Off-line commissioning of EBIS and plans for its integration into ATLAS and CARIBU

Science.gov (United States)

Ostroumov, P. N.; Barcikowski, A.; Dickerson, C. A.; Mustapha, B.; Perry, A.; Sharamentov, S. I.; Vondrasek, R. C.; Zinkann, G.

2016-02-01

An Electron Beam Ion Source Charge Breeder (EBIS-CB) has been developed at Argonne to breed radioactive beams from the CAlifornium Rare Isotope Breeder Upgrade (CARIBU) facility at Argonne Tandem Linac Accelerator System (ATLAS). The EBIS-CB will replace the existing ECR charge breeder to increase the intensity and significantly improve the purity of reaccelerated radioactive ion beams. The CARIBU EBIS-CB has been successfully commissioned offline with an external singly charged cesium ion source. The performance of the EBIS fully meets the specifications to breed rare isotope beams delivered from CARIBU. The EBIS is being relocated and integrated into ATLAS and CARIBU. A long electrostatic beam transport system including two 180° bends in the vertical plane has been designed. The commissioning of the EBIS and the beam transport system in their permanent location will start at the end of this year.

Design of the low energy beam transport line between CARIBU and the EBIS charge breeder

Energy Technology Data Exchange (ETDEWEB)

Perry, A., E-mail: aperry4@hawk.iit.edu [Argonne National Laboratory, Argonne, IL 60439, USA and Illinois Institute of Technology, Chicago, IL 60616 (United States); Ostroumov, P. N.; Barcikowski, A.; Dickerson, C.; Kondrashev, S. A.; Mustapha, B.; Savard, G. [Argonne National Laboratory, Argonne, IL 60439 (United States)

2015-01-09

An Electron Beam Ion Source Charge Breeder (EBIS-CB) has been developed to breed radioactive beams from the CAlifornium Rare Isotope Breeder Upgrade (CARIBU) facility at ATLAS. The EBIS-CB will replace the existing ECR charge breeder to increase the intensity and improve the purity of reaccelerated radioactive ion beams. The EBIS-CB is in the final stage of off-line commissioning. Currently, we are developing a low energy beam transport (LEBT) system to transfer CARIBU beams to the EBIS-CB. As was originally planned, an RFQ cooler-buncher will precede the EBIS-CB. Recently, it was decided to include a multi-reflection time-of-flight (MR-TOF) mass-spectrometer following the RFQ. MR-TOF is a relatively new technology used to purify beams with a mass-resolving power up to 3×10{sup 5} as was demonstrated in experiments at CERN/ISOLDE. Very high purity singly-charged radioactive ion beams will be injected into the EBIS for charge breeding and due to its inherent properties, the EBIS-CB will maintain the purity of the charge bred beams. Possible contamination of residual gas ions will be greatly suppressed by achieving ultra-high vacuum in the EBIS trap. This paper will present and discuss the design of the LEBT and the overall integration of the EBIS-CB into ATLAS.

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.

The EBI2 signalling pathway plays a role in cellular crosstalk between astrocytes and macrophages.

Science.gov (United States)

Rutkowska, Aleksandra; O'Sullivan, Sinead A; Christen, Isabelle; Zhang, Juan; Sailer, Andreas W; Dev, Kumlesh K

2016-05-11

EBI2 is a G protein-coupled receptor activated by oxysterol 7α, 25-dihydroxycholesterol (7α25HC) and regulates T cell-dependant antibody response and B cell migration. We recently found EBI2 is expressed in human astrocytes, regulates intracellular signalling and modulates astrocyte migration. Here, we report that LPS treatment of mouse astrocytes alters mRNA levels of EBI2 and oxysterols suggesting that the EBI2 signalling pathway is sensitive to LPS-mediated immune challenge. We also find that conditioned media obtained from LPS-stimulated mouse astrocytes induces macrophage migration, which is inhibited by the EBI2 antagonist NIBR189. These results demonstrate a role for the EBI2 signalling pathway in astrocytes as a sensor for immune challenge and for communication with innate immune cells such as macrophages.

PROPOSAL FOR AN EBIS BASED RHIC PREINJECTOR.

Energy Technology Data Exchange (ETDEWEB)

ALESSI,J.G.; BEEBE,E.; KPONOU,A.; PIKIN,A.; PRELEC,K.; RAPARIA,D.; RITTER,J.; ZHANG,S.Y.

2000-11-06

A proposed new heavy ion preinjector for RHIC is described. The progress made at BNL on the development of an Electron Beam Ion Source (EBIS) has increased our confidence that one can build a preinjector meeting RHIC requirements using an EBIS producing intermediate charge state heavy ions. A new RFQ and Linac will be required to accelerate beams from this source to an energy sufficient for injection into the AGS Booster. These are both straightforward devices, very similar to ones already in operation at other laboratories. Injection into the Booster will occur at the same location as the existing heavy ion injection from the Tandem Van de Graaff.

PROPOSAL FOR AN EBIS-BASED RHIC PREINJECTOR

International Nuclear Information System (INIS)

ALESSI, J.G.; BEEBE, E.; KPONOU, A.; PIKIN, A.; PRELEC, K.; RAPARIA, D.; RITTER, J.; ZHANG, S.Y.

2000-01-01

A proposed new heavy ion preinjector for RHIC is described. The progress made at BNL on the development of an Electron Beam Ion Source (EBIS) has increased our confidence that one can build a preinjector meeting RHIC requirements using an EBIS producing intermediate charge state heavy ions. A new RFQ and Linac will be required to accelerate beams from this source to an energy sufficient for injection into the AGS Booster. These are both straightforward devices, very similar to ones already in operation at other laboratories. Injection into the Booster will occur at the same location as the existing heavy ion injection from the Tandem Van de Graaff

Laser ion source with long pulse width for RHIC-EBIS

International Nuclear Information System (INIS)

Kondo, K.; Kanesue, T.; Okamura, M.

2011-01-01

The Electron Beam Ion Source (EBIS) at Brookhaven National Laboratory is a new heavy ion-projector for RHIC and NASA Space Radiation Laboratory. Laser Ion Source (LIS) with solenoid can supply many kinds of ion from solid targets and is suitable for long pulse length with low current as ion provider for RHIC-EBIS. In order to understand a plasma behavior for fringe field of solenoid, we measure current, pulse width and total ion charges by a new ion probe. The experimental result indicates that the solenoid confines the laser ablation plasma transversely. Laser ion source needs long pulse length with limited current as primary ion provider for RHIC-EBIS. New ion probe can measure current distribution for the radial positions along z axis. The beam pulse length is not effected by magnetic field strength. However, the currents and charges decay with the distance from the end of solenoid. These results indicate that solenoid field has important role for plasma confinement not longitudinally but transversely and solenoid is able to have long pulse length with sufficient total ion charges. Moreover, the results are useful for a design of the extraction system for RHIC-EBIS.

Report on EBIS studies for a RHIC preinjector

International Nuclear Information System (INIS)

Beebe, E.; Hershcovitch, A.; Kponou, A.; Prelec, K.; Alessi, J.

1995-01-01

Bookhaven, an Electron Beam Ion Source (EBIS) is now operational. This source is being used as a test bed to answer questions relevant to the eventual design of an EBIS-based heavy ion injector for RHIC. Such a source can easily produce ions such as Au 43+ but the challenge lies in reaching intensities of interest for RHIC (3 x 10 9 particles/pulse). The source studies are planned to address issues such as scaling of the electron beam to 10 A, possible onset (and control) of instabilities, ion injection, and parametric studies of output emittance

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

An EBIS system for rare isotope science project in Korea

International Nuclear Information System (INIS)

Kim, Jongwon; Han, Jae-Eun; Son, Hyock-Jun; Yi, Kun-Hui; Zhao, Liangji; Kim, Jin-Soo

2015-01-01

An EBIS system has been designed to be used as a charge breeder for the post accelerator of an ISOL system. An electron gun, which is designed to produce a maximum current of 3 A at the beam energy of 20 kV, will be acquired from the Budker Institute, Novosibirsk. Electron beam optics calculations of the EBIS system as well as of the gun assembly have been performed using PBGUNS and TRAK. A superconducting solenoid with a maximum field of 6 T is to be used to compress the electron beam. A test stand, which includes the gun assembly and a high-power electron beam collector, is being designed and will be ready for the gun test in the end of this year. Charge breeding simulation using EBIS0D and CBSIM has been performed for a few key isotopes

BRIC: An EBIS design for charge state breeding in RIB applications

International Nuclear Information System (INIS)

Brautti, G.; Clauser, T.; Raino, A.; Stagno, V.; Variale, V.; Logatchov, P.

2001-01-01

This work deals with the 'charge state breeder' that will be tested at INFN Laboratory of Bari (Italy). The breeder, based on the Electron Beam Ion Source (EBIS) scheme, is designed for applications in Radioactive Ion Beam (RIB) production facilities based on the Isotope Separation On-Line (ISOL) method in the framework of the SPES project of the INFN LNL laboratory (Legnaro). Some modifications with respect to the classical EBIS have been proposed to increase the containment efficiency. The insertion in the ion chamber of a RF-Quadrupole, aiming to filtering the unwanted masses, is the most relevant change with respect to the classical EBIS. The breeder design and numerical simulation results of the electron and ion beam propagation are reported

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.

The CARIBU EBIS control and synchronization system

Energy Technology Data Exchange (ETDEWEB)

Dickerson, Clayton, E-mail: cdickerson@anl.gov; Peters, Christopher, E-mail: cdickerson@anl.gov [Argonne National Laboratory, Argonne, IL 60439 (United States)

2015-01-09

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.

Development of an EBIS charge breeder for the Rare Isotope Science Project

Science.gov (United States)

Son, Hyock-Jun; Park, Young-Ho; Kondrashev, Sergey; Kim, Jongwon; Lee, Bong Ju; Chung, Moses

2017-10-01

In Korea, a heavy ion accelerator facility called RAON is being designed to produce various rare isotopes for the Rare Isotope Science Project (RISP) (Jeong, 2016) [1], (Moon, 2014) [2]. This facility is designed to use both In-flight Fragment (IF) and Isotope Separation On-Line (ISOL) techniques in order to produce a wide variety of RI beams for nuclear physics experiments. An Electron Beam Ion Source (EBIS) will be used for charge breeding of Rare Isotope (RI) beams in the ISOL system. The charge-to-mass ratio (q/A) of the RI beams after charge breeding is ≥1/4. The highly charged RI beams will be accelerated by a linac post-accelerator and delivered to a low energy (∼18 MeV/u) experimental hall or the IF system. The RAON EBIS will use a 3 A electron gun and a 6 T superconducting solenoid for high capacity, high efficiency, and short breeding time. In front of the charge breeder, an RFQ cooler-buncher will be used to deliver a bunched beam with small emittance to the EBIS charge breeder. The main design of the RAON EBIS has been carried out on the basis of several beam analyses and technical reviews. In this paper, current progress of the development of the RAON EBIS charge breeder will be presented.

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

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.

Advantages of combining an EBIS with the PIGMI technology

International Nuclear Information System (INIS)

Hamm, R.W.

1980-01-01

The Electron Beam Ion Source (EBIS) produces highly charged heavy ions by electron impact ionization of ions electrostatically trapped within a dense energetic electron beam. Because of its pulsed operation and the highly charged ions produced, the EBIS is ideally suited as an injector for a high-gradient, low duty-cycle linac such as that being developed at the Los Alamos Scientific Laboratory (LASL) in the program to design a Pion Generator for Medical Irradiation (PIGMI). This combination of new technologies would produce an efficient, small heavy ion linac useful in a variety of research and practical applications

Commissioning and performance of the BNL EBIS LLRF system

International Nuclear Information System (INIS)

Yuan, S.; Smith, K.S.; Hayes, T.; Severino, F.; Harvey, M.; Narayan, G.; Zaltsman, A.

2011-01-01

The Electron Beam Ion Source (EBIS) LLRF system utilizes the RHIC LLRF upgrade platform to achieve the required functionality and flexibility. The LLRF system provides drive to the EBIS high-level RF system, employs I-Q feedback to provide required amplitude and phase stability, and implements a cavity resonance control scheme. The embedded system provides the interface to the existing Controls System, making remote system control and diagnostics possible. The flexibility of the system allows us to reuse VHDL codes, develop new functionalities, improve current designs, and implement new features with relative ease. In this paper, we will discuss the commissioning process, issues encountered, and performance of the system.

Commissioning and performance of the BNL EBIS LLRF system

Energy Technology Data Exchange (ETDEWEB)

Yuan, S.; Smith, K.S.; Hayes, T.; Severino, F.; Harvey, M.; Narayan, G.; Zaltsman, A.

2011-03-28

The Electron Beam Ion Source (EBIS) LLRF system utilizes the RHIC LLRF upgrade platform to achieve the required functionality and flexibility. The LLRF system provides drive to the EBIS high-level RF system, employs I-Q feedback to provide required amplitude and phase stability, and implements a cavity resonance control scheme. The embedded system provides the interface to the existing Controls System, making remote system control and diagnostics possible. The flexibility of the system allows us to reuse VHDL codes, develop new functionalities, improve current designs, and implement new features with relative ease. In this paper, we will discuss the commissioning process, issues encountered, and performance of the system.

Searching and Extracting Data from the EMBL-EBI Complex Portal.

Science.gov (United States)

Meldal, Birgit H M; Orchard, Sandra

2018-01-01

The Complex Portal ( www.ebi.ac.uk/complexportal ) is an encyclopedia of macromolecular complexes. Complexes are assigned unique, stable IDs, are species specific, and list all participating members with links to an appropriate reference database (UniProtKB, ChEBI, RNAcentral). Each complex is annotated extensively with its functions, properties, structure, stoichiometry, tissue expression profile, and subcellular location. Links to domain-specific databases allow the user to access additional information and enable data searching and filtering. Complexes can be saved and downloaded in PSI-MI XML, MI-JSON, and tab-delimited formats.

Ebi3 Prevents Trypanosoma cruzi-Induced Myocarditis by Dampening IFN-γ-Driven Inflammation

Directory of Open Access Journals (Sweden)

Tiago Silva Medina

2017-09-01

Full Text Available The identification of anti-inflammatory mediators can reveal important targetable molecules capable of counterbalancing Trypanosoma cruzi-induced myocarditis. Composed of Ebi3 and IL-27p28 subunits, IL-27 is produced by myeloid cells and is able to suppress inflammation by inducing IL-10-producing Tr1 cells, thus emerging as a potential candidate to ameliorate cardiac inflammation induced by T. cruzi. Although IL-27 has been extensively characterized as a suppressive cytokine that prevents liver immunopathogenesis after T. cruzi infection, the mechanisms underlying its effects on T. cruzi-induced myocarditis remain largely unknown. Here, wild-type (WT and Ebi3-deficient animals were intraperitoneally infected with trypomastigotes of T. cruzi Y strain and used to evaluate the potential anti-inflammatory properties of Ebi3 during T. cruzi infection. The survival rates of mice were daily recorded, the frequency of inflammatory cells was analyzed by flow cytometry and inflammatory mediators were measured by ELISA, real-time PCR and PCR array. We reported that T. cruzi-induced myocarditis was prevented by Ebi3. Stressors mainly recognized by TLR2 and TLR4 receptors on myeloid cells were essential to trigger IL-27p28 production. In addition, Ebi3 regulated IFN-γ-mediated myocarditis by promoting an anti-inflammatory environment through IL-10, which was most likely produced by Tr1 cells rather than classical regulatory T cells (Tregs, in the heart tissue of T. cruzi-infected animals. Furthermore, in vivo IFN-γ blockade ameliorated the host survival without compromising the parasite control in the bloodstream. In humans, IL-27p28 was correlated with cardiac protection during Chagas disease. Patients with mild clinical forms of the disease produced high levels of IL-27p28, whereas lower levels were found in those with severe forms. In addition, polymorphic sites at Ebi3 gene were associated with severe cardiomyopathy in patients with Chagas disease

Ebi3 Prevents Trypanosoma cruzi-Induced Myocarditis by Dampening IFN-γ-Driven Inflammation

Science.gov (United States)

Medina, Tiago Silva; Oliveira, Gabriela Gonçalves; Silva, Maria Cláudia; David, Bruna Araújo; Silva, Grace Kelly; Fonseca, Denise Morais; Sesti-Costa, Renata; Frade, Amanda Farage; Baron, Monique Andrade; Ianni, Barbara; Pereira, Alexandre Costa; Chevillard, Christophe; Cunha-Neto, Edécio; Marin-Neto, José Antonio; Silva, João Santana

2017-01-01

The identification of anti-inflammatory mediators can reveal important targetable molecules capable of counterbalancing Trypanosoma cruzi-induced myocarditis. Composed of Ebi3 and IL-27p28 subunits, IL-27 is produced by myeloid cells and is able to suppress inflammation by inducing IL-10-producing Tr1 cells, thus emerging as a potential candidate to ameliorate cardiac inflammation induced by T. cruzi. Although IL-27 has been extensively characterized as a suppressive cytokine that prevents liver immunopathogenesis after T. cruzi infection, the mechanisms underlying its effects on T. cruzi-induced myocarditis remain largely unknown. Here, wild-type (WT) and Ebi3-deficient animals were intraperitoneally infected with trypomastigotes of T. cruzi Y strain and used to evaluate the potential anti-inflammatory properties of Ebi3 during T. cruzi infection. The survival rates of mice were daily recorded, the frequency of inflammatory cells was analyzed by flow cytometry and inflammatory mediators were measured by ELISA, real-time PCR and PCR array. We reported that T. cruzi-induced myocarditis was prevented by Ebi3. Stressors mainly recognized by TLR2 and TLR4 receptors on myeloid cells were essential to trigger IL-27p28 production. In addition, Ebi3 regulated IFN-γ-mediated myocarditis by promoting an anti-inflammatory environment through IL-10, which was most likely produced by Tr1 cells rather than classical regulatory T cells (Tregs), in the heart tissue of T. cruzi-infected animals. Furthermore, in vivo IFN-γ blockade ameliorated the host survival without compromising the parasite control in the bloodstream. In humans, IL-27p28 was correlated with cardiac protection during Chagas disease. Patients with mild clinical forms of the disease produced high levels of IL-27p28, whereas lower levels were found in those with severe forms. In addition, polymorphic sites at Ebi3 gene were associated with severe cardiomyopathy in patients with Chagas disease. Collectively, we

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...

Simulation of 10 A electron beam formation and collection for a high current EBIS

International Nuclear Information System (INIS)

Kponou, A.; Beebe, E.; Pikin, A.; Kuznetsov, G.; Batazova, M.; Tiunov, M.

1997-01-01

Development of an Electron Beam Ion Source (EBIS) for the Relativistic Heavy Ion Collider (RHIC) at BNL requires operating with a 10 A electron beam, which is approximately an order of magnitude higher current than in any existing EBIS device. A test stand is presently being designed and constructed where EBIS components will be twisted. It will be reported in a separate paper at this Conference. The design of the 10 A electron gun, drift tubes and electron collector requires extensive computer simulations. Calculations have been performed at Novosibirsk and BNL using two different programs, SAM and EGUN. Results of these simulations will be presented

On-line charge breeding using ECRIS and EBIS

Energy Technology Data Exchange (ETDEWEB)

Vondrasek, Richard, E-mail: Vondrasek@anl.gov

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.

Epstein-Barr virus-induced gene 3 (EBI3) polymorphisms and expression are associated with susceptibility to pulmonary tuberculosis.

Science.gov (United States)

Zheng, Ruijuan; Liu, Haipeng; Song, Peng; Feng, Yonghong; Qin, Lianhua; Huang, Xiaochen; Chen, Jianxia; Yang, Hua; Liu, Zhonghua; Cui, Zhenglin; Hu, Zhongyi; Ge, Baoxue

2015-07-01

Tuberculosis (TB) remains a major global health problem and host genetic factors play a critical role in susceptibility and resistance to TB. The aim of this study was to identify novel candidate genes associated with TB susceptibility. We performed a population-based case-control study to genotype 13 tag SNPs spanning Epstein-Barr virus-induced gene 3 (EBI3), colony stimulating factor 2 (CSF2), IL-4, interferon beta 1 (IFNB1), chemokine (C-X-C motif) ligand 14 (CXCL14) and myeloid differentiation primary response gene 88 (Myd88) genes in 435 pulmonary TB patients and 375 health donors from China. We observed that EBI3 gene rs4740 polymorphism was associated with susceptibility to pulmonary tuberculosis (PTB) and the allele G was associated with a protective effect against PTB. Furthermore, EBI3 deficiency led to reduced bacterial burden and histopathological impairment in the lung of mice infected with Mycobacterium bovis BCG. Meanwhile, higher abundance of EBI3 was observed in the granuloma of PTB patients and in the lung tissue of BCG-infected mice. Of note, the expression of EBI3 in macrophages was remarkably induced by mycobacteria infection at both mRNA and protein level. In conclusion, EBI3 gene rs4740 polymorphism is closely associated with susceptibility to PTB and the elevation and enrichment of EBI3 in the lung which at least partially derived from macrophages may contribute to the exacerbation of mycobacterial infection. Copyright © 2015 Elsevier Ltd. All rights reserved.

Small molecule antagonism of oxysterol-induced Epstein-Barr virus induced gene 2 (EBI2) activation

DEFF Research Database (Denmark)

Benned-Jensen, Tau; Madsen, Christian M; Arfelt, Kristine N

2013-01-01

The Epstein-Barr virus induced gene 2 (EBI2) was recently identified as the first oxysterol-activated 7TM receptor. EBI2 is essential for B cell trafficking within lymphoid tissues and thus the humoral immune response in general. Here we characterize the antagonism of the non-peptide molecule GSK...

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

Numerical simulation of ion production processes in EBIS

International Nuclear Information System (INIS)

Kalagin, I.V.; Ovsyannikov, V.P.

1996-01-01

The numerical model of EBIS is presented. The calculation of Kr ionization by cooling with Ne ions was carried out taking into account charge exchange, ion heating by electrons, ion-ion energy exchange and ion escape processes. A good agreement with experimental data was observed. 19 refs., 13 figs

Construction of the BNL EBIS preinjector

Energy Technology Data Exchange (ETDEWEB)

Alessi,J.; Barton, D.; Beebe, E.; Bellavia, S.; Gould, O.; Kponou, A.; Lambiase, R.; Lessard, E.; Lockey, R.; LoDestro, V.; Mapes, M.; McCafferty, D.; McNerney, A.; Okamura, M.; Pendzick, A.; Phillips, D.; Pikin, A. I.; Raparia, D.; Ritter, J.; Scaduto, J.; Snydstrup, L.; Wilinski, M.; Zaltsman, A. et al.

2009-05-04

A new heavy ion preinjector, consisting of an Electron Beam Ion Source (EBIS), an RFQ, and IH linac, is under construction at Brookhaven National Laboratory. This preinjector win provide ions of any species at an energy of 2 MeV/u, resulting in increased capabilities for the Relativistic Heavy Ion Collider, and the NASA Space Radiation Laboratory programs. The RF'Q has been commissioned with beam, and most of the remaining elements are either installed or being assembled.

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.

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

An EBIS for charge state breeding in the SPES project

International Nuclear Information System (INIS)

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

2002-01-01

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. (author)

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

International Nuclear Information System (INIS)

Balleza, M; Vargas, M; Delgadillo, I; Kashina, S; Huerta, M R; 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. (paper)

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

Science.gov (United States)

Niss Arfelt, Kristine; Barington, Line; Benned-Jensen, Tau; Kubale, Valentina; Kovalchuk, Alexander L; Daugvilaite, Viktorija; Christensen, Jan Pravsgaard; Thomsen, Allan Randrup; Egerod, Kristoffer L; Bassi, Maria R; Spiess, Katja; Schwartz, Thue W; Wang, Hongsheng; Morse, Herbert C; Holst, Peter J; Rosenkilde, Mette M

2017-02-16

Human and mouse chronic lymphocytic leukemia (CLL) develops 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 (GC) development, and the B1a cell population is increased in mice with reduced GC formation. As a major mediator of follicular B-cell migration, the G protein-coupled receptor 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 toward the extrafollicular area, whereas downregulation is essential for GC formation. We therefore speculated whether increased expression of EBI2 would lead to an expanded B1 cell subset and, ultimately, progression to CLL. Here, we demonstrate that B-cell-targeted expression of human EBI2 (hEBI2) in mice reduces GC-dependent immune responses, reduces total immunoglobulin M (IgM) and IgG levels, and leads to increased proliferation and upregulation of cellular oncogenes. Furthermore, hEBI2 overexpression leads to an abnormally expanded CD5 + B1a B-cell subset (present as early as 4 days after birth), late-onset lymphoid cancer development, and premature death. These findings are highly similar to those observed in CLL patients and identify EBI2 as a promoter of B-cell malignancies.

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.

An EBIS for charge state breeding in the SPES project

Indian Academy of Sciences (India)

development and testing of a charge state breeder device based on an EBIS source ... the number of particles that can be accumulated in a Penning source is limited. ... accounting for the magnetic field and the electron beam space charge.

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.

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.

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

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.

An EBIS for charge state breeding in the SPES project

Indian Academy of Sciences (India)

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 ...

Charge breeding of stable and radioactive ion beams with EBIS/T devices

CERN Document Server

Kester, Oliver; Becker, R

2004-01-01

Radioactive ion beams (RIBs) are an important tool for experiments at the foremost frontier of nuclear physics. The quasi-continuous radioactive beams from target ion sources of RIB-facilities have to be accelerated to energies at and beyond the Coulomb barrier. An efficient acceleration requires a suitable A/q of the ions determined by the accelerator design, which can be reached via the stripping method or by using a charge state breeder like the REX-ISOLDE system. In order to get comparable efficiencies for a charge state breeder with the stripping scheme, the breeding efficiency in one charge state has to be optimized by narrowing the charge state distribution. In addition good beam quality and thus small emittances are required to achieve best transmission in the following accelerator, which is mandatory for high intensity RIBs. For EBIS/T devices the maximum intensity of the radioactive ion beam is a critical issue, and high current EBIS/T devices will be necessary to deal with intensities of second gen...

Design and numerical characterization of a crossover EBIS

Energy Technology Data Exchange (ETDEWEB)

Geyer, Sabrina, E-mail: geyer@iap.uni-frankfurt.de; Langbein, A., E-mail: geyer@iap.uni-frankfurt.de; Meusel, Oliver, E-mail: geyer@iap.uni-frankfurt.de [Institute of Applied Physics, Goethe University Frankfurt, Frankfurt am Main, HE (Germany); Kester, Oliver [Institute of Applied Physics, Goethe University Frankfurt, Frankfurt am Main, HE, Germany and GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt, HE (Germany)

2015-01-09

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{sup −7} A/V{sup 3/2} for the realized gun system. In the interaction region the electron beam has a density of around 10 A/cm{sup 2} 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 1×10{sup 8} charges. Charge state breeding studies with CBSIM indicate for the noble gases as maximal achievable charge state Ar{sup 16+}, Kr{sup 30+} and Xe{sup 35+}. 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.

Design and numerical characterization of a crossover EBIS

International Nuclear Information System (INIS)

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/V 3/2 for the realized gun system. In the interaction region the electron beam has a density of around 10 A/cm 2 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 1×10 8 charges. Charge state breeding studies with CBSIM indicate for the noble gases as maximal achievable charge state Ar 16+ , Kr 30+ and Xe 35+ . 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

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.

Magnetic field measurements of the superEBIS superconducting magnet

International Nuclear Information System (INIS)

Herschcovitch, A.; Kponou, A.; Clipperton, R.; Hensel, W.; Usack, F.

1994-01-01

SuperEBIS was designed to have a solenoidal magnetic field of a 5 Tesla strength with a 120 cm long bore. The field was specified to be straight within 1 part in 10000 within the bore, and uniform to within 1 part in 1000 within the central 90 cm. Magnetic field measurements were performed with a computerized magnetic field measuring setup that was borrowed from W. Sampson's group. A preliminary test was made of a scheme to determine if the magnetic and mechanical axes of the solenoid coincided, and, if not, by how much

The initiation of EBIS/T-based HCI research in Japan

International Nuclear Information System (INIS)

Ohtani, Shunsuke

2004-01-01

This article reviews early EBIS/T-based HCI research in Japan designed to understand atomic processes of highly charged impurity ions in plasmas. In particular the work of the NICE (Naked Ion Collision Experiments) project is discussed. The NICE experiment showed for the first time that translational energy spectroscopy would give useful information about the intermediate multiple-excited states in the transfer ionization processes, and therefore it would be a powerful method for spectroscopy of so-called hollow atoms

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

-targeted expression of human EBI2 in mice reduces germinal center-dependent immune responses, reduces total IgM and IgG levels, and leads to increased proliferation and upregulation of cellular oncogenes. Furthermore, hEBI2 overexpression leads to an abnormally expanded CD5+ B1a B cell subset present as early as 4......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...... 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...

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

were identified by a systematic mutational analysis of 29 residues in EBI2. The cAMP response element-binding protein transcription factor was used as a measure of receptor activity and was correlated to the receptor surface expression. PheVI:13 (Phe257), and the neighboring CysVI:12 (Cys256......, 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...

Chemical Entity Recognition and Resolution to ChEBI

Science.gov (United States)

Grego, Tiago; Pesquita, Catia; Bastos, Hugo P.; Couto, Francisco M.

2012-01-01

Chemical entities are ubiquitous through the biomedical literature and the development of text-mining systems that can efficiently identify those entities are required. Due to the lack of available corpora and data resources, the community has focused its efforts in the development of gene and protein named entity recognition systems, but with the release of ChEBI and the availability of an annotated corpus, this task can be addressed. We developed a machine-learning-based method for chemical entity recognition and a lexical-similarity-based method for chemical entity resolution and compared them with Whatizit, a popular-dictionary-based method. Our methods outperformed the dictionary-based method in all tasks, yielding an improvement in F-measure of 20% for the entity recognition task, 2–5% for the entity-resolution task, and 15% for combined entity recognition and resolution tasks. PMID:25937941

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

Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.

Science.gov (United States)

Lopez, Rodrigo; Cowley, Andrew; Li, Weizhong; McWilliam, Hamish

2014-12-12

The European Bioinformatics Institute (EMBL-EBI) provides access to a wide range of databases and analysis tools that are of key importance in bioinformatics. As well as providing Web interfaces to these resources, Web Services are available using SOAP and REST protocols that enable programmatic access to our resources and allow their integration into other applications and analytical workflows. This unit describes the various options available to a typical researcher or bioinformatician who wishes to use our resources via Web interface or programmatically via a range of programming languages. Copyright © 2014 John Wiley & Sons, Inc.

Identification and characterization of small molecule modulators of the Epstein-Barr virus-induced gene 2 (EBI2) receptor

DEFF Research Database (Denmark)

Gessier, Francois; Preuss, Inga; Yin, Hong

2014-01-01

immune response and has been genetically linked to autoimmune diseases such as type I diabetes ( Nature 2010 , 467 , 460 ). Here we describe the isolation of a potent small molecule antagonist for the EBI2 receptor. First, we identified a small molecule agonist NIBR51 (1), which enabled identification...

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.

Interleukin (IL)‐39 [IL‐23p19/Epstein–Barr virus‐induced 3 (Ebi3)] induces differentiation/expansion of neutrophils in lupus‐prone mice

Science.gov (United States)

Liu, X.; Zhang, Y.; Wang, Z.; Zhu, G.; Han, G.; Chen, G.; Hou, C.; Wang, T.; Ma, N.; Shen, B.; Li, Y.; Wang, R.

2016-01-01

Summary Interleukin (IL)‐12 family cytokines play critical roles in autoimmune diseases. Our previous study has shown that IL‐23p19 and Epstein–Barr virus‐induced 3 (Ebi3) form a new IL‐12 family heterodimer, IL‐23p19/Ebi3, termed IL‐39, and knock‐down of p19 or Ebi3 reduced diseases by transferred GL7+ B cells in lupus‐prone mice. In the present study, we explore further the possible effect of IL‐39 on murine lupus. We found that IL‐39 in vitro and in vivo induces differentiation and/or expansion of neutrophils. GL7+ B cells up‐regulated neutrophils by secreting IL‐39, whereas IL‐39‐deficient GL7+ B cells lost the capacity to up‐regulate neutrophils in lupus‐prone mice and homozygous CD19cre (CD19‐deficient) mice. Finally, we found that IL‐39‐induced neutrophils had a positive feedback on IL‐39 expression in activated B cells by secreting B cell activation factor (BAFF). Taken together, our results suggest that IL‐39 induces differentiation and/or expansion of neutrophils in lupus‐prone mice. PMID:27400195

Significant reduction of peripheral blood interleukin-35 and CD4+EBI3+ T cells, which are negatively correlated with an increase in the plasma IL-17 and cTnI level, in viral myocarditis patients

Directory of Open Access Journals (Sweden)

Han Ouyang

2017-02-01

Full Text Available Introduction: Viral myocarditis (VMC has become an increasingly common heart disease that endangers human health. In the present study, the plasma interleukin-35 (IL-35 level and the percentage of CD4 + EBI3 + T cells in VMC patients were detected to investigate the significance of changes in these parameters in the plasma of VMC patients and their association with the disease. Material and methods: ELISA was performed to detect the plasma IL-35 level and the percentage of peripheral blood CD4 + EBI3 + T cells in 40 VMC patients and in 20 healthy individuals. Moreover, the plasma IL-17 levels in the VMC patients and in the healthy individuals were detected using an ELISA, and the cardiac Troponin-I (cTnI levels were detected using a chemiluminescent microparticle immunoassay to compare the differences in the groups. Results : Plasma IL-35 level and the percentage of CD4 + EBI3 + T cells in acute phase VMC patients was lower than that in the healthy control group and the convalescent phase VMC patients. Additionally, the plasma IL-35 level in the VMC patients exhibited a negative correlation with the levels of cTnI and IL-17. The percentage of CD4 + EBI3 + T cells also showed a negative correlation with the levels of cTnI and IL-17. Conclusions : The plasma IL-35 level and the percentage of CD4 + EBI3 + T cells in VMC patients was reduced, and the amount of the decrease was associated with the severity of the disease. These results suggest that IL-35 and CD4 + EBI3 + T might play important roles in the progression of VMC and could be used as indictors of the disease.

Selective containment in EBIS for charge breeding applications

International Nuclear Information System (INIS)

Variale, Vincenzo; Valentino, Vincenzo; Bak, Petr A.; Kuznetsov, Gennady I.; Skarbo, Boris; Tiunov, Michael A.; Clauser, Tarcisio; Boggia, Antonio; Raino, Antonio C.

2008-01-01

The production of radioactive ion beam (RIB) with the ISOL technique could require a charge breeder device to increase the ion acceleration efficiency and reduce greatly the production cost. The 'charge breeder' is a device designed to accept radioactive 1+ ions in order to increase their charge state up to n+. In the framework of the SPES project, proposed at the INFN-LNL (Padua) for RIB production, an R and D experiment of a charge breeder device, BRIC, has been carried out at LNL. BRIC is an EBIS-type ion charge state breeder in which a radio frequency (RF) quadrupolar field has been superimposed in the trapped ion region to introduce a selective containment with the aim of increasing the ion trapping efficiency. In this paper, the device and the test measurements that demonstrate the selective containment effect due to the RF quadrupolar field are presented. Furthermore, some comments on the possibility of using that device as charge state breeder for RIB production has been also discussed in the conclusions. This experiment has been also considered as R and D program of the RIB European project EURISOL D S

Ion Sources, Preinjectors and the Road to EBIS (459th Brookhaven Lecture)

International Nuclear Information System (INIS)

Alessi, James

2010-01-01

To meet the requirements of the scientific programs of the Relativistic Heavy Ion Collider and the NASA Space Radiation Lab, BNL's Collider-Accelerator Department needs a variety of ion sources. Although these sources are a relatively small and inexpensive part of an accelerator, they can have a big impact on the machine's overall performance. For the 459th Brookhaven Lecture, James Alessi will describe C-AD's long history of developing state-of-the-art ion sources for its accelerators, and its current process for source and pre-injector development. He will follow up with a discussion of the features and development status of EBIS, which, as the newest source and preinjector, is in the final stages of commissioning at the end of a five-year construction project.

Numerical design of an EBIS collector to optimize electron collection and ion extraction

International Nuclear Information System (INIS)

Dietrich, J.

1990-01-01

For the Frankfurt EBIS, a new collector was designed using the relativistic electron optics program EGUN and the magnetic field program INTMAG. To model the fringing field of the main solenoid, a bucking coil and a cylindrical shim is provided. The current of the bucking coil and the position and shape of the shim are optimized with INTMAG for minimum fringing field to allow expansion of the electron beam by its space charge. The magnetic field data output from INTMAG is directly used as input for EGUN to calculate the ectron and ion trajectories. The initial conditions for the trajectories were computed from the paraxial ray equation. Different operation modes of the collector are investigated including the behaviour of secondary electrons. (orig.)

Numerical design of an EBIS collector to optimize electron collection and ion extraction

Energy Technology Data Exchange (ETDEWEB)

Dietrich, J. (Frankfurt Univ. (Germany, F.R.). Inst. fuer Angewandte Physik)

1990-12-01

For the Frankfurt EBIS, a new collector was designed using the relativistic electron optics program EGUN and the magnetic field program INTMAG. To model the fringing field of the main solenoid, a bucking coil and a cylindrical shim is provided. The current of the bucking coil and the position and shape of the shim are optimized with INTMAG for minimum fringing field to allow expansion of the electron beam by its space charge. The magnetic field data output from INTMAG is directly used as input for EGUN to calculate the ectron and ion trajectories. The initial conditions for the trajectories were computed from the paraxial ray equation. Different operation modes of the collector are investigated including the behaviour of secondary electrons. (orig.).

The EBIS-RFQ couple: a fully matched heavy ion 3rd pre-injector for Saturne

International Nuclear Information System (INIS)

Olivier, M.; Faure, J.; Laclare, J.L.; Lefebvre, J.M.; Leleux, G.; Ropert, A.; Tkatchenko, A.; Tkatchenko, M.

1983-01-01

Since 1978, the 3 GeV Synchrotron Saturne is routinely operated with proton, deuteron, helium beams and, since 1981 with polarized protons and deuterons. Heavy ions are expected in the Summer of 1983 by using a new pre-injector presently under construction. As already proposed by R.W.Hamm, the marriage of an EBIS and an RFQ can be looked upon generally as a very good means of production of heavy ion beams at low energy because it combines high charges states, therefore low voltage on the terminal, and low velocity acceleration. After the RFQ, the beam is injected into Saturne through 20 MeV Alvarez linac

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...... have been deorphanized, many remain orphan, and these orphan receptors constitute a large pool of potential drug targets. This review focuses on one of these orphan targets, the Epstein-Barr Virus-induced receptor 2, EBI2 (or GPR183), together with two structurally related receptors, GPR17 and GPR18...

Reporting v spoločnosti BSH domácí spotřebiče s.r.o.

OpenAIRE

Cinkaničová, Martina

2011-01-01

Diploma thesis is focused on reporting process in the sale company BSH domácí spotřebiče s.r.o. In the beginning it explains differences between management, financial and tax accounting. There is the aim to emphasize the importance of management accounting in the broader sense, in the process of strategic, tactic and operative cost controlling. The source of information for cost accounting is controlling. Controller, in retrospect to content of diploma thesis, intermediate the results through...

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...

Numerical design of an EBIS collector to optimize electron collection and ion extraction

Science.gov (United States)

Dietrich, Jürgen

1990-12-01

For the Frankfurt EBIS (R. Becker et al., Nucl. Instr. and Meth. B24/25 (1987) 838, ref. [1]), a new collector was designed using the relativistic electron optics program EGUN (W.B. Herrmannsfeldt, SLAC-331 (1988), ref. [2]) and the magnetic field program INTMAG (R. Becker, Nucl. Instr. and Meth. B42 (1989) 303, ref. [3]). To model the fringing field of the main solenoid, a bucking coil and a cylindrical shim is provided. The current of the bucking coil and the position and shape of the shim are optimized with INTMAG for minimum fringing field to allow expansion of the electron beam by its space charge. The magnetic field data output from INTMAG is directly used as input for EGUN to calculate the electron and ion trajectories. The initial conditions for the trajectories were computed from the paraxial ray equation. Different operation modes of the collector are investigated including the behaviour of secondary electrons.

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...

Discovery of EBI-907: A highly potent and orally active B-Raf(V600E) inhibitor for the treatment of melanoma and associated cancers.

Science.gov (United States)

Lu, Biao; Cao, Hu; Cao, Jingsong; Huang, Song; Hu, Qiyue; Liu, Dong; Shen, Ru; Shen, Xiaodong; Tao, Weikang; Wan, Hong; Wang, Dan; Yan, Yinfa; Yang, Liuqing; Zhang, Jiayin; Zhang, Lei; Zhang, Lianshan; Zhang, Minsheng

2016-02-01

A novel series of pyrazolo[3,4-c]isoquinoline derivatives was discovered as B-Raf(V600E) inhibitors through scaffold hopping based on a literature lead PLX4720. Further SAR exploration and optimization led to the discovery of potent B-Raf(V600E) inhibitors with good oral bioavailability in rats and dogs. One of the compounds EBI-907 (13g) demonstrated excellent in vivo efficacy in B-Raf(V600E) dependent Colo-205 tumor xenograft models in mouse and is under preclinical studies for the treatment of melanoma and B-Raf(V600E) associated cancers. Copyright © 2015 Elsevier Ltd. All rights reserved.

Anti-IL-39 (IL-23p19/Ebi3) polyclonal antibodies ameliorate autoimmune symptoms in lupus-like mice

Science.gov (United States)

Wang, Xiaoqian; Zhang, Yu; Wang, Zhiding; Liu, Xiaoling; Zhu, Gaizhi; Han, Gencheng; Chen, Guojiang; Hou, Chunmei; Wang, Tianxiao; Shen, Beifen; Li, Yan; Xiao, He; Ma, Ning; Wang, Renxi

2018-01-01

The interleukin (IL)-12 family cytokines have been examined as therapeutic targets in the treatment of several autoimmune diseases. Our previous study showed that a novel IL-12 family cytokine, IL-39 (IL-23p19/Ebi3) mediates inflammation in lupus-like mice. In the present study, the effect of anti-mouse IL-39 polyclonal antibodies on autoimmune symptoms in lupus-like mice was investigated. Rabbit anti-mouse IL-39 polyclonal antibodies were produced by immunization with recombinant mouse IL-39, and purified using protein A chromatography. These antibodies were subsequently used to treat lupus-like mice. Flow cytometry, captured images, ELISA and H&E staining were used to determine the effect of anti-IL-39 polyclonal antibodies on inflammatory cells, autoantibody titers, proteinuria, infiltrating inflammatory cells and the structure of the glomerular region. The anti-IL-39 polyclonal antibodies effectively reduced the numbers of inflammatory cells, splenomegaly, autoantibody titers, proteinuria, infiltrating inflammatory cells, and restored the structure of the glomerular region in MRL/lpr mice. Taken together, these results suggested that anti-IL-39 polyclonal antibodies ameliorated autoimmune symptoms in lupus-like mice. Therefore, IL-39 may be used as a possible target for the treatment of systemic lupus erythematosus. PMID:29138852

Using Evidence-Based Interventions to Improve Cancer Screening in the National Breast and Cervical Cancer Early Detection Program.

