Performance on the low charge state laser ion source in BNL

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

Okamura, M.; Alessi, J.; Beebe, E.

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 Au 32+. 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 Heavymore » Ion Collider (RHIC) and NASA Space Radiation Laboratory (NSRL).« less

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

NASA Astrophysics Data System (ADS)

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 < 6, breeding times <30 ms, low background contamination, and charge breeding efficiencies >18% into a single charge state. The operation of this device, challenges during the commissioning phase, and future improvements will be discussed.

The Electron Beam Ion Source (EBIS)

ScienceCinema

Brookhaven Lab

2017-12-09

Brookhaven National Lab has successfully developed a new pre-injector system, called the Electron Beam Ion Source, for the Relativistic Heavy Ion Collider (RHIC) and NASA Space Radiation Laboratory science programs. The first of several planned improvemen

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

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

Alessi, James

2010-07-21

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 themore » newest source and preinjector, is in the final stages of commissioning at the end of a five-year construction project.« less

A hollow cathode ion source for production of primary ions for the BNL electron beam ion source.

PubMed

Alessi, James; Beebe, Edward; Carlson, Charles; McCafferty, Daniel; Pikin, Alexander; Ritter, John

2014-02-01

A hollow cathode ion source, based on one developed at Saclay, has been modified significantly and used for several years to produce all primary 1+ ions injected into the Relativistic Heavy Ion Collider Electron Beam Ion Source (EBIS) at Brookhaven. Currents of tens to hundreds of microamperes have been produced for 1+ ions of He, C, O, Ne, Si, Ar, Ti, Fe, Cu, Kr, Xe, Ta, Au, and U. The source is very simple, relying on a glow discharge using a noble gas, between anode and a solid cathode containing the desired species. Ions of both the working gas and ionized sputtered cathode material are extracted, and then the desired species is selected using an ExB filter before being transported into the EBIS trap for charge breeding. The source operates pulsed with long life and excellent stability for most species. Reliable ignition of the discharge at low gas pressure is facilitated by the use of capacitive coupling from a simple toy plasma globe. The source design, and operating experience for the various species, is presented.

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

PubMed

Schwarz, S; Lapierre, A

2016-02-01

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

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

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

Schwarz, S., E-mail: schwarz@nscl.msu.edu; Lapierre, A.

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

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

NASA Astrophysics Data System (ADS)

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.

Production of low-Z ions in the Dresden superconducting electron ion beam source for medical particle therapy.

PubMed

Zschornack, G; Schwan, A; Ullmann, F; Grossmann, F; Ovsyannikov, V P; Ritter, E

2012-02-01

We report on experiments with a new superconducting electron beam ion source (EBIS-SC), the Dresden EBIS-SC, with the objective to meet the main requirements for their application in particle-therapy facilities. Synchrotrons as well as innovative accelerator concepts, such as high-gradient linacs which are driven by a large-current cyclotron (CYCLINACS) and direct drive RF linear accelerators may benefit from the advantages of EBISs in regard to their functional principle. First experimental studies of the production of low-Z ions such as H(+), H(2)(+), H(3)(+), C(4+), and C(6+) are presented. Particular attention is paid to the ion output, i.e., the number of ions per pulse and per second, respectively. Important beam parameters in this context are, among others, ion pulse shaping, pulse repetition rates, beam emittance, and ion energy spread.

Charge breeding simulations for radioactive ion beam production

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

Variale, V.; Raino, A. C.; Clauser, T.

2012-02-15

The charge breeding technique is used for radioactive ion beam (RIB) production in order of optimizing the re-acceleration of the radioactive element ions produced by a primary beam in a thick target. Charge breeding is achieved by means of a device capable of increasing the ion charge state from 1+ to a desired value n+. In order to get high intensity RIB, experiments with charge breeding of very high efficiency could be required. To reach this goal, the charge breeding simulation could help to optimize the high charge state production efficiency by finding more proper parameters for the radioactive 1+more » ions. In this paper a device based on an electron beam ion source (EBIS) is considered. In order to study that problem, a code already developed for studying the ion selective containment in an EBIS with RF quadrupoles, BRICTEST, has been modified to simulate the ion charge state breeding rate for different 1+ ion injection conditions. Particularly, the charge breeding simulations for an EBIS with a hollow electron beam have been studied.« less

Surface and material analytics based on Dresden-EBIS platform technology

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

Schmidt, M., E-mail: mike.schmidt@dreebit.com; König, J., E-mail: mike.schmidt@dreebit.com; Bischoff, L.