Science.gov (United States)

DeGroff, Amy; Carter, Aundrea; Kenney, Kristy; Myles, Zachary; Melillo, Stephanie; Royalty, Janet; Rice, Ketra; Gressard, Lindsay; Miller, Jacqueline W

2016-01-01

The National Breast and Cervical Cancer Early Detection Program (NBCCEDP) provides cancer screening to low-income, un-, and underinsured women through more than 11 000 primary care clinics. The program is well-positioned to work with health systems to implement evidence-based interventions (EBIs) to increase screening among all women. To collect baseline data on EBI use, evaluation of EBIs, and related training needs among NBCCEDP grantees. The Centers for Disease Control and Prevention conducted a Web-based survey in late 2013 among NBCCEDP grantees for the period July 2012 to June 2013. This was the first systematic assessment of EBIs among NBCCEDP grantees. The Centers for Disease Control and Prevention's NBCCEDP. Primarily program directors/coordinators for all 67 NBCCEDP grantees. Data captured were used to assess implementation of 5 EBIs, their evaluation, and related training needs. Frequencies and proportions were determined. Cluster analysis identified grantees with similar patterns of EBI use for NBCCEDP clients and providers. On average, 4.1 of 5 EBIs were implemented per grantee for NBCCEDP clients and providers. Four clusters were identified including "high overall EBI users," "high provider EBI users," "high EBI users with no provider assessment and feedback," and "high client EBI users." Only 1.8 EBIs were implemented, on average, with non-NBCCEDP clients and providers. Fewer than half (n = 32, 47.8%) of grantees conducted process or outcome evaluation of 1 or more EBIs. Overall, 47.6% of grantees reported high or medium training needs for client-oriented EBIs and 54.3% for provider-oriented EBIs. The NBCCEDP grantees are implementing EBIs extensively with clients and providers. Increased EBI use among non-NBCCEDP clients/providers is needed to extend the NBCCEDP's reach and impact. Grantee training and technical assistance is necessary across EBIs. In addition, grantees' use of process and outcome evaluation of EBI implementation must be increased

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

International Nuclear Information System (INIS)

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

2013-01-01

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 cm 2 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.

INISIASI MENYUSU DINI MENJAGA KESTABILAN SUHU PADA BAYI BARU LAHIR

Directory of Open Access Journals (Sweden)

Nuli Nuryanti Zulala

2018-04-01

Full Text Available Background: Hypothermia contributes 6.3% to neonatal mortality. Interventions to keep newborns warm can reduce neonatal mortality by 18-42%. Early Breastfeeding Initiation (EBI is a simple intervention that reduces the risk of neonatal death. Objective: The aim of this study  to determine the difference of axillary temperature of newborn between improper EBI group and proper EBI group for 24 hours. Methods: This prospective cohort study was conducted at Aisyiyah Muntilan Hospital. Sixty-two healthy newborns from healthy mothers born in November 2016 who meet the inclusion and exclusion criteria. Subjects were grouped in improper EBI groups (n=32 and proper EBI groups (n=32. Axila temperature measurements were performed at 1st minute, 30th minute, 60th minute, 6th hour, 12th hour, 24th hour. Results: The result of the hypotermic occurrence is more happened on improper EBI than proper EBI. EBI is able to prevent hypothermia during the first 24 hours of newborn life Conclussions: Infants with proper EBI have a lower risk of hypothermia.

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

2017-02-01

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.

Unraveling Macrophage Heterogeneity in Erythroblastic Islands

Directory of Open Access Journals (Sweden)

Katie Giger Seu

2017-09-01

Full Text Available Mammalian erythropoiesis occurs within erythroblastic islands (EBIs, niches where maturing erythroblasts interact closely with a central macrophage. While it is generally accepted that EBI macrophages play an important role in erythropoiesis, thorough investigation of the mechanisms by which they support erythropoiesis is limited largely by inability to identify and isolate the specific macrophage sub-population that constitute the EBI. Early studies utilized immunohistochemistry or immunofluorescence to study EBI morphology and structure, while more recent efforts have used flow cytometry for high-throughput quantitative characterization of EBIs and their central macrophages. However, these approaches based on the expectation that EBI macrophages are a homogeneous population (F4/80+/CD169+/VCAM-1+ for example provide an incomplete picture and potentially overlook critical information about the nature and biology of the islands and their central macrophages. Here, we present a novel method for analysis of EBI macrophages from hematopoietic tissues of mice and rats using multispectral imaging flow cytometry (IFC, which combines the high-throughput advantage of flow cytometry with the morphological and fluorescence features derived from microscopy. This method provides both quantitative analysis of EBIs, as well as structural and morphological details of the central macrophages and associated cells. Importantly, the images, combined with quantitative software features, can be used to evaluate co-expression of phenotypic markers which is crucial since some antigens used to identify macrophages (e.g., F4/80 and CD11b can be expressed on non-erythroid cells associated with the islands instead of, or in addition to the central macrophage itself. We have used this method to analyze native EBIs from different hematopoietic tissues and evaluated the expression of several markers that have been previously reported to be expressed on EBI macrophages. We

Retting effect of kenaf bast fiber by electron beam irradiation

Energy Technology Data Exchange (ETDEWEB)

Shin, Hye Kyoung; Kangm Hyo Kyoung; Jeun, Joon Pyo; Kang, Phil Hyun [Korea Atomic Energy Research Institute, Jeongeup (Korea, Republic of)

2010-06-15

Kenaf (Hibiscus cannabinus) retting were separated from a kenaf bast fiber by a combination of Electron beam irradiation (EBI) and NaOH solution treatment. The methods were based on a 6% NaOH solution treatment after various doses of EBI. FT-IR spectroscopy demonstrated that the content of lignin and hemicellulose in the retted kenaf fibers decreased as the EBI dose increased. Specifically, the lignin in the retted kenaf fiber treated with 300 kGy of EBI was almost completely removed. The morphology of retted kenaf fibers were characterized by SEM image, and the studies showed that the fibrillated degree of retted kenaf fibers treated with various EBI doses and was increased as EBI dose increased. The retted kenaf fibers treated with the EBI at 300 kGy was uniformly fibrillated with 10 {approx} 30 {mu}m diameters.

Retting effect of kenaf bast fiber by electron beam irradiation

International Nuclear Information System (INIS)

Shin, Hye Kyoung; Kangm Hyo Kyoung; Jeun, Joon Pyo; Kang, Phil Hyun

2010-01-01

Kenaf (Hibiscus cannabinus) retting were separated from a kenaf bast fiber by a combination of Electron beam irradiation (EBI) and NaOH solution treatment. The methods were based on a 6% NaOH solution treatment after various doses of EBI. FT-IR spectroscopy demonstrated that the content of lignin and hemicellulose in the retted kenaf fibers decreased as the EBI dose increased. Specifically, the lignin in the retted kenaf fiber treated with 300 kGy of EBI was almost completely removed. The morphology of retted kenaf fibers were characterized by SEM image, and the studies showed that the fibrillated degree of retted kenaf fibers treated with various EBI doses and was increased as EBI dose increased. The retted kenaf fibers treated with the EBI at 300 kGy was uniformly fibrillated with 10 ∼ 30 μm diameters

ICFA Beam Dynamics Newsletter

Energy Technology Data Exchange (ETDEWEB)

Pikin, A. [Brookhaven National Lab. (BNL), Upton, NY (United States)

2017-11-21

Electron beam ion sources technology made significant progress since 1968 when this method of producing highly charged ions in a potential trap within electron beam was proposed by E. Donets. Better understanding of physical processes in EBIS, technological advances and better simulation tools determined significant progress in key EBIS parameters: electron beam current and current density, ion trap capacity, attainable charge states. Greatly increased the scope of EBIS and EBIT applications. An attempt is made to compile some of EBIS engineering problems and solutions and to demonstrate a present stage of understanding the processes and approaches to build a better EBIS.

Intervention Mapping to Adapt Evidence-Based Interventions for Use in Practice: Increasing Mammography among African American Women.

Science.gov (United States)

Highfield, Linda; Hartman, Marieke A; Mullen, Patricia Dolan; Rodriguez, Serena A; Fernandez, Maria E; Bartholomew, L Kay

2015-01-01

This paper describes and demonstrates the use of the systematic planning process, Intervention Mapping, to adapt an evidence-based public health intervention (EBI). We used a simplified version of Intervention Mapping (IM Adapt) to increase an intervention's fit with a new setting and population. IM Adapt guides researchers and practitioners in selecting an EBI, making decisions about whether and what to adapt, and executing the adaptation while guarding the EBI's essential elements (those responsible for effectiveness). We present a case study of a project in which we used IM Adapt to find, adapt, implement, and evaluate an EBI to improve mammography adherence for African American women in a new practice setting in Houston, Texas. IM Adapt includes the following (1) assess needs and organizational capacity; (2) find EBIs; (3) plan adaptations based on fit assessments; (4) make adaptations; (5) plan for implementation; and (6) plan for evaluation of the adapted EBI. The case study shows an example of how public health researchers and practitioners can use the tool to make it easier to find and use EBIs, thus encouraging greater uptake. IM Adapt adds to existing dissemination and adaptation models by providing detailed guidance on how to decide on effective adaptation, while maintaining the essential elements of the EBI.

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.

Isolation of cellulose fibers from kenaf using electron beam

International Nuclear Information System (INIS)

Shin, Hye Kyoung; Pyo Jeun, Joon; Bin Kim, Hyun; Hyun Kang, Phil

2012-01-01

Cellulose fibers were isolated from a kenaf bast fiber using a electron beam irradiation (EBI) treatment. The methods of isolation were based on a hot water treatment after EBI and two-step bleaching processes. FT-IR spectroscopy demonstrated that the content of lignin and hemicellulose in the bleached cellulose fibers treated with various EBI doses decreased with increasing doses of EBI. Specifically, the lignin in the bleached cellulose fibers treated at 300 kGy, was almost completely removed. Moreover, XRD analyses showed that the bleached cellulose fibers treated at 300 kGy presented the highest crystallinity of all the samples treated with EBI. Finally, the morphology of the bleached fiber was characterized by SEM imagery, and the studies showed that the separated degree of bleached cellulose fibers treated with various EBI doses increased with an increase of EBI dose, and the bleached cellulose fibers obtained by EBI treatment at 300 kGy was separated more uniformly than the bleached cellulose fiber obtained by alkali cooking with non-irradiated kenaf fiber. - Highlights: ► This study was to provide a progressive and convenient cellulose isolation process. ► Using an electron beam irradiation, we can obtain cellulose fibers using only water without chemicals during cooking process. ► We think that this cellulose isolation method will have an effect on enormous environmental and economic benefits.

Implementing Evidence-Based Teen Pregnancy-Prevention Interventions in a Community-Wide Initiative: Building Capacity and Reaching Youth.

Science.gov (United States)

House, L Duane; Tevendale, Heather D; Martinez-Garcia, Genevieve

2017-03-01

To describe efforts to implement evidence-based interventions (EBIs) within multicomponent, community-wide initiatives to reduce teen pregnancy. During 2011-2014, we collected information about the capacity (i.e., knowledge, confidence, training, and experience) of state and community-based organizations to support implementation of the following: EBIs, number and characteristics of youth served by EBIs, type of EBIs implemented, EBI settings, hours of training, and technical assistance provided. State and community-based organizations reported these data annually; however, training and technical assistance was reported monthly. We used aggregated data from these annual and monthly reports to describe the implementation of EBIs in the community-wide initiative project. From baseline in 2011-2014, state and community-based organizations increased their capacities to support program partners in delivering EBIs. They provided 5,015 hours of technical assistance and training on topics, including ensuring adequate capacity, process and outcome evaluation, program planning, and continuous quality improvement. Program partners increased the number of youth reached by an EBI in targeted communities by 349%, from 4,304 in the first year of implementation in 2012 to 19,344 in 2014. Most youth in 2014 received sexuality education programs (59%), whereas smaller percentages received abstinence-based, youth development, and clinic-based programs. Most youth were reached through schools (72%) and community-based organizations (16%), and smaller numbers were reached in other settings (e.g., faith-based organizations, health centers). Building and monitoring the capacity of program partners to deliver EBIs through technical assistance and training is important. In addition, partnering with schools leads to reaching more youth. Copyright © 2016 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

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.

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…

Smart E-Beam for Defect Identification & Analysis in the Nanoscale Technology Nodes: Technical Perspectives

Directory of Open Access Journals (Sweden)

Ankush Oberai

2017-10-01

Full Text Available Optical beam has been the veteran inspector of semiconductor wafer production house, ever since the birth of integrated circuit (IC. As technology and market place raise the bar on chip density, Moore’s law stretches to the limit. Due to its inherent physical limitations, the optical method just cannot see the measuring rod of silicon industry getting recalibrated to finer nano-scales. Electron Beam Inspection (EBI, by virtue of its high resolution, has started to rule the nodes at 10 nm and below. As the geometries shrink, defects can reside deep within the structures. EBI can find those tiny defects, which otherwise go scot-free with optical tools. However, EBI suffers the handicap of poor performance and low throughput. It is therefore essential to complement EBI by judiciously crafting out the methods for getting the desired performance, a subject matter to which, this article is committed to. The research torchlights the critical EBI throughput problem to round-up “care-areas”. Such guided and focused inspection augments throughput, thereby positioning EBI as the industrial grade candidate in finer nanometer segment. Besides gearing up to current trends, the smart EBI school of thought is inspirational, to fuel the aspirations for 1 nanometer scale.

Intervention Mapping to Adapt Evidence-Based Interventions for Use in Practice: Increasing Mammography among African American Women

Directory of Open Access Journals (Sweden)

Linda Highfield

2015-01-01

Full Text Available This paper describes and demonstrates the use of the systematic planning process, Intervention Mapping, to adapt an evidence-based public health intervention (EBI. We used a simplified version of Intervention Mapping (IM Adapt to increase an intervention’s fit with a new setting and population. IM Adapt guides researchers and practitioners in selecting an EBI, making decisions about whether and what to adapt, and executing the adaptation while guarding the EBI’s essential elements (those responsible for effectiveness. We present a case study of a project in which we used IM Adapt to find, adapt, implement, and evaluate an EBI to improve mammography adherence for African American women in a new practice setting in Houston, Texas. IM Adapt includes the following (1 assess needs and organizational capacity; (2 find EBIs; (3 plan adaptations based on fit assessments; (4 make adaptations; (5 plan for implementation; and (6 plan for evaluation of the adapted EBI. The case study shows an example of how public health researchers and practitioners can use the tool to make it easier to find and use EBIs, thus encouraging greater uptake. IM Adapt adds to existing dissemination and adaptation models by providing detailed guidance on how to decide on effective adaptation, while maintaining the essential elements of the EBI.

The dynamic influence of human resources on evidence-based intervention sustainability and population outcomes: an agent-based modeling approach.

Science.gov (United States)

McKay, Virginia R; Hoffer, Lee D; Combs, Todd B; Margaret Dolcini, M

2018-06-05

Sustaining evidence-based interventions (EBIs) is an ongoing challenge for dissemination and implementation science in public health and social services. Characterizing the relationship among human resource capacity within an agency and subsequent population outcomes is an important step to improving our understanding of how EBIs are sustained. Although human resource capacity and population outcomes are theoretically related, examining them over time within real-world experiments is difficult. Simulation approaches, especially agent-based models, offer advantages that complement existing methods. We used an agent-based model to examine the relationships among human resources, EBI delivery, and population outcomes by simulating provision of an EBI through a hypothetical agency and its staff. We used data from existing studies examining a widely implemented HIV prevention intervention to inform simulation design, calibration, and validity. Once we developed a baseline model, we used the model as a simulated laboratory by systematically varying three human resource variables: the number of staff positions, the staff turnover rate, and timing in training. We tracked the subsequent influence on EBI delivery and the level of population risk over time to describe the overall and dynamic relationships among these variables. Higher overall levels of human resource capacity at an agency (more positions) led to more extensive EBI delivery over time and lowered population risk earlier in time. In simulations representing the typical human resource investments, substantial influences on population risk were visible after approximately 2 years and peaked around 4 years. Human resources, especially staff positions, have an important impact on EBI sustainability and ultimately population health. A minimum level of human resources based on the context (e.g., size of the initial population and characteristics of the EBI) is likely needed for an EBI to have a meaningful impact on

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.

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

International Nuclear Information System (INIS)

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

2012-01-01

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.

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.

Early Brain Injury Associated with Systemic Inflammation After Subarachnoid Hemorrhage.

Science.gov (United States)

Savarraj, Jude; Parsha, Kaushik; Hergenroeder, Georgene; Ahn, Sungho; Chang, Tiffany R; Kim, Dong H; Choi, H Alex

2018-04-01

Early brain injury (EBI) after aneurysmal subarachnoid hemorrhage (aSAH) is defined as brain injury occurring within 72 h of aneurysmal rupture. Although EBI is the most significant predictor of outcomes after aSAH, its underlying pathophysiology is not well understood. We hypothesize that EBI after aSAH is associated with an increase in peripheral inflammation measured by cytokine expression levels and changes in associations between cytokines. aSAH patients were enrolled into a prospective observational study and were assessed for markers of EBI: global cerebral edema (GCE), subarachnoid hemorrhage early brain edema score (SEBES), and Hunt-Hess grade. Serum samples collected at ≤ 48 h of admission were analyzed using multiplex bead-based assays to determine levels of 13 pro- and anti-inflammatory cytokines. Pairwise correlation coefficients between cytokines were represented as networks. Cytokine levels and differences in correlation networks were compared between EBI groups. Of the 71 patients enrolled in the study, 17 (24%) subjects had GCE, 31 (44%) subjects had SEBES ≥ 3, and 21 (29%) had HH ≥ 4. IL-6 was elevated in groups with GCE, SEBES ≥ 3, and HH ≥ 4. MIP1β was independently associated with high-grade SEBES. Correlation network analysis suggests higher systematic inflammation in subjects with SEBES ≥ 3. EBI after SAH is associated with increased levels of specific cytokines. Peripheral levels of IL-10, IL-6, and MIP1β may be important markers of EBI. Investigating systematic correlations in addition to expression levels of individual cytokines may offer deeper insight into the underlying mechanisms related to EBI.

Fast and efficient charge breeding of the Californium rare isotope breeder upgrade electron beam ion source

International Nuclear Information System (INIS)

Ostroumov, P. N.; Barcikowski, A.; Dickerson, C. A.; Perry, A.; Sharamentov, S. I.; Vondrasek, R. C.; Zinkann, G. P.; Pikin, A. I.

2015-01-01

The Electron Beam Ion Source (EBIS), developed to breed Californium Rare Isotope Breeder Upgrade (CARIBU) radioactive beams at Argonne Tandem Linac Accelerator System (ATLAS), is being tested off-line. A unique property of the EBIS is a combination of short breeding times, high repetition rates, and a large acceptance. Overall, we have implemented many innovative features during the design and construction of the CARIBU EBIS as compared to the existing EBIS breeders. The off-line charge breeding tests are being performed using a surface ionization source that produces singly charged cesium ions. The main goal of the off-line commissioning is to demonstrate stable operation of the EBIS at a 10 Hz repetition rate and a breeding efficiency into single charge state higher than 15%. These goals have been successfully achieved and exceeded. We have measured (20% ± 0.7%) breeding efficiency into the single charge state of 28+ cesium ions with the breeding time of 28 ms. In general, the current CARIBU EBIS operational parameters can provide charge breeding of any ions in the full mass range of periodic table with high efficiency, short breeding times, and sufficiently low charge-to-mass ratio, 1/6.3 for the heaviest masses, for further acceleration in ATLAS. In this paper, we discuss the parameters of the EBIS and the charge breeding results in a pulsed injection mode with repetition rates up to 10 Hz

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.

Intervention Mapping to Adapt Evidence-Based Interventions for Use in Practice: Increasing Mammography among African American Women

OpenAIRE

Highfield, Linda; Hartman, Marieke A.; Mullen, Patricia Dolan; Rodriguez, Serena A.; Fernandez, Maria E.; Bartholomew, L. Kay

2015-01-01

This paper describes and demonstrates the use of the systematic planning process, Intervention Mapping, to adapt an evidence-based public health intervention (EBI). We used a simplified version of Intervention Mapping (IM Adapt) to increase an intervention's fit with a new setting and population. IM Adapt guides researchers and practitioners in selecting an EBI, making decisions about whether and what to adapt, and executing the adaptation while guarding the EBI's essential elements (those re...

Electrical bioimpedance enabling prompt intervention in traumatic brain injury

Science.gov (United States)

Seoane, Fernando; Atefi, S. Reza

2017-05-01

Electrical Bioimpedance (EBI) is a well spread technology used in clinical practice across the world. Advancements in Textile material technology with conductive textile fabrics and textile-electronics integration have allowed exploring potential applications for Wearable Measurement Sensors and Systems exploiting. The sensing principle of electrical bioimpedance is based on the intrinsic passive dielectric properties of biological tissue. Using a pair of electrodes, tissue is electrically stimulated and the electrical response can be sensed with another pair of surface electrodes. EBI spectroscopy application for cerebral monitoring of neurological conditions such as stroke and perinatal asphyxia in newborns have been justified using animal studies and computational simulations. Such studies have shown proof of principle that neurological pathologies indeed modify the dielectric composition of the brain that is detectable via EBI. Similar to stroke, Traumatic Brain Injury (TBI) also affects the dielectric properties of brain tissue that can be detected via EBI measurements. Considering the portable and noninvasive characteristics of EBI it is potentially useful for prehospital triage of TBI patients where. In the battlefield blast induced Traumatic Brain Injuries are very common. Brain damage must be assessed promptly to have a chance to prevent severe damage or eventually death. The relatively low-complexity of the sensing hardware required for EBI sensing and the already proven compatibility with textile electrodes suggest the EBI technology is indeed a candidate for developing a handheld device equipped with a sensorized textile cap to produce an examination in minutes for enabling medically-guided prompt intervention.

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

Impact of Human Resources on Implementing an Evidence-based HIV Prevention Intervention

Science.gov (United States)

McKay, Virginia R.; Dolcini, M. Margaret; Catania, Joseph A.

2016-01-01

Evidence-based interventions (EBIs) often require competent staff, or human resources (HR), for implementation. The empirical evidence characterizing the influence of HR fluctuations on EBI delivery is limited and conflicting. Using the Interactive Systems Framework, we explored staff fluctuation and the subsequent influence on RESPECT, an HIV prevention EBI. Methods We conducted interviews with staff in two waves (n=53, Wave I; n=37, Wave II) in a national sample of organizations delivering RESPECT (N=29). We analyzed interviews qualitatively to describe changes among RESPECT staff and explore the subsequent influences on RESPECT implementation. Results Organizations reported downsizing, turnover, and expansion of staff positions. Staff changes had multiple influences on RESPECT implementation including clients reached, fidelity to specific RESPECT protocols, and overall sustainability of RESPECT over time. Discussion HR fluctuations are common, and our analyses provide an initial characterization of the relationship between HR fluctuation and EBI implementation. Given the prominent influence of HR on EBI implementation, the Interactive Systems Framework is a useful guiding tool for future examinations. PMID:27150896

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

International Nuclear Information System (INIS)

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

2010-01-01

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, Z meas (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

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.

Wearable Vector Electrical Bioimpedance System to Assess Knee Joint Health.

Science.gov (United States)

Hersek, Sinan; Toreyin, Hakan; Teague, Caitlin N; Millard-Stafford, Mindy L; Jeong, Hyeon-Ki; Bavare, Miheer M; Wolkoff, Paul; Sawka, Michael N; Inan, Omer T

2017-10-01

We designed and validated a portable electrical bioimpedance (EBI) system to quantify knee joint health. Five separate experiments were performed to demonstrate the: 1) ability of the EBI system to assess knee injury and recovery; 2) interday variability of knee EBI measurements; 3) sensitivity of the system to small changes in interstitial fluid volume; 4) reducing the error of EBI measurements using acceleration signals; and 5) use of the system with dry electrodes integrated to a wearable knee wrap. 1) The absolute difference in resistance ( R) and reactance (X) from the left to the right knee was able to distinguish injured and healthy knees (p knee R was 2.5 Ω and for X was 1.2 Ω. 3) Local heating/cooling resulted in a significant decrease/increase in knee R (p knee R and X measured using the wet electrodes and the designed wearable knee wrap were highly correlated ( R 2 = 0.8 and 0.9, respectively). This study demonstrates the use of wearable EBI measurements in monitoring knee joint health. The proposed wearable system has the potential for assessing knee joint health outside the clinic/lab and help guide rehabilitation.

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.

Changes in mechanical and chemical wood properties by electron beam irradiation

International Nuclear Information System (INIS)

Schnabel, Thomas; Huber, Hermann; Grünewald, Tilman A.; Petutschnigg, Alexander

2015-01-01

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

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.

Run 16 Tandem gold performance in the injectors and possible improvement with AGS type 6:3:1 bunch merge in the Booster

Energy Technology Data Exchange (ETDEWEB)

Zeno, Keith [Brookhaven National Lab. (BNL), Upton, NY (United States)

2016-10-21

During Run 16 the Tandem was used as the Gold pre-injector for a brief time so that RHIC could continue running while EBIS was down for repairs. Given the time constraints, the setup was largely derived from the EBIS Au setup. The EBIS Au setup used a 4:2:1 bunch merge in the Booster and a 12:6:2 bunch merge in the AGS.1 This note will describe the Tandem Au setup and compare it to that used for EBIS Au. The bunch merge in the Booster for Tandem Au did not work well, and it seems likely that the performance would’ve been significantly better if it did. An AGS type 6:3:1 merge in the Booster is described which might improve matters.2 Somewhat speculative estimates for the AGS bunch intensity and emittance, if that merge were successful in reducing the Booster extraction emittance to EBIS Au levels, are also given for several potential setups. Using 6 Booster loads from the Tandem, the AGS bunch intensity at extraction reached about 2.5e9 ions with a longitudinal emittance (ε) of about 0.59 eV·s/n.3 Using 12 Booster loads from EBIS, the peak bunch intensity and ε was about 3.1e9 ions and 0.75 eV·s/n, respectively. A 6.4 sec supercycle was used for both at the time, but the Tandem Au supercycle (barring any potential issues with Tandem) could probably have been reduced to about 4.6 sec.

Development and persistence of resistance to fungicides in Sphaerotheca fuliginea in cucumbers in the Netherlands

NARCIS (Netherlands)

Schepers, H.T.A.M.

1985-01-01

Ergosterol biosynthesis inhibitors (EBIs) have a remarkably broad spectrum of antifungal activity. They belong to the commercial fungicides which exhibit the highest activity known to date. Resistance to EBIs was found in vitro, but the level of resistance and the decreased fitness of resistant

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.

Beam Dynamics Simulations of the REX-ISOLDE A/q-separator

CERN Document Server

Fraser, M A; Wenander, F

2014-01-01

The REX-ISOLDE A=q-separator selects the radioactive species of interest from the background of residual gas ions coming from the EBIS ion source. In the context of the HIE-ISOLDE upgrade, including the implementation of a multi-harmonic buncher and an upgraded EBIS, the separator and the beam line between the EBIS and RFQ, which we will call the Low Energy Beam Transfer (LEBT) line, has been simulated by tracking particles through the field maps of each active element using the TRACK [4] code. The simulations were benchmarked with a COSY-1 model that was improved to take into account the fringe fields of the electrostatic quadrupoles, electrostatic deflector and magnetic bender; the model can be used to tune and optimise the separator with higher-order effects taken into account. In this note the beam dynamics simulations are documented and the transverse and longitudinal acceptance of the separator line studied to provide design constraints for the EBIS upgrade.

The ninth International Symposium on Electron Beam Ion Sources and Traps and Their Applications, 15-17 April 2004

International Nuclear Information System (INIS)

Nakamura, Nobuyuki; Ohtani, Shunsuke

2004-01-01

The ninth International Symposium on Electron Beam Ion Sources and Traps and Their Applications - EBIS/T 2004 was held at the Tokyo Metropolitan University (TMU), 15-17 April 2004. There were about 40 participants and about 30 papers presented. The meeting has shown the remarkable progress in science and technology with the EBIS/T machines. In this meeting, besides the normal presentations related to the EBIS/T works, a special session was organized on the last day which was dedicated to Professors N Kobayashi and K Okuno, who have contributed to the EBIS/T development and to the physics of highly charged ions (HCI), to mark their retirement from the TMU in March 2004. In the evening of the first day, there was a laboratory tour where the participants enjoyed seeing the Tokyo EBIT facility and also a beer party in a small hall next to the laboratory. The banquet was held in a traditional Japanese restaurant in a village under Mt Takao with the Japanese meals and performances, after seeing the HCI-research activities in the TMU. The next EBIS/T symposium will be held in Heidelberg in the summer of 2007 as a satellite meeting of XXV ICPEAC. We are looking forward to the next exciting meeting there. Finally, we thank all of TMU staffs and students for their help during the meeting. (preface)

Children's Executive Functions: Are They Poorer after Very Early Brain Insult

Science.gov (United States)

Anderson, Vicki; Spencer-Smith, Megan; Coleman, Lee; Anderson, Peter; Williams, Jackie; Greenham, Mardee; Leventer, Richard J.; Jacobs, Rani

2010-01-01

Traditionally early brain insult (EBI) has been considered to have better outcome than later injury, consistent with the notion that the young brain is flexible and able to reorganize. Recent research findings question this view, suggesting that EBI might lead to poorer outcome than brain insult at any other age. Exploring this early vulnerability…

The effect of the PROSPER partnership model on cultivating local stakeholder knowledge of evidence-based programs: a five-year longitudinal study of 28 communities.

Science.gov (United States)

Crowley, D Max; Greenberg, Mark T; Feinberg, Mark E; Spoth, Richard L; Redmond, Cleve R

2012-02-01

A substantial challenge in improving public health is how to facilitate the local adoption of evidence-based interventions (EBIs). To do so, an important step is to build local stakeholders' knowledge and decision-making skills regarding the adoption and implementation of EBIs. One EBI delivery system, called PROSPER (PROmoting School-community-university Partnerships to Enhance Resilience), has effectively mobilized community prevention efforts, implemented prevention programming with quality, and consequently decreased youth substance abuse. While these results are encouraging, another objective is to increase local stakeholder knowledge of best practices for adoption, implementation and evaluation of EBIs. Using a mixed methods approach, we assessed local stakeholder knowledge of these best practices over 5 years, in 28 intervention and control communities. Results indicated that the PROSPER partnership model led to significant increases in expert knowledge regarding the selection, implementation, and evaluation of evidence-based interventions. Findings illustrate the limited programming knowledge possessed by members of local prevention efforts, the difficulty of complete knowledge transfer, and highlight one method for cultivating that knowledge.

Simulation of 10 A electron-beam formation and collection for a high current electron-beam ion source

Science.gov (United States)

Kponou, A.; Beebe, E.; Pikin, A.; Kuznetsov, G.; Batazova, M.; Tiunov, M.

1998-02-01

Presented is a report on the development of an electron-beam ion source (EBIS) for the relativistic heavy ion collider at Brookhaven National Laboratory (BNL) which requires operating with a 10 A electron beam. This is approximately an order of magnitude higher current than in any existing EBIS device. A test stand is presently being designed and constructed where EBIS components will be tested. It will be reported in a separate paper at this conference. The design of the 10 A electron gun, drift tubes, and electron collector requires extensive computer simulations. Calculations have been performed at Novosibirsk and BNL using two different programs, SAM and EGUN. Results of these simulations will be presented.

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).

ELECTRON BEAM ION SOURCE PRE-INJECTOR DIGNOSTICS

International Nuclear Information System (INIS)

WILINSKI, M.; ALESSI, J.; BEEBE, E.; BELLAVIA, S.; PIKIN, A.

2006-01-01

A new ion pre-injector line is currently under design at Brookhaven National Laboratory (BNL) for the Relativistic Heavy Ion Collider (RHIC) and the NASA Space Radiation Laboratory (NSRL,). Collectively, this new line is referred to as the EBIS project. This pre-injector is based on an Electron Beam Ion Source (EBIS), a Radio Frequency Quadrupole (R-FQ) accelerator, and a linear accelerator. The new EBIS will be able to produce a wide range of heavy ion species as well as rapidly switching between species. To aid in operation of the pre-injector line, a suite of diagnostics is currently proposed which includes faraday cups, current transformers, profile monitors, and a pepperpot emittance measurement device

Beyond Evidence-Based Interventions for Teen Pregnancy Prevention

OpenAIRE

Emily Scribner-O'Pray

2017-01-01

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.

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.

Simulation of 10 A electron-beam formation and collection for a high current electron-beam ion source

International Nuclear Information System (INIS)

Kponou, A.; Beebe, E.; Pikin, A.; Kuznetsov, G.; Batazova, M.; Tiunov, M.

1998-01-01

Presented is a report on the development of an electron-beam ion source (EBIS) for the relativistic heavy ion collider at Brookhaven National Laboratory (BNL) which requires operating with a 10 A electron beam. This is approximately an order of magnitude higher current than in any existing EBIS device. A test stand is presently being designed and constructed where EBIS components will be tested. It will be reported in a separate paper at this conference. The design of the 10 A electron gun, drift tubes, and electron collector requires extensive computer simulations. Calculations have been performed at Novosibirsk and BNL using two different programs, SAM and EGUN. Results of these simulations will be presented. copyright 1998 American Institute of Physics

Nationally Certified School Psychologists' use and reported barriers to using evidence-based interventions in schools: the influence of graduate program training and education.

Science.gov (United States)

Hicks, Taylor B; Shahidullah, Jeffrey D; Carlson, John S; Palejwala, Mohammed H

2014-12-01

The purpose of this study was to empirically investigate Nationally Certified School Psychologists' (NCSP) training in and use of evidence-based interventions (EBIs) for child behavior concerns as well as their reported implementation barriers. A modified Tailored Design Method (TDM; Dillman, Smyth, & Christian, 2009) using up to four mail-based participant contacts was used to obtain survey data (72% usable response rate; n = 392) from a randomly selected national sample of 548 currently practicing NCSPs. Lack of time was rated as the most serious barrier to behavioral EBI implementation, followed by a lack of necessary resources, and financial constraints. Nearly three-quarters (71%) of respondents reported a perceived inadequacy of graduate program training in behavioral EBIs, with a statistically significant difference found between respondents who attended American Psychological Association (APA)-accredited/National Association of School Psychologists (NASP)-approved programs and those who did not. These findings highlight the significant barriers school psychologists encounter when attempting to implement behavioral EBIs within applied practice, as well as the importance of graduate program training in implementation science. Implications for training, practice, and research are discussed. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Assessment of electron beam irradiation induced proteomic changes and its effect on the development of silkworm, Bombyx mori (Bombycidae: Lepidoptera

Directory of Open Access Journals (Sweden)

Mani Kannan

2016-01-01

Full Text Available The present study has been designed to determine the hemolymph protein changes induced by EBI using Microtron (ranges from 20 to 100 Gy on the 5th instar larvae of silkworm, Bombyx mori using SDS–PAGE. The EBI did not caused any impact on 5th instar larval hemolymph proteins, however a significant reduction of pupal hemolymph proteins such as lipophorin (250 kDa, vitellogenin (180 kDa, storage protein (76–80 kDa and a 30 kDa protein was observed through SDS–PAGE and densitometry analysis. These proteins are known to play a crucial role in various developmental processes including transport of lipids, as amino acid reservoir for providing precursors for egg and cuticle formation and immunity of B. mori. Further, a decrease of antioxidant enzymes such as Superoxide Dismutase (SOD and Catalase (CAT in the EBI treated larval and pupal hemolymph was observed. In addition, a negative influence on growth characteristics and appearance of pupal deformity was noted. This may be due to damage in hemolymph proteins, when the larvae were exposed to EBI at >80 Gy.

Apolipoprotein E-Mimetic Peptide COG1410 Promotes Autophagy by Phosphorylating GSK-3β in Early Brain Injury Following Experimental Subarachnoid Hemorrhage

Directory of Open Access Journals (Sweden)

Xinshen Li

2018-03-01

Full Text Available COG1410, a mimetic peptide derived from the apolipoprotein E (apoE receptor binding region, exerts positive effect on neurological deficits in early brain injury (EBI after experimental subarachnoid hemorrhage (SAH. Currently the neuroprotective effect of COG1410 includes inhibiting BBB disruption, reducing neuronal apoptosis, and neuroinflammation. However, the effect and mechanism of COG1410 to subcellular organelles disorder have not been fully investigated. As the main pathway for recycling long-lived proteins and damaged organelles, neuronal autophagy is activated in SAH and exhibits neuroprotective effects by reducing the insults of EBI. Pharmacologically elevated autophagy usually contributes to alleviated brain injury, while few of the agents achieved clinical transformation. In this study, we explored the activation of autophagy during EBI by measuring the Beclin-1 and LC3B-II protein levels. Administration of COG1410 notably elevated the autophagic markers expression in neurons, simultaneously reversed the neurological deficits. Furthermore, the up-regulated autophagy by COG1410 was further promoted by p-GSK-3β agonist, whereas decreased by p-GSK-3β inhibitor. Taken together, these data suggest that the COG1410 might be a promising therapeutic strategy for EBI via promoting autophagy in SAH.

CRYEBIS, an exotic source for the synchrotron Saturne 2

International Nuclear Information System (INIS)

Arianer, J.; Buhler, S.; Cabrespine, A.; Goldstein, C.; Ulrich, M.; Abd El Baki, M.

1979-01-01

An EBIS has been built to provide nuclei up to Ne 10+ (10 10 ppp) and polarized particles (3.10 11 with storage). This EBIS uses a superconducting solenoid (3T, 1.5m long). The electron density is higher than 10 3 A.cm -2 by space charge neutralization. Results of preliminary experiments show spectra with Ne 10+ , A 18+ , Kr 34+ and Xe 44+ [fr

Identification and characterisation of the IL-27 p28 subunits in fish: Cloning and comparative expression analysis of two p28 paralogues in Atlantic salmon Salmo salar.

Science.gov (United States)

Husain, Mansourah; Martin, Samuel A M; Wang, Tiehui

2014-11-01

Interleukin (IL)-27 is an IL-6/IL-12 family member with pro-inflammatory and anti-inflammatory properties. It is a heterodimeric cytokine composed of an α-chain p28 and a β-chain Ebi3 (Epstein-Barr virus induce gene 3). The p28 subunit can also be secreted as a monomer and function as IL-30 that acts as an inhibitor of IL-27 signalling. At present, the p28 gene has only been described in mammals. Thus, for the first time outwith mammals, we have identified seven p28 molecules in six divergent teleost fish species, Atlantic salmon, two cichlids, two cyprinids and a yellowtail. The fish p28 molecules have higher similarities to mammalian p28 than other IL-6/12 family members. Critical residues involved in the interaction with Ebi3 and the receptor gp130 are highly conserved. The prediction that these are true orthologues is supported by phylogenetic and synteny analysis. Two p28 paralogues (p28a and p28b) sharing 72% aa identity have been identified and characterised in Atlantic salmon. There are multiple upstream ATGs in the 5'-UTR and ATTTA motifs in the 3'-UTR of both cDNA sequences, suggesting regulation at the post-transcriptional and translational level. Both salmon p28 genes are highly expressed in immune relevant tissues, such as thymus, gills, spleen and head kidney. Conversely salmon Ebi3 is highly expressed in other organs, such as liver and caudal kidney. The expression of p28 but not Ebi3 was induced by PAMPs and recombinant cytokines in head kidney cells, and in spleen by Poly I:C challenge in vivo. The dissociation of the expression and modulation of p28 and Ebi3 suggest that both p28 and Ebi3 may be secreted alone or with other partners. Copyright © 2014 Elsevier Ltd. All rights reserved.

A mixed methods study of individual and organizational factors that affect implementation of interventions for children with autism in public schools.

Science.gov (United States)

Locke, Jill; Beidas, Rinad S; Marcus, Steven; Stahmer, Aubyn; Aarons, Gregory A; Lyon, Aaron R; Cannuscio, Carolyn; Barg, Frances; Dorsey, Shannon; Mandell, David S

2016-10-10

The significant lifelong impairments associated with autism spectrum disorder (ASD), combined with the growing number of children diagnosed with ASD, have created urgency in improving school-based quality of care. Although many interventions have shown efficacy in university-based research, few have been effectively implemented and sustained in schools, the primary setting in which children with ASD receive services. Individual- and organizational-level factors have been shown to predict the implementation of evidence-based interventions (EBIs) for the prevention and treatment of other mental disorders in schools, and may be potential targets for implementation strategies in the successful use of autism EBIs in schools. The purpose of this study is to examine the individual- and organizational-level factors associated with the implementation of EBIs for children with ASD in public schools. We will apply the Domitrovich and colleagues (2008) framework that examines the influence of contextual factors (i.e., individual- and organizational-level factors) on intervention implementation in schools. We utilize mixed methods to quantitatively test whether the factors identified in the Domitrovich and colleagues (2008) framework are associated with the implementation of autism EBIs, and use qualitative methods to provide a more comprehensive understanding of the factors associated with successful implementation and sustainment of these interventions with the goal of tailoring implementation strategies. The results of this study will provide an in-depth understanding of individual- and organizational-level factors that influence the successful implementation of EBIs for children with ASD in public schools. These data will inform potential implementation targets and tailoring of strategies that will help schools overcome barriers to implementation and ultimately improve the services and outcomes for children with ASD.

Phosphorylation of Akt by SC79 Prevents Iron Accumulation and Ameliorates Early Brain Injury in a Model of Experimental Subarachnoid Hemorrhage

Directory of Open Access Journals (Sweden)

Shuangying Hao

2016-03-01

Full Text Available Previous studies have demonstrated that activation of Akt may alleviate early brain injury (EBI following subarachnoid hemorrhage (SAH. This study is undertaken to determine whether iron metabolism is involved in the beneficial effect of Akt activation after SAH. Therefore, we used a novel molecule, SC79, to activate Akt in an experimental Sprague–Dawley rat model of SAH. Rats were randomly divided into four groups as follows: sham, SAH, SAH + vehicle, SAH + SC79. The results confirmed that SC79 effectively enhanced the defense against oxidative stress and alleviated EBI in the temporal lobe after SAH. Interestingly, we found that phosphorylation of Akt by SC79 reduced cell surface transferrin receptor-mediated iron uptake and promoted ferroportin-mediated iron transport after SAH. As a result, SC79 administration diminished the iron content in the brain tissue. Moreover, the impaired Fe-S cluster biogenesis was recovered and loss of the activities of the Fe-S cluster-containing enzymes were regained, indicating that injured mitochondrial functions are restored to healthy levels. These findings suggest that disrupted iron homeostasis could contribute to EBI and Akt activation may regulate iron metabolism to relieve iron toxicity, further protecting neurons from EBI after SAH.

Charge breeding of radioactive isotopes at the CARIBU facility with an electron beam ion source

Science.gov (United States)

Vondrasek, R. C.; Dickerson, C. A.; Hendricks, M.; Ostroumov, P.; Pardo, R.; Savard, G.; Scott, R.; Zinkann, G.

2018-05-01

An Electron Beam Ion Source Charge Breeder (EBIS-CB) has been developed at Argonne National Laboratory as part of the californium rare ion breeder upgrade. For the past year, the EBIS-CB has been undergoing commissioning as part of the ATLAS accelerator complex. It has delivered both stable and radioactive beams with A/Q 18% into a single charge state. The operation of this device, challenges during the commissioning phase, and future improvements will be discussed.

Industry Study, Environment Industry, Spring 2009

Science.gov (United States)

2009-01-01

practices. For example, the cruising sector of the tourism industry has widely- acknowledged negative environmental impacts (carbon emissions and ocean...Services: An Industry Analysis ,” (2009): 4. http://www.berr.gov.uk/files/file50253.pdf 18 Ibid., 5. 19 EBI, 21 20 Department for Business...Ibid., 26. 50 DataMonitor Country Analysis Report, “Korea: In-Depth PESTLE Insights,” (June 2008): 4. 51 EBI, “3000,” 1-22. 52 Ibid., 5-130, 5

Statistika spotřeby obyvatelstva

OpenAIRE

Orendáčová, Jana

2008-01-01

Main goal of the diploma thesis is to describe household consumption and its survey in the Czech Republic not only from the macroeconomic but mainly from the microeconomic standpoint. Consumption expenditures are the main subject of many long-term analysis and forecasts which help by implementation of economic and politcal precautions. In connection with the historical development of statistic as a scientific disciplin there is also a significant stress on a methodical development of househol...

Enhancing capacity among faith-based organizations to implement evidence-based cancer control programs: a community-engaged approach.

Science.gov (United States)

Leyva, Bryan; Allen, Jennifer D; Ospino, Hosffman; Tom, Laura S; Negrón, Rosalyn; Buesa, Richard; Torres, Maria Idalí

2017-09-01

Evidence-based interventions (EBIs) to promote cancer control among Latinos have proliferated in recent years, though adoption and implementation of these interventions by faith-based organizations (FBOs) is limited. Capacity building may be one strategy to promote implementation. In this qualitative study, 18 community key informants were interviewed to (a) understand existing capacity for health programming among Catholic parishes, (b) characterize parishes' resource gaps and capacity-building needs implementing cancer control EBIs, and (c) elucidate strategies for delivering capacity-building assistance to parishes to facilitate implementation of EBIs. Semi-structured qualitative interviews were conducted. Key informants concurred about the capacity of Catholic parishes to deliver health programs, and described attributes of parishes that make them strong partners in health promotion initiatives, including a mission to address physical and mental health, outreach to marginalized groups, altruism among members, and existing engagement in health programming. However, resource gaps and capacity building needs were also identified. Specific recommendations participants made about how existing resources might be leveraged to address challenges include to: establish parish wellness committees; provide "hands-on" learning opportunities for parishioners to gain program planning skills; offer continuous, tailored, on-site technical assistance; facilitate relationships between parishes and community resources; and provide financial support for parishes. Leveraging parishes' existing resources and addressing their implementation needs may improve adoption of cancer control EBIs.

A zone-specific fish-based biotic index as a management tool for the Zeeschelde estuary (Belgium).

Science.gov (United States)

Breine, Jan; Quataert, Paul; Stevens, Maarten; Ollevier, Frans; Volckaert, Filip A M; Van den Bergh, Ericia; Maes, Joachim

2010-07-01

Fish-based indices monitor changes in surface waters and are a valuable aid in communication by summarising complex information about the environment (Harrison and Whitfield, 2004). A zone-specific fish-based multimetric estuarine index of biotic integrity (Z-EBI) was developed based on a 13 year time series of fish surveys from the Zeeschelde estuary (Belgium). Sites were pre-classified using indicators of anthropogenic impact. Metrics showing a monotone response with pressure classes were selected for further analysis. Thresholds for the good ecological potential (GEP) were defined from references. A modified trisection was applied for the other thresholds. The Z-EBI is defined by the average of the metric scores calculated over a one year period and translated into an ecological quality ratio (EQR). The indices integrate structural and functional qualities of the estuarine fish communities. The Z-EBI performances were successfully validated for habitat degradation in the various habitat zones. Copyright 2010 Elsevier Ltd. All rights reserved.

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

Science.gov (United States)

Greville, W James; Dymond, Simon; Newton, Philip M

2016-01-01

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. 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. 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. 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.

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.

EBTS: DESIGN AND EXPERIMENTAL STUDY

International Nuclear Information System (INIS)

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

2000-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Vali, Indudhar Panduranga [Manipal Institute of Technology, Manipal University, Manipal 576104 (India); Shetty, Pramoda Kumara, E-mail: pramod.shetty@manipal.edu [Manipal Institute of Technology, Manipal University, Manipal 576104 (India); Mahesha, M.G. [Manipal Institute of Technology, Manipal University, Manipal 576104 (India); Petwal, V.C.; Dwivedi, Jishnu [Raja Ramanna Centre for Advanced Technology, Department of Atomic Energy, Government of India, Indore 452012 (India); Choudhary, R.J. [UGC-DAE Consortium for Scientific Research, University Campus, Khandwa Road, Indore 452017 (India)

2017-06-15

Highlights: • Tuning of Schottky barrier height has been achieved by electron beam irradiation at different doses on n-Si wafer prior to the fabrication of Schottky contact. • The XPS analyses have shown irradiation induced defects and the formation of several localized chemical states in Si/SiOx interface that influences the Schottky barrier height. • High ideality factor indicates metal-insulator-semiconductor configuration of the Schottky diode and the inhomogeneous nature of the Schottky barrier height. • The modifications in I–V characteristics have been observed as a function of electron dose. This is caused due to changes in the Schottky diode parameters and different transport mechanisms. - Abstract: 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 (Φ{sub B}), ideality factor (n) and series resistance (R{sub s}). 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 Φ{sub B} was observed as a function of EBI dose. The improved n with increased Φ{sub B} 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

Interstitial high-dose-rate brachytherapy in the treatment of base of tongue carcinoma

Energy Technology Data Exchange (ETDEWEB)

Takacsi-Nagy, Z.; Polgar, C.; Somogyi, A.; Major, T.; Fodor, J.; Nemeth, G. [Dept. of Radiotherapy, National Inst. of Oncology, Budapest (Hungary); Oberna, F. [Dept. of Maxillofacial Surgery, St. Rokus Hospital, Budapest (Hungary); Remenar, E.; Kasler, M. [Dept. of Head and Neck, Maxillofacial and Reconstructive Plastic Surgery, National Inst. of Oncology, Budapest (Hungary)

2004-12-01

Background and purpose: to date none of the studies examined the feasibility and efficacy of interstitial high-dose-rate (HDR) brachytherapy in the treatment of carcinoma of the tongue base. Therefore the aim of this study was to contribute to this issue. Patients and methods: between 1992 and 2000 37 patients (mean age 55 years) with T1-4 and NO-3 carcinoma of the base of tongue were presented. Neck dissection was carried out in twelve cases (32%). 30 patients with advanced stage received brachytherapy boost after 50-66.5 Gy (mean, 60 Gy) locoregional external beam irradiation (EBI) and 7 patients with early stage (T1-2, NO) were managed locally with wide tumor excision and sole brachytherapy. 4 of them underwent neck dissection and the others were subjected to 50 Gy regional EBI. The mean dose of boost and sole brachytherapy was 18 Gy and 28 Gy, respectively. Results: the median follow-up time for surviving patients was 51 months. The 7 sole brachytherapy patients are living with no evidence of disease. For patients treated with EBI and brachytherapy boost, the 5-year actuarial rate of local, locoregional recurrence-free and overall survival was 60%, 52% and 46%, respectively. For all patients in univariate analysis larger tumor size (T4 vs. T1-3) was significant negative predictor of local (RR: 7.23) and locoregional control (RR: 3.87), but nodal involvement was not. Delayed soft tissue ulceration and osteoradionecrosis occurred in 4 (13%) EBI and brachytherapy treated patients. None of the sole brachytherapy patients experienced severe late radiation toxicity. Conclusion: EBI combined with interstitial HDR brachytherapy boost result in acceptable local tumor control with low incidence of late side effects in patients with advanced disease. Fractionated sole HDR brachytherapy following tumor excision is a feasible treatment option for patients with early stage cancer and gives excellent local results. (orig.)

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...

Brookhaven National Laboratory electron beam test stand

International Nuclear Information System (INIS)

Pikin, A.; Alessi, J.; Beebe, E.; Kponou, A.; Prelec, K.; Snydstrup, L.

1998-01-01

The main purpose of the electron beam test stand (EBTS) project at the Brookhaven National Laboratory is to build a versatile device to develop technologies that are relevant for a high intensity electron beam ion source (EBIS) and to study the physics of ion confinement in a trap. The EBTS will have all the main attributes of EBIS: a 1-m-long, 5 T superconducting solenoid, electron gun, drift tube structure, electron collector, vacuum system, ion injection system, appropriate control, and instrumentation. Therefore it can be considered a short prototype of an EBIS for a relativistic heavy ion collider. The drift tube structure will be mounted in a vacuum tube inside a open-quotes warmclose quotes bore of a superconducting solenoid, it will be at room temperature, and its design will employ ultrahigh vacuum technology to reach the 10 -10 Torr level. The first gun to be tested will be a 10 A electron gun with high emission density and magnetic compression of the electron beam. copyright 1998 American Institute of Physics

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.

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. © The Author(s) 2017. Published by Oxford University Press.

Hyperion II: a heavy ion pre-injector for Saturne

International Nuclear Information System (INIS)

Olivier, M.; Auclair, J.P.; Courtois, A.

1983-01-01

Since 1978, the 3GeV synchrotron Saturne is routinely operated with proton, deuteron, helium beams and, since 1981 with polarized protons and deuterons. Heavy ions are expected in 1983 by using a new pre-injector presently under construction. The marriage of an EBIS and an RFQ can be looked upon generally as a very good means of production of heavy ion beams at low energy. In the first paragraph, the cryogenic version of EBIS, called CRYEBIS, is described, while the RFQ design is studied in detail in paragraph two. The construction status is given in a third paragraph

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.

Cellular and molecular properties of {sup 90}Y-labeled cetuximab in combination with radiotherapy on human tumor cells in vitro

Energy Technology Data Exchange (ETDEWEB)

Saki, M.; Toulany, M.; Rodemann, H.P. [Tuebingen Univ. (Germany). Div. of Radiobiology and Molecular Environmental Research; Sihver, W.; Zenker, M.; Heldt, J.M.; Mosch, B.; Pietzsch, H.J.; Steinbach, J. [Helmholtz-Zentrum Dresden-Rossendorf (HZDR) e.V., Dresden (Germany). Inst. of Radiopharmacy; Baumann, M. [Technische Univ. Dresden (Germany). Dept. of Radiation Oncology

2012-09-15

Purpose: Anti-EGFR antibody cetuximab (C225) is used in combination with radiotherapy of head and neck squamous cell carcinoma (HNSCC) patients. We investigated whether conjugation of cetuximab with trans-cyclohexyl-diethylene-triamine-pentaacetic acid (CHX-A''-DTPA) and radiolabeling with {sup 90}Yttrium affect the molecular and cellular function of cetuximab and improve its combined effect with external-beam irradiation (EBI). Methods: The following cell lines were used: HNSCC UT5, SAS, FaDu, as well as A43, Chinese hamster ovary cells (CHO), and human skin fibroblast HSF7. Binding affinity and kinetics, specificity, retention, and the combination of {sup 90}Y-cetuximab with EBI were evaluated. Results: Control cetuximab and CHX-A''-DTPA-cetuximab blocked the proliferation activity of UT5 cells. In combination with EBI, CHX-A''-DTPA-cetuximab increased the radiosensitivity of UT5 to a similar degree as control cetuximab did. In contrast, in SAS and HSF7 cells neither proliferation nor radiosensitivity was affected by either of the antibodies. Binding [{sup 90}Y]Y-CHX-A''-DTPA-cetuximab ({sup 90}Y-cetuximab) to EGFR in HNSCC cells occurred time dependently with a maximum binding at 24 h. Retention of {sup 90}Y-cetuximab was similar in both HNSCC cell lines; 24 h after treatment, approximately 90% of bound activity remained in the cell layer. Competition assays, using cell membranes in the absence of an internalized fraction of cetuximab, showed that the cetuximab affinity is not lost as a result of conjugation with CHX-A''-DTPA. Cetuximab and CHX-A''-DTPA-cetuximab blocked EGF-induced Y1068 phosphorylation of EGFR. The lack of an effect of cetuximab on EGF-induced Akt and ERK1/2 phosphorylation and the inhibition of irradiation (IR)-induced Akt and ERK1/2 phosphorylation by cetuximab were not affected by DTPA conjugation. {sup 90}Y-cetuximab in combination with EBI resulted in a pronounced inhibition of

Cellular and molecular properties of 90Y-labeled cetuximab in combination with radiotherapy on human tumor cells in vitro

International Nuclear Information System (INIS)

Saki, M.; Toulany, M.; Rodemann, H.P.; Sihver, W.; Zenker, M.; Heldt, J.M.; Mosch, B.; Pietzsch, H.J.; Steinbach, J.; Baumann, M.

2012-01-01

Purpose: Anti-EGFR antibody cetuximab (C225) is used in combination with radiotherapy of head and neck squamous cell carcinoma (HNSCC) patients. We investigated whether conjugation of cetuximab with trans-cyclohexyl-diethylene-triamine-pentaacetic acid (CHX-A''-DTPA) and radiolabeling with 90 Yttrium affect the molecular and cellular function of cetuximab and improve its combined effect with external-beam irradiation (EBI). Methods: The following cell lines were used: HNSCC UT5, SAS, FaDu, as well as A43, Chinese hamster ovary cells (CHO), and human skin fibroblast HSF7. Binding affinity and kinetics, specificity, retention, and the combination of 90 Y-cetuximab with EBI were evaluated. Results: Control cetuximab and CHX-A''-DTPA-cetuximab blocked the proliferation activity of UT5 cells. In combination with EBI, CHX-A''-DTPA-cetuximab increased the radiosensitivity of UT5 to a similar degree as control cetuximab did. In contrast, in SAS and HSF7 cells neither proliferation nor radiosensitivity was affected by either of the antibodies. Binding [ 90 Y]Y-CHX-A''-DTPA-cetuximab ( 90 Y-cetuximab) to EGFR in HNSCC cells occurred time dependently with a maximum binding at 24 h. Retention of 90 Y-cetuximab was similar in both HNSCC cell lines; 24 h after treatment, approximately 90% of bound activity remained in the cell layer. Competition assays, using cell membranes in the absence of an internalized fraction of cetuximab, showed that the cetuximab affinity is not lost as a result of conjugation with CHX-A''-DTPA. Cetuximab and CHX-A''-DTPA-cetuximab blocked EGF-induced Y1068 phosphorylation of EGFR. The lack of an effect of cetuximab on EGF-induced Akt and ERK1/2 phosphorylation and the inhibition of irradiation (IR)-induced Akt and ERK1/2 phosphorylation by cetuximab were not affected by DTPA conjugation. 90 Y-cetuximab in combination with EBI resulted in a pronounced inhibition of colony formation of HNSCC cells. Conclusions: Conjugation of CHX-A''-DTPA to cetuximab

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

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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

Adapting an Evidence-Based HIV Prevention Intervention Targeting High-Risk Migrant Workers: The Process and Outcome of Formative Research

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Roman eShrestha

2016-03-01

Full Text Available BackgroundHistorically, HIV prevention efforts in Nepal have primarily focused on heterosexual transmission, particularly, among female sex workers (FSWs and their male clients, with little acknowledgment of the contribution of migrant workers to the epidemic. The very few HIV prevention efforts that have been attempted with migrants have been unsuccessful primarily due to stigma, discrimination, and insufficient availability of culturally relevant evidence-based interventions (EBIs. As an initial step toward addressing this unmet need, we conducted formative research aimed at adapting an evidence-based HIV risk reduction intervention for implementation among migrants in Nepal.MethodsOur formative work involved a critical examination of established EBIs and associated published reports complemented by data elicited through structured interviews with members of the target population and key stakeholders. Between July and August, 2014, we conducted structured one-on-one interview with migrants (n = 5 and key stakeholder (e.g., counselors, field workers, and project coordinator; n = 5, which focused on the HIV risk profiles of the migrants and on ways to optimize intervention content, delivery, and placement within the community-based settings. Data analysis followed a thematic analysis approach utilizing several qualitative data analysis techniques, including inductive analysis, cross-case analysis, and analytical coding of textual data.ResultsBased on formative research, we adapted the Holistic Health Recovery Program (HHRP, an EBI, to consist of four 30-minute sessions that cover a range of topics relevant to migrants in Nepal. The intervention was adapted with flexibility so that it could be provided in an individual format, implemented within or outside the CBO, and can be delivered in either consecutive or weekly sessions based on time constraints. ConclusionsThis paper provides a detailed description of the formative research process

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

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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.

The status of the Electron Beam Ion Sources

Energy Technology Data Exchange (ETDEWEB)

Stockli, M.P.

1990-01-01

More than twenty years after its invention, 13 examples of the Electron Beam Ion Sources (EBIS) are in operation worldwide. The substantial progress in operation and insight, achieved over the last few years, made the EBISes become reliable tools for the production of beams of very highly charged, low-energy ions. For example, 8 EBISes produce bare argon on a standard basis. The successful production of hydrogen-like xenon presents the ions with the highest ionization energy, whereas the production of Th80+ presents the highest achieved charge state. Several synchrotrons are fed by EBIS injectors, taking advantage of the EBIS batch mode production, which yields the highest charge states. A few EBISes are used for ion source development. However, most of the EBISes' efforts are directed to research the physics of highly charged ions. Some of those are used to study the electron--ion interaction inside the source. But normally, most EBISes deliver the ions for external experiments, which so far concentrate on the recombination of the highly charged ions with atoms, molecules and surfaces. The ions are typically produced at a potential of 1 to a few kilovolts per charge; but in most cases, the EBIS is mounted on a high voltage platform or is followed by an RFQ, and therefore can generate ion energies from a few hundred volts up to a few hundred kilovolts per charge. The delivered beams have a low emittance and a low energy spread, which is an advantage for high-resolution experiments. This paper presents briefly all operational EBISes, their capabilities, their achievements, and their contribution to physics research. 5 figs., 1 tab., 59 refs.

The status of the Electron Beam Ion Sources

International Nuclear Information System (INIS)

Stockli, M.P.

1990-01-01

More than twenty years after its invention, 13 examples of the Electron Beam Ion Sources (EBIS) are in operation worldwide. The substantial progress in operation and insight, achieved over the last few years, made the EBISes become reliable tools for the production of beams of very highly charged, low-energy ions. For example, 8 EBISes produce bare argon on a standard basis. The successful production of hydrogen-like xenon presents the ions with the highest ionization energy, whereas the production of Th80+ presents the highest achieved charge state. Several synchrotrons are fed by EBIS injectors, taking advantage of the EBIS batch mode production, which yields the highest charge states. A few EBISes are used for ion source development. However, most of the EBISes' efforts are directed to research the physics of highly charged ions. Some of those are used to study the electron--ion interaction inside the source. But normally, most EBISes deliver the ions for external experiments, which so far concentrate on the recombination of the highly charged ions with atoms, molecules and surfaces. The ions are typically produced at a potential of 1 to a few kilovolts per charge; but in most cases, the EBIS is mounted on a high voltage platform or is followed by an RFQ, and therefore can generate ion energies from a few hundred volts up to a few hundred kilovolts per charge. The delivered beams have a low emittance and a low energy spread, which is an advantage for high-resolution experiments. This paper presents briefly all operational EBISes, their capabilities, their achievements, and their contribution to physics research. 5 figs., 1 tab., 59 refs

The status of the Electron Beam Ion Sources

Energy Technology Data Exchange (ETDEWEB)

Stockli, M.P.

1990-12-31

More than twenty years after its invention, 13 examples of the Electron Beam Ion Sources (EBIS) are in operation worldwide. The substantial progress in operation and insight, achieved over the last few years, made the EBISes become reliable tools for the production of beams of very highly charged, low-energy ions. For example, 8 EBISes produce bare argon on a standard basis. The successful production of hydrogen-like xenon presents the ions with the highest ionization energy, whereas the production of Th80+ presents the highest achieved charge state. Several synchrotrons are fed by EBIS injectors, taking advantage of the EBIS batch mode production, which yields the highest charge states. A few EBISes are used for ion source development. However, most of the EBISes` efforts are directed to research the physics of highly charged ions. Some of those are used to study the electron--ion interaction inside the source. But normally, most EBISes deliver the ions for external experiments, which so far concentrate on the recombination of the highly charged ions with atoms, molecules and surfaces. The ions are typically produced at a potential of 1 to a few kilovolts per charge; but in most cases, the EBIS is mounted on a high voltage platform or is followed by an RFQ, and therefore can generate ion energies from a few hundred volts up to a few hundred kilovolts per charge. The delivered beams have a low emittance and a low energy spread, which is an advantage for high-resolution experiments. This paper presents briefly all operational EBISes, their capabilities, their achievements, and their contribution to physics research. 5 figs., 1 tab., 59 refs.

Metagenomic sequence of saline desert microbiota from wild ass sanctuary, Little Rann of Kutch, Gujarat, India.

Science.gov (United States)

Patel, Rajesh; Mevada, Vishal; Prajapati, Dhaval; Dudhagara, Pravin; Koringa, Prakash; Joshi, C G

2015-03-01

We report Metagenome from the saline desert soil sample of Little Rann of Kutch, Gujarat State, India. Metagenome consisted of 633,760 sequences with size 141,307,202 bp and 56% G + C content. Metagenome sequence data are available at EBI under EBI Metagenomics database with accession no. ERP005612. Community metagenomics revealed total 1802 species belonged to 43 different phyla with dominating Marinobacter (48.7%) and Halobacterium (4.6%) genus in bacterial and archaeal domain respectively. Remarkably, 18.2% sequences in a poorly characterized group and 4% gene for various stress responses along with versatile presence of commercial enzyme were evident in a functional metagenome analysis.

Experimental study of interactions of highly charged ions with atoms at keV energies. Progress report, February 16, 1993--April 15, 1994

International Nuclear Information System (INIS)

Kostroun, V.O.

1994-01-01

Experimental study of low energy, highly charged ions with other atomic species requires an advanced ion source such as an electron beam ion source, EBIS or an electron cyclotron ion source, ECRIS. Five years ago we finished the design and construction of the Cornell superconducting solenoid, cryogenic EBIS (CEBIS). Since then, this source has been in continuous operation in a program whose main purpose is the experimental study of interactions of highly charged ions with atoms at keV energies. This progress report for the period February 16, 1993 to April 15, 1994 describes the work accomplished during this time in the form of short abstracts

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database.

Science.gov (United States)

Boutselakis, H; Dimitropoulos, D; Fillon, J; Golovin, A; Henrick, K; Hussain, A; Ionides, J; John, M; Keller, P A; Krissinel, E; McNeil, P; Naim, A; Newman, R; Oldfield, T; Pineda, J; Rachedi, A; Copeland, J; Sitnov, A; Sobhany, S; Suarez-Uruena, A; Swaminathan, J; Tagari, M; Tate, J; Tromm, S; Velankar, S; Vranken, W

2003-01-01

The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.

Cattle manure, fertilizer, inoculants both singly and in combination on growth performance in the common bean=Esterco bovino, biofertilizante, inoculante e combinações no desempenho produtivo do feijão comum

Directory of Open Access Journals (Sweden)

Jéssyca Dellinhares Lopes Martins

2016-02-01

Full Text Available In places where beans are cultivated by family farmers without major investment in inputs, in the long run organic fertilisers can come to supplement or even replace chemical fertilisers in the field. In view of this, the aim was to evaluate productive performance in plants of the common bean cultivated with cattle manure, biofertiliser, inoculants and mineral fertiliser, both singly and in combination. The experiment was conducted under rainfed conditions in the town of São João, in the State of Pernambuco, Brazil (PE, during the 2013 crop year. The experimental design was of randomised blocks, comprising nine treatments with three replications: T - control; E - cattle manure; B - biofertiliser; I - inoculant; EI - cattle manure + inoculant; BI - biofertiliser + inoculant; EB - cattle manure + biofertiliser; EBI - cattle manure + biofertiliser + inoculant; AM - mineral fertiliser. The cattle manure (40 t ha-1, whether applied singly (E or together with biofertiliser and/ or inoculant (EI, EB, EBI, gave a significant increase in pod length and the number of pods per plant, as well as in straw yield and crop productivity. Alternative methods of fertilisation (E, EI, EB, EBI can replace mineral fertiliser in the cultivation of beans, however, inoculant or biofertiliser should not be used singly for production of the common bean under rainfed conditions.= Onde o cultivo do feijão é realizado por agricultores familiares sem grandes investimentos em insumos, a adubação orgânica pode vir a suplementar ou, até mesmo, substituir os adubos químicos, a longo prazo, na lavoura. Diante disso, objetivou-se avaliar o desempenho produtivo do feijão comum cultivado com esterco bovino, biofertilizante, inoculante, adubação mineral e diferentes combinações desses. O experimento foi realizado em condições de sequeiro, no município de São João-PE, no ano agrícola de 2013. O delineamento experimental foi em blocos ao acaso, com três repeti

Culturable bacterial endophytes isolated from Mangrove tree (Rhizophora apiculata Blume) enhance seedling growth in Rice.

Science.gov (United States)

Deivanai, Subramanian; Bindusara, Amitraghata Santhanam; Prabhakaran, Guruswamy; Bhore, Subhash Janardhan

2014-07-01

Endophytic bacteria do have several potential applications in medicine and in other various sectors of biotechnology including agriculture. Bacterial endophytes need to be explored for their potential applications in agricultural biotechnology. One of the potential applications of bacterial endophytes in agricultural is to enhance the growth of the agricultural crops. Hence, this study was undertaken to explore the plant growth promoting potential application of bacterial endophytes. The objective of this study was to examine the effect of endophytic bacteria from mangrove tree (Rhizophora apiculata Blume) for their efficacy in promoting seedling growth in rice. Eight endophytic bacterial isolates (EBIs) isolated from twig and petiole tissues of the mangrove were identified based on their 16S ribosomal ribonucleic acid (rRNA) gene sequence homology. Separately, surface sterilized paddy seeds were treated with cell-free broth and cell suspension of the EBIs. Rice seedlings were analyzed by various bioassays and data was recorded. The gene sequences of the isolates were closely related to two genera namely, Bacillus and Pantoea. Inoculation of EBIs from R. apiculata with rice seeds resulted in accelerated root and shoot growth with significant increase in chlorophyll content. Among the isolates, Pantoea ananatis (1MSE1) and Bacillus amyloliquefaciens (3MPE1) had shown predominance of activity. Endophytic invasion was recognized by the non-host by rapid accumulation of reactive oxygen species (ROS) and was counteracted by the production of hydrogen peroxide (H2O2) and lipid peroxide. The results demonstrated that EBIs from mangrove tree can increase the fitness of the rice seedlings under controlled conditions. These research findings could be useful to enhance the seedling growth and could serve as foundation in further research on enhancing the growth of the rice crop using endophytic bacteria.

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

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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.

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

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.

The ATLAS multi-user upgrade and potential applications

Energy Technology Data Exchange (ETDEWEB)

Mustapha, B.; Nolen, J. A.; Savard, G.; Ostroumov, P. N.

2017-12-01

With the recent integration of the CARIBU-EBIS charge breeder into the ATLAS accelerator system to provide for more pure and efficient charge breeding of radioactive beams, a multi-user upgrade of the ATLAS facility is being proposed to serve multiple users simultaneously. ATLAS was the first superconducting ion linac in the world and is the US DOE low-energy Nuclear Physics National User Facility. The proposed upgrade will take advantage of the continuous-wave nature of ATLAS and the pulsed nature of the EBIS charge breeder in order to simultaneously accelerate two beams with very close mass-to-charge ratios; one stable from the existing ECR ion source and one radioactive from the newly commissioned EBIS charge breeder. In addition to enhancing the nuclear physics program, beam extraction at different points along the linac will open up the opportunity for other potential applications; for instance, material irradiation studies at ~ 1 MeV/u and isotope production at ~ 6 MeV/u or at the full ATLAS energy of ~ 15 MeV/u. The concept and proposed implementation of the ATLAS multi-user upgrade will be presented. Future plans to enhance the flexibility of this upgrade will also be presented.

The European Bioinformatics Institute in 2017: data coordination and integration

Science.gov (United States)

Cochrane, Guy; Apweiler, Rolf; Birney, Ewan

2018-01-01

Abstract The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https://www.ebi.ac.uk). We accommodate an increasingly diverse range of data types and integrate them, so that biologists in all disciplines can explore life in ever-increasing detail. We maintain over 40 data resources, many of which are run collaboratively with partners in 16 countries (https://www.ebi.ac.uk/services). Submissions continue to increase exponentially: our data storage has doubled in less than two years to 120 petabytes. Recent advances in cellular imaging and single-cell sequencing techniques are generating a vast amount of high-dimensional data, bringing to light new cell types and new perspectives on anatomy. Accordingly, one of our main focus areas is integrating high-quality information from bioimaging, biobanking and other types of molecular data. This is reflected in our deep involvement in Open Targets, stewarding of plant phenotyping standards (MIAPPE) and partnership in the Human Cell Atlas data coordination platform, as well as the 2017 launch of the Omics Discovery Index. This update gives a birds-eye view of EMBL-EBI’s approach to data integration and service development as genomics begins to enter the clinic. PMID:29186510

Enhanced Therapeutic Potential of Nano-Curcumin Against Subarachnoid Hemorrhage-Induced Blood-Brain Barrier Disruption Through Inhibition of Inflammatory Response and Oxidative Stress.

Science.gov (United States)

Zhang, Zong-Yong; Jiang, Ming; Fang, Jie; Yang, Ming-Feng; Zhang, Shuai; Yin, Yan-Xin; Li, Da-Wei; Mao, Lei-Lei; Fu, Xiao-Yan; Hou, Ya-Jun; Fu, Xiao-Ting; Fan, Cun-Dong; Sun, Bao-Liang

2017-01-01

Curcumin and nano-curcumin both exhibit neuroprotective effects in early brain injury (EBI) after experimental subarachnoid hemorrhage (SAH). However, the mechanism that whether curcumin and its nanoparticles affect the blood-brain barrier (BBB) following SAH remains unclear. This study investigated the effect of curcumin and the poly(lactide-co-glycolide) (PLGA)-encapsulated curcumin nanoparticles (Cur-NPs) on BBB disruption and evaluated the possible mechanism underlying BBB dysfunction in EBI using the endovascular perforation rat SAH model. The results indicated that Cur-NPs showed enhanced therapeutic effects than that of curcumin in improving neurological function, reducing brain water content, and Evans blue dye extravasation after SAH. Mechanically, Cur-NPs attenuated BBB dysfunction after SAH by preventing the disruption of tight junction protein (ZO-1, occludin, and claudin-5). Cur-NPs also up-regulated glutamate transporter-1 and attenuated glutamate concentration of cerebrospinal fluid following SAH. Moreover, inhibition of inflammatory response and microglia activation both contributed to Cur-NPs' protective effects. Additionally, Cur-NPs markedly suppressed SAH-mediated oxidative stress and eventually reversed SAH-induced cell apoptosis in rats. Our findings revealed that the strategy of using Cur-NPs could be a promising way in improving neurological function in EBI after experimental rat SAH.

Multicharged and intense heavy ion beam sources

International Nuclear Information System (INIS)

Kutner, V.B.

1981-01-01

The cyclotron plasma-are source (PIG), duoplasmatron (DP), laser source (LS), electron beam ion source (EBIS) and electron cyclotron resonance source (ECRS) from the viewpoint of generating intense and high charge state beams are considered. It is pointed out that for the last years three types of multicharged ion sources-EBIS, ECR and LS have been essentially developed. In the EBIS source the Xe 48+ ions are produced. The present day level of the development of the electron-beam ionization technique shows that by means of this technique intensive uranium nuclei beams production becomes a reality. On the ECR source Xe 26+ approximately 4x10 10 h/s, Asub(r)sup(12+) approximately 10 12 h/s intensive ion beams are produced. In the laser source a full number of C 6+ ions during one laser pulse constitutes not less than 10 10 from the 5x10mm 2 emission slit. At the present time important results are obtained pointing to the possibility to separate the ion component of laser plasma in the cyclotron central region. On the PIG source the Xe 15+ ion current up to 10μA per pulse is produced. In the duoplasmatron the 11-charge state of xenon ion beams is reached [ru

ASO EBI: FASHIONING SELF THROUGH PHOTOGRAPHY AND ...

African Journals Online (AJOL)

Precious

In Nigeria, fashion and photography have become powerful forces in the ... grown every year since the first photography studios opened in. Lagos in the 1880s. ..... Uchendu was determined to take as many as "fifty pictures and deliver them to ...

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).

Drug: D04616 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available 2190 3222 ATC code: B03AB02 ... Iron preparation Treatment of iron deficiency anemia and ... related ... indications (hematinic) ... CAS: 8047-67-4 PubChem: 17398130 ChEBI: 82530 ...

Restoration of stormwater retention capacity at the allotment-scale through a novel economic instrument.

Science.gov (United States)

Fletcher, Tim D; Walsh, Chistopher J; Bos, Darren; Nemes, Veronika; RossRakesh, Sharyn; Prosser, Toby; Hatt, Belinda; Birch, Rhiannon

2011-01-01

Urbanisation results in changes to runoff behaviour which, if not addressed, inevitably degrade receiving waters. To date, most stormwater management has focussed on the streetscape and public open space. Given that much of the catchment imperviousness is located on private land, we developed and tested a novel economic instrument (a uniform price auction) for encouraging allotment-scale stormwater retention. We evaluated bids using an integrated environmental benefit index (EBI), based on the ability of the proposed works to reduce runoff frequency, pollutant loads and to reduce potable water demand. The uniform price auction resulted in 1.4 ha of impervious areas being effectively 'disconnected' from the stormwater system. The EBI provided an objective and transparent method of comparing bids, which varied in the type of works proposed (e.g. rainwater tank, rain-garden), the cost and the resulting environmental benefit. Whilst the pilot auction was a success, the public subsidy of works undertaken was around 85%, meaning that property owners a relatively small private benefit in the works. Future auction rounds will be revised to (i) test an EBI which is more focussed on the protection of streams (assessing changes to runoff frequency, baseflow volumes and water quality) and (ii) provide an auction process which is simpler to understand, and provides greater practical support for landholders who wish to undertake works.

The Determinants of Visitor’s Revisit Intention: A Lesson from Ijen Car Free Day

Directory of Open Access Journals (Sweden)

Cesya Rizkika Parahiyanti

2015-09-01

Full Text Available Event industry currently is considered as one of interesting business opportunity in contributing major positive economic impact. Event could be categorized into some activities conducted by an event management or event organizer in the case of achieving some specific outcomes. An event is also recognized as an essential marketing tool in branding of particular destination. It has a powerful function to make a differentiation between one destination and others. This study aims to establish a theoretical event brand equity for which the key components of the brand equity were evaluated from visitor perspective in the tourism context. Brand equity is constructed by four multidimensions which are event brand awareness (EBA, event brand image (EBI, event brand quality (EBQ, and event revisit intention (ERI. By using convenience sampling, 205 visitors of Ijen Car Free Day (ICFD as the event object were used as respondents to obtain the data. This study uses Partial Least Square (PLS to analyze the data both in outer model and inner model measurements. The finding of this study indicate that EBA has positive and significant influence to EBI, EBQ, and ERI. Then, EBI is also proven giving positive and significant influence to EBQ and ERI. In contrary, EBQ does not show significant influence to ERI. The significance movement of this study could be useful measurement in assessing event brand equity management in the future.

E-MSD: an integrated data resource for bioinformatics.

Science.gov (United States)

Velankar, S; McNeil, P; Mittard-Runte, V; Suarez, A; Barrell, D; Apweiler, R; Henrick, K

2005-01-01

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the 'Structure Integration with Function, Taxonomy and Sequences (SIFTS)' initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group.

Drug: D08665 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available euromutilin Same as: C12066 Chemical group: DG01438 ... Veterinary medicine Pleuromutilin [CPD:C09169] derivative ... CAS: 101312-92-9 PubChem: 96025348 ChEBI: 29705 LigandBox: D08665 ...

KONTRIBUSI DAN PELUANG PENINGKATAN PENDAPATAN ISTERI NELAYAN TERHADAP PENDAPATAN KELUARGA DI KECAMATAN ALUH-ALUH KABUPATEN BANJAR KALIMANTAN SELATAN

Directory of Open Access Journals (Sweden)

Ulfah Nurul Hidayah

2016-06-01

The research method used a descriptive method and survey method. Data collection performed with observation and interview techniques. Technique of sampling locations use purposive sampling and respondents sampling use purposive random sampling. The results showed that types of work fisherman’s wife performed in fisheries include : salted fish processing, shrimp paste processing, processing ebi, ang processing of prawn crackers, revenue contribution fisherman’s wife who worked as a salted fish processing amounted to 32,32%, as processing shirmp paste amounted to 31,29%, as processing ebi amounted to 31,01%, as processing shrimp crackers amounted to 23,95%. Average revenue contribution amounting to 29,64%, fish crackers opportunies amounted to 48,58%, shrimp meatball amounted to 30,36%, shrimp amplangs amounted to 10,12%, and shrimp nuggets amounted to 10,93%.

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.

Drug: D10442 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available inhibitor Chemical group: DG01818 ... Treatment of chronic hepatitis C infection HCV NS5A [CPD:C18292] ... CAS: 1256388-51-8 PubChem: 172232535 ChEBI: 85089 ChEMBL: CHEMBL2374220 ...

Pramana – Journal of Physics | Indian Academy of Sciences

Indian Academy of Sciences (India)

Proceedings of the Ninth International Conference on Heavy Ion Accelerator Technology - Part I .... An EBIS for charge state breeding in the SPES project .... Preliminary design of high-power wave-guide/transmission system for multimegawatt ...

Consent Codes: Upholding Standard Data Use Conditions.

Directory of Open Access Journals (Sweden)

Stephanie O M Dyke

2016-01-01

Full Text Available A systematic way of recording data use conditions that are based on consent permissions as found in the datasets of the main public genome archives (NCBI dbGaP and EMBL-EBI/CRG EGA.

An assessment of two off-shore igniter concepts

International Nuclear Information System (INIS)

Guenette, C. C.

1997-01-01

On June 12, 1996, two controlled in-situ oil spill burns (ISB), using a response-prepared ISB system, were conducted in the North Sea, 40 miles off the U. K. coast. The first burn involved fresh crude oil and was ignited with a hand-held igniter using a standard gelled fuel mixture. In the second burn an emulsified crude was used, ignited with a prototype emulsion breaking igniter (EBI) deployed using the Helitorch. The objective was to determine operational practicalities under realistic conditions when responding to a weathered oil situation in an offshore location. This paper is devoted to an assessment of the two igniter systems used during the trials. Results showed that oil aged by 12 hours with a 25 per cent water content burned down to a three-to-four per cent residue. The fire burn survived the two burns intact. The hand-held ignition system worked with fresh oil and the Helitorch lit emulsified oil using EBI. These trials were the first time that the EBI was deployed from a Helitorch slung beneath a helicopter. It was concluded that (1) the simplicity of the logistics required for the hand-held igniter would favour its use over the Helitorch method for fresh or lightly weathered oil, (2) more heavily weathered oils would require the use of an emulsion-breaking type igniter, and (3) aerial deployment of igniters offer the advantage of allowing more accurate positioning. 10 refs.,5 tabs., 3 figs

Interstitial brachytherapy for stage I and II squamous cell carcinoma of the oral tongue: factors influencing local control and soft tissue complications

International Nuclear Information System (INIS)

Fujita, Minoru; Hirokawa, Yutaka; Kashiwado, Kouzo; Akagi, Yukio; Kashimoto, Kazuki; Kiriu, Hiroshi; Matsuura, Kanji; Ito, Katsuhide

1999-01-01

Purpose: Our aim was to study the treatment parameters that influence local control and soft tissue complications (STC) in a series of 207 Stage I and II squamous cell carcinomas of the oral tongue treated by interstitial brachytherapy (BRT) alone (127 patients), or by a combination using external beam irradiation (EBI) (80 patients) between 1980 and 1993. Methods and Materials: The patient distribution was 93 T1, 72 T2a, and 42 T2b. The prescribed BRT dose at the plane 5 mm from the plane of the radioactive sources was 65-70 Gy in BRT alone, and 50-60 Gy in the combined treatment using EBI. Generally, an EBI dose of 30 Gy was used. No prophylactic neck treatment was performed. Results: The 5-year local recurrence-free rate for T1, T2a, and T2b was 92.9%, 81.9%, and 71.8%, respectively (p 85 Gy (p = 0.01), BRT dose > 55 Gy (p = 0.04), and a dose rate = 0.6 Gy/h was significantly related to more STC in BRT alone (p = 0.03), and that a dose rate > = 0.55 Gy/h (p 70 Gy (p 100 Gy (p 85 Gy and 55 Gy and < = 70 Gy, and < 0.55 Gy/h, respectively. We also recommend longer follow-up periods; more than 5 years might be necessary for late local recurrences and for secondary cancers

Drug: D01798 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available l group: DG00147 ... Treatment of mild-to-moderate phenylketonuria (PKU) ... CAS: 69056-38-8 PubChem: 7848860 ChEBI: 32120 ChEMBL: CHEMBL1201775 LigandBox: D01798 NIKKAJI: J1.219.960K ...

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).

ComplexViewer: visualization of curated macromolecular complexes.

Science.gov (United States)

Combe, Colin W; Sivade, Marine Dumousseau; Hermjakob, Henning; Heimbach, Joshua; Meldal, Birgit H M; Micklem, Gos; Orchard, Sandra; Rappsilber, Juri

2017-11-15

Proteins frequently function as parts of complexes, assemblages of multiple proteins and other biomolecules, yet network visualizations usually only show proteins as parts of binary interactions. ComplexViewer visualizes interactions with more than two participants and thereby avoids the need to first expand these into multiple binary interactions. Furthermore, if binding regions between molecules are known then these can be displayed in the context of the larger complex. freely available under Apache version 2 license; EMBL-EBI Complex Portal: http://www.ebi.ac.uk/complexportal; Source code: https://github.com/MICommunity/ComplexViewer; Package: https://www.npmjs.com/package/complexviewer; http://biojs.io/d/complexviewer. Language: JavaScript; Web technology: Scalable Vector Graphics; Libraries: D3.js. colin.combe@ed.ac.uk or juri.rappsilber@ed.ac.uk. © The Author 2017. Published by Oxford University Press.

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.

Characterization of Pseudomonas aeruginosa PB112 (JN996498 ...

African Journals Online (AJOL)

Saradindu Panda

www.ebi.ac.uk/clustalw) and analyzed by ClustalW software (Thompson et al., 1994). Evolutionary distances were calculated using the method of Jukes and Cantor (Jukes et al., 1969) and phylogenetic tree was constructed following Tamura et al.

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

Drug: D02106 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available 9 Therapeutic category: 4291 ATC code: L01XX27 ... Genomic biomarker: PML-RARA [HSA:5371 5914] CAS: 1327-53-3 PubChem: 7849167 ChEBI: 30621 49900 DrugBank: DB01169 NIKKAJI: J44.421I ...

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

Effect of prenatal education on breastfeeding initiation and exclusive ...

African Journals Online (AJOL)

Background: The prevalence of breastfeeding initiation and exclusive breastfeeding is low globally in both developing and developed countries despite the promotion interventions on breastfeeding rates in early infancy. In Ethiopia, the proportion of women who practiced early breastfeeding initiation (EBI) and exclusive ...

Drug: D05406 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D05406 Drug Penamecillin (USAN/INN) ... C19H22N2O6S D05406.gif ... Antibacterial ... DG01...PubChem: 47207081 ChEBI: 131733 ChEMBL: CHEMBL2106988 LigandBox: D05406 NIKKAJI: J7.208G ...

Drug: D01883 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available e as: C13355 ATC code: N06BX11 ... Mental performance enhancer ... CAS: 72432-10-1 PubChem: 7848945 ChEBI: 47943 ChEMBL: CHEMBL36994 PDB-CCD: 4MP LigandBox: D01883 NIKKAJI: J18.602C ...

75 FR 72822 - Nationwide Categorical Waivers Under Section 1605 (Buy American) of the American Recovery and...

Science.gov (United States)

2010-11-26

...) software for integration of water management and HVAC systems including: Customized Dell PowerEdge T610... Honeywell Enterprise Buildings Integrator (EBI) software for integration of water management and HVAC... Coordinator worked with labor unions, trade associations and other manufacturing stakeholders to scout for...