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 themore » 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 applications connected to analyzing the biosphere, hydrosphere, lithosphere, cosmosphere and technosphere.« less

Kinetic energy offsets for multicharged ions from an electron beam ion source.

PubMed

Kulkarni, D D; Ahl, C D; Shore, A M; Miller, A J; Harriss, J E; Sosolik, C E; Marler, J P

2017-08-01

Using a retarding field analyzer, we have measured offsets between the nominal and measured kinetic energy of multicharged ions extracted from an electron beam ion source (EBIS). By varying source parameters, a shift in ion kinetic energy was attributed to the trapping potential produced by the space charge of the electron beam within the EBIS. The space charge of the electron beam depends on its charge density, which in turn depends on the amount of negative charge (electron beam current) and its velocity (electron beam energy). The electron beam current and electron beam energy were both varied to obtain electron beams of varying space charge and these were related to the observed kinetic energy offsets for Ar 4+ and Ar 8+ ion beams. Knowledge of these offsets is important for studies that seek to utilize slow, i.e., low kinetic energy, multicharged ions to exploit their high potential energies for processes such as surface modification. In addition, we show that these offsets can be utilized to estimate the effective radius of the electron beam inside the trap.

The REX-ISOLDE charge breeder as an operational machine

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

Wenander, F.; Delahaye, P.; Scrivens, R.

2006-03-15

The charge breeding system of radioactive beam experiment at ISOLDE (REX-ISOLDE), consisting of a large Penning trap in combination with an electron-beam ion source (EBIS), is now a mature concept after having delivered radioactive beams for postacceleration to a number of experiments for three years. The system, preparing ions prior to injection into a compact linear accelerator, has shown to be versatile in terms of the ion species and energies that can be delivered. During the experimental periods 2004 and 2005 a significant part of the ISOLDE beam time was dedicated to REX-ISOLDE experiments. Ion masses in the range betweenmore » A=7 and 153 have been handled with record efficiencies. High-intensity as well as very-short-lived isotope beams were proven to be feasible. Continuous injection into the EBIS has also been successfully tested. Two means of suppressing unwanted beam contaminations were tested and are now in use. In addition, the experience gained from the trap-EBIS concept from a machine operational point of view will be discussed and the limitations described.« less

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

NASA Astrophysics Data System (ADS)

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.

Electron beam ion sources for use in second generation synchrotrons for medical particle therapy

NASA Astrophysics Data System (ADS)

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.

Modification of electron beam ion source instability by longitudinal kinetic effects

NASA Astrophysics Data System (ADS)

Krafft, G. A.; Mark, J. W.-K.

1982-07-01

The electron beam ion source (EBIS) was proposed and subsequently realized by Donets. Further development has been done by the Orsay group and by the Berkeley group. Much theoretical work has been done on EBIS and, in particular, Litwin, Vella, and Sessler find that an electrostatic mode of the electron beam-ion system is unstable using a fluid calculation. The present work indicates that the inclusion of a longitudinal velocity spread in the electron beam decreases the instability growth rate, but their conclusions are not significantly modified. Numerically it is shown that substantial linear instability remains, even when sizeable longitudinal velocity spread is included. The principal result of the work is fig. 1; it gives the complex frequency of the mode as a function of σ/ υ0 z, σ being the spread and υ0 z being the average electron axial velocity.

Electron string phenomenon: physics and use

NASA Astrophysics Data System (ADS)

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.

Application and development of ion-source technology for radiation-effects testing of electronics

NASA Astrophysics Data System (ADS)

Kalvas, T.; Javanainen, A.; Kettunen, H.; Koivisto, H.; Tarvainen, O.; Virtanen, A.