Indexes to Volume 59

Indian Academy of Sciences (India)

Critical exponents in the transition to chaos in one-dimensional discrete sys- tems. G Ambika and N V ... simulations of inertial confinement fusion plasmas. N K Gupta and B K ... An EBIS for charge state breeding in the SPES project. V Variale,.

Drug: D00801 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D00801 Drug Lithium carbonate (JP17/USP); Eskalith (TN); Lithobid (TN) ... CO3. 2Li D00801...: 554-13-2 PubChem: 7847866 ChEBI: 6504 ChEMBL: CHEMBL1200826 LigandBox: D00801 NIKKAJI: J425A ...

Ion accumulation and space charge neutralization in intensive electron beams for ion sources and electron cooling

International Nuclear Information System (INIS)

Shirkov, G.D.

1996-01-01

The Electron Beam Ion Sources (EBIS), Electron Beam Ion Traps (EBIT) and electron beams for electron cooling application have the beam parameters in the same ranges of magnitudes. EBIS and EBIT produce and accumulate ions in the beam due to electron impact ionization. The cooling electron beam accumulates positive ions from the residual gas in the accelerator chamber during the cooling cycle. The space charge neutralization of cooling beam is also used to reduce the electron energy spread and enhance the cooling ability. The advanced results of experimental investigations and theoretical models of the EBIS electron beams are applied to analyze the problem of beam neutralization in the electron cooling techniques. The report presents the analysis of the most important processes connected with ion production, accumulation and losses in the intensive electron beams of ion sources and electron cooling systems for proton and ion colliders. The inelastic and elastic collision processes of charged particles in the electron beams are considered. The inelastic processes such as ionization, charge exchange and recombination change the charge states of ions and neutral atoms in the beam. The elastic Coulomb collisions change the energy of particles and cause the energy redistribution among components in the electron-ion beams. The characteristic times and specific features of ionization, beam neutralization, ion heating and loss in the ion sources and electron cooling beams are determined. The dependence of negative potential in the beam cross section on neutralization factor is studied. 17 refs., 5 figs., 1 tab

The process of adapting a universal dating abuse prevention program to adolescents exposed to domestic violence.

Science.gov (United States)

Foshee, Vangie A; Dixon, Kimberly S; Ennett, Susan T; Moracco, Kathryn E; Bowling, J Michael; Chang, Ling-Yin; Moss, Jennifer L

2015-07-01

Adolescents exposed to domestic violence are at increased risk of dating abuse, yet no evaluated dating abuse prevention programs have been designed specifically for this high-risk population. This article describes the process of adapting Families for Safe Dates (FSD), an evidenced-based universal dating abuse prevention program, to this high-risk population, including conducting 12 focus groups and 107 interviews with the target audience. FSD includes six booklets of dating abuse prevention information, and activities for parents and adolescents to do together at home. We adapted FSD for mothers who were victims of domestic violence, but who no longer lived with the abuser, to do with their adolescents who had been exposed to the violence. Through the adaptation process, we learned that families liked the program structure and valued being offered the program and that some of our initial assumptions about this population were incorrect. We identified practices and beliefs of mother victims and attributes of these adolescents that might increase their risk of dating abuse that we had not previously considered. In addition, we learned that some of the content of the original program generated negative family interactions for some. The findings demonstrate the utility of using a careful process to adapt evidence-based interventions (EBIs) to cultural sub-groups, particularly the importance of obtaining feedback on the program from the target audience. Others can follow this process to adapt EBIs to groups other than the ones for which the original EBI was designed. © The Author(s) 2014.

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.

Transportability of an Evidence-Based Early Childhood Intervention in a Low-Income African Country: Results of a Cluster Randomized Controlled Study.

Science.gov (United States)

Huang, Keng-Yen; Nakigudde, Janet; Rhule, Dana; Gumikiriza-Onoria, Joy Louise; Abura, Gloria; Kolawole, Bukky; Ndyanabangi, Sheila; Kim, Sharon; Seidman, Edward; Ogedegbe, Gbenga; Brotman, Laurie Miller

2017-11-01

Children in Sub-Saharan Africa (SSA) are burdened by significant unmet mental health needs. Despite the successes of numerous school-based interventions for promoting child mental health, most evidence-based interventions (EBIs) are not available in SSA. This study investigated the implementation quality and effectiveness of one component of an EBI from a developed country (USA) in a SSA country (Uganda). The EBI component, Professional Development, was provided by trained Ugandan mental health professionals to Ugandan primary school teachers. It included large-group experiential training and small-group coaching to introduce and support a range of evidence-based practices (EBPs) to create nurturing and predictable classroom experiences. The study was guided by the Consolidated Framework for Implementation Research, the Teacher Training Implementation Model, and the RE-AIM evaluation framework. Effectiveness outcomes were studied using a cluster randomized design, in which 10 schools were randomized to intervention and wait-list control conditions. A total of 79 early childhood teachers participated. Teacher knowledge and the use of EBPs were assessed at baseline and immediately post-intervention (4-5 months later). A sample of 154 parents was randomly selected to report on child behavior at baseline and post-intervention. Linear mixed effect modeling was applied to examine effectiveness outcomes. Findings support the feasibility of training Ugandan mental health professionals to provide Professional Development for Ugandan teachers. Professional Development was delivered with high levels of fidelity and resulted in improved teacher EBP knowledge and the use of EBPs in the classroom, and child social competence.

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.

DESM: portal for microbial knowledge exploration systems

KAUST Repository

Salhi, Adil; Essack, Magbubah; Radovanovic, Aleksandar; Marchand, Benoit; Bougouffa, Salim; Antunes, Andre; Simoes, Marta; Lafi, Feras Fawzi; Motwalli, Olaa Amin; Bokhari, Ameerah; Malas, Tareq Majed Yasin; Al Amoudi, Soha; Othum, Ghofran; Alam, Intikhab; Mineta, Katsuhiko; Gao, Xin; Hoehndorf, Robert; Archer, John A.C.; Gojobori, Takashi; Bajic, Vladimir B.

2015-01-01

Med 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

COLLABORATIVE RESEARCH AND DEVELOPMENT CONTRACT. Delivery Order 0038: Microbial Biotechnology and Biocatalysis

Science.gov (United States)

2010-04-01

Insights into Bacillus Spore Coat Assembly. Eby, D.M., and Johnson, G.R. Air Force Research Laboratory Materials Directorate, Biotechnology Group...integration with the HVAC intake to building. The sensitivity and detection limits demonstrate the potential f the system as a proof of concept, but

Drug: D04194 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available rinary) ... CAS: 73231-34-2 PubChem: 47206140 ChEBI: 87185 ChEMBL: CHEMBL1241590 LigandBox: D04194 NIKKAJI: J128.612I ... ...bacterial ... DG01576 ... Amphenicol type antibacterial Chemical group: DG02449 ... Amphenicol derivative Target: 50S ribosomal subunit (vete

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.…

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

Drug: D01878 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available hiatric agent ... DG02030 ... Anesthetics ... DG01675 ... Local anesthetic ... DG01673 ... Amide type local anesthetic ... DG01675 ... Local anesthetic... ... DG01673 ... Amide type local anesthetic ... CAS: 7210-92-6 PubChem: 7848940 ChEBI: 32247 LigandBox: D01878 NIKKAJI: J231.527K ...

Road Materials and Pavement Design volume 17(2)

CSIR Research Space (South Africa)

De Beer, Morris

2016-03-01

Full Text Available Materials and Pavement Design Volume 17, 2016 - Issue 2 Editorial Board Page ebi | Published online: 03 Oct 2016  http://dx.doi.org/10.1080/14680629.2016.1244475 Editors-in-Chief Hervé DI BENEDETTO - University of Lyon/ENTPE, Vaulx-en-Velin, France...

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...

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...

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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes

Directory of Open Access Journals (Sweden)

Sadhna Phanse

2016-03-01

Full Text Available Our analysis examines the conservation of multiprotein complexes among metazoa through use of high resolution biochemical fractionation and precision mass spectrometry applied to soluble cell extracts from 5 representative model organisms Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Strongylocentrotus purpuratus, and Homo sapiens. The interaction network obtained from the data was validated globally in 4 distant species (Xenopus laevis, Nematostella vectensis, Dictyostelium discoideum, Saccharomyces cerevisiae and locally by targeted affinity-purification experiments. Here we provide details of our massive set of supporting biochemical fractionation data available via ProteomeXchange (http://www.ebi.ac.uk/pride/archive/projects/PXD002319-http://www.ebi.ac.uk/pride/archive/projects/PXD002328, PPIs via BioGRID (185267; and interaction network projections via (http://metazoa.med.utoronto.ca made fully accessible to allow further exploration. The datasets here are related to the research article on metazoan macromolecular complexes in Nature [1]. Keywords: Proteomics, Metazoa, Protein complexes, Biochemical, Fractionation

Gene structure, phylogeny and expression profile of the sucrose ...

Indian Academy of Sciences (India)

2015-09-16

Sep 16, 2015 ... serine residue for phosphorylation by Ser/Thr protein kinase is indicated by a red star. The characteristic sucrose synthase domain (single underline) and a glycosyltransferases domain (double underline) were identified by the Interproscan algorithm (http://www.ebi.ac.uk/Tools/ pfa/iprscan/). 464. Journal of ...

Drug: D02959 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D02959 Drug Antimony potassium tartrate (USP) ... C8H4O12Sb2. 2K. 3H2O D02959.gif ... Same as: C11340 ... Antimo...ny compound ... CAS: 28300-74-5 PubChem: 17397116 ChEBI: 2761 NIKKAJI: J365.136C ...

Drug: D01406 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D01406 Drug Tocopherol calcium succinate (JP17); Vitamin-E (TN) ... (C33H53O5)2. Ca D01406....gif ... ATC code: A11HA03 Chemical group: DG00129 ... CAS: 14638-18-7 PubChem: 7848469 ChEBI: 32238 LigandBox: D01406 ...

A Structural and Correlational Analysis of Two Common Measures of Personal Epistemology

Science.gov (United States)

Laster, Bonnie Bost

2010-01-01

Scope and Method of Study: The current inquiry is a factor analytic study which utilizes first and second order factor analytic methods to examine the internal structures of two measurements of personal epistemological beliefs: the Schommer Epistemological Questionnaire (SEQ) and Epistemic Belief Inventory (EBI). The study also examines the…

Using a Virtual Environment to Deliver Evidence-Based Interventions: The Facilitator's Experience

Science.gov (United States)

Villarruel, Antonia; Tschannen, Dana; Valladares, Angel; Yaksich, Joseph; Yeagley, Emily; Hawes, Armani

2015-01-01

Background Evidence-based interventions (EBIs) have the potential to maximize positive impact on communities. However, despite the quantity and quality of EBIs for prevention, the need for formalized training and associated training-related expenses, such as travel costs, program materials, and input of personnel hours, pose implementation challenges for many community-based organizations. In this study, the community of inquiry (CoI) framework was used to develop the virtual learning environment to support the adaptation of the ¡Cuídate! (Take Care of Yourself!) Training of Facilitators curriculum (an EBI) to train facilitators from community-based organizations. Objective The purpose of this study was to examine the feasibility of adapting a traditional face-to-face facilitator training program for ¡Cuídate!, a sexual risk reduction EBI for Latino youth, for use in a multi-user virtual environment (MUVE). Additionally, two aims of the study were explored: the acceptability of the facilitator training and the level of the facilitators’ knowledge and self-efficacy to implement the training. Methods A total of 35 facilitators were trained in the virtual environment. We evaluated the facilitators' experience in the virtual training environment and determined if the learning environment was acceptable and supported the acquisition of learning outcomes. To this end, the facilitators were surveyed using a modified community of inquiry survey, with questions specific to the Second Life environment and an open-ended questionnaire. In addition, a comparison to face-to-face training was conducted using survey methods. Results Results of the community of inquiry survey demonstrated a subscale mean of 23.11 (SD 4.12) out of a possible 30 on social presence, a subscale mean of 8.74 (SD 1.01) out of a possible 10 on teaching presence, and a subscale mean of 16.69 (SD 1.97) out of a possible 20 on cognitive presence. The comparison to face-to-face training showed no

A UK and Ireland Survey of Educational Psychologists' Intervention Practices for Students with Autism Spectrum Disorder

Science.gov (United States)

Robinson, Lee; Bond, Caroline; Oldfield, Jeremy

2018-01-01

Although evidence-based interventions (EBIs) for autism spectrum disorder (ASD) have been identified in recent systematic literature reviews, the extent to which the practice of educational psychologists (EPs) in the UK and Ireland is informed by these is unknown. This study presents the results of a questionnaire that surveyed 146 EP…

IPN and AFI collaboration balance. The SIS source (Crysis)

International Nuclear Information System (INIS)

Goldstein, C.

1985-01-01

The fabrication and development of a source with confined electron beam (EBIS) is the result of a collaboration between IPN (Institut de Physique Nucleaire) and AFI (Forskningstitutet for Atom-fysik) First tests have confirmed the good operation of the whole elements. A critical balance is made, and conclusions are drawn [fr

Cu(ll) mediated ATRP of MMA by using a novel tetradentate amine ligand with oligo(ethylene glycol) pendant groups

NARCIS (Netherlands)

Becer, C.R.; Hoogenboom, R.; Founier, D.; Schubert, U.S.

2007-01-01

A novel tetradentate amine ligand namely N,N,N,N,N;,N;-hexaoligo(ethylene glycol) triethylenetetramine (HOEGTETA) was employed in the homogenous ATRP of MMA in anisole using CuBr and CuBr2 as the catalyst and ethyl 2-bromoisobutyrate (EBiB) as an initiator. The effect of the polymerization

ADAPTIVE CAPACITY IN RURAL SOUTH AFRICA Sam Schramski

African Journals Online (AJOL)

sam schramski

2017-02-02

Feb 2, 2017 ... such as the authors of Panarchy, state that adaptive capacity is ―the ... with this definition that the ‗potential' represents a society's response to ... closely linked together in case studies on water and health (Ebi ... water insecurity; weak institutions and governance (Füssel and ...... Stockholm, Sweden, 2005.

Application of InterPro for the functional classification of the proteins ...

Indian Academy of Sciences (India)

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 ...

Using Stimulus Equivalence-Based Instruction to Teach Graduate Students in Applied Behavior Analysis to Interpret Operant Functions of Behavior

Science.gov (United States)

Albright, Leif; Schnell, Lauren; Reeve, Kenneth F.; Sidener, Tina M.

2016-01-01

Stimulus equivalence-based instruction (EBI) was used to teach four, 4-member classes representing functions of behavior to ten graduate students. The classes represented behavior maintained by attention (Class 1), escape (Class 2), access to tangibles (Class 3), and automatic reinforcement (Class 4). Stimuli within each class consisted of a…

Drug: D08014 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D08014 Drug Glaucine; Tusidil (TN) ... C21H25NO4 D08014.gif ... Same as: C09446 Chemi...cal group: DG02011 ... CAS: 475-81-0 PubChem: 96024707 ChEBI: 5373 ChEMBL: CHEMBL228082 LigandBox: D08014 NIKKAJI: J12.036G ...

Drug: D02406 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D02406 Drug Cefatrizine (USAN); CFT ... C18H18N6O5S2 D02406.gif ... Antibacterial ... DG0...m cephalosporin penicillin binding protein ... CAS: 51627-14-6 PubChem: 7849464 ChEBI: 131730 ChEMBL: CHEMBL1095284 LigandBox: D02406 NIKKAJI: J11.176G ...

Drug: D10002 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D10002 Drug Florbetaben (18F) (JAN/INN); Neuraceq (TN) ... C21H26FNO3 D10002.gif ... ...ATC code: V09AX06 ... beta-Amyloid tracer Diagnosis of Alzheimer disease ... CAS: 902143-01-5 PubChem: 135626723 ChEBI: 79033 ChEMBL: CHEMBL566752 LigandBox: D10002 ...

Drug: D02534 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D02534 Drug Nitrovin (BAN); Difurazone; Nitrovin (TN) ... C14H12N6O6 D02534.gif ... Same as: C19487 ... veterina...ry medicine ... CAS: 804-36-4 PubChem: 17396705 ChEBI: 82516 ChEMBL: CHEMBL1395447 LigandBox: D02534 NIKKAJI: J4.527F ...

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…

Electron string phenomenon: physics and use

International Nuclear Information System (INIS)

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 N 7+ , Ar 16+ and Fe 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

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.

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.

In Vivo Assessment of Gamma Rays, Electron-beam Irradiation plus a Commercial Toxin Binder (Milbond-TX As an Anti-Aflatoxin B1 in a Chicken Model

Directory of Open Access Journals (Sweden)

Saeed Hasanpour

2018-02-01

Full Text Available Background: Aspergillus flavus is the most important fungus for production of Aflatoxin B1 (AFB1. This study evaluated the ability of gamma rays (GRs and electron-beam irradiation (EBI to counteract the deleterious effects of aflatoxin B1 (AFB1 in a chicken model. Methods: Overall, 168 one-day-old male Coturnix quails were assigned to eight treatments for 42 d in Tehran, Iran, in 2010 and 2011. Two dietary inclusion rates of AFB1 (0 and 2 ppm and toxin binders, such as 0, 27 kGy doses of GRs, 27 kGy doses of EBI, and 0.3% of commercial toxin binder-milbond-TX, were tested in a 2×4 factorial manner. Serum biochemical parameters, immune response, and dietary treatments on factors associated with kidney and lipid profiles were determined on day 42. Results: AFB1 significantly decreased the hematological parameters (Hematocrit in 21 and 42 d, immune response (White blood cell (WBC, heterophil to lymphocyte ratio (H/L and sheep red blood cell (SRBC, and blood chemical factors (glucose, albumin, total protein, and triglycerides compared to the control diet (P<0.05. It also significantly increased the calcium, phosphorus, uric acid, and low-density lipoprotein (LDL levels (P<0.05. The addition of toxin binders, such as GRs, EBI, and milbond-TX, in the contaminated diets significantly diminished the inhibitory effects of dietary AFB1 (P<0.05 on the hematological parameters, immune response, blood chemical factors, and factors associated with kidney and lipids profile with no differences compared to the control diet. Conclusion: The addition of these toxin binders may reduce the adverse effects produced by the presence of AFB1 in Japanese quails’ diets.

Identification of OBO nonalignments and its implications for OBO enrichment.

Science.gov (United States)

Bada, Michael; Hunter, Lawrence

2008-06-15

Existing projects that focus on the semiautomatic addition of links between existing terms in the Open Biomedical Ontologies can take advantage of reasoners that can make new inferences between terms that are based on the added formal definitions and that reflect nonalignments between the linked terms. However, these projects require that these definitions be necessary and sufficient, a strong requirement that often does not hold. If such definitions cannot be added, the reasoners cannot point to the nonalignments through the suggestion of new inferences. We describe a methodology by which we have identified over 1900 instances of nonredundant nonalignments between terms from the Gene Ontology (GO) biological process (BP), cellular component (CC) and molecular function (MF) ontologies, Chemical Entities of Biological Interest (ChEBI) and the Cell Type Ontology (CL). Many of the 39.8% of these nonalignments whose object terms are more atomic than the subject terms are not currently examined in other ontology-enrichment projects due to the fact that the necessary and sufficient conditions required for the inferences are not currently examined. Analysis of the ratios of nonalignments to assertions from which the nonalignments were identified suggests that BP-MF, BP-BP, BP-CL and CC-CC terms are relatively well-aligned, while ChEBI-MF, BP-ChEBI and CC-MF terms are relatively not aligned well. We propose four ways to resolve an identified nonalignment and recommend an analogous implementation of our methodology in ontology-enrichment tools to identify types of nonalignments that are currently not detected. The nonalignments discussed in this article may be viewed at http://compbio.uchsc.edu/Hunter_lab/Bada/nonalignments_2008_03_06.html. Code for the generation of these nonalignments is available upon request. mike.bada@uchsc.edu.

Drug: D01212 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D01212 Drug Simfibrate (JAN/INN); Cholesolvin (TN) ... C23H26Cl2O6 D01212.gif ... Card...ibrates ATC code: C10AB06 ... Clofibrate derivative ... CAS: 14929-11-4 PubChem: 7848275 ChEBI: 32131 ChEMBL: CHEMBL2105435 LigandBox: D01212 NIKKAJI: J3.444D ...

Molecular characterization of oxysterol binding to the Epstein-Barr virus-induced gene 2 (GPR183)

DEFF Research Database (Denmark)

Benned-Jensen, Tau; Norn, Christoffer; Laurent, Stephane

2012-01-01

, the family of G protein-coupled seven transmembrane-spanning receptors (7TM receptors) was added to this group. Specifically, the Epstein-Barr virus-induced gene 2 (EBI2 or GPR183) was shown to be activated by several oxysterols, most potently by 7α,25-dihydroxycholesterol (7α,25-OHC). Nothing is known about...

The physical protection systems at the Czech nuclear installations and the Y2K issue

International Nuclear Information System (INIS)

Malach, J.; Seifert, Z.; Sedlacek, J.; Bartak, L.; Polanka, J.

1999-01-01

The paper describes the joint effort of the State Office for Nuclear Safety, EZ, a.s., Nuclear Power Plant Dukovany and EBIS Ltd., as a subcontractor, to solve the problem of the Y2K particularly in connection with real time operation of the integrated physical protection system at Nuclear Power Plant Dukovany. (author)

Drug: D07829 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available erinary medicine ... CAS: 35367-38-5 PubChem: 96024526 ChEBI: 34703 ChEMBL: CHEMBL49338 LigandBox: D07829 NIKKAJI: J1.888K ... ... D07829 Drug Diflubenzuron ... C14H9ClF2N2O2 D07829.gif ... Same as: C14427 ... Benzoyl phenylurea derivative vet

Permanent magnet electron beam ion source/trap systems with bakeable magnets for improved operation conditions

Energy Technology Data Exchange (ETDEWEB)

Schmidt, M., E-mail: mike.schmidt@dreebit.com [DREEBIT GmbH, 01109 Dresden (Germany); Zschornack, G.; Kentsch, U.; Ritter, E. [Department of Physics, Dresden University of Technology, 01062 Dresden, Germany and Helmholtz-Zentrum Dresden-Rossendorf e.V., Institute of Ion Beam Physics and Materials Research, 01328 Dresden (Germany)

2014-02-15

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.

First radioactive ions charge bred in REXEBIS at the REX-ISOLDE accelerator

CERN Document Server

Wolf, B H; Fostner, O; Wenander, F; Ames, F; Reisinger, K; Liljeby, L; Skeppstedt, Ö; Jonson, B; Nyman, G H

2003-01-01

REXEBIS is the charge breeder of the REX-ISOLDE post accelerator. The radioactive 1$^{+}$ ions produced at ISOLDE are accumulated, phase-space cooled and bunched in the REXTRAP, and thereafter injected into the EBIS with an energy up to 60 keV. The REXEBIS produced the first charge bred ions in August 2001 and has been running nearly non-stop during September to December 2001. It has delivered stable $^{39}$K$^{10+}$ and $^{23}$Na$^{6+}$ beams generated in the ion source in front of REXTRAP with a Na$^{7+}$ current exceeding 70 pA (6x10$^{7}$ p/s). Stable $^{27}$Al$^{7+}$ and $^{23}$Na$^{6+}$ from ISOLDE and also the first radioactive $^{26}$Na$^{7+}$ and $^{24}$Na$^{7+}$ beams (just 5x10$^{5}$ p/s) have been charge bred and accelerated for tests of the experimental setup. Despite some problems with the electron gun, which had one breakdown after about 1500 hours of operation and displays slow changes of the emission conditions, the EBIS is working remarkably stable (24 hours / 7 days a week). We will report ...

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

Science.gov (United States)

Orchard, Sandra; Ammari, Mais; Aranda, Bruno; Breuza, Lionel; Briganti, Leonardo; Broackes-Carter, Fiona; Campbell, Nancy H.; Chavali, Gayatri; Chen, Carol; del-Toro, Noemi; Duesbury, Margaret; Dumousseau, Marine; Galeota, Eugenia; Hinz, Ursula; Iannuccelli, Marta; Jagannathan, Sruthi; Jimenez, Rafael; Khadake, Jyoti; Lagreid, Astrid; Licata, Luana; Lovering, Ruth C.; Meldal, Birgit; Melidoni, Anna N.; Milagros, Mila; Peluso, Daniele; Perfetto, Livia; Porras, Pablo; Raghunath, Arathi; Ricard-Blum, Sylvie; Roechert, Bernd; Stutz, Andre; Tognolli, Michael; van Roey, Kim; Cesareni, Gianni; Hermjakob, Henning

2014-01-01

IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset. Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org). PMID:24234451

The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments.

Science.gov (United States)

Kodama, Yuichi; Mashima, Jun; Kaminuma, Eli; Gojobori, Takashi; Ogasawara, Osamu; Takagi, Toshihisa; Okubo, Kousaku; Nakamura, Yasukazu

2012-01-01

The DNA Data Bank of Japan (DDBJ; http://www.ddbj.nig.ac.jp) maintains and provides archival, retrieval and analytical resources for biological information. The central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: the 'DDBJ Omics Archive' (DOR; http://trace.ddbj.nig.ac.jp/dor) and BioProject (http://trace.ddbj.nig.ac.jp/bioproject). DOR is an archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. In this article, we describe major changes and improvements introduced to the DDBJ services, and the launch of two new resources: DOR and BioProject.

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.

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.

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.

"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.

ESI-LC-MS based-metabolomics data of mangosteen (Garcinia mangostana Linn. fruit pericarp, aril and seed at different ripening stages

Directory of Open Access Journals (Sweden)

Siti Farah Mamat

2018-04-01

Full Text Available Fruit ripening is a complex phenomenon involving a series of biochemical, physiological and organoleptic changes. Ripening process in mangosteen (Garcinia mangostana Linn. is unique of which the fruit will only ripen properly if harvested during its middle stage (emergence of purple/pink colour but not earlier (green stage. The knowledge on the molecular mechanism and regulation behind this phenomenon is still limited. Hence, electrospray ionization liquid chromatography mass spectrometry (ESI-LC-MS based metabolomics analysis was applied to determine the metabolome of mangosteen ripening. Specifically, mangosteen pericarp, aril and seed were collected at four different ripening stages (stage 0: green, stage 2: yellowish with pink patches, stage 4: brownish red and stage 6: dark purple and subjected to metabolite profiling analysis. The data provided in this article have been deposited to the EMBL-EBI MetaboLights database (DOI: 10.1093/nar/gks1004. PubMed PMID: 23109552 with the identifier MTBLS595. The complete dataset can be accessed here https://www.ebi.ac.uk/metabolights/MTBLS595. Keywords: Ripening, Garcinia mangostana Linn., Metabolomics, ESI-LC-MS

Permanent magnet electron beam ion source/trap systems with bakeable magnets for improved operation conditions

International Nuclear Information System (INIS)

Schmidt, M.; Zschornack, G.; Kentsch, U.; Ritter, E.

2014-01-01

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

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...

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).

Drug: D01000 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D01000 Drug Bethanechol chloride (JP17/USP); Urecholine (TN) ... C7H17N2O2. Cl D01000...31 K04132 K04133] ... CAS: 590-63-6 PubChem: 7848063 ChEBI: 3085 ChEMBL: CHEMBL1768 DrugBank: DB01019 LigandBox: D01000 NIKKAJI: J277.869F ...

Drug: D08442 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available icine acetylcholinesterase (AChE) [KO:K01049] ... CAS: 114-26-1 PubChem: 96025128 ChEBI: 34938 ChEMBL: CHEMBL446060 LigandBox: D08442 NIKKAJI: J2.893B ... ... D08442 Drug Propoxur (BAN); Bolfo (TN) ... C11H15NO3 D08442.gif ... Same as: C14334 ... Carbamate veterinary med

Drug: D04140 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D04140 Drug Fenbendazole (USP/INN); Panacur [veterinary] (TN) ... C15H13N3O2S D04140....gif ... ATC code: P02CA06 ... Benzimidazole derivative veterinary medicine ... CAS: 43210-67-9 PubChem: 47206087 ChEBI: 77092 ChEMBL: CHEMBL37161 LigandBox: D04140 NIKKAJI: J15.833J ...

Drug: D08150 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D08150 Drug Lufenuron (INN); Program [veterinary] (TN) ... C17H8Cl2F8N2O3 D08150.gif ... ... Same as: C18434 ... Benzoyl phenylurea derivative veterinary medicine ... CAS: 103055-07-8 PubChem: 96024840 ChEBI: 39384 ChEMBL: CHEMBL1364906 LigandBox: D08150 NIKKAJI: J481.190I ...

Drug: D03636 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D03636 Drug Cystine (USAN/INN); L-Cystine (JAN) ... C6H12N2O4S2 D03636.gif ... Other ... ...DG01672 ... Amino acid Same as: C00491 ... CAS: 56-89-3 PubChem: 47205875 ChEBI: 16283 ChEMBL: CHEMBL590540 DrugBank: DB00138 LigandBox: D03636 NIKKAJI: J9.172C ...

A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk

Czech Academy of Sciences Publication Activity Database

Heinig, M.; Petretto, E.; Wallace, C.; Bottolo, L.; Rotival, M.; Lu, H.; Li, Y.; Sarwar, R.; Langley, S. R.; Bauerfeind, A.; Hummel, O.; Lee, Y. A.; Paskas, S.; Rintisch, C.; Saar, K.; Cooper, J.; Buchan, R.; Gray, C. C.; Cyster, J. G.; Erdmann, J.; Hengstenberg, C.; Maouche, S.; Ouwehand, W. H.; Rice, C. M.; Samani, N. J.; Schunkert, H.; Goodall, A. H.; Schulz, H.; Roider, H. G.; Vingron, M.; Blankenberg, S.; Münzel, T.; Zeller, T.; Szymczak, S.; Ziegler, A.; Tiret, L.; Smyth, D. J.; Pravenec, Michal; Aitman, T. J.; Cambien, F.; Clayton, D.; Todd, J. A.; Hubner, N.; Cook, S.A.

2010-01-01

Roč. 467, č. 7314 (2010), s. 460-464 ISSN 0028-0836 R&D Projects: GA MŠk(CZ) 1M0520; GA ČR GAP301/10/0290 Institutional research plan: CEZ:AV0Z50110509 Keywords : IRF7 driven inflammatory network * Ebi2 * type 1 diabetes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 36.101, year: 2010

Drug: D10001 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D10001 Drug Fingolimod (INN); Gilenya (TN) ... C19H33NO2 D10001.gif ... ATC code: L04...AA27 Chemical group: DG00741 ... Sphingosine [CPD:C00319] analog S1PR1 [HSA:1901] [KO:K04288] ... CAS: 162359-55-9 PubChem: 135626722 ChEBI: 63115 ChEMBL: CHEMBL314854 LigandBox: D10001 ...

A light ion four rod RFQ injector

International Nuclear Information System (INIS)

Schempp, A.; Ferch, M.; Klein, H.

1987-01-01

The four-rod RFQ has been developed in Frankfurt as an alternative solution for ion injectors. A 202 MHz resonator has been built with design parameters taken from the HERA injector (18keV-750keV, 20mA H - ). Properties of this structure are described and applications as light ion accelerator for particles from an EBIS ion source are discussed

An EBIS for charge state breeding in the SPES project

Indian Academy of Sciences (India)

increases the total efficiency of the beam transmission and lowers the cost of the .... accounting for the magnetic field and the electron beam space charge. .... the TOF system that will be placed at the end of the BRIC to analyze the ion charge ...

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

Straightforward and complete deposition of NMR data to the PDBe

International Nuclear Information System (INIS)

Penkett, Christopher J.; Ginkel, Glen van; Velankar, Sameer; Swaminathan, Jawahar; Ulrich, Eldon L.; Mading, Steve; Stevens, Tim J.; Fogh, Rasmus H.; Gutmanas, Aleksandras; Kleywegt, Gerard J.; Henrick, Kim; Vranken, Wim F.

2010-01-01

We present a suite of software for the complete and easy deposition of NMR data to the PDB and BMRB. This suite uses the CCPN framework and introduces a freely downloadable, graphical desktop application called CcpNmr Entry Completion Interface (ECI) for the secure editing of experimental information and associated datasets through the lifetime of an NMR project. CCPN projects can be created within the CcpNmr Analysis software or by importing existing NMR data files using the CcpNmr FormatConverter. After further data entry and checking with the ECI, the project can then be rapidly deposited to the PDBe using AutoDep, or exported as a complete deposition NMR-STAR file. In full CCPN projects created with ECI, it is straightforward to select chemical shift lists, restraint data sets, structural ensembles and all relevant associated experimental collection details, which all are or will become mandatory when depositing to the PDB. Instructions and download information for the ECI are available from the PDBe web site at http://www.ebi.ac.uk/pdbe/nmr/deposition/eci.htmlhttp://www.ebi.ac.uk/pdbe/nmr/deposition/eci.html.

New trends in RFQ-development

International Nuclear Information System (INIS)

Schempp, A.

1987-01-01

New trends in RFQ-development depending on the design goals are presented. Designs for heavy ion RFQs and for highly charged light ions from EBIS source are given. The use of the RFQ to accelerate beams, to accelerate very heavy clusters is shown. The application of the procedure funnel beams with RFQs is outlined. The beam dynamic parameters of the 4-vane RFQ for HERA are given

Phenotype abnormality - Arabidopsis Phenome Database | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available ion of ontology terms and properties. Phenotypes for morphology are standardized using Plant Ontology... (PO) or Trait Ontology (TO), with Phenotype Ontology (PATO). PATO is the vocabulary cov... tolerance can be expressed using Gene Ontology (GO), ChEBI etc. Some phenotypes are observed under some spe...h URL http://togodb.biosciencedbc.jp/togodb/view/cpp_abnormality#en Data acquisition method Plant Ontology, Phenotype Ontology

ELIXIR Handbook of Operations

OpenAIRE

Niklas Blomberg; Martin Cook; Pablo Roman Garcia; Stephanie Suhr; Premysl Velek; Montserrat Gonzalez; Susanna Repo

2017-01-01

ELIXIR is a distributed infrastructure, built around existing centres of excellence throughout the European member states represented through national Nodes, and incorporating the internationally supported European Bioinformatics Institute (EMBL-EBI). There are currently over 160 institutes from 20 member states taking part in ELIXIR. Operating a large, distributed, ‘virtual’ organisation such as ELIXIR requires strong coordination capabilities with clear roles and effective and simple proces...

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.

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

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.

Radiofrequency quadrupole-based beam cooler and buncher for the CANREB project at TRIUMF

Science.gov (United States)

Barquest, Brad; Pearson, Matt; Ames, Friedhelm; Dilling, Jens; Gwinner, Gerald; Kanungo, Rituparna; Kruecken, Reiner

2016-09-01

A new radiofrequency quadrupole-based ion beam cooler and buncher (BCB) and pulsed drift tube (PDT) have been designed as part of the CANREB project at TRIUMF. The BCB is designed to accept continuous 60 keV rare isotope beams from the ARIEL or ISAC production targets and efficiently deliver low-emittance, bunched beams of up to 107 ions per bunch to an electron beam ion source (EBIS) to charge-breed the bunch for post-acceleration. The PDT will adjust the energy of the bunched beam from 60 keV to 10-14 keV for injection into the EBIS. The injection energy is determined by the acceptance of the post-accelerating RFQ. The design of the BCB is nearing completion, and fabrication and assembly effort will proceed shortly. In addition, a PDT prototype is under development to test that the design concept satisfies the voltage and switching time requirements. Design features of the BCB and PDT will be discussed, and an update on BCB assembly and PDT testing progress will be presented. CANREB is funded by CFI, NSRIT, Manitoba Research and Innovation Fund, AAPS, Saint Mary's U, U of Manitoba and TRIUMF. TRIUMF receives federal funding via a contribution agreement with the National Research Council of Canada.

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.

BRICTEST: a code for charge breeding simulations in RF quadrupolar field

International Nuclear Information System (INIS)

Variale, V.; Claudione, M.

2005-01-01

In the framework of the SPES project (Study for Production of Exotic Species), funded by Istituto Nazionale Fisica Nucleare (INFN) at the Laboratori Nazionali Legnaro (LNL) (Padua) for Radioactive Ion Beam (RIB) production, an R and D experiment of a charge breeder device, called BRIC (BReeding Ion Charge), is in progress at LNL. BRIC is an Electron Beam Ion Source (EBIS) type ion charge state breeder in which a radio frequency (RF) quadrupolar field has been superimposed in the trapped ion region to introduce a selective containment with the aim of increasing the wanted ion trapping efficiency. A code that studies the motion and the ion charge state evolution in the trap region of the BRIC device has been recently developed in the Bari INFN section. That code has the aim of showing if, in the presence of an axial magnetic field and electron beam space charge force, the RF quadrupole field can still give a selective ion containment in the EBIS trap region. The code, furthermore, should allow choosing the RF quadrupole parameters to optimize the ion charge containment efficiency. In this paper the main feature of the code, named BRICTEST, and the simulation test will be presented and shortly discussed

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

African Journals Online (AJOL)

Introduction: Cytokeratin fragment 21.1 (CYFRA 21.1) assay detects a serum fragment of cytokeratin 19 (CK19) and is employed in the diagnosis and management of lung cancer, particularly of squamous cell histotype. Breast carcinoma has been demonstrated to express CK19 fragments in the primary and metastatic ...

De novo transcriptome assembly and its annotation for the aposematic wood tiger moth (Parasemia plantaginis

Directory of Open Access Journals (Sweden)

Juan A. Galarza

2017-06-01

Full Text Available In this paper we report the public availability of transcriptome resources for the aposematic wood tiger moth (Parasemia plantaginis. A comprehensive assembly methods, quality statistics, and annotation are provided. This reference transcriptome may serve as a useful resource for investigating functional gene activity in aposematic Lepidopteran species. All data is freely available at the European Nucleotide Archive (http://www.ebi.ac.uk/ena under study accession number: PRJEB14172.

Drug: D07284 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D07284 Drug Butanilicaine (INN) ... C13H19ClN2O D07284.gif ... Neuropsychiatric agent ... DG02030 ... Anesthetic...s ... DG01675 ... Local anesthetic ... DG01673 ... Amide type local anesthetic ... DG01675 ... Local anesthetic... ... DG01673 ... Amide type local anesthetic ATC code: N01BB05 ... CAS: 3785-21-5 PubChem: 51091621 ChEBI: 55518 ChEMBL: CHEMBL2104238 LigandBox: D07284 NIKKAJI: J8.254F ...

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

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

International Nuclear Information System (INIS)

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

2017-01-01

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. - Highlights: • Idli (traditional Indian fermented food) was prepared in ready-to-eat (RTE) form. • Ready-to-eat Idli was then subjected to combination processing comprised of lowest irradiation dosage of 2.5 kGy with mild heat treatment to extend its shelf life. • Increase in hardness and decrease in brightness of combination processed Idli was observed. • Combination processed Idli was microbiologically safe and

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

Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism.

Science.gov (United States)

Liu, Qingping; Wang, Jiahao; Zhu, Yan; He, Yongqun

2017-12-21

Rheumatism represents any disease condition marked with inflammation and pain in the joints, muscles, or connective tissues. Many traditional Chinese drugs have been used for a long time to treat rheumatism. However, a comprehensive information source for these drugs is still missing, and their anti-rheumatism mechanisms remain unclear. An ontology for anti-rheumatism traditional Chinese drugs would strongly support the representation, analysis, and understanding of these drugs. In this study, we first systematically collected reported information about 26 traditional Chinese decoction pieces drugs, including their chemical ingredients and adverse events (AEs). By mostly reusing terms from existing ontologies (e.g., TCMDPO for traditional Chinese medicines, NCBITaxon for taxonomy, ChEBI for chemical elements, and OAE for adverse events) and making semantic axioms linking different entities, we developed the Ontology of Chinese Medicine for Rheumatism (OCMR) that includes over 3000 class terms. Our OCMR analysis found that these 26 traditional Chinese decoction pieces are made from anatomic entities (e.g., root and stem) from 3 Bilateria animals and 23 Mesangiospermae plants. Anti-inflammatory and antineoplastic roles are important for anti-rheumatism drugs. Using the total of 555 unique ChEBI chemical entities identified from these drugs, our ChEBI-based classification analysis identified 18 anti-inflammatory, 33 antineoplastic chemicals, and 9 chemicals (including 3 diterpenoids and 3 triterpenoids) having both anti-inflammatory and antineoplastic roles. Furthermore, our study detected 22 diterpenoids and 23 triterpenoids, including 16 pentacyclic triterpenoids that are likely bioactive against rheumatism. Six drugs were found to be associated with 184 unique AEs, including three AEs (i.e., dizziness, nausea and vomiting, and anorexia) each associated with 5 drugs. Several chemical entities are classified as neurotoxins (e.g., diethyl phthalate) and allergens (e

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 milk at PBE in relation to the subsequent PS (P = 0.04). Cows in lactation number 5 or more were less likely (r = 0.69) to get in calf before the end of the breeding season than cows in their first lactation. Cows that calved later in the season were less likely to become pregnant before the end of the breeding season (P mucus evaluation with the Metricheck device and an ultrasound scan of the uterus serve as a good predictor of the subsequent PS. There is overlap between the

Isolasi Dan Analisis Kimia Minyak Atsiri Dari Bunga Kecombrang (Etlingera Elatior) Dengan Gas Kromatografi-Spektrometer Massa (GC-MS) Dan Uji Aktivitas Anti Bakteri

OpenAIRE

Perangin Angin, Mawar Indah

2016-01-01

In this study has been treated isolation and analyze its chemical component of volatile oil of Etlingera e. obtained from district of Nang Belawan sub district of Simpang Empat in Karo Regency. The isolated volatile oil used Stahl tool. Chemical composition for each outcome of isolation was treated analysis using Gas chromatography Mass Spectrophotometer (GC-MS) device and Infra Red Spectrophotometer. The outcome isolation of Etlingera e.by distillation using Stahl device some 450 gram sa...

Drug: D08247 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D08247 Drug Nalorphine (INN); Nalorphine serb (TN) ... C19H21NO3 D08247.gif ... Analgesic ... DG01586 ... Opioid receptor antagonist Other ... DG01718 ... Drugs for addictive disorder ... DG01717 ... Drugs for opioid dependence Same as: C11787 ATC code: V03AB02 Chemical group: DG01151 ... CAS: 62-67-9 PubChem: 96024935 ChEBI: 7458 ChEMBL: CHEMBL415284 LigandBox: D08247 NIKKAJI: J4.825I ...

Cornell electron beam ion source

International Nuclear Information System (INIS)

Kostroun, V.O.; Ghanbari, E.; Beebe, E.N.; Janson, S.W.

1981-01-01

An electron beam ion source (EBIS) for the production of low energy, multiply charged ion beams to be used in atomic physics experiments has been designed and constructed. An external high perveance electron gun is used to launch the electron beam into a conventional solenoid. Novel features of the design include a distributed sputter ion pump to create the ultrahigh vacuum environment in the ionization region of the source and microprocessor control of the axial trap voltage supplies

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.

The complex portal--an encyclopaedia of macromolecular complexes.

Science.gov (United States)

Meldal, Birgit H M; Forner-Martinez, Oscar; Costanzo, Maria C; Dana, Jose; Demeter, Janos; Dumousseau, Marine; Dwight, Selina S; Gaulton, Anna; Licata, Luana; Melidoni, Anna N; Ricard-Blum, Sylvie; Roechert, Bernd; Skyzypek, Marek S; Tiwari, Manu; Velankar, Sameer; Wong, Edith D; Hermjakob, Henning; Orchard, Sandra

2015-01-01

The IntAct molecular interaction database has created a new, free, open-source, manually curated resource, the Complex Portal (www.ebi.ac.uk/intact/complex), through which protein complexes from major model organisms are being collated and made available for search, viewing and download. It has been built in close collaboration with other bioinformatics services and populated with data from ChEMBL, MatrixDB, PDBe, Reactome and UniProtKB. Each entry contains information about the participating molecules (including small molecules and nucleic acids), their stoichiometry, topology and structural assembly. Complexes are annotated with details about their function, properties and complex-specific Gene Ontology (GO) terms. Consistent nomenclature is used throughout the resource with systematic names, recommended names and a list of synonyms all provided. The use of the Evidence Code Ontology allows us to indicate for which entries direct experimental evidence is available or if the complex has been inferred based on homology or orthology. The data are searchable using standard identifiers, such as UniProt, ChEBI and GO IDs, protein, gene and complex names or synonyms. This reference resource will be maintained and grow to encompass an increasing number of organisms. Input from groups and individuals with specific areas of expertise is welcome. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Design for simultaneous acceleration of stable and unstable beams in a superconducting heavy-ion linear accelerator for RISP

Science.gov (United States)

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

2017-11-01

The post-accelerator of isotope separation on-line (ISOL) system for rare isotope science project (RISP) is a superconducting linear accelerator (SC-linac) with a DC equivalent voltage of around 160 MV. An isotope beam extracted from the ISOL is in a charge state of 1+ and its charge state is increased to n+ by charge breeding with an electron beam ion source (EBIS). The charge breeding takes tens of ms and the pulse width of extracted beam from the EBIS is tens of μs, which operates at up to 30 Hz. Consequently a large portion of radio frequency (rf) time of the post SC-linac is unused. The post-linac is equipped also with an electron cyclotron resonance (ECR) ion source for stable ion acceleration. Thanks to the large phase acceptance of SC-linac, it is possible to accelerate simultaneously both stable and radioisotope ions with a similar charge to mass ratio by sharing rf time. This operation scheme is implemented for RISP with the addition of an electric chopper and magnetic kickers. The facility will be capable of providing the users of the ISOL and in-flight fragmentation (IF) systems with different beams simultaneously, which would help nuclear science users in obtaining a beam time as high-precision measurements often need long hours.

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.

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.

The application of the rapid assessment and response methodology for cannabis prevention research among youth in the Netherlands.

Science.gov (United States)

Dupont, Hans B; Kaplan, Charles D; Braam, Richard V; Verbraeck, Hans T; de Vries, Nanne K

2015-08-01

Drug prevention methods tailored to specific target groups have become increasingly important. There is a growing need to find ways to rapidly assess and situate target groups in their particular contexts. This need is associated with the implementation of evidence-based interventions (EBIs) for these specific target groups. This article describes the application of Rapid Assessment and Response (RAR) as a necessary first step in designing and implementing a prevention intervention plan for problematic cannabis use among "loitering" youth in the South of the Netherlands. Seven RAR studies were conducted using an innovative stepwise model in which the prevention field worker is central. The normative structure for the use of cannabis was found to vary across the neighborhoods of the RAR studies and emerged as the focal point in designing a suitable response. The RAR studies also identified the need in the prevention toolbox for a tailored, low-threshold, effective, individual brief intervention for youth problematic cannabis use. The RAR was found to provide a powerful methodology for detecting target groups and generating contextual and normative data that enable the prevention field worker to select and adapt from the spectrum of existing Evidence based Interventions (EBIs) or develop the most promising model for implementation with the specific target group. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

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

European Bioinformatics Institute: Research Infrastructure needed for Life Science

CERN Multimedia

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.

Road Materials and Pavement Design Volume 17(1)

CSIR Research Space (South Africa)

De Beer, Morris

2016-03-01

Full Text Available Materials and Pavement Design Volume 17, 2016 - Issue 1 Editorial Board Page ebi | Published online: 03 Oct 2016  http://dx.doi.org/10.1080/14680629.2016.1244475 Editors-in-Chief Hervé DI BENEDETTO - University of Lyon/ENTPE, Vaulx-en-Velin, France... Andrew Charles COLLOP - De Montfort University, Leicester, UK William G. BUTTLAR - University of Missouri, Urbana-Champaign, USA Editor-in-Chief at Large Jorge B. Sousa - Consulpav, Oeiras, Portugal Associate Editors Morris de Beer - CSIR Built...

The synthesis method for design of electron flow sources

Science.gov (United States)

Alexahin, Yu I.; Molodozhenzev, A. Yu

1997-01-01

The synthesis method to design a relativistic magnetically - focused beam source is described in this paper. It allows to find a shape of electrodes necessary to produce laminar space charge flows. Electron guns with shielded cathodes designed with this method were analyzed using the EGUN code. The obtained results have shown the coincidence of the synthesis and analysis calculations [1]. This method of electron gun calculation may be applied for immersed electron flows - of interest for the EBIS electron gun design.

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases

OpenAIRE

Orchard, S; Ammari, M; Aranda, B; Breuza, L; Briganti, L; Broackes-Carter, F; Campbell, N; Chavali, G; Chen, C; del-Toro, N; Duesbury, M; Dumousseau, M; Galeota, E; Hinz, U; Iannuccelli, M

2014-01-01

IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate l...

Predikce spotřeby elektrické energie a zemního plynu

Czech Academy of Sciences Publication Activity Database

Pelikán, Emil; Eben, Kryštof; Šimůnek, Milan

2001-01-01

Roč. 7, č. 4 (2001), s. 15-17 ISSN 1210-9592 Institutional research plan: AV0Z1030915 Keywords : prediction systems * statistical data analysis * neural networks * software implementation Subject RIV: BA - General Mathematics

5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.

Science.gov (United States)

Stephan, Christian; Hamacher, Michael; Blüggel, Martin; Körting, Gerhard; Chamrad, Daniel; Scheer, Christian; Marcus, Katrin; Reidegeld, Kai A; Lohaus, Christiane; Schäfer, Heike; Martens, Lennart; Jones, Philip; Müller, Michael; Auyeung, Kevin; Taylor, Chris; Binz, Pierre-Alain; Thiele, Herbert; Parkinson, David; Meyer, Helmut E; Apweiler, Rolf

2005-09-01

The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On July 7, 2005 the members came together for the 5th time at the European Bioinformatics Institute (EBI) in Hinxton, UK, hosted by Rolf Apweiler. As a main result, the parameter set of the semi-automated data re-analysis of MS/MS spectra has been elaborated and the subsequent work steps have been defined.

Soluble serum VCAM-1, whole blood mRNA expression and treatment response in natalizumab-treated multiple sclerosis

DEFF Research Database (Denmark)

Petersen, E R; Søndergaard, H B; Oturai, A B

2016-01-01

Background Natalizumab reduces disease activity in multiple sclerosis (MS). Natalizumab binds to the very late antigen-4 and inhibits vascular cell adhesion molecule-1 (VCAM-1)-mediated transmigration of immune cells across the blood-brain-barrier. This is associated with decreased serum...... levels of a panel of immunomarkers, associated with natalizumab-treatment, are not sensitive markers of MS disease activity. However, decreased expression of pro-inflammatory HLX1 and IL1B and increased expression of immunoregulatory EBI3 may indicate a less pathogenic immune activation status...

11. international conference on ion sources

International Nuclear Information System (INIS)

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

2005-01-01

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

Bibliografía

OpenAIRE

2015-01-01

Abram, Matthias1992. Lengua, cultura e identidad. El proyecto EBl 1985-1990. Quito: Proyecto EBI/Abya Yala. Academia Mayor de la Lengua Quechua1995 Diccionario Quechua-Español-Quechua. Qheswa-Español-Qheswa Simi Taqe. Cuzco: Municipalidad del Cuzco. Adelaar, Willem1977. Tarma Quechua. Grammar, Texts, Dictionary. Lisse: Peter de Ridder Press.1986 “La relación quechua-aru: perspectivas para la separación del léxico”. Revista Andina 4 (2): 379426.1999. “Unprotected Languages: The Silent Death of...

Downscaled climate change projections over northeastern South Africa: Implications for streamflow

CSIR Research Space (South Africa)

Mkhwanazi, M

2015-09-01

Full Text Available health, agriculture and biodiversity. A comprehensive assessment and understanding of the long-term impacts of climate change on water resources is therefore vital. This information, if applied in planning processes and decision making can... of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change [Barros, V.R., Field, C.B., Dokken, D.J., Mastrandrea, M.D., Mach, K.J., Bilir, T.E., Chatterjee, M., Ebi, K.L., Estrada, Y.O., Genova, R.C., Girma, B...

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.

Building a drug ontology based on RxNorm and other sources.

Science.gov (United States)

Hanna, Josh; Joseph, Eric; Brochhausen, Mathias; Hogan, William R

2013-12-18

We built the Drug Ontology (DrOn) because we required correct and consistent drug information in a format for use in semantic web applications, and no existing resource met this requirement or could be altered to meet it. One of the obstacles we faced when creating DrOn was the difficulty in reusing drug information from existing sources. The primary external source we have used at this stage in DrOn's development is RxNorm, a standard drug terminology curated by the National Library of Medicine (NLM). To build DrOn, we (1) mined data from historical releases of RxNorm and (2) mapped many RxNorm entities to Chemical Entities of Biological Interest (ChEBI) classes, pulling relevant information from ChEBI while doing so. We built DrOn in a modular fashion to facilitate simpler extension and development of the ontology and to allow reasoning and construction to scale. Classes derived from each source are serialized in separate modules. For example, the classes in DrOn that are programmatically derived from RxNorm are stored in a separate module and subsumed by classes in a manually-curated, realist, upper-level module of DrOn with terms such as 'clinical drug role', 'tablet', 'capsule', etc. DrOn is a modular, extensible ontology of drug products, their ingredients, and their biological activity that avoids many of the fundamental flaws found in other, similar artifacts and meets the requirements of our comparative-effectiveness research use-case.

Indications, techniques and results of postoperative brachytherapy in cancer of the oral cavity

International Nuclear Information System (INIS)

Pernot, M.; Aletti, P.; Carolus, J.M.; Marquis, I.; Hoffstetter, S.; Maaloul, F.; Peiffert, D.; Lapeyre, M.; Luporsi, E.; Marchal, C.; Noeel, A.; Bey, P.

1995-01-01

Purpose/objective: We tried to reduce the number of local recurrences after surgery and external beam irradiation (EBI) in carcinoma of the oral cavity, when margins were positive or close. Material and methods: From 1980 to 1992, we treated 97 cases of carcinomas of the oral cavity by postoperative brachytherapy. Surgery was combined with EBI+brachytherapy in 51 cases and with brachytherapy alone in 46 cases. We treated 29 T1, 34 T2, 30 T3T4 and four Tx (73% were N0 at first examination and 23% had positive nodes). The type of surgery is analysed. Brachytherapy was performed in one or two planes along the surgical scar. If the mandibular rim was resected, especially when the tongue or the remaining floor were sutured to the internal face of the inferior lip or to the buccal mucosa, the bridge technique was used. To decrease the dose to the inferior part of the mandible, the bridge was modified thanks to experimental dosimetry. Results: At 5 years, the local control (LC) is 89%, the locoregional control (LRC) 82%, the specific survival (SS) 74% and the overall survival (OS) 67%. Complications: We noted 19% of grade 1 (minor), 12% of grade 2 (moderate) and 6% of grade 3 (major) complications. Conclusion: Compared with the results of the literature, we think that postoperative brachytherapy can improve classical radiosurgical results in selected cases with a risk of local recurrence

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.

The design of electron and ion guns, beams, and collectors

Energy Technology Data Exchange (ETDEWEB)

Becker, Reinard [Institut fuer Angewandte Physik der Universitaet Frankfurt/M, Fach 180, D-60054 (Germany); Herrmannsfeldt, William B [Stanford Linear Accclerator Center, Stanford University, CA (United States)

2004-01-01

The well known 'SLAC Electron Trajectory Program' (EGUN) has been ported to PCs and has been developed into a family of programs for the design and the optimization of particle optics devices including electron and ion guns, beam transport sections and collectors. We will discuss the application of these tools for the design and the optimization of the essential parts of EBIS/T devices. The discussion will include conditions in which restrictions in the reliability of simulations may occur due to the mathematical modeling and how to overcome them.

The design of electron and ion guns, beams, and collectors

Science.gov (United States)

Becker, Reinard; Herrmannsfeldt, William B.

2004-01-01

The well known `SLAC Electron Trajectory Program' (EGUN) has been ported to PCs and has been developed into a family of programs for the design and the optimization of particle optics devices including electron and ion guns, beam transport sections and collectors. We will discuss the application of these tools for the design and the optimization of the essential parts of EBIS/T devices. The discussion will include conditions in which restrictions in the reliability of simulations may occur due to the mathematical modeling and how to overcome them.

The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.

Science.gov (United States)

Côté, Richard G; Jones, Philip; Martens, Lennart; Apweiler, Rolf; Hermjakob, Henning

2008-07-01

The Ontology Lookup Service (OLS) (http://www.ebi.ac.uk/ols) provides interactive and programmatic interfaces to query, browse and navigate an ever increasing number of biomedical ontologies and controlled vocabularies. The volume of data available for querying has more than quadrupled since it went into production and OLS functionality has been integrated into several high-usage databases and data entry tools. Improvements have been made to both OLS query interfaces, based on user feedback and requirements, to improve usability and service interoperability and provide novel ways to perform queries.

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.

uvby and Hβ photometry of the open cluster IC 4996

International Nuclear Information System (INIS)

Alfaro, E.J.; Delgado, A.J.; Garcia-Pelayo, J.M.; Garrido, R.; Saez, M.

1985-01-01

Photoelectric uvby and Hβ observations have been obtained for 15 stars in the field of the open cluster IC 4996. An average colour excess of E(b-y)=0.473 is estimated for six observed members of the cluster, in good agreement with previous results. A comparison between the β-Msub(v) calibrations given by Crawford and by Eggen suggests that the first one takes better into account the evolutionary effects on the Hβ index. We have calculated a true distance modulus of 11.43 and an age of 7.5x10 6 years

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.

Advantages and disadvantages for receiving Internet-based HIV/AIDS interventions at home or at community-based organizations.

Science.gov (United States)

Green, Shana M; Lockhart, Elizabeth; Marhefka, Stephanie L

2015-01-01

Within recent years, public health interventions have become technology based to reflect the digital age we currently live in and appeal to the public in innovative and novel ways. The Internet breaks down boundaries distance imposes and increases our ability to reach and connect with people. Internet-based interventions have the potential to expand access to effective behavioral interventions (EBIs). The US National HIV/AIDS Strategy states that people living with HIV should have access to EBIs such as healthy relationships (HR) to help them develop safe sex and disclosure skills. However, access to HR is limited across the country, especially for people in remote or rural areas. Internet-based healthy relationships video groups (HR-VG) delivered at home or community-based organizations (CBOs) can possibly expand access. This study assesses the preferences of women living with HIV (WLH) for participation in HR-VG among 21 WLH who participated in a randomized control trial (RCT) testing HR-VG and completed open-ended semi-structured telephone interviews. Transcripts were thematically analyzed to determine advantages and disadvantages of home or CBO delivery of HR-VG. Themes relating to convenience, technology access, privacy, distractions, HIV serostatus disclosure, and social opportunities were identified as advantages or disadvantages to participating in HR-VG at each location. Overall, privacy was the most salient concern of accessing HR-VG at home or at a CBO. Considering the concerns expressed by WLH, further studies are needed to assess how an Internet-based intervention delivered at home for WLH can maintain privacy while being cost effective.

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.

Reactome diagram viewer: data structures and strategies to boost performance.

Science.gov (United States)

Fabregat, Antonio; Sidiropoulos, Konstantinos; Viteri, Guilherme; Marin-Garcia, Pablo; Ping, Peipei; Stein, Lincoln; D'Eustachio, Peter; Hermjakob, Henning

2018-04-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. Here, we present comprehensive enhancements in usability and performance based on extensive usability testing sessions and technology developments, aiming to optimize the viewer towards the needs of the community. The pathway diagram viewer version 3 achieves consistently better performance, loading and rendering of 97% of the diagrams in Reactome in less than 1 s. Combining the multi-layer html5 canvas strategy with a space partitioning data structure minimizes CPU workload, enabling the introduction of new features that further enhance user experience. Through the use of highly optimized data structures and algorithms, Reactome has boosted the performance and usability of the new pathway diagram viewer, providing a robust, scalable and easy-to-integrate solution to pathway visualization. As graph-based visualization of complex data is a frequent challenge in bioinformatics, many of the individual strategies presented here are applicable to a wide range of web-based bioinformatics resources. Reactome is available online at: https://reactome.org. The diagram viewer is part of the Reactome pathway browser (https://reactome.org/PathwayBrowser/) and also available as a stand-alone widget at: https://reactome.org/dev/diagram/. The source code is freely available at: https://github.com/reactome-pwp/diagram. fabregat@ebi.ac.uk or hhe@ebi.ac.uk. Supplementary data are available at Bioinformatics online.

LigSearch: a knowledge-based web server to identify likely ligands for a protein target

Energy Technology Data Exchange (ETDEWEB)

Beer, Tjaart A. P. de; Laskowski, Roman A. [European Bioinformatics Institute (EMBL–EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD (United Kingdom); Duban, Mark-Eugene [Northwestern University Feinberg School of Medicine, Chicago, Illinois (United States); Chan, A. W. Edith [University College London, London WC1E 6BT (United Kingdom); Anderson, Wayne F. [Northwestern University Feinberg School of Medicine, Chicago, Illinois (United States); Thornton, Janet M., E-mail: thornton@ebi.ac.uk [European Bioinformatics Institute (EMBL–EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD (United Kingdom)

2013-12-01

LigSearch is a web server for identifying ligands likely to bind to a given protein. Identifying which ligands might bind to a protein before crystallization trials could provide a significant saving in time and resources. LigSearch, a web server aimed at predicting ligands that might bind to and stabilize a given protein, has been developed. Using a protein sequence and/or structure, the system searches against a variety of databases, combining available knowledge, and provides a clustered and ranked output of possible ligands. LigSearch can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/LigSearch.

Organic halogen compounds and surface water pollution; Composti organoalogenati alifatici e contaminazione delle acque superficiali

Energy Technology Data Exchange (ETDEWEB)

Cocchioni, M.; Pellegrini, M. G.; Grappasonni, I.; Nacciarriti, L.; Bernacchia, G. [Camerino, Univ. (Italy). Dipt. di Scienze Igienistiche e Sanitarie-Ambientali

1997-03-01

A brief review of the effects of halogenated organic compounds on the fluvial ecosystem is followed by results from a detailed monitoring of these substances in all the Marches Region rivers. The results show generally modest concentrations, except for sporadic peaks for chloroform. Sites revealing significant concentrations of halogenated organic compounds also manifested a worsening of the biological quality of the waters with lessening of E.B.I. Attention is drawn to the negative effects of indiscriminate chlorination of purification plant outputs, as this practice often fails to resolve infective problems and in itself adds toxicity to the watercourse.

Maize MeJA-responsive proteins identified by high-resolution 2-DE PAGE

Directory of Open Access Journals (Sweden)

Yuliang Zhang

2015-12-01

Full Text Available Exogenous methyl jasmonate (MeJA is well-known to induce plant defense mechanisms effective against a wide variety of insect and microbial pests. High-resolution 2-DE gel electrophoresis was used to discover changes in the leaf proteome of maize exposed to MeJA. We sequenced 62 MeJA-responsive proteins by tandem mass spectroscopy, and deposited the mass spectra and identities in the EMBL-EBI PRIDE repository under reference number PXD001793. An analysis and discussion of the identified proteins in relation to maize defense against Asian corn borer is published by Zhang et al. (2015 [1].

Effect of ammonia and electron beam irradiation on lignocelulosic materials

International Nuclear Information System (INIS)

Mastro, N.L. del; Gennari, S.M.; Castagnet, A.C.G.

1986-01-01

Reports on some of the effects produced on sugarcane bagasse and eucaliptus wood saccharification by combining irradiation and NH 3 treatment. The samples irradiated at 10 5 Gy, 2x10 5 Gy and 5x10 5 Gy with an electron accelerator were treated with anhydrous gaseous ammonia. Cellulase complex from T. reesei was used for hydrolysis assays. Bromatological analysis and 'in vitro' digestibility tests were performed. The combination of EBI and ammonia treatments produced and increase in the saccharification yield, 'in vitro' digestibility and protein content for the two kinds of sample. (Author) [pt

Simulation-based Investigations of Electrostatic Beam Energy Analysers

CERN Document Server

Pahl, Hannes

2015-01-01

An energy analyser is needed to measure the beam energy profile behind the REX-EBIS at ISOLDE. The device should be able to operate with an accuracy of 1 V at voltages up to 30 kV. In order to find a working concept for an electrostatic energy analyser different designs were evaluated with simulations. A spherical device and its design issues are presented. The potential deformation effects of grids at high voltages and their influence on the energy resolution were investigated. First tests were made with a grid-free ring electrode device and show promising results.

PDBsum: Structural summaries of PDB entries.

Science.gov (United States)

Laskowski, Roman A; Jabłońska, Jagoda; Pravda, Lukáš; Vařeková, Radka Svobodová; Thornton, Janet M

2018-01-01

PDBsum is a web server providing structural information on the entries in the Protein Data Bank (PDB). The analyses are primarily image-based and include protein secondary structure, protein-ligand and protein-DNA interactions, PROCHECK analyses of structural quality, and many others. The 3D structures can be viewed interactively in RasMol, PyMOL, and a JavaScript viewer called 3Dmol.js. Users can upload their own PDB files and obtain a set of password-protected PDBsum analyses for each. The server is freely accessible to all at: http://www.ebi.ac.uk/pdbsum. © 2017 The Protein Society.

Increasing milk solids production across lactation through genetic selection and intensive pasture-based feed system.

Science.gov (United States)

Coleman, J; Pierce, K M; Berry, D P; Brennan, A; Horan, B

2010-09-01

The objective of the study was to quantify the effect of genetic improvement using the Irish total merit index, the Economic Breeding Index (EBI), on overall performance and lactation profiles for milk, milk solids, body weight (BW), and body condition score (BCS) within 2 pasture-based systems of milk production likely to be used in the future, following abolition of the European Union's milk quota system. Three genotypes of Holstein-Friesian dairy cattle were established from within the Moorepark dairy research herd: LowNA, indicative of animals with North American origin and average or lower genetic merit at the time of the study; HighNA, North American Holstein-Friesians of high genetic merit; and HighNZ, New Zealand Holstein-Friesians of high genetic merit. Animals from within each genotype were randomly allocated to 1 of 2 possible pasture-based feeding systems (FS): 1) The Moorepark pasture (MP) system (2.64 cows/ha and 344 kg of concentrate supplement per cow per lactation) and 2) a high output per hectare (HC) system (2.85 cows/ha and 1,056 kg of concentrate supplement per cow per lactation). Pasture was allocated to achieve similar postgrazing residual sward heights for both treatments. A total of 126, 128, and 140 spring-calving dairy cows were used during the years 2006, 2007, and 2008, respectively. Each group had an individual farmlet of 17 paddocks and all groups were managed similarly throughout the study. The effects of genotype, FS, and the interaction between genotype and FS on milk production, BW, and BCS across lactation were studied using mixed models with factorial arrangements of genotype and FS accounting for the repeated cow records across years. No significant genotype by FS interaction was observed for any of the variables measured. Results show that milk solids production of the national average dairy cow can be increased across lactation through increased EBI. High EBI genotypes (HighNA and HighNZ) produced more milk solids per cow and

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

Acute cardiac support with intravenous milrinone promotes recovery from early brain injury in a murine model of severe subarachnoid haemorrhage.

Science.gov (United States)

Mutoh, Tomoko; Mutoh, Tatsushi; Nakamura, Kazuhiro; Yamamoto, Yukiko; Tsuru, Yoshiharu; Tsubone, Hirokazu; Ishikawa, Tatsuya; Taki, Yasuyuki

2017-04-01

Early brain injury/ischaemia (EBI) is a serious complication early after subarachnoid haemorrhage (SAH) that contributes to development of delayed cerebral ischaemia (DCI). This study aimed to determine the role of inotropic cardiac support using milrinone (MIL) on restoring acute cerebral hypoperfusion attributable to EBI and improving outcomes after experimental SAH. Forty-three male C57BL/6 mice were assigned to either sham surgery (SAH-sham), SAH induced by endovascular perforation plus postconditioning with 2% isoflurane (Control), or SAH plus isoflurane combined with MIL with and without hypoxia-inducible factor inhibitor (HIF-I) pretreatment. Cardiac output (CO) during intravenous MIL infusion (0.25-0.75 μg/kg/min) between 1.5 and 2.5 hours after SAH induction was monitored with Doppler echocardiography. Magnetic resonance imaging (MRI)-continuous arterial spin labelling was used for quantitative cerebral blood flow (CBF) measurements. Neurobehavioral function was assessed daily by neurological score and open field test. DCI was analyzed 3 days later by determining infarction on MRI. Mild reduction of cardiac output (CO) and global cerebral blood flow (CBF) depression were notable early after SAH. MIL increased CO in a dose-dependent manner (P<.001), which was accompanied by improved hypoperfusion, incidence of DCI and functional recovery than Control (P<.05). The neuroprotective effects afforded by MIL or Control were attenuated by hypoxia-inducible factor (HIF) inhibition (P<.05). These results suggest that MIL improves acute hypoperfusion by its inotropic effect, leading to neurobehavioral improvement in mice after severe SAH, in which HIF may be acting as a critical mediator. © 2017 John Wiley & Sons Australia, Ltd.

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.

Test measurements on the RF charge breeder device BRIC

International Nuclear Information System (INIS)

Variale, Vincenzo; Boggia, Antonio; Clauser, Tarcisio; Raino, Antonio; Valentino, Vincenzo; Verrone, Grazia; Bak, Petr; Kustenzov, Gennady; Skarbo, Boris; Tiunov, Michael

2004-01-01

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 state +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 and where, in the future, with some implementation, it will be tested as charge breeder at ISOL/TS facility of that laboratory. BRIC could be considered as a solution for the charge state breeder of the SPES project under study also at the LNL. 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 filter the unwanted masses and then making a more efficient containment of the wanted ions. In this paper, the first ion charge state measurements and analysis and the effect of the RF field applied on the ion chamber will be reported and discussed. The first RF test measurements seem confirm, as foreseen by simulation results carried out previously, that a selective containment can be obtained. However, most accurate measurements needed to study with more details the effect. For this reason, few implementations of the system are in order to improve the accuracy of the measurements. The proposed modifications of the BRIC device, then, will be also presented and shortly discussed

ProCarDB: a database of bacterial carotenoids.

Science.gov (United States)

Nupur, L N U; Vats, Asheema; Dhanda, Sandeep Kumar; Raghava, Gajendra P S; Pinnaka, Anil Kumar; Kumar, Ashwani

2016-05-26

Carotenoids have important functions in bacteria, ranging from harvesting light energy to neutralizing oxidants and acting as virulence factors. However, information pertaining to the carotenoids is scattered throughout the literature. Furthermore, information about the genes/proteins involved in the biosynthesis of carotenoids has tremendously increased in the post-genomic era. A web server providing the information about microbial carotenoids in a structured manner is required and will be a valuable resource for the scientific community working with microbial carotenoids. Here, we have created a manually curated, open access, comprehensive compilation of bacterial carotenoids named as ProCarDB- Prokaryotic Carotenoid Database. ProCarDB includes 304 unique carotenoids arising from 50 biosynthetic pathways distributed among 611 prokaryotes. ProCarDB provides important information on carotenoids, such as 2D and 3D structures, molecular weight, molecular formula, SMILES, InChI, InChIKey, IUPAC name, KEGG Id, PubChem Id, and ChEBI Id. The database also provides NMR data, UV-vis absorption data, IR data, MS data and HPLC data that play key roles in the identification of carotenoids. An important feature of this database is the extension of biosynthetic pathways from the literature and through the presence of the genes/enzymes in different organisms. The information contained in the database was mined from published literature and databases such as KEGG, PubChem, ChEBI, LipidBank, LPSN, and Uniprot. The database integrates user-friendly browsing and searching with carotenoid analysis tools to help the user. We believe that this database will serve as a major information centre for researchers working on bacterial carotenoids.

Vývoj webové aplikace s ohledem na specifické potřeby zadavatele

OpenAIRE

Nývlt, David

2009-01-01

Bachelor's thesis deals with development of web applications and is divided into 2 parts, the first one is theoretical and the other is practical. The theoretical part discusses about the history and todays status of web applications and web as a whole with a small view into the future. Another section deals with an architecture of web applications (modularity, database design, structure of storage, etc.). The last section of the first part describes elements which are needed for developing o...

myChEMBL: a virtual machine implementation of open data and cheminformatics tools.

Science.gov (United States)

Ochoa, Rodrigo; Davies, Mark; Papadatos, George; Atkinson, Francis; Overington, John P

2014-01-15

myChEMBL is a completely open platform, which combines public domain bioactivity data with open source database and cheminformatics technologies. myChEMBL consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest version of the ChEMBL database, as well as the latest RDKit cheminformatics libraries. In addition, a self-contained web interface is available, which can be modified and improved according to user specifications. The VM is available at: ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current. The web interface and web services code is available at: https://github.com/rochoa85/myChEMBL.

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+

The activity of detoxifying enzymes in the infective juveniles of Heterorhabditis bacteriophora strains: Purification and characterization of two acetylcholinesterases.

Science.gov (United States)

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

2016-02-01

The infectivity and detoxifying enzyme activities including glutathione-S-transferase (GST), acetylcholinesterase (AChE) and carboxylesterase (CaE) are investigated in the infective juveniles (IJs) of six different strains of Heterorhabditis bacteriophora as a biocontrol agent against insect pests. The specific activities ranged from 10.8-29.8 and 50-220units/mg protein for GST and AChE, respectively; and from 24.7-129 and 22.6-77.3units/mg protein for CaE as estimated by P-nitrophenyl and α-naphthyl acetates, respectively. H. bacteriophora EM2 strain has the highest infectivity and the highest enzymatic activities as well. AChE is the predominant detoxifying enzyme that might imply its major role in the detoxification of insecticide(s). The isoenzyme pattern demonstrated two major slow-moving isoforms in all EPN strains examined. Purification of two AChE isoforms, AChEAII and AChEBI, from H. bacteriophora EM2 strain is performed by ammonium sulfate precipitation, gel filtration on Sephacryl S-200 and chromatography on DEAE-Sepharose. AChEAII and AChEBII have specific activities of 1207 and 1560unit/mg protein, native molecular weights of 180 and 68kDa, and are found in dimeric and monomeric forms, respectively. Both isoforms showed optimum activity at pH8.5 and 35°C. AChEBI exhibited higher thermal stability and higher activation energy than AChEAII. The enzymatic activities of purified AChEs are completely inhibited by Hg(+2) and Ni(+2) and greatly enhanced by Mn(+2). The substrate specificity, the relative efficiency of substrates hydrolysis, substrate inhibition and inhibition by BW284C51, but not by iso-OMPA, clearly indicated that they are true AChEs; their properties are compared with those recorded for insects as target hosts for H. bacteriophora EM2. Copyright © 2015 Elsevier Inc. All rights reserved.

Evaluating and optimizing horticultural regimes in space plant growth facilities

Science.gov (United States)

Berkovich, Y.; Chetirkin, R.; Wheeler, R.; Sager, J.

In designing innovative Space Plant Growth Facilities (SPGF) for long duration space f ightl 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 of 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 a 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. We analyzed the efficiency of plant crops and the environmental parameters by examining the criteria for 15 salad and 12 wheat crops from the data in the ALS database at Kennedy Space Center. Some following conclusion have been established: 1. The technology involved in growing salad crops on a cylindrical type surface provides a more meaningful Q-criterion; 2. Wheat crops were less efficient than leafy greens (salad crops) when examining resource utilization; 3. By increasing light intensity of the crop the efficiency of the resource utilization could decrease. Using the existing databases and Q-criteria we have found that the criteria can be used in optimizing design and horticultural regimes in the SPGF.

Effect of psychological stress on gastric motility assessed by electrical bio-impedance.

Science.gov (United States)

Huerta-Franco, María Raquel; Vargas-Luna, Miguel; Montes-Frausto, Juana Berenice; Morales-Mata, Ismael; Ramirez-Padilla, Lorena

2012-09-28

To evaluate gastric motility using electrical bio-impedance (EBI) and gastric changes as a result of stress induced by psychological tests. A group of 57 healthy women, aged 40-60 years, 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-150 system. 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 T dependent and Wilcoxon T tests. 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 (1-4 cpm), 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 stress test showed significant changes (F = 5.5, P stress test (P stress can be evaluated by short-term EBI.

Carbon dioxide emission and bio-capacity indexing for transportation activities: A methodological development in determining the sustainability of vehicular transportation systems.

Science.gov (United States)

Labib, S M; Neema, Meher Nigar; Rahaman, Zahidur; Patwary, Shahadath Hossain; Shakil, Shahadat Hossain

2018-06-09

CO 2 emissions from urban traffic are a major concern in an era of increasing ecological disequilibrium. Adding to the problem net CO 2 emissions in urban settings are worsened due to the decline of bio-productive areas in many cities. This decline exacerbates the lack of capacity to sequestrate CO 2 at the micro and meso-scales resulting in increased temperatures and decreased air quality within city boundaries. Various transportation and environmental strategies have been implemented to address traffic related CO 2 emissions, however current literature identifies difficulties in pinpointing these critical areas of maximal net emissions in urban transport networks. This study attempts to close this gap in the literature by creating a new lay-person friendly index that combines CO 2 emissions from vehicles and the bio-capacity of specific traffic zones to identify these areas at the meso-scale within four ranges of values with the lowest index values representing the highest net CO 2 levels. The study used traffic volume, fuel types, and vehicular travel distance to estimate CO 2 emissions at major links in Dhaka, Bangladesh's capital city's transportation network. Additionally, using remote-sensing tools, adjacent bio-productive areas were identified and their bio-capacity for CO 2 sequestration estimated. The bio-productive areas were correlated with each traffic zone under study resulting in an Emission Bio-Capacity index (EBI) value estimate for each traffic node. Among the ten studied nodes in Dhaka City, nine had very low EBI values, correlating to very high CO 2 emissions and low bio-capacity. As a result, the study considered these areas unsustainable as traffic nodes going forward. Key reasons for unsustainability included increasing use of motorized traffic, absence of optimized signal systems, inadequate public transit options, disincentives for fuel free transport (FFT), and a decline in bio-productive areas. Copyright © 2018 Elsevier Ltd. All rights

Chimira: analysis of small RNA sequencing data and microRNA modifications.

Science.gov (United States)

Vitsios, Dimitrios M; Enright, Anton J

2015-10-15

Chimira is a web-based system for microRNA (miRNA) analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences. Supported modification types include multiple types of 3'-modifications (e.g. uridylation, adenylation), 5'-modifications and also internal modifications or variation (ADAR editing or single nucleotide polymorphisms). Besides cleaning and mapping of input sequences to miRNAs, Chimira provides a simple and intuitive set of tools for the analysis and interpretation of the results (see also Supplementary Material). These allow the visual study of the differential expression between two specific samples or sets of samples, the identification of the most highly expressed miRNAs within sample pairs (or sets of samples) and also the projection of the modification profile for specific miRNAs across all samples. Other tools have already been published in the past for various types of small RNA-Seq analysis, such as UEA workbench, seqBuster, MAGI, OASIS and CAP-miRSeq, CPSS for modifications identification. A comprehensive comparison of Chimira with each of these tools is provided in the Supplementary Material. Chimira outperforms all of these tools in total execution speed and aims to facilitate simple, fast and reliable analysis of small RNA-Seq data allowing also, for the first time, identification of global microRNA modification profiles in a simple intuitive interface. Chimira has been developed as a web application and it is accessible here: http://www.ebi.ac.uk/research/enright/software/chimira. aje@ebi.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

A chemical specialty semantic network for the Unified Medical Language System

Directory of Open Access Journals (Sweden)

Morrey C

2012-05-01

Full Text Available Abstract Background Terms representing chemical concepts found the Unified Medical Language System (UMLS are used to derive an expanded semantic network with mutually exclusive semantic types. The UMLS Semantic Network (SN is composed of a collection of broad categories called semantic types (STs that are assigned to concepts. Within the UMLS’s coverage of the chemical domain, we find a great deal of concepts being assigned more than one ST. This leads to the situation where the extent of a given ST may contain concepts elaborating variegated semantics. A methodology for expanding the chemical subhierarchy of the SN into a finer-grained categorization of mutually exclusive types with semantically uniform extents is presented. We call this network a Chemical Specialty Semantic Network (CSSN. A CSSN is derived automatically from the existing chemical STs and their assignments. The methodology incorporates a threshold value governing the minimum size of a type’s extent needed for inclusion in the CSSN. Thus, different CSSNs can be created by choosing different threshold values based on varying requirements. Results A complete CSSN is derived using a threshold value of 300 and having 68 STs. It is used effectively to provide high-level categorizations for a random sample of compounds from the “Chemical Entities of Biological Interest” (ChEBI ontology. The effect on the size of the CSSN using various threshold parameter values between one and 500 is shown. Conclusions The methodology has several potential applications, including its use to derive a pre-coordinated guide for ST assignments to new UMLS chemical concepts, as a tool for auditing existing concepts, inter-terminology mapping, and to serve as an upper-level network for ChEBI.

Validation, optimisation, and application data in support of the development of a targeted selected ion monitoring assay for degraded cardiac troponin T

Directory of Open Access Journals (Sweden)

Alexander S. Streng

2016-06-01

Full Text Available Cardiac troponin T (cTnT fragmentation in human serum was investigated using a newly developed targeted selected ion monitoring assay, as described in the accompanying article: “Development of a targeted selected ion monitoring assay for the elucidation of protease induced structural changes in cardiac troponin T” [1]. This article presents data describing aspects of the validation and optimisation of this assay. The data consists of several figures, an excel file containing the results of a sequence identity search, and a description of the raw mass spectrometry (MS data files, deposited in the ProteomeXchange repository with id PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD003187.

Remediation of the protein data bank archive

Science.gov (United States)

Henrick, Kim; Feng, Zukang; Bluhm, Wolfgang F.; Dimitropoulos, Dimitris; Doreleijers, Jurgen F.; Dutta, Shuchismita; Flippen-Anderson, Judith L.; Ionides, John; Kamada, Chisa; Krissinel, Eugene; Lawson, Catherine L.; Markley, John L.; Nakamura, Haruki; Newman, Richard; Shimizu, Yukiko; Swaminathan, Jawahar; Velankar, Sameer; Ory, Jeramia; Ulrich, Eldon L.; Vranken, Wim; Westbrook, John; Yamashita, Reiko; Yang, Huanwang; Young, Jasmine; Yousufuddin, Muhammed; Berman, Helen M.

2008-01-01

The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive at ftp://ftp.wwpdb.org is the repository for the coordinates and related information for more than 47 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The members of the wwPDB–RCSB PDB (USA), MSD-EBI (Europe), PDBj (Japan) and BMRB (USA)–have remediated this archive to address inconsistencies that have been introduced over the years. The scope and methods used in this project are presented. PMID:18073189

The biological quality of Sieve downriver the Sabatta waster water plant

International Nuclear Information System (INIS)

Banchetti, Rosalba; Gasperini, Federico; Bicocchi, Allegra; Cecchini, Agnese; Nolan, Brigitte; Stramaccia, Tania

2005-01-01

An evaluation study of the environmental condition of Sieve river, based on the Extended Biotic Index method (E.B.I.) applied to macro invertebrates was carried out in 2003. Three sampling locations were selected upriver and downriver a depuration plant and upriver of the confluence of a tributary that flow into the Sieve, the Ensa. The monitoring, carried out in two separate campaigns, in winter and spring, revealed how efficient is the sludge-active plant in determining a good quality of the water. Moreover Bilancino reservoir, with constant discharges, keeps Sieve river flow with a constant regime all through the year, avoiding the summer dry-up of the river and allowing the settlement of a biodiversified macrobenthonic community [it

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.

Velkomoravská pohřebiště v Rajhradě a Rajhradicích

Czech Academy of Sciences Publication Activity Database

Hendrychová, Soňa

2016-01-01

Roč. 41, č. 1 (2016), s. 87-99 ISSN 0231-5823 Institutional support: RVO:67985912 Keywords : burial ground * Great Moravia * Rajhrad * Rajhradice Subject RIV: AC - Archeology, Anthropology, Ethnology

Changes over lactation in breast milk serum proteins involved in the maturation of immune and digestive system of the infant

Directory of Open Access Journals (Sweden)

Lina Zhang

2016-06-01

Full Text Available Here we provide data from shot-gun proteomics, using filtered-aided sample preparation (FASP, dimethyl labeling and LC–MS/MS, to quantify the changes in the repertoire of human milk proteins over lactation. Milk serum proteins were analyzed at week 1, 2, 3 4, 8, 16, and 24 in milk from four individual mothers. A total of 247 proteins were identified, of which 200 proteins were quantified. The data supplied in this article supports the accompanying publication (Zhang et al., 2006 [1]. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaíno et al., 2016 [2] via the PRIDE partner repository with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD003465.

Podnikatelský plán

OpenAIRE

Štefančík, Jozef

2007-01-01

Práce se zabývá podstatnými skutečnostmi, které mají vliv na založení internetového obchodu se skate doplňky v ČR. Zmiňuje legislativní, technologické, marktetingové, finanční a jiné aspekty. Praktická část používá zjištěné poznatky k navržení podoby hypotetického internetového obchodu se skate doplňky Skate stuff, s.r.o. a je tak podnikatelským plánem pro potřeby případného začínajícího podnikatele.

Dynamic inequalities on time scales

CERN Document Server

Agarwal, Ravi; Saker, Samir

2014-01-01

This is a monograph devoted to recent research and results on dynamic inequalities on time scales. The study of dynamic inequalities on time scales has been covered extensively in the literature in recent years and has now become a major sub-field in pure and applied mathematics. In particular, this book will cover recent results on integral inequalities, including Young's inequality, Jensen's inequality, Holder's inequality, Minkowski's inequality, Steffensen's inequality, Hermite-Hadamard inequality and Čebyšv's inequality. Opial type inequalities on time scales and their extensions with weighted functions, Lyapunov type inequalities, Halanay type inequalities for dynamic equations on time scales, and Wirtinger type inequalities on time scales and their extensions will also be discussed here in detail.

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.

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.)

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

International Nuclear Information System (INIS)

Sokolov, Alexey

2010-01-01

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.)

Self-organizing ontology of biochemically relevant small molecules.

Science.gov (United States)

Chepelev, Leonid L; Hastings, Janna; Ennis, Marcus; Steinbeck, Christoph; Dumontier, Michel

2012-01-06

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. 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. We conclude that the proposed methodology can ease the burden of chemical data annotators and

The Synthesis of Cellulose Graft Copolymers Using Cu(0)-Mediated Polymerization

Science.gov (United States)

Donaldson, Jason L.