2017-09-01

Studies of heavy-ion induced single event effect (SEE) on space electronics are necessary to verify the operation of the components in the harsh radiation environment. These studies are conducted by using high-energy heavy-ion beams to simulate the radiation effects in space. The ion beams are accelerated as so-called ion cocktails, containing several ion beam species with similar mass-to-charge ratio, covering a wide range of linear energy transfer (LET) values also present in space. The use of cocktails enables fast switching between beam species during testing. Production of these high-energy ion cocktails poses challenging requirements to the ion sources because in most laboratories reaching the necessary beam energies requires very high charge state ions. There are two main technologies producing these beams: The electron beam ion source EBIS and the electron cyclotron resonance ion source ECRIS. The EBIS is most suitable for pulsed accelerators, while ECRIS is most suitable for use with cyclotrons, which are the most common accelerators used in these applications. At the Accelerator Laboratory of the University of Jyväskylä (JYFL), radiation effects testing is currently performed using a K130 cyclotron and a 14 GHz ECRIS at a beam energy of 9.3 MeV/u. A new 18 GHz ECRIS, pushing the limits of the normal conducting ECR technology is under development at JYFL. The performances of existing 18 GHz ion sources have been compared, and based on this analysis, a 16.2 MeV/u beam cocktail with 1999 MeV 126Xe44+ being the most challenging component to has been chosen for development at JYFL. The properties of the suggested beam cocktail are introduced and discussed.

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

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

Schmidt, M., E-mail: mike.schmidt@dreebit.com; Zschornack, G.; Kentsch, U.

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 ofmore » 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.« less

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

PubMed

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.

Quightness: A proposed figure of merit for sources of low-energy, high-charge-state ions

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

Schmieder, R.W.

A variety of ion sources, including the EBIS and ECRIS, are distinguished by their ability to produce low-energy ions of very high charge state. It would be useful to have some figure of merit that is particularly sensitive to this performance. I propose here such a quantity, called Quightness,'' which is related to brightness but which enhances the contrast between sources supplying multicharged ions of low energy. The rationale for introducing this quantity, its etymology and relationship to other figures of merit, and some representative values are presented.

Electronics for fast ion extraction from EBIS devices

NASA Astrophysics Data System (ADS)

Höltermann, H.; Becker, R.; Kleinod, M.; Müller, I.

2004-05-01

Future synchrotrons for cancer therapy could profit from single turn injection in terms of size, costs, and ease of operation [O. Kester, R. Becker, and M. Kleinod, Rev. Sci. Instrum. 67 (1996)]. Short (˜1.5 μs) and intense (˜1.3 mA) pulses of highly charged light ions (C6+, N7+, O8+) are a requirement for these future therapy facilities which can be provided by an EBIS ion source. Such a medically dedicated EBIS has an electron beam of 400 mA at 5 keV and needs an electron current density of 100 A/cm2 for a repetition rate of 10 Hz. To obtain a 1.5 μs ion pulse it is necessary to switch the drift tube potentials up to 1.6 kV (for a ratio of beam to drift tube of 1/20) in some 100 ns. To avoid spreading out of the pulse due to the restoration of the full space charge depression at locations where ions have already been extracted, the potentials applied to the drift tubes are changed with time. They will be adjusted for each drift tube according to the transit time of the ion pulse. Furthermore, the drift tubes are fully interpenetrating each other with tapered fingers in order to locally distribute the action of the applied potentials. This provides a potential wall, which is following the extracted ion pulse and results in a compressed short ion pulse for single turn injection into a synchrotron.

Generation of magneto-immersed electron beams

NASA Astrophysics Data System (ADS)

Pikin, A.; Raparia, D.

2018-05-01

There are many applications of electron beams in accelerator facilities: for electron coolers, electron lenses, and electron beam ion sources (EBIS) to mention a few. Most of these applications require magnetic compression of the electron beam to reduce the beam radius with the goal of either matching the circulating ion beam (electron lenses and electron coolers) or increasing the ionization capability for the production of highly charged ions (EBIS). The magnetic compression of the electron beam comes at a cost of increasing share of the transverse component of energy and therefore increased angles of the electron trajectories to the longitudinal axis. Considering the effect of the magnetic mirror, it is highly desirable to produce a laminar electron beam in the electron gun. The analysis of electron guns with different configurations is given in this paper with emphasis on generating laminar electron beams.

The CARIBU EBIS control and synchronization system

NASA Astrophysics Data System (ADS)

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.

Charge state breeding experiences and plans at TRIUMF

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

Ames, F., E-mail: ames@triumf.ca; Marchetto, M.; Mjøs, A.