Cellulose is the most abundant renewable polymer on the planet and there is great interest in expanding its use beyond its traditional applications. However, its hydrophilicity and insolubility in most common solvent systems are obstacles to its widespread use in advanced materials. One way to counteract this is to attach hydrophobic polymer chains to cellulose: this allows the properties of the copolymer to be tailored by the molecular weight, density, and physical properties of the grafts. Two methods were used here to synthesize the graft copolymers: a 'grafting-from' approach, where synthetic chains were grown outward from bromoester moieties on cellulose (Cell-BiB) via Cu(0)-mediated polymerization; and a 'grafting-to' approach, where fully formed synthetic chains with terminal sulfide functionality were added to cellulose acetate with methacrylate functionality (CA-MAA) via thiol-ene Michael addition. The Cell-BiB was synthesized in the ionic liquid 1-butyl-3-methylimidazolium chloride and had a degree of substitution of 1.13. Polymerization from Cell-BiB proceeded at similar but slightly slower rate than an analogous non-polymeric initiator (EBiB). The average graft density of poly(methyl acrylate) chains was 0.71 chains/ring, with a maximum of 1.0 obtained. The graft density when grafting poly(methyl methacrylate) was only 0.15, and this appeared to be due to the slow initiation of BiB groups. Using EBiB to model the reaction and improve the design should allow this to be overcome. Chain extension experiments demonstrated the living behaviour of the polymer. The CA-MAA was synthesized by esterification with methacrylic acid. Reactions of CA-MAA with thiophenol and dodecanethiol resulted in quantitative addition of the thiol to the alkene. The grafts were synthesized by Cu(0)-mediated polymerization from a bifunctional initiator containing a disulfide bond, followed by reduction to sulfides. The synthetic polymers were successfully grafted to CA-MAA but the

An Integrated Recovery-oriented Model (IRM) for mental health services: evolution and challenges.

Science.gov (United States)

Frost, Barry G; Tirupati, Srinivasan; Johnston, Suzanne; Turrell, Megan; Lewin, Terry J; Sly, Ketrina A; Conrad, Agatha M

2017-01-17

Over past decades, improvements in longer-term clinical and personal outcomes for individuals experiencing serious mental illness (SMI) have been moderate, although recovery has clearly been shown to be possible. Recovery experiences are inherently personal, and recovery can be complex and non-linear; however, there are a broad range of potential recovery contexts and contributors, both non-professional and professional. Ongoing refinement of recovery-oriented models for mental health (MH) services needs to be fostered. This descriptive paper outlines a service-wide Integrated Recovery-oriented Model (IRM) for MH services, designed to enhance personally valued health, wellbeing and social inclusion outcomes by increasing access to evidenced-based psychosocial interventions (EBIs) within a service context that supports recovery as both a process and an outcome. Evolution of the IRM is characterised as a series of five broad challenges, which draw together: relevant recovery perspectives; overall service delivery frameworks; psychiatric and psychosocial rehabilitation approaches and literature; our own clinical and service delivery experience; and implementation, evaluation and review strategies. The model revolves around the person's changing recovery needs, focusing on underlying processes and the service frameworks to support and reinforce hope as a primary catalyst for symptomatic and functional recovery. Within the IRM, clinical rehabilitation (CR) practices, processes and partnerships facilitate access to psychosocial EBIs to promote hope, recovery, self-agency and social inclusion. Core IRM components are detailed (remediation of functioning; collaborative restoration of skills and competencies; and active community reconnection), together with associated phases, processes, evaluation strategies, and an illustrative IRM scenario. The achievement of these goals requires ongoing collaboration with community organisations. Improved outcomes are achievable for

Benzocyclobutene-based electric micromachines supported on microball bearings: Design, fabrication, and characterization

Science.gov (United States)

Modafe, Alireza

This dissertation summarizes the research activities that led to the development of the first microball-bearing-supported linear electrostatic micromotor with benzocyclobutene (BCB) low-k polymer insulating layers. The primary application of this device is long-range, high-speed linear micropositioning. The future generations of this device include rotary electrostatic micromotors and microgenerators. The development of the first generation of microball-bearing-supported micromachines, including device theory, design, and modeling, material characterization, process development, device fabrication, and device test and characterization is presented. The first generation of these devices is based on a 6-phase, bottom-drive, linear, variable-capacitance micromotor (B-LVCM). The design of the electrical and mechanical components of the micromotor, lumped-circuit modeling of the device and electromechanical characteristics, including variable capacitance, force, power, and speed are presented. Electrical characterization of BCB polymers, characterization of BCB chemical mechanical planarization (CMP), development of embedded BCB in silicon (EBiS) process, and integration of device components using microfabrication techniques are also presented. The micromotor consists of a silicon stator, a silicon slider, and four stainless-steel microballs. The aligning force profile of the micromotor was extracted from simulated and measured capacitances of all phases. An average total aligning force of 0.27 mN with a maximum of 0.41 mN, assuming a 100 V peak-to-peak square-wave voltage, was measured. The operation of the micromotor was verified by applying square-wave voltages and characterizing the slider motion. An average slider speed of 7.32 mm/s when excited by a 40 Hz, 120 V square-wave voltage was reached without losing the synchronization. This research has a pivotal impact in the field of power microelectromechanical systems (MEMS). It establishes the foundation for the

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

Self-organizing ontology of biochemically relevant small molecules

Science.gov (United States)

2012-01-01

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 can ease the burden of

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

Engineering Design of Electrostatic Quadrupole for ISOL Beam Lines

International Nuclear Information System (INIS)

Kim, H. S.; Kwon, H. J.; Cho, Y. S.

2014-01-01

In the ISOL system, the RI beam should be transported from the target ion source to post accelerator through various analyzing and charge-breeding systems such as PS (pre-seperator), HRMS (High Resolution Mass Seperator), RF cooler and A/q separator. A reference particle for the beam dynamics calculation is 132 Sn 1+ . After charge breeder system, the charge state is boosted from +1 to +19 with ECR charge breeder and to +33 with EBIS charge breeder. Because the beam energy is as low as 50 keV, the electrostatic optics was adopted rather than the magnetic optics. The electrostatic quadrupole triplets were used for the beam focusing and the electrostatic bender is used for 90-degree bending. In this paper, the design procedure and engineering design of the electrostatic quadrupole are presented

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study.

Science.gov (United States)

Wimalaratne, Sarala M; Grenon, Pierre; Hoehndorf, Robert; Gkoutos, Georgios V; de Bono, Bernard

2012-02-01

The article presents an infrastructure for supporting the semantic interoperability of biomedical resources based on the management (storing and inference-based querying) of their ontology-based annotations. This infrastructure consists of: (i) a repository to store and query ontology-based annotations; (ii) a knowledge base server with an inference engine to support the storage of and reasoning over ontologies used in the annotation of resources; (iii) a set of applications and services allowing interaction with the integrated repository and knowledge base. The infrastructure is being prototyped and developed and evaluated by the RICORDO project in support of the knowledge management of biomedical resources, including physiology and pharmacology models and associated clinical data. The RICORDO toolkit and its source code are freely available from http://ricordo.eu/relevant-resources. sarala@ebi.ac.uk.

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.

Aether: leveraging linear programming for optimal cloud computing in genomics.

Science.gov (United States)

Luber, Jacob M; Tierney, Braden T; Cofer, Evan M; Patel, Chirag J; Kostic, Aleksandar D

2018-05-01

Across biology, we are seeing rapid developments in scale of data production without a corresponding increase in data analysis capabilities. Here, we present Aether (http://aether.kosticlab.org), an intuitive, easy-to-use, cost-effective and scalable framework that uses linear programming to optimally bid on and deploy combinations of underutilized cloud computing resources. Our approach simultaneously minimizes the cost of data analysis and provides an easy transition from users' existing HPC pipelines. Data utilized are available at https://pubs.broadinstitute.org/diabimmune and with EBI SRA accession ERP005989. Source code is available at (https://github.com/kosticlab/aether). Examples, documentation and a tutorial are available at http://aether.kosticlab.org. chirag_patel@hms.harvard.edu or aleksandar.kostic@joslin.harvard.edu. Supplementary data are available at Bioinformatics online.

BioContainers: an open-source and community-driven framework for software standardization

Science.gov (United States)

da Veiga Leprevost, Felipe; Grüning, Björn A.; Alves Aflitos, Saulo; Röst, Hannes L.; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C.; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I.; Perez-Riverol, Yasset

2017-01-01

Abstract Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). Availability and Implementation The software is freely available at github.com/BioContainers/. Contact yperez@ebi.ac.uk PMID:28379341

Dataset of the Botrytis cinerea phosphoproteome induced by different plant-based elicitors.

Science.gov (United States)

Liñeiro, Eva; Chiva, Cristina; Cantoral, Jesús M; Sabido, Eduard; Fernández-Acero, Francisco Javier

2016-06-01

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].

ArrayExpress update--trends in database growth and links to data analysis tools.

Science.gov (United States)

Rustici, Gabriella; Kolesnikov, Nikolay; Brandizi, Marco; Burdett, Tony; Dylag, Miroslaw; Emam, Ibrahim; Farne, Anna; Hastings, Emma; Ison, Jon; Keays, Maria; Kurbatova, Natalja; Malone, James; Mani, Roby; Mupo, Annalisa; Pedro Pereira, Rui; Pilicheva, Ekaterina; Rung, Johan; Sharma, Anjan; Tang, Y Amy; Ternent, Tobias; Tikhonov, Andrew; Welter, Danielle; Williams, Eleanor; Brazma, Alvis; Parkinson, Helen; Sarkans, Ugis

2013-01-01

The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is one of three international functional genomics public data repositories, alongside the Gene Expression Omnibus at NCBI and the DDBJ Omics Archive, supporting peer-reviewed publications. It accepts data generated by sequencing or array-based technologies and currently contains data from almost a million assays, from over 30 000 experiments. The proportion of sequencing-based submissions has grown significantly over the last 2 years and has reached, in 2012, 15% of all new data. All data are available from ArrayExpress in MAGE-TAB format, which allows robust linking to data analysis and visualization tools, including Bioconductor and GenomeSpace. Additionally, R objects, for microarray data, and binary alignment format files, for sequencing data, have been generated for a significant proportion of ArrayExpress data.

Aplikace pro výuku jazyků pro Firefox OS

OpenAIRE

Chudík, Jakub

2015-01-01

Tato práce se zabývá vytvořením aplikace pro výuku jazyků specificky pro mobilní operační systém Firefox OS. Vzhledem k své povaze, uživatelské rozhraní aplikace se snaží uspokojit ergonomické potřeby aplikací určených pro kapesní zařízení. Aplikuje několik konceptů gamifikace ke zlepšení procesu učení, jehož výsledky jsou prezentovány a vyhodnoceny. Aplikace také přináší své vlastní jedinečné vlastnosti, které jí pomáhají vyniknout mezi ostatními aplikacemi pro výuku jazyků. This thesis d...

BioContainers: an open-source and community-driven framework for software standardization.

Science.gov (United States)

da Veiga Leprevost, Felipe; Grüning, Björn A; Alves Aflitos, Saulo; Röst, Hannes L; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I; Perez-Riverol, Yasset

2017-08-15

BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). The software is freely available at github.com/BioContainers/. yperez@ebi.ac.uk. © The Author(s) 2017. Published by Oxford University Press.

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

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.

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

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

Science.gov (United States)

Passman, Dina B.

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 Preparedness and Response (ASPR). Fusion Analytics meaningfully augments traditional public and population health surveillance reporting by providing web-based data analysis and visualization tools. Methods Fusion Analytics serves as a one-stop-shop for the web-based data visualizations of multiple real-time data sources within ASPR. The 24-7 web availability makes it an ideal analytic tool for situational awareness and response allowing stakeholders to access the portal from any internet-enabled device without installing any software. The Fusion Analytics data integration system was built using off-the-shelf EBI software. Fusion Analytics leverages the full power of statistical analysis software and delivers reports to users in a secure web-based environment. Fusion Analytics provides an example of how public health staff can develop and deploy a robust public health informatics solution using an off-the shelf product and with limited development funding. It also provides the unique example of a public health information system that combines patient data for traditional disease surveillance with manpower and resource data to provide overall decision support for federal public health and medical disaster response operations. Conclusions We are currently in a unique position within public health. One the one hand, we have been gaining greater and greater access to electronic data of all kinds over the last few years. On the other, we are working in a time of reduced government spending

Ekonomické systémy MMORPG, jejich výhody a nevýhody

OpenAIRE

Havel, Vojtěch

2008-01-01

Cílem mé práce je popsat vnitřní ekonomiky MMORPG a diskutovat jejich potenciál jakožto vhodných virtuálních simulací reálného světa pro potřeby výzkumu ekonomických teorií a vztahů. První kapitola je zaměřena na postupný historický vznik žánru RPG a MMORPG a jejich základní pravidla. Druhá se zabývá metodami a postupy ekonomického výzkumu v dnešní době. Třetí navrhuje, proč by použití MMORPG bylo v tomto kontextu výhodné. Ve čtvrté se zabývám nedostatky, neduhy a limity těchto virtuálních sv...

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.

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).

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.

SPARQL-enabled identifier conversion with Identifiers.org

Science.gov (United States)

Wimalaratne, Sarala M.; Bolleman, Jerven; Juty, Nick; Katayama, Toshiaki; Dumontier, Michel; Redaschi, Nicole; Le Novère, Nicolas; Hermjakob, Henning; Laibe, Camille

2015-01-01

Motivation: On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data. Results: We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data. Availability and implementation: The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql. Contact: sarala@ebi.ac.uk PMID:25638809

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].

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

Band gap opening of bilayer graphene by F4-TCNQ molecular doping and externally applied electric field.

Science.gov (United States)

Tian, Xiaoqing; Xu, Jianbin; Wang, Xiaomu

2010-09-09

The band gap opening of bilayer graphene with one side surface adsorption of F4-TCNQ is reported. F4-TCNQ doped bilayer graphene shows p-type semiconductor characteristics. With a F4-TCNQ concentration of 1.3 x 10(-10) mol/cm(2), the charge transfer between each F4-TCNQ molecule and graphene is 0.45e, and the built-in electric field, E(bi), between the graphene layers could reach 0.070 V/A. The charge transfer and band gap opening of the F4-TCNQ-doped graphene can be further modulated by an externally applied electric field (E(ext)). At 0.077 V/A, the gap opening at the Dirac point (K), DeltaE(K) = 306 meV, and the band gap, E(g) = 253 meV, are around 71% and 49% larger than those of the pristine bilayer under the same E(ext).

A first dataset toward a standardized community-driven global mapping of the human immunopeptidome

Directory of Open Access Journals (Sweden)

Pouya Faridi

2016-06-01

Full Text Available We present the first standardized HLA peptidomics dataset generated by the immunopeptidomics community. The dataset is composed of native HLA class I peptides as well as synthetic HLA class II peptides that were acquired in data-dependent acquisition mode using multiple types of mass spectrometers. All laboratories used the spiked-in landmark iRT peptides for retention time normalization and data analysis. The mass spectrometric data were deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD001872. The generated data were used to build HLA allele-specific peptide spectral and assay libraries, which were stored in the SWATHAtlas database. Data presented here are described in more detail in the original eLife article entitled ‘An open-source computational and data resource to analyze digital maps of immunopeptidomes’.

Pohřebiště únětické kultury v Klecanech, okr. Praha-východ

Czech Academy of Sciences Publication Activity Database

Ernée, Michal; Profantová, Naďa; Březinová, Helena; Frána, Jaroslav; Majer, A.; Stránská, Petra

2011-01-01

Roč. 63, č. 2 (2011), s. 307-330 ISSN 0323-1267 R&D Projects: GA ČR GA404/09/1135 Institutional research plan: CEZ:AV0Z80020508; CEZ:AV0Z10480505 Keywords : Early Bronze Age * Únětice culture * cemetery * 14C * anthropology * metal analyses * corrosion layers Subject RIV: AC - Archeology, Anthropology, Ethnology

Predikční systém ELVÍRA pro predikci spotřeby zemního plynu

Czech Academy of Sciences Publication Activity Database

Pelikán, Emil; Eben, Kryštof; Šimůnek, Milan; Kolman, M.; Hais, J.

2000-01-01

Roč. 80, č. 11 (2000), s. 253-255 ISSN 0032-1761 Institutional research plan: AV0Z1030915 Keywords : predikční modely * systémy pro podporu rozhodování * regresní metody * umělé neuronové sítě Subject RIV: BB - Applied Statistics, Operational Research

Proteome identification of the silkworm middle silk gland

Directory of Open Access Journals (Sweden)

Jian-ying Li

2016-03-01

Full Text Available To investigate the functional differentiation among the anterior (A, middle (M, and posterior (P regions of silkworm middle silk gland (MSG, their proteomes were characterized by shotgun LC–MS/MS analysis with a LTQ-Orbitrap mass spectrometer. To get better proteome identification and quantification, triplicate replicates of mass spectrometry analysis were performed for each sample. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaíno et al., 2014 [1] via the PRIDE partner repository (Vizcaino, 2013 [2] with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD003371. The peptide identifications that were further processed by PeptideProphet program in Trans-Proteomic Pipeline (TPP after database search with Mascot software were also available in .XML format files. Data presented here are related to a research article published in Journal of Proteomics by Li et al. (2015 [3]. Keywords: Bombyx mori, Middle silk gland, Silk protein synthesis, Shotgun proteomics, Label-free

MS-analysis of SILAC-labeled MYC-driven B lymphoma cells overexpressing miR-17-19b

Directory of Open Access Journals (Sweden)

Marija Mihailovich

2016-06-01

Full Text Available Micro RNAs (miRNAs are small non-coding RNAs, which dampen gene expression by repressing translation and/or inducing degradation of target-mRNAs. Although the role of miR-17-19b (a truncated version of miR-17-92 cluster is well documented in MYC-driven B cell lymphomagenesis, little is known about the function of the cluster in the maintenance of full-blown lymphomas. We employed SILAC-based quantitative proteomics to identify miR-17-19b targets upon a mild overexpression of the cluster in B cell lymphomas, established from λ-MYC transgenic mice. The proteomics data described in detail in this study, whose follow up analysis with MaxQuant algorithm is part of the recent publication (Mihailovich et al., 2015 [1], are deposited to the ProteomeXchange Consortium via the PRIDE partner repository, with the accession code PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002810.

Proteome-wide dataset supporting functional study of tyrosine kinases in breast cancer

Directory of Open Access Journals (Sweden)

Nicos Angelopoulos

2016-06-01

Full Text Available Tyrosine kinases (TKs play an essential role in regulating various cellular activities and dysregulation of TK signaling contributes to oncogenesis. However, less than half of the TKs have been thoroughly studied. Through a combined use of RNAi and stable isotope labeling with amino acids in cell culture (SILAC-based quantitative proteomics, a global functional proteomic landscape of TKs in breast cancer was recently revealed highlighting a comprehensive and highly integrated signaling network regulated by TKs (Stebbing et al., 2015 [1]. We collate the enormous amount of the proteomic data in an open access platform, providing a valuable resource for studying the function of TKs in cancer and benefiting the science community. Here we present a detailed description related to this study (Stebbing et al., 2015 [1] and the raw data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the identifier http://www.ebi.ac.uk/pride/archive/projects/PXD002065.

Lecture 10: The European Bioinformatics Institute - "Big data" for biomedical sciences

CERN Multimedia

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...

Charge Breeding of Radioactive Ions in an Electron Cyclotron Resonance Ion Source(ECRIS) at ISOLDE

CERN Multimedia

Lindroos, M

2002-01-01

The development of an efficient charge breeding scheme for the next generation of RIB facilities will have a strong impact on the post-accelerator for several Radioactive Ion Beam (RIB) projects at European large scale facilities. At ISOLDE/CERN there will be the unique possibility to carry out experiments with the two possible charge breeding set-ups with a large variety of radioactive isotopes using identical injection conditions. One charge breeding set-up is the Penning trap/EBIS combination which feeds the REX-ISOLDE linear accelerator and which is in commissioning now. The second charge breeder is a new ECRIS PHOENIX developed at the ISN ion source laboratory at Grenoble. This ECRIS is now under investigation with a 14 GHz amplifier to characterize its performance. The experiments are accompanied by theoretical studies in computer simulations in order to optimize the capture of the ions in the ECRIS plasma. A second identical PHOENIX ECRIS which is under investigation at the Daresbury Laboratory is avai...

Production of High-Intensity, Highly Charged Ions

CERN Document Server

Gammino, S.

2013-12-16

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...

Domain wall universe in the Einstein-Born-Infeld theory

International Nuclear Information System (INIS)

Lee, Bum-Hoon; Lee, Wonwoo; Minamitsuji, Masato

2009-01-01

In this Letter, we discuss the dynamics of a domain wall universe embedded into the charged black hole spacetime of the Einstein-Born-Infeld (EBI) theory. There are four kinds of possible spacetime structures, i.e., those with no horizon, the extremal one, those with two horizons (as the Reissner-Nordstroem black hole), and those with a single horizon (as the Schwarzshild black hole). We derive the effective cosmological equations on the wall. In contrast to the previous works, we take the contribution of the electrostatic energy on the wall into account. By examining the properties of the effective potential, we find that a bounce can always happen outside the (outer) horizon. For larger masses of the black hole, the height of the barrier between the horizon and bouncing point in the effective potential becomes smaller, leading to longer time scales of bouncing process. These results are compared with those in the previous works.

Proposed LLNL electron beam ion trap

International Nuclear Information System (INIS)

Marrs, R.E.; Egan, P.O.; Proctor, I.; Levine, M.A.; Hansen, L.; Kajiyama, Y.; Wolgast, R.

1985-01-01

The interaction of energetic electrons with highly charged ions is of great importance to several research fields such as astrophysics, laser fusion and magnetic fusion. In spite of this importance there are almost no measurements of electron interaction cross sections for ions more than a few times ionized. To address this problem an electron beam ion trap (EBIT) is being developed at LLNL. The device is essentially an EBIS except that it is not intended as a source of extracted ions. Instead the (variable energy) electron beam interacting with the confined ions will be used to obtain measurements of ionization cross sections, dielectronic recombination cross sections, radiative recombination cross sections, energy levels and oscillator strengths. Charge-exchange recombinaion cross sections with neutral gasses could also be measured. The goal is to produce and study elements in many different charge states up to He-like xenon and Ne-like uranium. 5 refs., 2 figs

The Nursing Care And Education Plan For A Child With Epidermolys is Bullosa (A Case Report

Directory of Open Access Journals (Sweden)

Esra Karaca Çiftçi

2016-05-01

Full Text Available Epidermolysis Bullosa (EBis a chronic disease, some types of which may have morbidity and mortality. That is why the patients must receive multidisciplinary care in case any complications arise. Families must be informed about the disease, about home care and receive genetic counselling. The importance of genetic counselling cannot be stressed enough, since both M.C. and his younger brother were diagnosed with EB. If the family had received genetic counselling, this tragic situation could have been prevented. Home care education for the families of EB patients is also of great importance. Relatives of the patient must also be educated about wound care, infection control, patient nutrition and physical treatment. They must also be educated about how to use the medications and about bandaging, dressing, Vaseline bandages, antiseptics, bathing procedures, and the use of antibiotic cream ointment. It was obvious, therefore, that the nursing care given at home enhanced both the patient’s and the family’s quality of life.

Court rejects claim of mental illness from needlestick.

Science.gov (United States)

1998-05-29

The Montana Supreme Court rejected the bid of a medical technician to remain on workers' compensation, based on his claims that he suffered from psychosis, depression, and hallucinations after pricking himself with a needle used on an HIV-positive patient. [Name removed], a respiratory therapist at Community Medical Center in Missoula, tested negative for HIV, but claimed that the psychological trauma from the needlestick injury caused him to become disabled. Based on expert testimony, the Workers' Compensation Court determined that [name removed] was faking his symptoms to collect benefits from his employer's insurer, EBI/Orion Group. [Name removed] appealed, and the Supreme Court remanded the case, stating that psychologists are not included among the medical professionals able to conduct medical reviews. The Workers' Compensation Court again found that [name removed] was faking his symptoms, and [name removed] unsuccessfully appealed. The compensation panel cited conflicting evidence from psychological tests, [name removed]'s friends' testimonies, and [name removed]'s personal diary. The Supreme Court upheld the verdict.

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). Copyright 1999 Wiley-Liss, Inc.

The VOICES/VOCES success story: effective strategies for training, technical assistance and community-based organization implementation.

Science.gov (United States)

Hamdallah, Myriam; Vargo, Sue; Herrera, Jennifer

2006-08-01

The Centers for Disease Control and Prevention's Diffusion of Effective Behavioral Interventions (DEBI) project successfully disseminated VOICES/VOCES, a brief video-based HIV risk reduction intervention targeting African American and Latino heterosexual men and women at risk for HIV infection. Elements of the dissemination strategy included a comprehensive and user-friendly intervention kit, comprising (a) an implementationmanual and othermaterials necessary for conducting the intervention (b) a Training of Facilitators (TOF) curriculum used to teach agency staff how to implement the EBI in their setting, (c) a network of expert trainers who attend a training institute to become adept at using the TOF curriculum to train facilitators, (d) a comprehensive training coordination center to plan and deliver TOF trainings, (e) proactive technical assistance to trainers, and (f) post-TOF technical assistance for local implementers. This article reports on those strategies and a local CBO's successful participation in DEBI, resulting implementation of VOICES/VOCES, with unique approaches to adaptation and tailoring.

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.

ggseqlogo: a versatile R package for drawing sequence logos.

Science.gov (United States)

Wagih, Omar

2017-11-15

Sequence logos have become a crucial visualization method for studying underlying sequence patterns in the genome. Despite this, there remains a scarcity of software packages that provide the versatility often required for such visualizations. ggseqlogo is an R package built on the ggplot2 package that aims to address this issue. ggseqlogo offers native illustration of publication-ready DNA, RNA and protein sequence logos in a highly customizable fashion with features including multi-logo plots, qualitative and quantitative colour schemes, annotation of logos and integration with other plots. The package is intuitive to use and seamlessly integrates into R analysis pipelines. ggseqlogo is released under the GNU licence and is freely available via CRAN-The Comprehensive R Archive Network https://cran.r-project.org/web/packages/ggseqlogo. A detailed tutorial can be found at https://omarwagih.github.io/ggseqlogo. wagih@ebi.ac.uk. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Neurocardiac protection with milrinone for restoring acute cerebral hypoperfusion and delayed ischemic injury after experimental subarachnoid hemorrhage.

Science.gov (United States)

Mutoh, Tomoko; Mutoh, Tatsushi; Sasaki, Kazumasu; Nakamura, Kazuhiro; Tatewaki, Yasuko; Ishikawa, Tatsuya; Taki, Yasuyuki

2017-02-15

Acute cerebral hypoperfusion following subarachnoid hemorrhage (SAH) is highly related to the pathogenesis of delayed cerebral ischemia (DCI), but the therapeutic option is poorly available. This study aimed to clarify the effect of milrinone (MIL) on cerebral blood flow (CBF) and related outcomes after experimental SAH. Twenty-seven male C57BL/6 mice were assigned to either sham surgery (SAH-sham; n=6), SAH induced by endovascular perforation (control; n=10), or SAH followed by cardiac support with intravenous MIL (n=11) performed 1.5-h after SAH induction. CBF, neurobehavioral function, occurrence of DCI were assessed by MR-continuous arterial spin labeling, daily neurological score testing, and diffusion- and T2-weighted MR images on days 1 and 3, respectively. Initial global CBF depression was notable in mice of control and MIL groups as compared to the SAH-sham group (Pprotective agent against EBI. Copyright © 2017 Elsevier B.V. All rights reserved.

OntoVIP: an ontology for the annotation of object models used for medical image simulation.

Science.gov (United States)

Gibaud, Bernard; Forestier, Germain; Benoit-Cattin, Hugues; Cervenansky, Frédéric; Clarysse, Patrick; Friboulet, Denis; Gaignard, Alban; Hugonnard, Patrick; Lartizien, Carole; Liebgott, Hervé; Montagnat, Johan; Tabary, Joachim; Glatard, Tristan

2014-12-01

This paper describes the creation of a comprehensive conceptualization of object models used in medical image simulation, suitable for major imaging modalities and simulators. The goal is to create an application ontology that can be used to annotate the models in a repository integrated in the Virtual Imaging Platform (VIP), to facilitate their sharing and reuse. Annotations make the anatomical, physiological and pathophysiological content of the object models explicit. In such an interdisciplinary context we chose to rely on a common integration framework provided by a foundational ontology, that facilitates the consistent integration of the various modules extracted from several existing ontologies, i.e. FMA, PATO, MPATH, RadLex and ChEBI. Emphasis is put on methodology for achieving this extraction and integration. The most salient aspects of the ontology are presented, especially the organization in model layers, as well as its use to browse and query the model repository. Copyright © 2014 Elsevier Inc. All rights reserved.

Electron beam based transversal profile measurements of intense ion beams

International Nuclear Information System (INIS)

El Moussati, Said

2014-01-01

A non-invasive diagnostic method for the experimental determination of the transverse profile of an intense ion beam has been developed and investigated theoretically as well as experimentally within the framework of the present work. The method is based on the deflection of electrons when passing the electromagnetic field of an ion beam. To achieve this an electron beam is employed with a specifically prepared transversal profile. This distinguish this method from similar ones which use thin electron beams for scanning the electromagnetic field [Roy et al. 2005; Blockland10]. The diagnostic method presented in this work will be subsequently called ''Electron-Beam-Imaging'' (EBI). First of all the influence of the electromagnetic field of the ion beam on the electrons has been theoretically analyzed. It was found that the magnetic field causes only a shift of the electrons along the ion beam axis, while the electric field only causes a shift in a plane transverse to the ion beam. Moreover, in the non-relativistic case the magnetic force is significantly smaller than the Coulomb one and the electrons suffer due to the magnetic field just a shift and continue to move parallel to their initial trajectory. Under the influence of the electric field, the electrons move away from the ion beam axis, their resulting trajectory shows a specific angle compared to the original direction. This deflection angle practically depends just on the electric field of the ion beam. Thus the magnetic field has been neglected when analysing the experimental data. The theoretical model provides a relationship between the deflection angle of the electrons and the charge distribution in the cross section of the ion beam. The model however only can be applied for small deflection angles. This implies a relationship between the line-charge density of the ion beam and the initial kinetic energy of the electrons. Numerical investigations have been carried out to clarify the

Electron beam based transversal profile measurements of intense ion beams; Elektronenstrahl-Diagnostik zur Bestimmung vom transversalen Profil intensiver Ionenstrahlen

Energy Technology Data Exchange (ETDEWEB)

El Moussati, Said

2014-11-03

A non-invasive diagnostic method for the experimental determination of the transverse profile of an intense ion beam has been developed and investigated theoretically as well as experimentally within the framework of the present work. The method is based on the deflection of electrons when passing the electromagnetic field of an ion beam. To achieve this an electron beam is employed with a specifically prepared transversal profile. This distinguish this method from similar ones which use thin electron beams for scanning the electromagnetic field [Roy et al. 2005; Blockland10]. The diagnostic method presented in this work will be subsequently called ''Electron-Beam-Imaging'' (EBI). First of all the influence of the electromagnetic field of the ion beam on the electrons has been theoretically analyzed. It was found that the magnetic field causes only a shift of the electrons along the ion beam axis, while the electric field only causes a shift in a plane transverse to the ion beam. Moreover, in the non-relativistic case the magnetic force is significantly smaller than the Coulomb one and the electrons suffer due to the magnetic field just a shift and continue to move parallel to their initial trajectory. Under the influence of the electric field, the electrons move away from the ion beam axis, their resulting trajectory shows a specific angle compared to the original direction. This deflection angle practically depends just on the electric field of the ion beam. Thus the magnetic field has been neglected when analysing the experimental data. The theoretical model provides a relationship between the deflection angle of the electrons and the charge distribution in the cross section of the ion beam. The model however only can be applied for small deflection angles. This implies a relationship between the line-charge density of the ion beam and the initial kinetic energy of the electrons. Numerical investigations have been carried out to clarify the

Laténské pohřebiště v Bašti, okr. Praha-východ

Czech Academy of Sciences Publication Activity Database

Pecinovská, Monika; Baloun, L.; Sankot, P.

2014-01-01

Roč. 18, č. 2 (2014), s. 745-766 ISSN 1214-3553 Grant - others:GA UK(CZ) 564512 Institutional support: RVO:67985912 Keywords : warrior's grave * sword * rod-shaped object * microregion * Danube area Subject RIV: AC - Archeology, Anthropology, Ethnology

Effectiveness of a multi-level implementation strategy for ASD interventions: study protocol for two linked cluster randomized trials.

Science.gov (United States)

Brookman-Frazee, Lauren; Stahmer, Aubyn C

2018-05-09

The Centers for Disease Control (2018) estimates that 1 in 59 children has autism spectrum disorder, and the annual cost of ASD in the U.S. is estimated to be $236 billion. Evidence-based interventions have been developed and demonstrate effectiveness in improving child outcomes. However, research on generalizable methods to scale up these practices in the multiple service systems caring for these children has been limited and is critical to meet this growing public health need. This project includes two, coordinated studies testing the effectiveness of the Translating Evidence-based Interventions (EBI) for ASD: Multi-Level Implementation Strategy (TEAMS) model. TEAMS focuses on improving implementation leadership, organizational climate, and provider attitudes and motivation in order to improve two key implementation outcomes-provider training completion and intervention fidelity and subsequent child outcomes. The TEAMS Leadership Institute applies implementation leadership strategies and TEAMS Individualized Provider Strategies for training applies motivational interviewing strategies to facilitate provider and organizational behavior change. A cluster randomized implementation/effectiveness Hybrid, type 3, trial with a dismantling design will be used to understand the effectiveness of TEAMS and the mechanisms of change across settings and participants. Study #1 will test the TEAMS model with AIM HI (An Individualized Mental Health Intervention for ASD) in publicly funded mental health services. Study #2 will test TEAMS with CPRT (Classroom Pivotal Response Teaching) in education settings. Thirty-seven mental health programs and 37 school districts will be randomized, stratified by county and study, to one of four groups (Standard Provider Training Only, Standard Provider Training + Leader Training, Enhanced Provider Training, Enhanced Provider Training + Leader Training) to test the effectiveness of combining standard, EBI-specific training with the two TEAMS

Renewable Energy at NASA's Johnson Space Center

Science.gov (United States)

McDowall, Lindsay

2014-01-01

has two solar inverters, located on the second floor, that collected the data from the solar photovoltaic arrays. The data displayed here is the total energy produced by the system. These are cumulative amounts, so the last point on the graph shows all of the energy collected from the system since the start of its operation. The data shown here was manually collected from the solar inverters. However, the data is also automatically recorded through EBI. Through analysis of both sets of data it was determined that the EBI data was faulty. For example, from the manually collected data it can be determined that a total of 73 kWh of energy was collected between the dates of 1/16/2014 – 1/22/2014. The EBI data reports that approximately 17800 kWh of energy was collected during the same time frame. Not only does this exceed the time frame examined, but it also exceeds the total energy collected from the start of collection as recorded from the inverters. This leads to the belief that there is a malfunction with the automatic recording of the energy. In Building 20, data was examined from the solar water heater dating back many months and found that the pump for the solar water heater system was not operating properly, as exhibited in the graph shown below. The pump operates on a solar energy system, meaning that it collects energy throughout the day from the sun. Because of this, the system would stop operating shortly after the sun set because of a lack of sunlight. At that point, the graph should show a zero flow rate, but as exhibited in the graph below, that is not the case. It is clearly shown that the pump is continuously operating, even during the night. It was also observed that the majority of the time the pump would not turn on at all, despite good weather conditions. This led to the conclusion that the pump is malfunctioning, and needs to be examined and fixed.

Potřeby a zájmy mládeže v oblasti cestovního ruchu

OpenAIRE

Černá, Jana

2009-01-01

The thesis is devoted to tourism of youth with focusing on the needs and interests. The theoretical part deals with issues of tourism of this segment and marketing research. The practical part focuses on a survey to determine preferences of students of selected universities in relation to the services provided by travel agencies. Collected data are then compared with information contained in the theoretical part and serves as a base for marketing advice to the Autoturist travel agency, Plc.

Úvěry sloužící k financování bytové potřeby

OpenAIRE

Součková, Barbora

2011-01-01

The thesis is focused on loans for the financing of housing needs (mortgage loans, construction loans and consumer loans on the property). The work deals with the important parameters of each product. In particular, the definition of the purpose of financing, interest calculation, interest rate guarantees, collateral, repayment duration. Furthermore, the work focuses on state aid granted in these products, as well as credit risk, which is the issue of lending inextricably linked.

Active site specificity profiling datasets of matrix metalloproteinases (MMPs 1, 2, 3, 7, 8, 9, 12, 13 and 14

Directory of Open Access Journals (Sweden)

Ulrich Eckhard

2016-06-01

Full Text Available The data described provide a comprehensive resource for the family-wide active site specificity portrayal of the human matrix metalloproteinase family. We used the high-throughput proteomic technique PICS (Proteomic Identification of protease Cleavage Sites to comprehensively assay 9 different MMPs. We identified more than 4300 peptide cleavage sites, spanning both the prime and non-prime sides of the scissile peptide bond allowing detailed subsite cooperativity analysis. The proteomic cleavage data were expanded by kinetic analysis using a set of 6 quenched-fluorescent peptide substrates designed using these results. These datasets represent one of the largest specificity profiling efforts with subsequent structural follow up for any protease family and put the spotlight on the specificity similarities and differences of the MMP family. A detailed analysis of this data may be found in Eckhard et al. (2015 [1]. The raw mass spectrometry data and the corresponding metadata have been deposited in PRIDE/ProteomeXchange with the accession number http://www.ebi.ac.uk/pride/archive/projects/PXD002265.

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.

Charge breeding of intense radioactive beams

CERN Document Server

Kester, O

2001-01-01

The efficient transformation of radioactive beams by charge breeding devices will critically influence the lay-out of the post accelerator of presently built first generation radioactive ion beam (RIB) facilities as well as new second generation facilities. The size of the post-accelerator needed to bring the unstable nuclei to the energies required to study nuclear reactions depends on the charge state of the radioactive ions. The capability to raise that charge state from 1+ to n+, where n may correspond to a charge-to- mass ratio of 0.15 or higher, will therefore produce an enormous reduction in cost as well as the possibility to accelerate heavier masses. Thus the efficiency of the charge breeding scheme in comparison to the stripping scheme will be explored in the frame of the EU-network charge breeding. The two possible charge breeding schemes using either an Electron Beam Ion Source (EBIS) or an Electron Cyclotron Resonance Ion Source (ECRIS), the demands to the sources and the present status of existi...

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.

BioModels: expanding horizons to include more modelling approaches and formats.

Science.gov (United States)

Glont, Mihai; Nguyen, Tung V N; Graesslin, Martin; Hälke, Robert; Ali, Raza; Schramm, Jochen; Wimalaratne, Sarala M; Kothamachu, Varun B; Rodriguez, Nicolas; Swat, Maciej J; Eils, Jurgen; Eils, Roland; Laibe, Camille; Malik-Sheriff, Rahuman S; Chelliah, Vijayalakshmi; Le Novère, Nicolas; Hermjakob, Henning

2018-01-04

BioModels serves as a central repository of mathematical models representing biological processes. It offers a platform to make mathematical models easily shareable across the systems modelling community, thereby supporting model reuse. To facilitate hosting a broader range of model formats derived from diverse modelling approaches and tools, a new infrastructure for BioModels has been developed that is available at http://www.ebi.ac.uk/biomodels. This new system allows submitting and sharing of a wide range of models with improved support for formats other than SBML. It also offers a version-control backed environment in which authors and curators can work collaboratively to curate models. This article summarises the features available in the current system and discusses the potential benefit they offer to the users over the previous system. In summary, the new portal broadens the scope of models accepted in BioModels and supports collaborative model curation which is crucial for model reproducibility and sharing. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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...

Comparative In silico Study of Sex-Determining Region Y (SRY) Protein Sequences Involved in Sex-Determining.

Science.gov (United States)

Vakili Azghandi, Masoume; Nasiri, Mohammadreza; Shamsa, Ali; Jalali, Mohsen; Shariati, Mohammad Mahdi

2016-04-01

The SRY gene (SRY) provides instructions for making a transcription factor called the sex-determining region Y protein. The sex-determining region Y protein causes a fetus to develop as a male. In this study, SRY of 15 spices included of human, chimpanzee, dog, pig, rat, cattle, buffalo, goat, sheep, horse, zebra, frog, urial, dolphin and killer whale were used for determine of bioinformatic differences. Nucleotide sequences of SRY were retrieved from the NCBI databank. Bioinformatic analysis of SRY is done by CLC Main Workbench version 5.5 and ClustalW (http:/www.ebi.ac.uk/clustalw/) and MEGA6 softwares. The multiple sequence alignment results indicated that SRY protein sequences from Orcinus orca (killer whale) and Tursiopsaduncus (dolphin) have least genetic distance of 0.33 in these 15 species and are 99.67% identical at the amino acid level. Homosapiens and Pantroglodytes (chimpanzee) have the next lowest genetic distance of 1.35 and are 98.65% identical at the amino acid level. These findings indicate that the SRY proteins are conserved in the 15 species, and their evolutionary relationships are similar.

Ginger extracts influence the expression of IL-27 and IL-33 in the central nervous system in experimental autoimmune encephalomyelitis and ameliorates the clinical symptoms of disease.

Science.gov (United States)

Jafarzadeh, A; Mohammadi-Kordkhayli, M; Ahangar-Parvin, R; Azizi, V; Khoramdel-Azad, H; Shamsizadeh, A; Ayoobi, A; Nemati, M; Hassan, Z M; Moazeni, S M; Khaksari, M

2014-11-15

The immunomodulatory effects of the IL-27 and IL-33 and the anti-inflammatory effects of ginger have been reported in some studies. The aim was to evaluate the effects of the ginger extract on the expression of IL-27 and IL-33 in a model of experimental autoimmune encephalomyelitis (EAE). In PBS-treated EAE mice the expression of IL-27 P28 was significantly lower whereas the expression of IL-33 was significantly higher than unimmunized control mice. In 200 and 300 mg/kg ginger-treated EAE groups the expression of IL-27 P28 and IL-27 EBI3 was significantly higher whereas the expression of IL-33 was significantly lower than PBS-treated EAE mice. The EAE clinical symptoms and the pathological scores were significantly lower in ginger-treated EAE groups. These results showed that the ginger extract modulates the expression of the IL-27 and IL-33 in the spinal cord of EAE mice and ameliorates the clinical symptoms of disease. Copyright © 2014 Elsevier B.V. All rights reserved.

Hydrogeochemical Investigation of Recharge Pathways to Intermediate and Regional Groundwater in Canon de Valle and Technical Area 16, Los Alamos National Laboratory

Energy Technology Data Exchange (ETDEWEB)

Brady, Brendan W. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-11-14

In aquifers consisting of fractured or porous igneous rocks, as well as conglomerate and sandstone products of volcanic formations, silicate minerals actively dissolve and precipitate (Eby, 2004; Eriksson, 1985; Drever, 1982). Dissolution of hydrated volcanic glass is also known to influence the character of groundwater to which it is exposed (White et al., 1980). Hydrochemical evolution, within saturated zones of volcanic formations, is modeled here as a means to resolve the sources feeding a perched groundwater zone. By observation of solute mass balances in groundwater, together with rock chemistry, this study characterizes the chemical weathering processes active along recharge pathways in a mountain front system. Inverse mass balance modeling, which accounts for mass fluxes between solid phases and solution, is used to contrive sets of quantitative reactions that explain chemical variability of water between sampling points. Model results are used, together with chloride mass balance estimation, to evaluate subsurface mixing scenarios generated by further modeling. Final model simulations estimate contributions of mountain block and local recharge to various contaminated zones.

Ion colliders

Energy Technology Data Exchange (ETDEWEB)

Fischer, W.