At the Isotope Separation and ACceleration (ISAC) facility at TRIUMF, an electron cyclotron resonance ion source (ECRIS) has been set up for the charge state breeding of radioactive ions. In order to reduce background from stable ions generated in the ECRIS, several measures, including changing materials for the plasma chamber and the surrounding components, have been implemented. Further reduction has been achieved by using the post-accelerator chain as a mass filter. Since the implementation of those measures in 2013, physics experiments with accelerated radioactive isotopes of Rb, Sr, K, and Mg have been performed. In most cases, a charge breedingmore » efficiency of several percent has been achieved. With the planned expansion of the isotope production capabilities at TRIUMF within the Advanced Rare IsotopE Laboratory project, two new target stations, one using photo-fission induced by a high-power electron beam at 50 MeV and the other one using 480 MeV protons as at ISAC, will be put into operation within the next 5 yr. Additionally, a new electron beam ion source (EBIS) based charge state breeding system will be installed. Background from such a source is expected to be much lower. The drawback is that for the efficient operation of such a system, pulsed beam operation is required, which makes the installation of an additional ion buncher in front of the EBIS necessary.« less

The CARIBU EBIS control and synchronization system

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

Dickerson, Clayton, E-mail: cdickerson@anl.gov; Peters, Christopher, E-mail: cdickerson@anl.gov

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. Themore » 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.« less

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

PubMed

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

2013-03-01

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

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

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

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

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

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

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

The ATLAS multi-user upgrade and potential applications

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

Mustapha, B.; Nolen, J. A.; Savard, G.

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 existingmore » 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.« less

The ATLAS multi-user upgrade and potential applications

NASA Astrophysics Data System (ADS)

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, isotope production and radiobiological studies at ~6 MeV/u and at the full ATLAS energy of ~15 MeV/u. The concept and proposed implementation of the ATLAS multi-user upgrade will be discussed. Future plans to enhance the flexibility of this upgrade will be presented.

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

NASA Astrophysics Data System (ADS)

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.

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

NASA Astrophysics Data System (ADS)

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.

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

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

Delahaye, P., E-mail: delahaye@ganil.fr; Jardin, P.; Maunoury, L.

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 structuremore » 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.« less

Design and numerical characterization of a crossover EBIS

NASA Astrophysics Data System (ADS)

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.

libChEBI: an API for accessing the ChEBI database.

PubMed

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

2016-01-01

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

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

NASA Astrophysics Data System (ADS)

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.

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

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

Zeno, Keith

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 beenmore » 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.« less

InterProScan 5: genome-scale protein function classification

PubMed Central

Jones, Philip; Binns, David; Chang, Hsin-Yu; Fraser, Matthew; Li, Weizhong; McAnulla, Craig; McWilliam, Hamish; Maslen, John; Mitchell, Alex; Nuka, Gift; Pesseat, Sebastien; Quinn, Antony F.; Sangrador-Vegas, Amaia; Scheremetjew, Maxim; Yong, Siew-Yit; Lopez, Rodrigo; Hunter, Sarah

2014-01-01

Motivation: Robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences. Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan. Developments include improvements and additions to the outputs of the software and the complete reimplementation of the software framework, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis. InterProScan is freely available for download from the EMBl-EBI FTP site and the open source code is hosted at Google Code. Availability and implementation: InterProScan is distributed via FTP at ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/ and the source code is available from http://code.google.com/p/interproscan/. Contact: http://www.ebi.ac.uk/support or interhelp@ebi.ac.uk or mitchell@ebi.ac.uk PMID:24451626

Fast Ion extraction from the MedEBIS

NASA Astrophysics Data System (ADS)

Höltermann, H.; Becker, R.; Kleinod, M.; Müller, I.

2004-01-01

Cancer therapy synchrotrons profit from single turn injection in terms of size, costs and easy operation. The MEdically Dedicated EBIS (MEDEBIS), built in Frankfurt, will deliver short (~1.5 µs) and intense (~1.3 mA) pulses of highly charged light ions (C, N, O) to meet the requirements for therapy facilities. The MEDEBIS operates with an electron beam of 400 mA at 5 keV and a ratio of beam to drift tube of 1/20. Drift tube potentials up to 1.6 kV are switched in some 100 ns to deliver a 1.5 µs ion pulse at an axial field gradient of 6.5 kV/m. On extraction, all potentials applied to the drift tubes are set to a given primary potential to define the extraction gradient. During extraction the drift tubes are not held at constant voltage to avoid spreading out of the pulse due to the restoration of the full space charge depression at locations where ions have already been extracted. To locally distribute the action of the applied potentials the drift tubes are fully interpenetrating each other with tapered fingers. Combining these features result in a potential wall, which follows the extracted ion pulse and produces a compressed short ion pulse for single turn injection. In the future similar constructions could be considered for the RHIS EBIS device or proposed for LHC to provide the advantage with respect to lowest emittance and highest luminosity to the accelerators at BNL and CERN.

Accelerating Radioactive Ion Beams With REX-ISOLDE

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

Ames, F.; Emhofer, S.; Habs, D.

2003-08-26

The post accelerator REX-ISOLDE is installed at the ISOLDE facility at CERN, where a broad variety of radioactive ions can be addressed. Since the end of 2001 beams at the final energy of 2.2 MeV/u are available. REX-ISOLDE uses a unique system of beam bunching and charge breeding. First a Penning trap accumulates and bunches the ions, which are delivered as a quasi-continuous beam from the ISOLDE target-ion-source, and then an electron beam ion source (EBIS) charge-breeds them to a mass-to-charge ratio below 4.5. This enables a very compact design for the following LINAC, consisting of a 4 rod RFQ,more » an IH structure and three 7-gap-resonators. The later ones allow a variation of the final energy between 0.8 and 2.2 MeV/u. Although the machine is still in the commissioning phase, first physics experiments have been done with neutron rich Na and Mg isotopes and 9Li. A total efficiency of several percent has already been obtained.« less

Ion Sources

NASA Astrophysics Data System (ADS)

Haseroth, Helmut; Hora, Heinrich

1993-03-01

Ion sources for accelerators are based on plasma configurations with an extraction system in order to gain a very high number of ions within an appropriately short pulse and of sufficiently high charge number Z for advanced research. Beginning with the duoplasmatron, all established ion sources are based on low-density plasmas, of which the electron beam ionization source (EBIS) and the electron cyclotron resonance (ECR) source are the most advanced; for example they result in pulses of nearly 6 × 108 fully stripped sulfur ions per pulse in the Super Proton Synchrotron (SPS) at CERN with energies of 200 GeV/u. As an example of a forthcoming development, we are reporting about the lead ion source for the same purpose. Contrary to these cases of low-density plasmas, where a rather long time is always necessary to generate sufficiently high charge states, the laser ion source uses very high density plasmas and therefore produced, for example in 1983, single shots of Au51+ ions of high directivity with energies above 300 MeV within 2 ns irradiation time of a gold target with a medium-to-large CO2 laser. Experiments at Dubna and Moscow, using small-size lasers, produced up to one million shots with 1 Hz sequence. After acceleration by a linac or otherwise, ion pulses of up to nearly 5 × 1010 ions of C4+ or Mg12+ with energies in the synchrotrons of up to 2 GeV/u were produced. The physics of the laser generation of the ions is most complex, as we know from laser fusion studies, including non-linear dynamic and dielectric effects, resonances, self-focusing, instabilities, double layers, and an irregular pulsation in the 20 ps range. This explains not only what difficulties are implied with the laser ion source, but also why it opens up a new direction of ion sources.

Implementation of Evidence-Based HIV Interventions for Gay, Bisexual, and Other Men Who Have Sex with Men.

PubMed

Jeffries, William L; Garrett, Sherese; Phields, Miriam; Olubajo, Babatunde; Lemon, Emily; Valdés-Salgado, Raydel; Collins, Charles B

2017-10-01

The Centers for Disease Control and Prevention provides trainings to support implementation of five evidence-based HIV prevention interventions (EBIs) for men who have sex with men (MSM): d-up: Defend Yourself!; Many Men, Many Voices; Mpowerment; Personalized Cognitive Counseling; and Popular Opinion Leader. We evaluated trainees' implementation of these EBIs and, using multivariable logistic regression, examined factors associated with implementation. Approximately 43% of trainees had implemented the EBIs for which they received training. Implementation was associated with working in community-based organizations (vs. health departments or other settings); acquiring training for Mpowerment or Popular Opinion Leader (vs. Personalized Cognitive Counseling); having ≥3 funding sources (vs. one); and having (vs. not having) sufficient time and necessary EBI resources. Findings suggest that implementation may vary by trainee characteristics, especially those related to employment setting, EBI training, funding, and perceived implementation barriers. Efforts that address these factors may help to improve EBI implementation among trainees.

Simulations of RF capture with barrier bucket in booster at injection

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

Gardner, C.J.