2011-12-01

RHIC and LHC injector chains for the heaviest ion species used to date. The RHIC pulsed sputter source (PSC) and Tandem electrostatic accelerator are being replaced by an Electron Beam Ion Source (EBIS), Radio Frequency Quadrupole (RFQ) and short linac [08Ale1]. With EBIS beams of any element can be prepared for RHIC including uranium and spin-polarized 3He. At CERN an ECR ion source is used, followed by an RFQ and Linac. The ions are then accumulated, electron cooled, and accelerated in LEIR. After transfer to and acceleration in the PS, ion beams are injected into the SPS.

Ion colliders

International Nuclear Information System (INIS)

Fischer, W.

2010-01-01

RHIC and LHC injector chains for the heaviest ion species used to date. The RHIC pulsed sputter source (PSC) and Tandem electrostatic accelerator are being replaced by an Electron Beam Ion Source (EBIS), Radio Frequency Quadrupole (RFQ) and short linac (08Ale1). With EBIS beams of any element can be prepared for RHIC including uranium and spin-polarized 3He. At CERN an ECR ion source is used, followed by an RFQ and Linac. The ions are then accumulated, electron cooled, and accelerated in LEIR. After transfer to and acceleration in the PS, ion beams are injected into the SPS.

Mass-spectrometry analysis of histone post-translational modifications in pathology tissue using the PAT-H-MS approach

Directory of Open Access Journals (Sweden)

Roberta Noberini

2016-06-01

Full Text Available Aberrant histone post-translational modifications (hPTMs have been implicated with various pathologies, including cancer, and may represent useful epigenetic biomarkers. The data described here provide a mass spectrometry-based quantitative analysis of hPTMs from formalin-fixed paraffin-embedded (FFPE tissues, from which histones were extracted through the recently developed PAT-H-MS method. First, we analyzed FFPE samples from mouse spleen and liver or human breast cancer up to six years old, together with their corresponding fresh frozen tissue. We then combined the PAT-H-MS approach with a histone-focused version of the super-SILAC strategy-using a mix of histones from four breast cancer cell lines as a spike-in standard- to accurately quantify hPTMs from breast cancer specimens belonging to different subtypes. The data, which are associated with a recent publication (Pathology tissue-quantitative mass spectrometry analysis to profile histone post-translational modification patterns in patient samples (Noberini, 2015 [1], are deposited at the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD002669.

Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies

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Tue Bjerg Bennike

2016-03-01

Full Text Available Large repositories of well characterized RNAlater preserved samples and formalin-fixed, paraffin-embedded samples have been generated worldwide. However, the impact on the proteome of the preservation methods remain poorly described. Therefore, we analyzed the impact on the proteome of preserving samples in RNAlater, and by formalin-fixation, paraffin-embedding on human soft tissue, using directly frozen samples as a control (“Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples” [1]. We here report the data from the analysis. The comparative analysis was performed on 24 colon mucosa biopsies, extracted from the sigmoideum of two gastroenterologically healthy participants for the purpose of this study. A set of biopsies were additionally stored for 30 min at room temperature prior to formalin-fixation. The samples were analyzed by high throughput gel free quantitative proteomics. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002029. Keywords: Human, Colon, Mucosa, RNAlater, FFPE, Snap-frozen, Stability, LC–MS, Proteomics

Data set from a comprehensive phosphoproteomic analysis of rice variety IRBB5 in response to bacterial blight

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Yuxuan Hou

2016-03-01

Full Text Available Bacterial blight (BB caused by Xanthomonas oryzae pv. oryzae (Xoo has become one of the most devastating diseases for rice, a major food source for over half of the world populations. To investigate the roles of protein phosphorylation in rice bacterial blight resistance, a quantitative phosphoproteomic study was conducted in rice variety IRBB5 at 0 h and 24 h after Xoo infection. 2367 and 2223 phosphosites on 1334 and 1297 representative proteins were identified in 0 h and 24 h after Xoo infection, respectively, out of which 762 proteins were found to be differentially phosphorylated. In associated with the published article “A comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight” in BMC Plant Biology (Hou et al., 2015 [1], this dataset article provided the detailed information of experimental designing, methods, features as well as the raw data of mass spectrometry (MS identification. The MS proteomics data could be fully accessed from the ProteomeXchange Consortium with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD002222. Keywords: Rice (Oryza sativa L., Bacterial blight, Phosphoproteome

Data in support of proteomic analysis of pneumococcal pediatric clinical isolates to construct a protein array

Directory of Open Access Journals (Sweden)

Alfonso Olaya-Abril

2016-03-01

Full Text Available Surface proteins play key roles in the interaction between cells and their environment, and in pathogenic microorganisms they are the best targets for drug or vaccine discovery and/or development. In addition, surface proteins can be the basis for serodiagnostic tools aiming at developing more affordable techniques for early diagnosis of infection in patients. We carried out a proteomic analysis of a collection of pediatric clinical isolates of Streptococcus pneumoniae, an important human pathogen responsible for more than 1.5 million child deaths worldwide. For that, cultured live bacterial cells were “shaved” with trypsin, and the recovered peptides were analyzed by LC/MS/MS. We selected 95 proteins to be produced as recombinant polypeptides, and printed them on an array. We probed the protein array with a collection of patient sera to define serodiagnostic antigens. The mass spectrometry proteomics data correspond to those published in [1] and have been deposited to the ProteomeXchange Consortium [2] via the PRIDE partner repository [3] with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD001740. The protein array raw data are provided as supplemental material in this article. Keywords: Pneumococcus, Protein arrays, Proteomics, Diagnostics

Electron beam irradiation of textile effluents and non-ionic ethoxylated surfactant for toxicity and color removal

Energy Technology Data Exchange (ETDEWEB)

Sole, Stephanie V. Del; Garcia, Vanessa S.G.; Boiani, Nathalia F.; Rosa, Jorge M.; Andrade e Silva, Leonardo G. de; Borrely, Sueli I., E-mail: vanessagranadeiro@gmail.com, E-mail: steh.vdsole@gmail.com, E-mail: jotarosa@hotmail.com [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil); SENAI, Faculdade de Tecnologia Antoine Skaf, Sao Paulo, SP (Brazil)

2017-11-01

Textile industry has an expressive scenario in the world economy and Brazil is the 5{sup th} in the textile production. By 2015, Brazilian textile production represented US $ 39.3 billion, accounting for more than 1.8 million tons of fabric (ABIT, 2017). The effluents from textile industry are highlighted by quantity of wastewater discharged and variety of substances (dyes, bleaching agents, surfactants, salts, acids, among others). Such compounds often prove to be toxic to aquatic biota. This present study aims to assess toxicity of whole effluents, before and after irradiation (by electron beam accelerator, EBI). In addition, the reduction of the effluent color after irradiation is also very important. Daphnia similis and Vibrio fischeri were the biological systems applied for toxicity evaluations. Previous results demonstrated the surfactant as the main toxic compound, in the untreated and irradiated forms, EC 50 = 0.44 ppm ± 0.02 (untreated); EC 50 = 0.46 % ± 0.07 (irradiated). The irradiation was effective in reducing the color of the effluent, starting from 0.5 kGy. EB radiation may be proposed as an alternative treatment for the final effluent from textile processing, mainly for reuse purposes. (author)

Comparative In silico Study of Sex-Determining Region Y (SRY Protein Sequences Involved in Sex-Determining

Directory of Open Access Journals (Sweden)

Masoume Vakili Azghandi

2016-05-01

Full Text Available Background: The SRY gene (SRY provides instructions for making a transcription factor called the sex-determining region Y protein. The sex-determining region Y protein causes a fetus to develop as a male. In this study, SRY of 15 spices included of human, chimpanzee, dog, pig, rat, cattle, buffalo, goat, sheep, horse, zebra, frog, urial, dolphin and killer whale were used for determine of bioinformatic differences. Methods: Nucleotide sequences of SRY were retrieved from the NCBI databank. Bioinformatic analysis of SRY is done by CLC Main Workbench version 5.5 and ClustalW (http:/www.ebi.ac.uk/clustalw/ and MEGA6 softwares. Results: The multiple sequence alignment results indicated that SRY protein sequences from Orcinus orca (killer whale and Tursiopsaduncus (dolphin have least genetic distance of 0.33 in these 15 species and are 99.67% identical at the amino acid level. Homosapiens and Pantroglodytes (chimpanzee have the next lowest genetic distance of 1.35 and are 98.65% identical at the amino acid level. Conclusion: These findings indicate that the SRY proteins are conserved in the 15 species, and their evolutionary relationships are similar.

eGenomics: Cataloguing Our Complete Genome Collection III

Directory of Open Access Journals (Sweden)

Dawn Field

2007-01-01

Full Text Available This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS, Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS specification (v1.1, consensus on a variety of features to be added to the Genome Catalogue (GCat, agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates and working towards a single, global list of all public genomes and metagenomes.

Electron beam irradiation of textile effluents and non-ionic ethoxylated surfactant for toxicity and color removal

International Nuclear Information System (INIS)

Sole, Stephanie V. Del; Garcia, Vanessa S.G.; Boiani, Nathalia F.; Rosa, Jorge M.; Andrade e Silva, Leonardo G. de; Borrely, Sueli I.

2017-01-01

Textile industry has an expressive scenario in the world economy and Brazil is the 5"t"h in the textile production. By 2015, Brazilian textile production represented US $ 39.3 billion, accounting for more than 1.8 million tons of fabric (ABIT, 2017). The effluents from textile industry are highlighted by quantity of wastewater discharged and variety of substances (dyes, bleaching agents, surfactants, salts, acids, among others). Such compounds often prove to be toxic to aquatic biota. This present study aims to assess toxicity of whole effluents, before and after irradiation (by electron beam accelerator, EBI). In addition, the reduction of the effluent color after irradiation is also very important. Daphnia similis and Vibrio fischeri were the biological systems applied for toxicity evaluations. Previous results demonstrated the surfactant as the main toxic compound, in the untreated and irradiated forms, EC 50 = 0.44 ppm ± 0.02 (untreated); EC 50 = 0.46 % ± 0.07 (irradiated). The irradiation was effective in reducing the color of the effluent, starting from 0.5 kGy. EB radiation may be proposed as an alternative treatment for the final effluent from textile processing, mainly for reuse purposes. (author)

A Coulomb explosion strategy to tailor the nano-architecture of α-MoO3 nanobelts and an insight into its intrinsic mechanism.

Science.gov (United States)

Zhang, Junli; Zhu, Liu; Yang, Yu; Yong, Huadong; Zhang, Junwei; Peng, Yong; Fu, Jiecai

2018-05-03

Tailoring the nanoarchitecture of materials is significant for the development of nanoscience and nanotechnology. To date, one of the most powerful strategies is convergent electron beam irradiation (EBI). However, only two main functions of knock-on or atomic displacement have been achieved to date. In this study, a Coulomb explosion phenomenon was found to occur in α-MoO3 nanobelts (NBs) under electron beam irradiation, which was controllable and could be used to efficiently create nanostructures such as holes, gaps, and other atomic/nanometer patterns on a single α-MoO3 NB. Theoretical simulations starting from the charging state, charging rate to the threshold time of Coulomb explosion reveal that the Coulomb explosion phenomenon should result from positive charging. The results also show that the multiple charged regions are quickly fragmented, and the monolayered α-MoO3 pieces can then be peeled off once the Coulombic repulsion is sufficient to break the Mo-O bonds in the crystalline structure. It is believed that this efficient and versatile strategy may open up a new avenue to tailor α-MoO3 NBs or other kind of transition metal dichalcogenides via the Coulomb explosion effect.

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.

Genenames.org: the HGNC and VGNC resources in 2017.

Science.gov (United States)

Yates, Bethan; Braschi, Bryony; Gray, Kristian A; Seal, Ruth L; Tweedie, Susan; Bruford, Elspeth A

2017-01-04

The HUGO Gene Nomenclature Committee (HGNC) based at the European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. Currently the HGNC database contains almost 40 000 approved gene symbols, over 19 000 of which represent protein-coding genes. In addition to naming genomic loci we manually curate genes into family sets based on shared characteristics such as homology, function or phenotype. We have recently updated our gene family resources and introduced new improved visualizations which can be seen alongside our gene symbol reports on our primary website http://www.genenames.org In 2016 we expanded our remit and formed the Vertebrate Gene Nomenclature Committee (VGNC) which is responsible for assigning names to vertebrate species lacking a dedicated nomenclature group. Using the chimpanzee genome as a pilot project we have approved symbols and names for over 14 500 protein-coding genes in chimpanzee, and have developed a new website http://vertebrate.genenames.org to distribute these data. Here, we review our online data and resources, focusing particularly on the improvements and new developments made during the last two years. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View.

Science.gov (United States)

Boutet, Emmanuel; Lieberherr, Damien; Tognolli, Michael; Schneider, Michel; Bansal, Parit; Bridge, Alan J; Poux, Sylvain; Bougueleret, Lydie; Xenarios, Ioannis

2016-01-01

The Universal Protein Resource (UniProt, http://www.uniprot.org ) consortium is an initiative of the SIB Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) to provide the scientific community with a central resource for protein sequences and functional information. The UniProt consortium maintains the UniProt KnowledgeBase (UniProtKB), updated every 4 weeks, and several supplementary databases including the UniProt Reference Clusters (UniRef) and the UniProt Archive (UniParc).The Swiss-Prot section of the UniProt KnowledgeBase (UniProtKB/Swiss-Prot) contains publicly available expertly manually annotated protein sequences obtained from a broad spectrum of organisms. Plant protein entries are produced in the frame of the Plant Proteome Annotation Program (PPAP), with an emphasis on characterized proteins of Arabidopsis thaliana and Oryza sativa. High level annotations provided by UniProtKB/Swiss-Prot are widely used to predict annotation of newly available proteins through automatic pipelines.The purpose of this chapter is to present a guided tour of a UniProtKB/Swiss-Prot entry. We will also present some of the tools and databases that are linked to each entry.

Advanced SPARQL querying in small molecule databases.

Science.gov (United States)

Galgonek, Jakub; Hurt, Tomáš; Michlíková, Vendula; Onderka, Petr; Schwarz, Jan; Vondrášek, Jiří

2016-01-01

In recent years, the Resource Description Framework (RDF) and the SPARQL query language have become more widely used in the area of cheminformatics and bioinformatics databases. These technologies allow better interoperability of various data sources and powerful searching facilities. However, we identified several deficiencies that make usage of such RDF databases restrictive or challenging for common users. We extended a SPARQL engine to be able to use special procedures inside SPARQL queries. This allows the user to work with data that cannot be simply precomputed and thus cannot be directly stored in the database. We designed an algorithm that checks a query against data ontology to identify possible user errors. This greatly improves query debugging. We also introduced an approach to visualize retrieved data in a user-friendly way, based on templates describing visualizations of resource classes. To integrate all of our approaches, we developed a simple web application. Our system was implemented successfully, and we demonstrated its usability on the ChEBI database transformed into RDF form. To demonstrate procedure call functions, we employed compound similarity searching based on OrChem. The application is publicly available at https://bioinfo.uochb.cas.cz/projects/chemRDF.

Şiî Kaynaklarda Ali B. Ebî Tâlib ve Fatıma Mushafı

Directory of Open Access Journals (Sweden)

Mehmet Atalan

2015-11-01

Full Text Available It isimportant to note that the issue of the mushaf of Ali b. Ebi Talib is neither based on inference nor is it a matter of belief but it is rather a historical and well-researched fact, and if there exists any dispute over this issue, it is regarding certain details and the eventual fate of this mushaf Most of the narrations indicate that Imam Ali mushaf was compiled on the basis of the order of the revelation of the surahs. However, there are differing views as regards the contents of the mushaf had whether it contained only the revealed text or the al-nuzul and the nasikh and mansukh. In one tradition it is said that Fatimah, after the Prophet passed away, used to write what she was told that would happen to her descendants and stories about other rulers to come. Fatimah recorded those information, which was kept in her family of Imams, and was called The Mushaf of Fatimah. But, The Mushaf of Fatimah is not a part of Quran. It does not have anything to do with Shari’ah and the religious practices

A comparison of three radiation models for the calculation of nozzle arcs

International Nuclear Information System (INIS)

Dixon, C M; Yan, J D; Fang, M T C

2004-01-01

Three radiation models, the semi-empirical model based on net emission coefficients (Zhang et al 1987 J. Phys. D: Appl. Phys. 20 386-79), the five-band P1 model (Eby et al 1998 J. Phys. D: Appl. Phys. 31 1578-88), and the method of partial characteristics (Aubrecht and Lowke 1994 J. Phys. D: Appl. Phys. 27 2066-73; Sevast'yanenko 1979 J. Eng. Phys. 36 138-48), are used to calculate the radiation transfer in an SF6 nozzle arc. The temperature distributions computed by the three models are compared with the measurements of Leseberg and Pietsch (1981 Proc. 4th Int. Symp. on Switching Arc Phenomena (Lodz, Poland) pp 236-40) and Leseberg (1982 PhD Thesis RWTH Aachen, Germany). It has been found that all three models give similar distributions of radiation loss per unit time and volume. For arcs burning in axially dominated flow, such as arcs in nozzle flow, the semi-empirical model and the P1 model give accurate predictions when compared with experimental results. The prediction by the method of partial characteristics is poorest. The computational cost is the lowest for the semi-empirical model

Glyco-centric lectin magnetic bead array (LeMBA − proteomics dataset of human serum samples from healthy, Barrett׳s esophagus and esophageal adenocarcinoma individuals

Directory of Open Access Journals (Sweden)

Alok K. Shah

2016-06-01

Full Text Available This data article describes serum glycoprotein biomarker discovery and qualification datasets generated using lectin magnetic bead array (LeMBA – mass spectrometry techniques, “Serum glycoprotein biomarker discovery and qualification pipeline reveals novel diagnostic biomarker candidates for esophageal adenocarcinoma” [1]. Serum samples collected from healthy, metaplastic Barrett׳s esophagus (BE and esophageal adenocarcinoma (EAC individuals were profiled for glycoprotein subsets via differential lectin binding. The biomarker discovery proteomics dataset consisting of 20 individual lectin pull-downs for 29 serum samples with a spiked-in internal standard chicken ovalbumin protein has been deposited in the PRIDE partner repository of the ProteomeXchange Consortium with the data set identifier PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002442. Annotated MS/MS spectra for the peptide identifications can be viewed using MS-Viewer (〈http://prospector2.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msviewer〉 using search key “jn7qafftux”. The qualification dataset contained 6-lectin pulldown-coupled multiple reaction monitoring-mass spectrometry (MRM-MS data for 41 protein candidates, from 60 serum samples. This dataset is available as a supplemental files with the original publication [1].

PRIDE and "Database on Demand" as valuable tools for computational proteomics.

Science.gov (United States)

Vizcaíno, Juan Antonio; Reisinger, Florian; Côté, Richard; Martens, Lennart

2011-01-01

The Proteomics Identifications Database (PRIDE, http://www.ebi.ac.uk/pride ) provides users with the ability to explore and compare mass spectrometry-based proteomics experiments that reveal details of the protein expression found in a broad range of taxonomic groups, tissues, and disease states. A PRIDE experiment typically includes identifications of proteins, peptides, and protein modifications. Additionally, many of the submitted experiments also include the mass spectra that provide the evidence for these identifications. Finally, one of the strongest advantages of PRIDE in comparison with other proteomics repositories is the amount of metadata it contains, a key point to put the above-mentioned data in biological and/or technical context. Several informatics tools have been developed in support of the PRIDE database. The most recent one is called "Database on Demand" (DoD), which allows custom sequence databases to be built in order to optimize the results from search engines. We describe the use of DoD in this chapter. Additionally, in order to show the potential of PRIDE as a source for data mining, we also explore complex queries using federated BioMart queries to integrate PRIDE data with other resources, such as Ensembl, Reactome, or UniProt.

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.

Genomic Analysis of a Marine Bacterium: Bioinformatics for Comparison, Evaluation, and Interpretation of DNA Sequences

Directory of Open Access Journals (Sweden)

Bhagwan N. Rekadwad

2016-01-01

Full Text Available A total of five highly related strains of an unidentified marine bacterium were analyzed through their short genome sequences (AM260709–AM260713. Genome-to-Genome Distance (GGDC showed high similarity to Pseudoalteromonas haloplanktis (X67024. The generated unique Quick Response (QR codes indicated no identity to other microbial species or gene sequences. Chaos Game Representation (CGR showed the number of bases concentrated in the area. Guanine residues were highest in number followed by cytosine. Frequency of Chaos Game Representation (FCGR indicated that CC and GG blocks have higher frequency in the sequence from the evaluated marine bacterium strains. Maximum GC content for the marine bacterium strains ranged 53-54%. The use of QR codes, CGR, FCGR, and GC dataset helped in identifying and interpreting short genome sequences from specific isolates. A phylogenetic tree was constructed with the bootstrap test (1000 replicates using MEGA6 software. Principal Component Analysis (PCA was carried out using EMBL-EBI MUSCLE program. Thus, generated genomic data are of great assistance for hierarchical classification in Bacterial Systematics which combined with phenotypic features represents a basic procedure for a polyphasic approach on unambiguous bacterial isolate taxonomic classification.

SYSTEMATIC ANALYSIS OF PERSPECTIVE TRENDS IN ECOLOGICAL AND BIOLOGICAL STUDIES OF THE CASPIAN SEA

Directory of Open Access Journals (Sweden)

G. M. Abdurakhmanov

2016-01-01

Full Text Available RETRACTED ARTICLEAim. The main purpose of the ecological and biological research (EBR of the Caspian Sea is the information and technical support of decision-making to ensure the environmental management in the region taking into account the increase of anthropogenic impact and change in climatic conditions.Methods. As a basis, we have adopted the method of theoretical and mathematical generalization of a number of scientific papers and systematic analysis of the proposed solutions.Results. Analysis and mathematical processing of published literature sources has convincingly demonstrated the need for international cooperation to optimize the ecological and biological research. It has also confirmed the usefulness of the ecological and biological studies of the Caspian Sea in different directions, and the distribution of effort (cost between them requires coordinated management.Conclusion. It is shown that the data obtained by EBI have both rapid and long-term value. In the future, it is rational to develop suitable approaches to unified structuring of the EBR data, including their spatial and timing. An important task is to create a single interstate information space on the results of EBR using information and communication technologies.

Biologické a sociální potřeby onkologicky léčeného dítěte

OpenAIRE

ŘÁDKOVÁ, Klára

2014-01-01

The theory portion of the thesis is dedicated to the issue of cancer during childhood. The first chapter concentrates on possible causes for the genesis of the oncological disease in children. It also describes the kinds and types of children's tuber. The next chapter focuses on the developmental psychology of a child from birth through adolescence. The thesis is focused on children's vital needs so the chapter describes biological, mental and social needs. The chapter which deals with the so...

Pohřebiště Pražského hradu a možnosti jejich sociální interpretace

Czech Academy of Sciences Publication Activity Database

Frolík, Jan; Kaupová, S.

2016-01-01

Roč. 41, č. 1 (2016), s. 101-122 ISSN 0231-5823 R&D Projects: GA ČR GB14-36938G Institutional support: RVO:67985912 Keywords : burial ground * Prague Castle * Early Middle Ages * elite * stable isotopes * social differentiation * nutrition Subject RIV: AC - Archeology, Anthropology, Ethnology

Raně středověké pohřebiště u Malých Hoštic (okr. Opava)

Czech Academy of Sciences Publication Activity Database

Juchelka, Jiří

2010-01-01

Roč. 2010, - (2010), s. 102-108. ISBN 978-83-85871-58-3. ISSN N Institutional research plan: CEZ:AV0Z80010507 Keywords : burial ground * early Middle Ages * Czech Silesia Subject RIV: AC - Archeology, Anthropology, Ethnology

Results of a Musa mapping project

International Nuclear Information System (INIS)

Lagoda, P.J.L.; Noyer, J.L.; Baurens, F.C.

1998-01-01

A completed map, based on two selfed progenies from two banana cultivars (M53 and SFB5) is presented (roughly 1200 cM). More than three hundred markers are linked in 11 linkage groups representing the genome (2n=22) of Musa acuminata. Roughly one third of the markers are co-dominant restriction fragment polymorphisms (RFLPs; one hundred) or micro satellites (thirty). Two thirds of the markers are dominant amplified fragment length polymorphisms (AFLPs; 10% could be considered to be co-dominant). The mean linkage distance is 3 cM, but marker density still should be increased on a couple of linkage groups. Particularities for a mapping job in banana are discussed. Due to Musa acuminata sub-species specific translocations, up to 36% of all the markers tested show important segregation distortions. The need for a cooperative mapping initiative based on a proposed ''frame-map'' harbouring evenly spaced co-dominant ''anchor'' markers is proposed. CIRAD has published 45 sequence tagged micro satellite sites (STMS) in the EMBL database which are accessible at: ''http://www.ebi.ac.uk/'' using the keywords LAGODA and MICROSATELLITE (EMBL accessions X87258 to X87265, X90740 to X90750 and Z85950 to Z85977). (author)

IRaPPA: information retrieval based integration of biophysical models for protein assembly selection.

Science.gov (United States)

Moal, Iain H; Barradas-Bautista, Didier; Jiménez-García, Brian; Torchala, Mieczyslaw; van der Velde, Arjan; Vreven, Thom; Weng, Zhiping; Bates, Paul A; Fernández-Recio, Juan

2017-06-15

In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can lead to disease, and facilitates the designing of drugs which prevent or mimic the interaction. Atomic modeling of protein-protein interactions requires the selection of near-native structures from a set of docked poses based on their calculable properties. By considering this as an information retrieval problem, we have adapted methods developed for Internet search ranking and electoral voting into IRaPPA, a pipeline integrating biophysical properties. The approach enhances the identification of near-native structures when applied to four docking methods, resulting in a near-native appearing in the top 10 solutions for up to 50% of complexes benchmarked, and up to 70% in the top 100. IRaPPA has been implemented in the SwarmDock server ( http://bmm.crick.ac.uk/∼SwarmDock/ ), pyDock server ( http://life.bsc.es/pid/pydockrescoring/ ) and ZDOCK server ( http://zdock.umassmed.edu/ ), with code available on request. moal@ebi.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

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.

Laboratory Directed Research and Development Program

International Nuclear Information System (INIS)

Ogeka, G.J.; Romano, A.J.

1992-12-01

This report briefly discusses the following research: Advances in Geoexploration; Transvenous Coronary Angiography with Synchrotron X-Rays; Borehole Measurements of Global Warming; Molecular Ecology: Development of Field Methods for Microbial Growth Rate and Activity Measurements; A New Malaria Enzyme - A Potential Source for a New Diagnostic Test for Malaria and a Target for a New Antimalarial Drug; Basic Studies on Thoron and Thoron Precursors; Cloning of the cDNA for a Human Serine/Threonine Protein Kinase that is Activated Specifically by Double-Stranded DNA; Development of an Ultra-Fast Laser System for Accelerator Applications; Cluster Impact Fusion; Effect of a Bacterial Spore Protein on Mutagenesis; Structure and Function of Adenovirus Penton Base Protein; High Resolution Fast X-Ray Detector; Coherent Synchrotron Radiation Longitudinal Bunch Shape Monitor; High Grain Harmonic Generation Experiment; BNL Maglev Studies; Structural Investigations of Pt-Based Catalysts; Studies on the Cellular Toxicity of Cocaine and Cocaethylene; Human Melanocyte Transformation; Exploratory Applications of X-Ray Microscopy; Determination of the Higher Ordered Structure of Eukaryotic Chromosomes; Uranium Neutron Capture Therapy; Tunneling Microscopy Studies of Nanoscale Structures; Nuclear Techiques for Study of Biological Channels; RF Sources for Accelerator Physics; Induction and Repair of Double-Strand Breaks in the DNA of Human Lymphocytes; and An EBIS Source of High Charge State Ions up to Uranium

Laboratory Directed Research and Development Program

Energy Technology Data Exchange (ETDEWEB)

Ogeka, G.J.; Romano, A.J.

1992-12-01

This report briefly discusses the following research: Advances in Geoexploration; Transvenous Coronary Angiography with Synchrotron X-Rays; Borehole Measurements of Global Warming; Molecular Ecology: Development of Field Methods for Microbial Growth Rate and Activity Measurements; A New Malaria Enzyme - A Potential Source for a New Diagnostic Test for Malaria and a Target for a New Antimalarial Drug; Basic Studies on Thoron and Thoron Precursors; Cloning of the cDNA for a Human Serine/Threonine Protein Kinase that is Activated Specifically by Double-Stranded DNA; Development of an Ultra-Fast Laser System for Accelerator Applications; Cluster Impact Fusion; Effect of a Bacterial Spore Protein on Mutagenesis; Structure and Function of Adenovirus Penton Base Protein; High Resolution Fast X-Ray Detector; Coherent Synchrotron Radiation Longitudinal Bunch Shape Monitor; High Grain Harmonic Generation Experiment; BNL Maglev Studies; Structural Investigations of Pt-Based Catalysts; Studies on the Cellular Toxicity of Cocaine and Cocaethylene; Human Melanocyte Transformation; Exploratory Applications of X-Ray Microscopy; Determination of the Higher Ordered Structure of Eukaryotic Chromosomes; Uranium Neutron Capture Therapy; Tunneling Microscopy Studies of Nanoscale Structures; Nuclear Techiques for Study of Biological Channels; RF Sources for Accelerator Physics; Induction and Repair of Double-Strand Breaks in the DNA of Human Lymphocytes; and An EBIS Source of High Charge State Ions up to Uranium.

Laboratory Directed Research and Development Program. Annual report

Energy Technology Data Exchange (ETDEWEB)

Ogeka, G.J.; Romano, A.J.

1992-12-01

This report briefly discusses the following research: Advances in Geoexploration; Transvenous Coronary Angiography with Synchrotron X-Rays; Borehole Measurements of Global Warming; Molecular Ecology: Development of Field Methods for Microbial Growth Rate and Activity Measurements; A New Malaria Enzyme - A Potential Source for a New Diagnostic Test for Malaria and a Target for a New Antimalarial Drug; Basic Studies on Thoron and Thoron Precursors; Cloning of the cDNA for a Human Serine/Threonine Protein Kinase that is Activated Specifically by Double-Stranded DNA; Development of an Ultra-Fast Laser System for Accelerator Applications; Cluster Impact Fusion; Effect of a Bacterial Spore Protein on Mutagenesis; Structure and Function of Adenovirus Penton Base Protein; High Resolution Fast X-Ray Detector; Coherent Synchrotron Radiation Longitudinal Bunch Shape Monitor; High Grain Harmonic Generation Experiment; BNL Maglev Studies; Structural Investigations of Pt-Based Catalysts; Studies on the Cellular Toxicity of Cocaine and Cocaethylene; Human Melanocyte Transformation; Exploratory Applications of X-Ray Microscopy; Determination of the Higher Ordered Structure of Eukaryotic Chromosomes; Uranium Neutron Capture Therapy; Tunneling Microscopy Studies of Nanoscale Structures; Nuclear Techiques for Study of Biological Channels; RF Sources for Accelerator Physics; Induction and Repair of Double-Strand Breaks in the DNA of Human Lymphocytes; and An EBIS Source of High Charge State Ions up to Uranium.

The biological quality of Sieve downriver the Sabatta waster water plant; La qualita biologica del fiume Sieve a valle del depuratore di Rabatta

Energy Technology Data Exchange (ETDEWEB)

Banchetti, Rosalba; Gasperini, Federico; Bicocchi, Allegra; Cecchini, Agnese; Nolan, Brigitte; Stramaccia, Tania [Pisa Univ., Pisa (Italy). Dipartimento di etologia, ecologia ed evoluzione

2005-10-15

An evaluation study of the environmental condition of Sieve river, based on the Extended Biotic Index method (E.B.I.) applied to macro invertebrates was carried out in 2003. Three sampling locations were selected upriver and downriver a depuration plant and upriver of the confluence of a tributary that flow into the Sieve, the Ensa. The monitoring, carried out in two separate campaigns, in winter and spring, revealed how efficient is the sludge-active plant in determining a good quality of the water. Moreover Bilancino reservoir, with constant discharges, keeps Sieve river flow with a constant regime all through the year, avoiding the summer dry-up of the river and allowing the settlement of a biodiversified macrobenthonic community. [Italian] Nal 2003 e stato condotto uno studio di valutazione dello stato ecologico del fiume Sieve sulla base della comunita di macroinvertebrati, usando il metodo dell'I.B.E. (Indice Biotico Esteso). Sono stati scelti tre punti di campionamento a monte e a valle dello scarico di un impianto di depurazione, in funzione dal 1998, che tratta reflui di origine civile. Il monitoraggio eseguito ha rivelato l'utilita dell'impianto a fanghi attivi nel determinare un netto miglioramento della qualita delle acque.

[Parenting stress and the reliability of parental information in the diagnostics of children and adolescents with symptoms of psychiatric and behavioral disorders].

Science.gov (United States)

Irlbauer-Müller, Viktoria; Eichler, Anna; Stemmler, Mark; Moll, Gunther H; Kratz, Oliver

2017-07-01

Information from parents is regularly used in the diagnostic process of children and adolescents with psychiatric symptoms. But the reliability of this information is debatable, because the parents’ own stress can distort their perceptions of the child’s symptoms. For each of N = 68 children and adolescents (11–18 years) who were using mental health services for the first time, we evaluated the ratings of a parent and a professional clinician (internalizing, externalizing symptoms, total-problem score). In addition, parenting stress was scored on the Eltern-Belastungs-Inventars (EBI, Tröster, 2011), which measures both child-related stress and parent-related stress as well as total stress. Highly stressed parent ratings differed more from the clinicians’ ratings than the ratings of less stressed parents. Additionally, correlations showed that higher parenting stress resulted in larger differences between the parent’s and the clinician’s assessments. Multiple regressions proved the predictive value of child-caused parenting stress for these differences. These results apply for internalizing symptoms, externalizing symptoms, and total-problem score. Parenting stress should be evaluated systematically in order to carefully assess the value of the information from parents and to determine how it should be included in diagnostic and therapeutical decisions.

High-speed two-frame gated camera for parameters measurement of Dragon-Ⅰ LIA

International Nuclear Information System (INIS)

Jiang Xiaoguo; Wang Yuan; Zhang Kaizhi; Shi Jinshui; Deng Jianjun; Li Jin

2012-01-01

The time-resolved measurement system which can work at very high speed is necessary in electron beam parameter diagnosis for Dragon-Ⅰ linear induction accelerator (LIA). A two-frame gated camera system has been developed and put into operation. The camera system adopts the optical principle of splitting the imaging light beam into two parts in the imaging space of a lens with long focus length. It includes lens coupled gated image intensifier, CCD camera, high speed shutter trigger device based on large scale field programmable gate array. The minimum exposure time for each image is about 3 ns, and the interval time between two images can be adjusted with a step of about 0.5 ns. The exposure time and the interval time can be independently adjusted and can reach about 1 s. The camera system features good linearity, good response uniformity, equivalent background illumination (EBI) as low as about 5 electrons per pixel per second, large adjustment range of sensitivity, and excel- lent flexibility and adaptability in applications. The camera system can capture two frame images at one time with the image size of 1024 x 1024. It meets the requirements of measurement for Dragon-Ⅰ LIA. (authors)

A Novel Non-Iterative Method for Real-Time Parameter Estimation of the Fricke-Morse Model

Directory of Open Access Journals (Sweden)

SIMIC, M.

2016-11-01

Full Text Available Parameter estimation of Fricke-Morse model of biological tissue is widely used in bioimpedance data processing and analysis. Complex nonlinear least squares (CNLS data fitting is often used for parameter estimation of the model, but limitations such as high processing time, converging into local minimums, need for good initial guess of model parameters and non-convergence have been reported. Thus, there is strong motivation to develop methods which can solve these flaws. In this paper a novel real-time method for parameter estimation of Fricke-Morse model of biological cells is presented. The proposed method uses the value of characteristic frequency estimated from the measured imaginary part of bioimpedance, whereupon the Fricke-Morse model parameters are calculated using the provided analytical expressions. The proposed method is compared with CNLS in frequency ranges of 1 kHz to 10 MHz (beta-dispersion and 10 kHz to 100 kHz, which is more suitable for low-cost microcontroller-based bioimpedance measurement systems. The obtained results are promising, and in both frequency ranges, CNLS and the proposed method have accuracies suitable for most electrical bioimpedance (EBI applications. However, the proposed algorithm has significantly lower computation complexity, so it was 20-80 times faster than CNLS.

Report on the 2011 Critical Assessment of Function Annotation (CAFA) meeting

Energy Technology Data Exchange (ETDEWEB)

Friedberg, Iddo [Miami Univ., Oxford, OH (United States)

2015-01-21

The Critical Assessment of Function Annotation meeting was held July 14-15, 2011 at the Austria Conference Center in Vienna, Austria. There were 73 registered delegates at the meeting. We thank the DOE for this award. It helped us organize and support a scientific meeting AFP 2011 as a special interest group (SIG) meeting associated with the ISMB 2011 conference. The conference was held in Vienna, Austria, in July 2011. The AFP SIG was held on July 15-16, 2011 (immediately preceding the conference). The meeting consisted of two components, the first being a series of talks (invited and contributed) and discussion sections dedicated to protein function research, with an emphasis on the theory and practice of computational methods utilized in functional annotation. The second component provided a large-scale assessment of computational methods through participation in the Critical Assessment of Functional Annotation (CAFA). The meeting was exciting and, based on feedback, quite successful. There were 73 registered participants. The schedule was only slightly different from the one proposed, due to two cancellations. Dr. Olga Troyanskaya has canceled and we invited Dr. David Jones instead. Similarly, instead of Dr. Richard Roberts, Dr. Simon Kasif gave a closing keynote. The remaining invited speakers were Janet Thornton (EBI) and Amos Bairoch (University of Geneva).

Proteomic Analysis of the Cell Cycle of Procylic Form Trypanosoma brucei.

Science.gov (United States)

Crozier, Thomas W M; Tinti, Michele; Wheeler, Richard J; Ly, Tony; Ferguson, Michael A J; Lamond, Angus I

2018-06-01

We describe a single-step centrifugal elutriation method to produce synchronous Gap1 (G1)-phase procyclic trypanosomes at a scale amenable for proteomic analysis of the cell cycle. Using ten-plex tandem mass tag (TMT) labeling and mass spectrometry (MS)-based proteomics technology, the expression levels of 5325 proteins were quantified across the cell cycle in this parasite. Of these, 384 proteins were classified as cell-cycle regulated and subdivided into nine clusters with distinct temporal regulation. These groups included many known cell cycle regulators in trypanosomes, which validates the approach. In addition, we identify 40 novel cell cycle regulated proteins that are essential for trypanosome survival and thus represent potential future drug targets for the prevention of trypanosomiasis. Through cross-comparison to the TrypTag endogenous tagging microscopy database, we were able to validate the cell-cycle regulated patterns of expression for many of the proteins of unknown function detected in our proteomic analysis. A convenient interface to access and interrogate these data is also presented, providing a useful resource for the scientific community. Data are available via ProteomeXchange with identifier PXD008741 (https://www.ebi.ac.uk/pride/archive/). © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

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.

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).

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.

Kształcenie brokerów informacji w Polsce / Education information brokers in Poland

Directory of Open Access Journals (Sweden)

Karolina Kustra

2013-07-01

Full Text Available We współczesnym świecie, w dobie Internetu, to informacja jest najważniejsza, ale żeby ocenić czy jest wiarygodna potrzebni są specjaliści – brokerzy informacji. W Polsce ten zawód jest jeszcze młody, a jego przedstawiciele nie mając własnego stowarzyszenia, stosują się do zasad kodeksu etyki infobrokerskiej stworzonego przez Association of Independent Information Professionals. Oferta kształcenia infobrokerów w Polsce jest coraz szersza i przyszli brokerzy informacji mogą się przygotowywać do zawodu na studiach I i II stopnia, studiach podyplomowych oraz na szkoleniach i kursach. English abstractIn the modern world, the age of the Internet, the information is important, but to assess whether there is credible experts are needed – information brokers. In Poland, the profession is still young, and it’s representatives don’t have their own associations, follow the rules of the Code of Ethical Business Practiced created by the Association of Independent Information Professionals. Offer infobrokerów education in Poland is getting wider and future information brokers can prepare for the profession at the undergraduate and secondary education, post-graduate studies and training courses.

Advancing stroke genomic research in the age of Trans-Omics big data science: Emerging priorities and opportunities.

Science.gov (United States)

Owolabi, Mayowa; Peprah, Emmanuel; Xu, Huichun; Akinyemi, Rufus; Tiwari, Hemant K; Irvin, Marguerite R; Wahab, Kolawole Wasiu; Arnett, Donna K; Ovbiagele, Bruce

2017-11-15

We systematically reviewed the genetic variants associated with stroke in genome-wide association studies (GWAS) and examined the emerging priorities and opportunities for rapidly advancing stroke research in the era of Trans-Omics science. Using the PRISMA guideline, we searched PubMed and NHGRI- EBI GWAS catalog for stroke studies from 2007 till May 2017. We included 31 studies. The major challenge is that the few validated variants could not account for the full genetic risk of stroke and have not been translated for clinical use. None of the studies included continental Africans. Genomic study of stroke among Africans presents a unique opportunity for the discovery, validation, functional annotation, Trans-Omics study and translation of genomic determinants of stroke with implications for global populations. This is because all humans originated from Africa, a continent with a unique genomic architecture and a distinctive epidemiology of stroke; as well as substantially higher heritability and resolution of fine mapping of stroke genes. Understanding the genomic determinants of stroke and the corresponding molecular mechanisms will revolutionize the development of a new set of precise biomarkers for stroke prediction, diagnosis and prognostic estimates as well as personalized interventions for reducing the global burden of stroke. Copyright © 2017 Elsevier B.V. All rights reserved.

Requirements for design of accelerator, beam transport, and target in a study of thermonuclear reaction cross section

Energy Technology Data Exchange (ETDEWEB)

Itahashi, T.; Takahisa, K.; Ohsumi, H.; Komori, M.; Fujiwara, M.; Toki, H. [Osaka Univ., Suita (Japan)

1997-02-01

The process of pp-de{sup +}{nu} is the basic fusion reaction for hydrogen burning in the sun and the prime reaction in chain producing photons and neutrinos. There are many works of the theoretical estimation of the reaction rate in the reaction chain in the sun. The precise measurement of the nutrinos from the sun is one of the most important current physics issues. The rate of the pp-de{sup +}{nu} is too small to be measured in laboratories. The construction of a compact ion accelerator facility with high current, low energy transport and plasma target is planned at the underground laboratory in Otoh Cosmo Observatory of Research Center for Nuclear Physics. The plasma target by using the EBIS type synthesized plasma was proposed as a bare {sup 3}He target. The production of helium ions of each charge state was tested by using the present NEOMAFIOS ECR ion source, and the obtained current is shown. For noncontaminated, high current beam transport, the strong focusing system was introduced. The design of windowless gas target, plasma target, the detection of the energetic reaction particles of protons, digital calorimeter, the couple of ECR ion source and plasma target, and the underground laboratory are reported. (K.I.)

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.

A dictionary to identify small molecules and drugs in free text.