2012-01-23

As part of the effort to increase the number of ions per bunch in RHIC, a new scheme for RF capture of EBIS ions in Booster at injection has been developed. The scheme was proposed by M. Blaskiewicz and J.M. Brennan. It employs a barrier bucket to hold a half turn of beam in place during capture into two adjacent harmonic 4 buckets. After acceleration, this allows for 8 transfers of 2 bunches from Booster into 16 buckets on the AGS injection porch. During the Fall of 2011 the necessary hardware was developed and implemented by the RF and Controlsmore » groups. The scheme is presently being commissioned by K.L. Zeno with Au32+ ions from EBIS. In this note we carry out simulations of the RF capture. These are meant to serve as benchmarks for what can be achieved in practice. They also allow for an estimate of the longitudinal emittance of the bunches on the AGS injection porch.« less

Charge breeding results and future prospects with electron cyclotron resonance ion source and electron beam ion source (invited)

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

Vondrasek, R.; Levand, A.; Pardo, R.

2012-02-15

The Californium Rare Ion Breeder Upgrade (CARIBU) of the Argonne National Laboratory ATLAS facility will provide low-energy and reaccelerated neutron-rich radioactive beams for the nuclear physics program. A 70 mCi {sup 252}Cf source produces fission fragments which are thermalized and collected by a helium gas catcher into a low-energy particle beam with a charge of 1+ or 2+. An electron cyclotron resonance (ECR) ion source functions as a charge breeder in order to raise the ion charge sufficiently for acceleration in the ATLAS linac. The final CARIBU configuration will utilize a 1 Ci {sup 252}Cf source to produce radioactive beamsmore » with intensities up to 10{sup 6} ions/s for use in the ATLAS facility. The ECR charge breeder has been tested with stable beam injection and has achieved charge breeding efficiencies of 3.6% for {sup 23}Na{sup 8+}, 15.6% for {sup 84}Kr{sup 17+}, and 13.7% for {sup 85}Rb{sup 19+} with typical breeding times of 10 ms/charge state. For the first radioactive beams, a charge breeding efficiency of 11.7% has been achieved for {sup 143}Cs{sup 27+} and 14.7% for {sup 143}Ba{sup 27+}. The project has been commissioned with a radioactive beam of {sup 143}Ba{sup 27+} accelerated to 6.1 MeV/u. In order to take advantage of its lower residual contamination, an EBIS charge breeder will replace the ECR charge breeder in the next two years. The advantages and disadvantages of the two techniques are compared taking into account the requirements of the next generation radioactive beam facilities.« less

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

PubMed

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.

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

NASA Astrophysics Data System (ADS)

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.

Degradation and acute toxicity removal of the antidepressant Fluoxetine (Prozac(®)) in aqueous systems by electron beam irradiation.

PubMed

Silva, Vanessa Honda Ogihara; Dos Santos Batista, Ana Paula; Silva Costa Teixeira, Antonio Carlos; Borrely, Sueli Ivone

2016-06-01

Electron beam irradiation (EBI) has been considered an advanced technology for the treatment of water and wastewater, whereas very few previous investigations reported its use for removing pharmaceutical pollutants. In this study, the degradation of fluoxetine (FLX), an antidepressant marketed as Prozac(®), was investigated by using EBI at FLX initial concentration of 19.4 ± 0.2 mg L(-1). More than 90 % FLX degradation was achieved at 0.5 kGy, with FLX below the detection limit (0.012 mg L(-1)) at doses higher than 2.5 kGy. The elucidation of organic byproducts performed using direct injection mass spectrometry, along with the results of ion chromatography, indicated hydroxylation of FLX molecules with release of fluoride and nitrate anions. Nevertheless, about 80 % of the total organic carbon concentration remained even for 7.5 kGy or higher doses. The decreases in acute toxicity achieved 86.8 and 9.6 % for Daphnia similis and Vibrio fischeri after EBI exposure at 5 kGy, respectively. These results suggest that EBI could be an alternative to eliminate FLX and to decrease residual toxicity from wastewater generated in pharmaceutical formulation facilities, although further investigation is needed for correlating the FLX degradation mechanism with the toxicity results.

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

PubMed

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 to inform effective program implementation.