Science.gov (United States)

Hettne, Kristina M; Stierum, Rob H; Schuemie, Martijn J; Hendriksen, Peter J M; Schijvenaars, Bob J A; Mulligen, Erik M van; Kleinjans, Jos; Kors, Jan A

2009-11-15

From the scientific community, a lot of effort has been spent on the correct identification of gene and protein names in text, while less effort has been spent on the correct identification of chemical names. Dictionary-based term identification has the power to recognize the diverse representation of chemical information in the literature and map the chemicals to their database identifiers. We developed a dictionary for the identification of small molecules and drugs in text, combining information from UMLS, MeSH, ChEBI, DrugBank, KEGG, HMDB and ChemIDplus. Rule-based term filtering, manual check of highly frequent terms and disambiguation rules were applied. We tested the combined dictionary and the dictionaries derived from the individual resources on an annotated corpus, and conclude the following: (i) each of the different processing steps increase precision with a minor loss of recall; (ii) the overall performance of the combined dictionary is acceptable (precision 0.67, recall 0.40 (0.80 for trivial names); (iii) the combined dictionary performed better than the dictionary in the chemical recognizer OSCAR3; (iv) the performance of a dictionary based on ChemIDplus alone is comparable to the performance of the combined dictionary. The combined dictionary is freely available as an XML file in Simple Knowledge Organization System format on the web site http://www.biosemantics.org/chemlist.

A Quantitative bgl Operon Model for E. coli Requires BglF Conformational Change for Sugar Transport

Science.gov (United States)

Chopra, Paras; Bender, Andreas

The bgl operon is responsible for the metabolism of β-glucoside sugars such as salicin or arbutin in E. coli. Its regulatory system involves both positive and negative feedback mechanisms and it can be assumed to be more complex than that of the more closely studied lac and trp operons. We have developed a quantitative model for the regulation of the bgl operon which is subject to in silico experiments investigating its behavior under different hypothetical conditions. Upon administration of 5mM salicin as an inducer our model shows 80-fold induction, which compares well with the 60-fold induction measured experimentally. Under practical conditions 5-10mM inducer are employed, which is in line with the minimum inducer concentration of 1mM required by our model. The necessity of BglF conformational change for sugar transport has been hypothesized previously, and in line with those hypotheses our model shows only minor induction if conformational change is not allowed. Overall, this first quantitative model for the bgl operon gives reasonable predictions that are close to experimental results (where measured). It will be further refined as values of the parameters are determined experimentally. The model was developed in Systems Biology Markup Language (SBML) and it is available from the authors and from the Biomodels repository [www.ebi.ac.uk/biomodels].

Solution of the Helmholtz-Poincare Wave Equation using the coupled boundary integral equations and optimal surface eigenfunctions

International Nuclear Information System (INIS)

Werby, M.F.; Broadhead, M.K.; Strayer, M.R.; Bottcher, C.

1992-01-01

The Helmholtz-Poincarf 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-PWECs. 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 be obtained in matrix form by expanding all relevant terms in partial wave expansions, including a bi-orthogonal expansion of the Green's function. However some freedom in the choice of the surface expansion is available since the unknown surface quantities may be expanded in a variety of ways so 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 Hermitian operator. The methodology will be explained in detail and examples will be presented

Classical scattering theory of waves from the view point of an eigenvalue problem and application to target identification

International Nuclear Information System (INIS)

Bottcher, C.; Strayer, M.R.; Werby, M.F.

1993-01-01

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

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.

Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

Science.gov (United States)

Tedersoo, Leho; Abarenkov, Kessy; Nilsson, R Henrik; Schüssler, Arthur; Grelet, Gwen-Aëlle; Kohout, Petr; Oja, Jane; Bonito, Gregory M; Veldre, Vilmar; Jairus, Teele; Ryberg, Martin; Larsson, Karl-Henrik; Kõljalg, Urmas

2011-01-01

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.

Synergistic interactions between a variety of insecticides and an ergosterol biosynthesis inhibitor fungicide in dietary exposures of bumble bees (Bombus terrestris L.).

Science.gov (United States)

Raimets, Risto; Karise, Reet; Mänd, Marika; Kaart, Tanel; Ponting, Sally; Song, Jimao; Cresswell, James E

2018-03-01

In recent years, concern has been raised over honey bee colony losses, and also among wild bees there is evidence for extinctions and range contractions in Europe and North America. Pesticides have been proposed as a potential cause of this decline. Bees are exposed simultaneously to a variety of agrochemicals, which may cause synergistically detrimental impacts, which are incompletely understood. We investigated the toxicity of the fungicide imazalil in mixture with four common insecticides: fipronil (phenylpyrazoid), cypermethrin (pyrethroid), thiamethoxam, and imidacloprid (neonicotinoids). Ergosterol biosynthesis inhibitor (EBI) fungicides like imazalil can inhibit P450 detoxification systems in insects and therefore fungicide - insecticide co-occurrence might produce synergistic toxicity in bees. We assessed the impact of dietary fungicide - insecticide mixtures on the mortality and feeding rates of laboratory bumble bees (Bombus terrestris L.). Regarding mortality, imazalil synergised the toxicity of fipronil, cypermethrin and thiamethoxam, but not imidacloprid. We found no synergistic effects on feeding rates. Our findings suggest that P450-based detoxification processes are differentially important in mitigating the toxicity of certain insecticides, even those of the same chemical class. Our evidence that cocktail effects can arise in bumble bees should extend concern about the potential impacts of agrochemical mixtures to include wild bee species in farmland. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Oxysterols and Their Cellular Effectors

Directory of Open Access Journals (Sweden)

Eija Nissilä

2012-02-01

Full Text Available Oxysterols are oxidized 27-carbon cholesterol derivatives or by-products of cholesterol biosynthesis, with a spectrum of biologic activities. Several oxysterols have cytotoxic and pro-apoptotic activities, the ability to interfere with the lateral domain organization, and packing of membrane lipids. These properties may account for their suggested roles in the pathology of diseases such as atherosclerosis, age-onset macular degeneration and Alzheimer’s disease. Oxysterols also have the capacity to induce inflammatory responses and play roles in cell differentiation processes. The functions of oxysterols as intermediates in the synthesis of bile acids and steroid hormones, and as readily transportable forms of sterol, are well established. Furthermore, their actions as endogenous regulators of gene expression in lipid metabolism via liver X receptors and the Insig (insulin-induced gene proteins have been investigated in detail. The cytoplasmic oxysterol-binding protein (OSBP homologues form a group of oxysterol/cholesterol sensors that has recently attracted a lot of attention. However, their mode of action is, as yet, poorly understood. Retinoic acid receptor-related orphan receptors (ROR α and γ, and Epstein-Barr virus induced gene 2 (EBI2 have been identified as novel oxysterol receptors, revealing new physiologic oxysterol effector mechanisms in development, metabolism, and immunity, and evoking enhanced interest in these compounds in the field of biomedicine.

Integr8: enhanced inter-operability of European molecular biology databases.

Science.gov (United States)

Kersey, P J; Morris, L; Hermjakob, H; Apweiler, R

2003-01-01

The increasing production of molecular biology data in the post-genomic era, and the proliferation of databases that store it, require the development of an integrative layer in database services to facilitate the synthesis of related information. The solution of this problem is made more difficult by the absence of universal identifiers for biological entities, and the breadth and variety of available data. Integr8 was modelled using UML (Universal Modelling Language). Integr8 is being implemented as an n-tier system using a modern object-oriented programming language (Java). An object-relational mapping tool, OJB, is being used to specify the interface between the upper layers and an underlying relational database. The European Bioinformatics Institute is launching the Integr8 project. Integr8 will be an automatically populated database in which we will maintain stable identifiers for biological entities, describe their relationships with each other (in accordance with the central dogma of biology), and store equivalences between identified entities in the source databases. Only core data will be stored in Integr8, with web links to the source databases providing further information. Integr8 will provide the integrative layer of the next generation of bioinformatics services from the EBI. Web-based interfaces will be developed to offer gene-centric views of the integrated data, presenting (where known) the links between genome, proteome and phenotype.

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/.

The Proteins API: accessing key integrated protein and genome information.

Science.gov (United States)

Nightingale, Andrew; Antunes, Ricardo; Alpi, Emanuele; Bursteinas, Borisas; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd; Martin, Maria

2017-07-03

The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to 'talk' to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

Science.gov (United States)

Pujar, Shashikant; O'Leary, Nuala A; Farrell, Catherine M; Loveland, Jane E; Mudge, Jonathan M; Wallin, Craig; Girón, Carlos G; Diekhans, Mark; Barnes, If; Bennett, Ruth; Berry, Andrew E; Cox, Eric; Davidson, Claire; Goldfarb, Tamara; Gonzalez, Jose M; Hunt, Toby; Jackson, John; Joardar, Vinita; Kay, Mike P; Kodali, Vamsi K; Martin, Fergal J; McAndrews, Monica; McGarvey, Kelly M; Murphy, Michael; Rajput, Bhanu; Rangwala, Sanjida H; Riddick, Lillian D; Seal, Ruth L; Suner, Marie-Marthe; Webb, David; Zhu, Sophia; Aken, Bronwen L; Bruford, Elspeth A; Bult, Carol J; Frankish, Adam; Murphy, Terence; Pruitt, Kim D

2018-01-04

The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

Laténské pohřebiště v pískovnách u Vliněvsi, okr. Mělník

Czech Academy of Sciences Publication Activity Database

Limburský, Petr; Sankot, P.; Březinová, Helena; Likovský, Jakub

2015-01-01

Roč. 106, prosinec (2015), s. 181-246 ISSN 0031-0506 Grant - others:GA UK(CZ) 564512 Institutional support: RVO:67985912 Keywords : Central Bohemia * Mělník region * cemetery * La Tène period * chronology * social structure * interregional ties to western Europe and the Danube region Subject RIV: AC - Archeology, Anthropology, Ethnology

Locus Reference Genomic sequences: An improved basis for describing human DNA variants

KAUST Repository

Dalgleish, Raymond; Flicek, Paul; Cunningham, Fiona; Astashyn, Alex; Tully, Raymond E; Proctor, Glenn; Chen, Yuan; McLaren, William M; Larsson, Pontus; Vaughan, Brendan W; Bé roud, Christophe; Dobson, Glen; Lehvä slaiho, Heikki; Taschner, Peter EM; den Dunnen, Johan T; Devereau, Andrew; Birney, Ewan; Brookes, Anthony J; Maglott, Donna R

2010-01-01

As our knowledge of the complexity of gene architecture grows, and we increase our understanding of the subtleties of gene expression, the process of accurately describing disease-causing gene variants has become increasingly problematic. In part, this is due to current reference DNA sequence formats that do not fully meet present needs. Here we present the Locus Reference Genomic (LRG) sequence format, which has been designed for the specifi c purpose of gene variant reporting. The format builds on the successful National Center for Biotechnology Information (NCBI) RefSeqGene project and provides a single-fi le record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants. In principle, LRGs can be created for any organism, not just human. In addition, we recognize the need to respect legacy numbering systems for exons and amino acids and the LRG format takes account of these. We hope that widespread adoption of LRGs - which will be created and maintained by the NCBI and the European Bioinformatics Institute (EBI) - along with consistent use of the Human Genome Variation Society (HGVS)- approved variant nomenclature will reduce errors in the reporting of variants in the literature and improve communication about variants aff ecting human health. Further information can be found on the LRG web site (http://www.lrg-sequence.org). 2010 Dalgleish et al.; licensee BioMed Central Ltd.

Bias to negative emotions: a depression state-dependent marker in adolescent major depressive disorder.

Science.gov (United States)

Maalouf, Fadi T; Clark, Luke; Tavitian, Lucy; Sahakian, Barbara J; Brent, David; Phillips, Mary L

2012-06-30

The aim of the current research was to examine for the first time the extent to which bias to negative emotions in an inhibitory control paradigm is a state or trait marker in major depressive disorder (MDD) in adolescents. We administered the affective go/no go task which measures the ability to switch attention to or away from positive or negative emotional stimuli to 40 adolescents with MDD (20 in acute episode (MDDa) and 20 in remission (MDDr)) and 17 healthy controls (HC). MDDa were significantly faster on the shift to negative target blocks as compared to shift to positive target blocks while HC and MDDr displayed the opposite pattern as measured by an "emotional bias index" (EBI=latency (shift to negative targets)-latency (shift to positive targets)). There was also a trend for an effect of group on commission errors, suggesting more impulsive responding by MDDa than both MDDr and HC independently of stimulus valence throughout the task. Negative bias was not associated with depression severity or medication status. In conclusion, bias to negative emotional stimuli appears to be present in the acute stage of MDD and absent in remission suggesting that it is a depression state-specific marker of MDD in adolescents. Latency emerges as a better proxy of negative bias than commission errors and accuracy on this inhibitory control task in adolescents with MDD. Copyright © 2012 Elsevier Ltd. All rights reserved.

From Here to ET

Science.gov (United States)

Mathews, J. D.

SETI (Search for ExtraTerrestrial Intelligence) has thus far proven negative. The assumptions that have driven these searches are reexamined to determine if a new paradigm for future searches can be identified. To this end, the apparent path of evolving human exploration of the solar system and the local galaxy is used to assess where it might lead in the relative near future while noting that we are not overtly intending to contact ET (ExtraTerrestrials). The basic premise is that human space exploration must be highly efficient, cost effective, and autonomous as placing humans beyond low Earth orbit is fraught with political, economic, and technical difficulties. With this basis, it is concluded that only by developing and deploying self-replicating robotic spacecraft--and the incumbent communication systems--can the human race efficiently explore even the asteroid belt let alone the vast reaches of the Kuiper Belt, Oort Cloud, and beyond. It is assumed that ET would have followed a similar path. The technical practicality of and our progress towards this autonomous, self-replicating exobot--Explorer roBot or EB--is further examined with the conclusion that the narrow-beam, laser-based communication network that would likely be em- ployed, would be difficult to detect from a nearby star systems thus offering an explanation of the failure of SETI to date. It is further argued, as have others, that EBs are likely a common feature of the galaxy.

mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.

Science.gov (United States)

Larralde, Martin; Lawson, Thomas N; Weber, Ralf J M; Moreno, Pablo; Haug, Kenneth; Rocca-Serra, Philippe; Viant, Mark R; Steinbeck, Christoph; Salek, Reza M

2017-08-15

Submission to the MetaboLights repository for metabolomics data currently places the burden of reporting instrument and acquisition parameters in ISA-Tab format on users, who have to do it manually, a process that is time consuming and prone to user input error. Since the large majority of these parameters are embedded in instrument raw data files, an opportunity exists to capture this metadata more accurately. Here we report a set of Python packages that can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files. The parsing packages are separated into mzML2ISA (encompassing mzML and imzML formats) and nmrML2ISA (nmrML format only). Overall, the use of mzML2ISA & nmrML2ISA reduces the time needed to capture metadata substantially (capturing 90% of metadata on assay and sample levels), is much less prone to user input errors, improves compliance with minimum information reporting guidelines and facilitates more finely grained data exploration and querying of datasets. mzML2ISA & nmrML2ISA are available under version 3 of the GNU General Public Licence at https://github.com/ISA-tools. Documentation is available from http://2isa.readthedocs.io/en/latest/. reza.salek@ebi.ac.uk or isatools@googlegroups.com. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Proceedings of the 'INS workshop on ECR ion sources for multiply-charged heavy ions'

International Nuclear Information System (INIS)

1995-02-01

This workshop was held on December 1 and 2, 1994 at the Institute for Nuclear Study, University of Tokyo. The performance of ion sources is crucial for all researches and applications that use ion beam. The performance of ECR ion sources is strongly dependent on heuristic knowledge and innovation. From these viewpoints, it is useful to exchange information on the status of the existing sources, the performance of the new sources, and the design of the future sources between the source builders and the users. There were unexpected more than 70 participants and 20 contributions. The lectures were given on the present status of NIRS-ECR, SF-ECR, INS ISOL-ECR, RCNP ECR and EBIS ion sources, the production of multiply charged metallic ions with Hyper ECR or by plasma cathode method, the processing of ceramic rods and the ion production with OCTOPUS, the modeling of multi-charged ion production, the design of an advanced minimum B for ECR multi-charged ion source, the design, construction and operation of 18 GHz HiECR ion source, the construction and test operation of JAERI 18 GHz ion source, the design of an ECR ion source for the HIMAC, a 14.5 GHz ECR ion source at RIKEN, TMU 14 GHz ECR ion source, ''NANOGAN'' ECR ion source and its irradiation system, the optimization of the ECR ion source for optically pumped polarized ion source and so on. (K.I.)

Cultural Adaptations: Conceptual, Ethical, Contextual, and Methodological Issues for Working with Ethnocultural and Majority-World Populations.

Science.gov (United States)

Bernal, Guillermo; Adames, Cristina

2017-08-01

Mayor advancements have been achieved in research on the cultural adaptation of prevention and treatment interventions that are conducted with diverse ethnocultural groups. This commentary addresses conceptual, ethical, contextual, and methodological issues related to cultural adaptations. The articles in this special issue represent a major contribution to the study of cultural adaptations in prevention science. We frame our analysis of fidelity to core intervention components using a conceptual approach that examines (a) the propositional model (theory of change), (b) the procedural model (theory of action, methods), and (c) the philosophical assumptions that undergird these models. Regarding ethics, we caution against imposing the norms, values, and world views of the Western dominant society onto vulnerable populations such as ethnocultural groups. Given that the assumption of universality in behavioral science has been questioned, and as randomized clinical trials (RCTs) seldom examine the ecological validity of evidence-based interventions and treatments (EBI/T), imposing such interventions onto ethnocultural groups is problematic since these interventions contain values, norms, beliefs, and worldviews that may be contrary to those held by many ethnocultural groups. Regarding methods, several innovative designs are discussed that serve as alternatives to the RCT and represent an important contribution to prevention science. Also, we discuss guidelines for conducting cultural adaptations. Finally, the articles in this special issue make a major contribution to the growing field of cultural adaptation of preventive interventions with ethnocultural groups and majority-world populations.

An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences.

Science.gov (United States)

Ye, Kai; Kosters, Walter A; Ijzerman, Adriaan P

2007-03-15

Pattern discovery in protein sequences is often based on multiple sequence alignments (MSA). The procedure can be computationally intensive and often requires manual adjustment, which may be particularly difficult for a set of deviating sequences. In contrast, two algorithms, PRATT2 (http//www.ebi.ac.uk/pratt/) and TEIRESIAS (http://cbcsrv.watson.ibm.com/) are used to directly identify frequent patterns from unaligned biological sequences without an attempt to align them. Here we propose a new algorithm with more efficiency and more functionality than both PRATT2 and TEIRESIAS, and discuss some of its applications to G protein-coupled receptors, a protein family of important drug targets. In this study, we designed and implemented six algorithms to mine three different pattern types from either one or two datasets using a pattern growth approach. We compared our approach to PRATT2 and TEIRESIAS in efficiency, completeness and the diversity of pattern types. Compared to PRATT2, our approach is faster, capable of processing large datasets and able to identify the so-called type III patterns. Our approach is comparable to TEIRESIAS in the discovery of the so-called type I patterns but has additional functionality such as mining the so-called type II and type III patterns and finding discriminating patterns between two datasets. The source code for pattern growth algorithms and their pseudo-code are available at http://www.liacs.nl/home/kosters/pg/.

Minocycline Protects Against NLRP3 Inflammasome-Induced Inflammation and P53-Associated Apoptosis in Early Brain Injury After Subarachnoid Hemorrhage.

Science.gov (United States)

Li, Jianru; Chen, Jingsen; Mo, Hangbo; Chen, Jingyin; Qian, Cong; Yan, Feng; Gu, Chi; Hu, Qiang; Wang, Lin; Chen, Gao

2016-05-01

Minocycline has beneficial effects in early brain injury (EBI) following subarachnoid hemorrhage (SAH); however, the molecular mechanisms underlying these effects have not been clearly identified. This study was undertaken to determine the influence of minocycline on inflammation and neural apoptosis and the possible mechanisms of these effects in early brain injury following subarachnoid hemorrhage. SAH was induced by the filament perforation model of SAH in male Sprague-Dawley rats. Minocycline or vehicle was given via an intraperitoneal injection 1 h after SAH induction. Minocycline treatment markedly attenuated brain edema secondary to blood-brain barrier (BBB) dysfunction by inhibiting NLRP3 inflammasome activation, which controls the maturation and release of pro-inflammatory cytokines, especially interleukin-1β (IL-1β). Minocycline treatment also markedly reduced the number of terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick-end labeling (TUNEL)-positive cells. To further identify the potential mechanisms, we demonstrated that minocycline increased Bcl2 expression and reduced the protein expression of P53, Bax, and cleaved caspase-3. In addition, minocycline reduced the cortical levels of reactive oxygen species (ROS), which are closely related to both NLRP3 inflammasome and P53 expression. Minocycline protects against NLRP3 inflammasome-induced inflammation and P53-associated apoptosis in early brain injury following SAH. Minocycline's anti-inflammatory and anti-apoptotic effect may involve the reduction of ROS. Minocycline treatment may exhibit important clinical potentials in the management of SAH.

Introducing the PRIDE Archive RESTful web services.

Science.gov (United States)

Reisinger, Florian; del-Toro, Noemi; Ternent, Tobias; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-07-01

The PRIDE (PRoteomics IDEntifications) database is one of the world-leading public repositories of mass spectrometry (MS)-based proteomics data and it is a founding member of the ProteomeXchange Consortium of proteomics resources. In the original PRIDE database system, users could access data programmatically by accessing the web services provided by the PRIDE BioMart interface. New REST (REpresentational State Transfer) web services have been developed to serve the most popular functionality provided by BioMart (now discontinued due to data scalability issues) and address the data access requirements of the newly developed PRIDE Archive. Using the API (Application Programming Interface) it is now possible to programmatically query for and retrieve peptide and protein identifications, project and assay metadata and the originally submitted files. Searching and filtering is also possible by metadata information, such as sample details (e.g. species and tissues), instrumentation (mass spectrometer), keywords and other provided annotations. The PRIDE Archive web services were first made available in April 2014. The API has already been adopted by a few applications and standalone tools such as PeptideShaker, PRIDE Inspector, the Unipept web application and the Python-based BioServices package. This application is free and open to all users with no login requirement and can be accessed at http://www.ebi.ac.uk/pride/ws/archive/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

Science.gov (United States)

Damkliang, Kasikrit; Tandayya, Pichaya; Sangket, Unitsa; Pasomsub, Ekawat

2016-11-28

At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. All local services have been deployed at our portal http://bioservices.sci.psu.ac.th.

Proceedings of the `INS workshop on ECR ion sources for multiply-charged heavy ions`

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-02-01

This workshop was held on December 1 and 2, 1994 at the Institute for Nuclear Study, University of Tokyo. The performance of ion sources is crucial for all researches and applications that use ion beam. The performance of ECR ion sources is strongly dependent on heuristic knowledge and innovation. From these viewpoints, it is useful to exchange information on the status of the existing sources, the performance of the new sources, and the design of the future sources between the source builders and the users. There were unexpected more than 70 participants and 20 contributions. The lectures were given on the present status of NIRS-ECR, SF-ECR, INS ISOL-ECR, RCNP ECR and EBIS ion sources, the production of multiply charged metallic ions with Hyper ECR or by plasma cathode method, the processing of ceramic rods and the ion production with OCTOPUS, the modeling of multi-charged ion production, the design of an advanced minimum B for ECR multi-charged ion source, the design, construction and operation of 18 GHz HiECR ion source, the construction and test operation of JAERI 18 GHz ion source, the design of an ECR ion source for the HIMAC, a 14.5 GHz ECR ion source at RIKEN, TMU 14 GHz ECR ion source, ``NANOGAN`` ECR ion source and its irradiation system, the optimization of the ECR ion source for optically pumped polarized ion source and so on. (K.I.).

Drying characteristic, enzyme inactivation and browning pigmentation kinetics of controlled humidity-convective drying of banana slices

Science.gov (United States)

Sarpong, Frederick; Yu, Xiaojie; Zhou, Cunshan; Oteng-Darko, Patricia; Amenorfe, Leticia Peace; Wu, Bengang; Bai, Junwen; Ma, Haile

2018-04-01

Investigating the kinetics of enzyme activities and browning indexes in food are very essential in understanding the enzyme inactivation and browning pigmentation reaction during drying processing. In order to understand and predict accurately the enzyme inactivation and browning pigmentation of banana slices using Relative Humidity (RH)-convective hot air dryer aided by ultrasound (US) pretreatment, this study was conducted. Drying was carried out with 20 kHz frequency of US-pretreatment using three durations (10 20 and 30 min) and RH (10 20 and 30%) conditions at 70 °C and 2.0 m/s air velocity. The kinetic study of both enzyme inactivation and browning pigmentation results were compared to their relevance of fit in terms of coefficient of correlation (R2), the root mean square error (RMSE) and the reduced chi-square (χ 2). First order and second-order polynomial kinetic model fitted well for enzyme inactivation and browning indexes respectively. Both enzymes inactivation kinetics and enzymatic browning index (EBI) declined significantly (p drying time in all drying conditions and rate of decrease intensified in longer US-pretreatment duration and lower RH conditions. However, shorter US-pretreatment duration and higher RH conditions reduced the non- enzymatic browning index (NBI) significantly. Again, longer US-pretreatment duration and lower RH shortened the drying time but adversely created more microspores from the micrograph study. Longer US pretreatment and lower RH decrease significantly (p < 0.05) the L* and b* values whereas the a* values was increased.

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.

JAMI: a Java library for molecular interactions and data interoperability.

Science.gov (United States)

Sivade Dumousseau, M; Koch, M; Shrivastava, A; Alonso-López, D; De Las Rivas, J; Del-Toro, N; Combe, C W; Meldal, B H M; Heimbach, J; Rappsilber, J; Sullivan, J; Yehudi, Y; Orchard, S

2018-04-11

A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types. A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats. Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI's model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.

Big Data Analysis of Human Genome Variations

KAUST Repository

Gojobori, Takashi

2016-01-25

Since the human genome draft sequence was in public for the first time in 2000, genomic analyses have been intensively extended to the population level. The following three international projects are good examples for large-scale studies of human genome variations: 1) HapMap Data (1,417 individuals) (http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/2010-08_phaseII+III/forward/), 2) HGDP (Human Genome Diversity Project) Data (940 individuals) (http://www.hagsc.org/hgdp/files.html), 3) 1000 genomes Data (2,504 individuals) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ If we can integrate all three data into a single volume of data, we should be able to conduct a more detailed analysis of human genome variations for a total number of 4,861 individuals (= 1,417+940+2,504 individuals). In fact, we successfully integrated these three data sets by use of information on the reference human genome sequence, and we conducted the big data analysis. In particular, we constructed a phylogenetic tree of about 5,000 human individuals at the genome level. As a result, we were able to identify clusters of ethnic groups, with detectable admixture, that were not possible by an analysis of each of the three data sets. Here, we report the outcome of this kind of big data analyses and discuss evolutionary significance of human genomic variations. Note that the present study was conducted in collaboration with Katsuhiko Mineta and Kosuke Goto at KAUST.

Impact of socioeconomic inequalities on geographic disparities in cancer incidence: comparison of methods for spatial disease mapping.

Science.gov (United States)

Goungounga, Juste Aristide; Gaudart, Jean; Colonna, Marc; Giorgi, Roch

2016-10-12

The reliability of spatial statistics is often put into question because real spatial variations may not be found, especially in heterogeneous areas. Our objective was to compare empirically different cluster detection methods. We assessed their ability to find spatial clusters of cancer cases and evaluated the impact of the socioeconomic status (e.g., the Townsend index) on cancer incidence. Moran's I, the empirical Bayes index (EBI), and Potthoff-Whittinghill test were used to investigate the general clustering. The local cluster detection methods were: i) the spatial oblique decision tree (SpODT); ii) the spatial scan statistic of Kulldorff (SaTScan); and, iii) the hierarchical Bayesian spatial modeling (HBSM) in a univariate and multivariate setting. These methods were used with and without introducing the Townsend index of socioeconomic deprivation known to be related to the distribution of cancer incidence. Incidence data stemmed from the Cancer Registry of Isère and were limited to prostate, lung, colon-rectum, and bladder cancers diagnosed between 1999 and 2007 in men only. The study found a spatial heterogeneity (p 1.2). The multivariate HBSM found a spatial correlation between lung and bladder cancers (r = 0.6). In spatial analysis of cancer incidence, SpODT and HBSM may be used not only for cluster detection but also for searching for confounding or etiological factors in small areas. Moreover, the multivariate HBSM offers a flexible and meaningful modeling of spatial variations; it shows plausible previously unknown associations between various cancers.

Locus Reference Genomic sequences: An improved basis for describing human DNA variants

KAUST Repository

Dalgleish, Raymond

2010-04-15

As our knowledge of the complexity of gene architecture grows, and we increase our understanding of the subtleties of gene expression, the process of accurately describing disease-causing gene variants has become increasingly problematic. In part, this is due to current reference DNA sequence formats that do not fully meet present needs. Here we present the Locus Reference Genomic (LRG) sequence format, which has been designed for the specifi c purpose of gene variant reporting. The format builds on the successful National Center for Biotechnology Information (NCBI) RefSeqGene project and provides a single-fi le record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants. In principle, LRGs can be created for any organism, not just human. In addition, we recognize the need to respect legacy numbering systems for exons and amino acids and the LRG format takes account of these. We hope that widespread adoption of LRGs - which will be created and maintained by the NCBI and the European Bioinformatics Institute (EBI) - along with consistent use of the Human Genome Variation Society (HGVS)- approved variant nomenclature will reduce errors in the reporting of variants in the literature and improve communication about variants aff ecting human health. Further information can be found on the LRG web site (http://www.lrg-sequence.org). 2010 Dalgleish et al.; licensee BioMed Central Ltd.

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.

Science.gov (United States)

Perez-Riverol, Yasset; Ternent, Tobias; Koch, Maximilian; Barsnes, Harald; Vrousgou, Olga; Jupp, Simon; Vizcaíno, Juan Antonio

2017-10-01

The availability of user-friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology Lookup Service (OLS, http://www.ebi.ac.uk/ols) is a popular centralized service to query, browse and navigate biomedical ontologies and controlled vocabularies. Recently, the OLS framework has been completely redeveloped (version 3.0), including enhancements in the data model, like the added support for Web Ontology Language based ontologies, among many other improvements. However, the new OLS is not backwards compatible and new software tools are needed to enable access to this widely used framework now that the previous version is no longer available. We here present the OLS Client as a free, open-source Java library to retrieve information from the new version of the OLS. It enables rapid tool creation by providing a robust, pluggable programming interface and common data model to programmatically access the OLS. The library has already been integrated and is routinely used by several bioinformatics resources and related data annotation tools. Secondly, we also introduce an updated version of the OLS Dialog (version 2.0), a Java graphical user interface that can be easily plugged into Java desktop applications to access the OLS. The software and related documentation are freely available at https://github.com/PRIDE-Utilities/ols-client and https://github.com/PRIDE-Toolsuite/ols-dialog. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dětské žárové hroby na pohřebišti lužické kultury v Opavě-Kateřinkách

Czech Academy of Sciences Publication Activity Database

Juchelka, Jiří

2007-01-01

Roč. 42, - (2007), s. 99-112 ISSN 0560-2793 Institutional research plan: CEZ:AV0Z80010507 Keywords : Lusatian culture * burial ground * urn graves * Czech Silesia * Upper Silesia Subject RIV: AC - Archeology, Anthropology, Ethnology

Psychosociální potřeby zdravých sourozenců onkologicky nemocných dětí aneb „zapomenuté děti“

Czech Academy of Sciences Publication Activity Database

Kárová, Š.; Blatný, Marek; Bendová, M.

2009-01-01

Roč. 53, č. 2 (2009), s. 149-157 ISSN 0009-062X R&D Projects: GA ČR GA406/09/1255 Institutional research plan: CEZ:AV0Z70250504 Keywords : siblings * oncology disease * psychosocial needs Subject RIV: AN - Psychology Impact factor: 0.226, year: 2009

Fasciola hepatica reinfection potentiates a mixed Th1/Th2/Th17/Treg response and correlates with the clinical phenotypes of anemia

Science.gov (United States)

Perez-Crespo, Ignacio; Chillón-Marinas, Carlos; Khoubbane, Messaoud; Quesada, Carla; Reguera-Gomez, Marta; Mas-Coma, Santiago; Fresno, Manuel; Gironès, Núria

2017-01-01

Background Fascioliasis is a severe zoonotic disease of worldwide extension caused by liver flukes. In human fascioliasis hyperendemic areas, reinfection and chronicity are the norm and anemia is the main sign. Herein, the profile of the Th1/Th2/Th17/Treg expression levels is analyzed after reinfection, correlating them with their corresponding hematological biomarkers of morbidity. Methodology/Principal findings The experimental design reproduces the usual reinfection/chronicity conditions in human fascioliasis endemic areas and included Fasciola hepatica primo-infected Wistar rats (PI) and rats reinfected at 8 weeks (R8), and at 12 weeks (R12), and negative control rats. In a cross-sectional study, the expression of the genes associated with Th1 (Ifng, Il12a, Il12b, Nos2), Th2 (Il4, Arg1), Treg (Foxp3, Il10, Tgfb, Ebi3), and Th17 (Il17) in the spleen and thymus was analyzed. After 20 weeks of primary infection, PI did not present significant changes in the expression of those genes when compared to non-infected rats (NI), but an increase of Il4, Arg1 and Ifng mRNA in the spleen was observed in R12, suggesting the existence of an active mixed Th1/Th2 systemic immune response in reinfection. Foxp3, Il10, Tgfb and Ebi3 levels increased in the spleen in R12 when compared to NI and PI, indicating that the Treg gene expression levels are potentiated in chronic phase reinfection. Il17 gene expression levels in R12 in the spleen increased when compared to NI, PI and R8. Gene expression levels of Il10 in the thymus increased when compared to NI and PI in R12. Ifng expression levels in the thymus increased in all reinfected rats, but not in PI. The clinical phenotype was determined by the fluke burden, the rat body weight and the hemogram. Multivariate mathematical models were built to describe the Th1/Th2/Th17/Treg expression levels and the clinical phenotype. In reinfection, two phenotypic patterns were detected: i) one which includes only increased splenic Ifng

Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods

Directory of Open Access Journals (Sweden)

Claire Ramus

2016-03-01

Full Text Available This data article describes a controlled, spiked proteomic dataset for which the “ground truth” of variant proteins is known. It is based on the LC-MS analysis of samples composed of a fixed background of yeast lysate and different spiked amounts of the UPS1 mixture of 48 recombinant proteins. It can be used to objectively evaluate bioinformatic pipelines for label-free quantitative analysis, and their ability to detect variant proteins with good sensitivity and low false discovery rate in large-scale proteomic studies. More specifically, it can be useful for tuning software tools parameters, but also testing new algorithms for label-free quantitative analysis, or for evaluation of downstream statistical methods. The raw MS files can be downloaded from ProteomeXchange with identifier http://www.ebi.ac.uk/pride/archive/projects/PXD001819. Starting from some raw files of this dataset, we also provide here some processed data obtained through various bioinformatics tools (including MaxQuant, Skyline, MFPaQ, IRMa-hEIDI and Scaffold in different workflows, to exemplify the use of such data in the context of software benchmarking, as discussed in details in the accompanying manuscript [1]. The experimental design used here for data processing takes advantage of the different spike levels introduced in the samples composing the dataset, and processed data are merged in a single file to facilitate the evaluation and illustration of software tools results for the detection of variant proteins with different absolute expression levels and fold change values.

Análisis de las metodologías de evaluación ex ante de Proyectos aplicados en los programas sociales en el Distrito Capital (2004-2008

Directory of Open Access Journals (Sweden)

Ramón Hernán Bojacá Martín

2007-06-01

Full Text Available El propósito de esta investigación, es el análisis y evaluación de las metodologías implementadas por el Distrito Capital para implementar los llamados "proyectos sociales" con el fin de establecer la influencia de la metodología en los resultados obtenidos de dichos proyectos. Para ello se hizo una selección de los proyectos asignados a la inversión y al gasto social a partir de las fichas EBI (Estadísticas Básicas de Información. Su análisis y evaluación se realizó con base en las reglas teóricas estándar de la Evaluación Ex Ante, definidas en los Manuales de uso frecuente por parte de las Entidades Multilaterales y Oficiales que aprueban dichos proyectos y asignan los recursos para su ejecución. De acuerdo con las 14 variables especificadas para que el proyecto cumpla con los parámetros definidos en el estándar, se encontró que casi todos los proyectos analizados adolecen de diagnósticos operativos de la situación sobre la que se quiere trabajar, no hay precisión ni se priorizan los objetivos en relación con las políticas sociales las inversiones, los costos y su factibilidad. Igualmente, se encontró que los proyectos no contemplan componentes que midan los impactos o indicadores que muestren el mejoramiento de la calidad de vida de las personas a quienes van orientados.

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries

Directory of Open Access Journals (Sweden)

Apweiler Rolf

2006-02-01

Full Text Available Abstract Background With the vast amounts of biomedical data being generated by high-throughput analysis methods, controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform controlled vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries. Results The Ontology Lookup Service (OLS was created to integrate publicly available biomedical ontologies into a single database. All modified ontologies are updated daily. A list of currently loaded ontologies is available online. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A programmatic interface is available to query the webservice using SOAP. The service is described by a WSDL descriptor file available online. A sample Java client to connect to the webservice using SOAP is available for download from SourceForge. All OLS source code is publicly available under the open source Apache Licence. Conclusion The OLS provides a user-friendly single entry point for publicly available ontologies in the Open Biomedical Ontology (OBO format. It can be accessed interactively or programmatically at http://www.ebi.ac.uk/ontology-lookup/.

Annotation-based feature extraction from sets of SBML models.

Science.gov (United States)

Alm, Rebekka; Waltemath, Dagmar; Wolfien, Markus; Wolkenhauer, Olaf; Henkel, Ron

2015-01-01

Model repositories such as BioModels Database provide computational models of biological systems for the scientific community. These models contain rich semantic annotations that link model entities to concepts in well-established bio-ontologies such as Gene Ontology. Consequently, thematically similar models are likely to share similar annotations. Based on this assumption, we argue that semantic annotations are a suitable tool to characterize sets of models. These characteristics improve model classification, allow to identify additional features for model retrieval tasks, and enable the comparison of sets of models. In this paper we discuss four methods for annotation-based feature extraction from model sets. We tested all methods on sets of models in SBML format which were composed from BioModels Database. To characterize each of these sets, we analyzed and extracted concepts from three frequently used ontologies, namely Gene Ontology, ChEBI and SBO. We find that three out of the methods are suitable to determine characteristic features for arbitrary sets of models: The selected features vary depending on the underlying model set, and they are also specific to the chosen model set. We show that the identified features map on concepts that are higher up in the hierarchy of the ontologies than the concepts used for model annotations. Our analysis also reveals that the information content of concepts in ontologies and their usage for model annotation do not correlate. Annotation-based feature extraction enables the comparison of model sets, as opposed to existing methods for model-to-keyword comparison, or model-to-model comparison.

Microencapsulated bitter compounds (from Gentiana lutea) reduce daily energy intakes in humans.

Science.gov (United States)

Mennella, Ilario; Fogliano, Vincenzo; Ferracane, Rosalia; Arlorio, Marco; Pattarino, Franco; Vitaglione, Paola

2016-11-10

Mounting evidence showed that bitter-tasting compounds modulate eating behaviour through bitter taste receptors in the gastrointestinal tract. This study aimed at evaluating the influence of microencapsulated bitter compounds on human appetite and energy intakes. A microencapsulated bitter ingredient (EBI) with a core of bitter Gentiana lutea root extract and a coating of ethylcellulose-stearate was developed and included in a vanilla microencapsulated bitter ingredient-enriched pudding (EBIP). The coating masked bitterness in the mouth, allowing the release of bitter secoiridoids in the gastrointestinal tract. A cross-over randomised study was performed: twenty healthy subjects consumed at breakfast EBIP (providing 100 mg of secoiridoids) or the control pudding (CP) on two different occasions. Blood samples, glycaemia and appetite ratings were collected at baseline and 30, 60, 120 and 180 min after breakfast. Gastrointestinal peptides, endocannabinoids (EC) and N-acylethanolamines (NAE) were measured in plasma samples. Energy intakes were measured at an ad libitum lunch 3 h after breakfast and over the rest of the day (post lunch) through food diaries. No significant difference in postprandial plasma responses of gastrointestinal hormones, glucose, EC and NAE and of appetite between EBIP and CP was found. However, a trend for a higher response of glucagon-like peptide-1 after EBIP than after CP was observed. EBIP determined a significant 30 % lower energy intake over the post-lunch period compared with CP. These findings were consistent with the tailored release of bitter-tasting compounds from EBIP along the gastrointestinal tract. This study demonstrated that microencapsulated bitter secoiridoids were effective in reducing daily energy intake in humans.

Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia.

Science.gov (United States)

Watson-Haigh, Nathan S; Shang, Catherine A; Haimel, Matthias; Kostadima, Myrto; Loos, Remco; Deshpande, Nandan; Duesing, Konsta; Li, Xi; McGrath, Annette; McWilliam, Sean; Michnowicz, Simon; Moolhuijzen, Paula; Quenette, Steve; Revote, Jerico Nico De Leon; Tyagi, Sonika; Schneider, Maria V

2013-09-01

The widespread adoption of high-throughput next-generation sequencing (NGS) technology among the Australian life science research community is highlighting an urgent need to up-skill biologists in tools required for handling and analysing their NGS data. There is currently a shortage of cutting-edge bioinformatics training courses in Australia as a consequence of a scarcity of skilled trainers with time and funding to develop and deliver training courses. To address this, a consortium of Australian research organizations, including Bioplatforms Australia, the Commonwealth Scientific and Industrial Research Organisation and the Australian Bioinformatics Network, have been collaborating with EMBL-EBI training team. A group of Australian bioinformaticians attended the train-the-trainer workshop to improve training skills in developing and delivering bioinformatics workshop curriculum. A 2-day NGS workshop was jointly developed to provide hands-on knowledge and understanding of typical NGS data analysis workflows. The road show-style workshop was successfully delivered at five geographically distant venues in Australia using the newly established Australian NeCTAR Research Cloud. We highlight the challenges we had to overcome at different stages from design to delivery, including the establishment of an Australian bioinformatics training network and the computing infrastructure and resource development. A virtual machine image, workshop materials and scripts for configuring a machine with workshop contents have all been made available under a Creative Commons Attribution 3.0 Unported License. This means participants continue to have convenient access to an environment they had become familiar and bioinformatics trainers are able to access and reuse these resources.

E-MSD: improving data deposition and structure quality.

Science.gov (United States)

Tagari, M; Tate, J; Swaminathan, G J; Newman, R; Naim, A; Vranken, W; Kapopoulou, A; Hussain, A; Fillon, J; Henrick, K; Velankar, S

2006-01-01

The Macromolecular Structure Database (MSD) (http://www.ebi.ac.uk/msd/) [H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Golovin, K. Henrick, A. Hussain, J. Ionides, M. John, P. A. Keller, E. Krissinel et al. (2003) E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res., 31, 458-462.] group is one of the three partners in the worldwide Protein DataBank (wwPDB), the consortium entrusted with the collation, maintenance and distribution of the global repository of macromolecular structure data [H. Berman, K. Henrick and H. Nakamura (2003) Announcing the worldwide Protein Data Bank. Nature Struct. Biol., 10, 980.]. Since its inception, the MSD group has worked with partners around the world to improve the quality of PDB data, through a clean up programme that addresses inconsistencies and inaccuracies in the legacy archive. The improvements in data quality in the legacy archive have been achieved largely through the creation of a unified data archive, in the form of a relational database that stores all of the data in the wwPDB. The three partners are working towards improving the tools and methods for the deposition of new data by the community at large. The implementation of the MSD database, together with the parallel development of improved tools and methodologies for data harvesting, validation and archival, has lead to significant improvements in the quality of data that enters the archive. Through this and related projects in the NMR and EM realms the MSD continues to improve the quality of publicly available structural data.