Disruptive Innovations for Designing and Diffusing Evidence-based Interventions

PubMed Central

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

2013-01-01

The numbers of evidence-based interventions (EBIs) have been growing exponentially, both therapeutic and prevention programs. Yet, EBIs have not been broadly adopted in the United States. In order for our EBI science to significantly reduce disease burden, we need to critically re-examine our scientific conventions and norms. Innovation may be spurred by re-examining the biomedical model for validating EBIs and the compartmentalization of EBIs as disease-specific, institutionally-based, counseling programs. The model of Disruptive Innovations suggests that we re-engineer EBIs based on their most robust features in order to reach more people in less time and at lower cost. Four new research agendas will be required to support disruptive innovations in EBI science: synthesize common elements across EBIs; experiment with new delivery formats (e.g., consumer controlled, self-directed, brief, paraprofessional, coaching, and technology and media strategies); adopt market strategies to promote and diffuse EBI science, knowledge, and products; and adopt continuous quality improvement as a research paradigm for systematically improving EBIs, based on ongoing data and feedback. EBI science can have more impact if it can better leverage what we know from existing EBIs in order to inspire, engage, inform, and support families and children to adopt and sustain healthy daily routines and lifestyles. PMID:22545596

ProtVista: visualization of protein sequence annotations.

PubMed

Watkins, Xavier; Garcia, Leyla J; Pundir, Sangya; Martin, Maria J

2017-07-01

ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity and relationships in this wealth of data pose a challenge in interpretation. Integrative visualization approaches such as provided by ProtVista are thus essential for researchers to understand the data and, for instance, discover patterns affecting function and disease associations. ProtVista is a JavaScript component released as an open source project under the Apache 2 License. Documentation and source code are available at http://ebi-uniprot.github.io/ProtVista/ . martin@ebi.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

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

PubMed Central

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

2017-01-01

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

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

PubMed

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.

Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI)

PubMed Central

Rebholz-Schuhmann, Dietrich; Kim, Jee-Hyub; Yan, Ying; Dixit, Abhishek; Friteyre, Caroline; Hoehndorf, Robert; Backofen, Rolf; Lewin, Ian

2013-01-01

Motivation Biomedical entities, their identifiers and names, are essential in the representation of biomedical facts and knowledge. In the same way, the complete set of biomedical and chemical terms, i.e. the biomedical “term space” (the “Lexeome”), forms a key resource to achieve the full integration of the scientific literature with biomedical data resources: any identified named entity can immediately be normalized to the correct database entry. This goal does not only require that we are aware of all existing terms, but would also profit from knowing all their senses and their semantic interpretation (ambiguities, nestedness). Result This study compiles a resource for lexical terms of biomedical interest in a standard format (called “LexEBI”), determines the overall number of terms, their reuse in different resources and the nestedness of terms. LexEBI comprises references for protein and gene entries and their term variants and chemical entities amongst other terms. In addition, disease terms have been identified from Medline and PubmedCentral and added to LexEBI. Our analysis demonstrates that the baseforms of terms from the different semantic types show only little polysemous use. Nonetheless, the term variants of protein and gene names (PGNs) frequently contain species mentions, which should have been avoided according to protein annotation guidelines. Furthermore, the protein and gene entities as well as the chemical entities, both do comprise enzymes leading to hierarchical polysemy, and a large portion of PGNs make reference to a chemical entity. Altogether, according to our analysis based on the Medline distribution, 401,869 unique PGNs in the documents contain a reference to 25,022 chemical entities, 3,125 disease terms or 1,576 species mentions. Conclusion LexEBI delivers the complete biomedical and chemical Lexeome in a standardized representation (http://www.ebi.ac.uk/Rebholz-srv/LexEBI/). The resource provides the disease terms as open source content, and fully interlinks terms across resources. PMID:24124474

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

NASA Astrophysics Data System (ADS)

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.

Technical design of RISP RFQ Cooler buncher

NASA Astrophysics Data System (ADS)

Boussaid, Ramzi; Park, Young-Ho; Kondrashev, Sergey

2017-12-01

An RFQCB is designed at Rare Isotope Science Project (RISP) project to efficiently accept high intensity continuous beams provided by ISOL-RISP facility and deliver to Electron Beam Ion Source (EBIS) charge breeder bunched beams with emittance around 3 π.mm.mrad, energy spread < 10 eV and short bunch width ( 10 μs). A new design concept to be implemented in this RFQCB have been developed, including a novel optics system with improved differential pumping system. An electric system providing RF voltages of high amplitudes going up to 10 kV is being also developed. The mechanical design of the various elements forming the radiofrequency quadrupole (RFQ) charge breeder (CB) and their matter are also performed. An overview of the RISP RFQCB design concept as well as the development of its sub-systems will be reported.

The EMBL-EBI bioinformatics web and programmatic tools framework.

PubMed

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

2015-07-01

Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces (https://www.ebi.ac.uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Oxysterol-EBI2 signaling in immune regulation and viral infection.

PubMed

Daugvilaite, Viktorija; Arfelt, Kristine Niss; Benned-Jensen, Tau; Sailer, Andreas W; Rosenkilde, Mette M

2014-07-01

The seven transmembrane G protein-coupled receptor Epstein-Barr virus (EBV) induced gene 2 (EBI2; also known as GPR183) was identified in 1993 on the basis of its substantial upregulation in EBV-infected cells. It is primarily expressed in lymphoid cells; most abundantly in B cells. EBI2 is central for the positioning of B cells within the lymphoid organs, a process that is regulated in part by a chemotactic gradient formed by the endogenous lipid agonists, and in part by a fine-tuned regulation of EBI2 cell surface expression. The most potent endogenous EBI2 agonist is 7α, 25-dihydroxyxcholesterol (7α,25-OHC), yet many structurally related oxysterols can bind to an EBI2 pocket that is defined by the upper parts of the transmembrane helices and extracellular receptor regions. EBI2 signals via Gαi, as well as via G protein-independent pathways like β-arrestin recruitment. The concerted action of these pathways leads to cell migration. By genetically interfering with its up- and downregulation, EBI2 was also recently shown to induce cell proliferation, an action that could be inhibited by small molecule antagonists. Here, we focus on the oxysterol-EBI2 axis in immune control, including its role in the EBV life cycle. We also summarize the structural and functional properties of EBI2 interaction with oxysterol agonists and small molecule antagonists and discuss EBI2 as therapeutic target for diseases of the immune system. © 2014 The Authors. European Journal of Immunology published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Disruptive innovations for designing and diffusing evidence-based interventions.

PubMed

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

2012-09-01

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

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

PubMed

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

2015-07-01

The European Bioinformatics Institute (EMBL-EBI-https://www.ebi.ac.uk) provides free and unrestricted access to data across all major areas of biology and biomedicine. Searching and extracting knowledge across these domains requires a fast and scalable solution that addresses the requirements of domain experts as well as casual users. We present the EBI Search engine, referred to here as 'EBI Search', an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities. API integration provides access to analytical tools, allowing users to further investigate the results of their search. The interconnectivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types including sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, together with relevant life science literature. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The EBI SRS server-new features.

PubMed

Zdobnov, Evgeny M; Lopez, Rodrigo; Apweiler, Rolf; Etzold, Thure

2002-08-01

Here we report on recent developments at the EBI SRS server (http://srs.ebi.ac.uk). SRS has become an integration system for both data retrieval and sequence analysis applications. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. The new additions include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in 'Nice views', SRSQuickSearch bookmarklets. SRS6 is a licensed product of LION Bioscience AG freely available for academics. The EBI SRS server (http://srs.ebi.ac.uk) is a free central resource for molecular biology data as well as a reference server for the latest developments in data integration.

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

PubMed

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 of Treg/CD4 + T/CD8 + T cells were decreased in the EBI3 mimics group, but the EBI3 inhibitors group exhibited an increase in apoptosis rate. In conclusion, over-expression of EBI3 could reduce the apoptosis of Treg/CD4 + T/CD8 + T cells and prevent radiation-induced immunosuppression of cervical cancer HeLa cells by inhibiting the activation of PD-1/PD-L1 signaling pathway.

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

Somerville, Chris

Berkeley Lab's Chris Somerville is a leading authority on the structure and function of plant cell walls, which comprise most of the body mass of higher plants. He views the knowledge of cell wall structure and function as furthering the development of plants with improved usefulness: these plants are strong potential sources of renewable materials and biofuel feedstocks. His scientific expertise defines an ideal match of his interest - in the development of cellulosic and other solar-to-fuel science - with his recent appointment as Director of the Energy Biosciences Institute (EBI). With colleagues in biology, physical sciences, engineering, and environmentalmore » and the social sciences, he now leads the EBI multidisciplinary teams' research efforts to develop next-generation, carbon-neutral transportation fuels.« less

The annotation-enriched non-redundant patent sequence databases.

PubMed

Li, Weizhong; Kondratowicz, Bartosz; McWilliam, Hamish; Nauche, Stephane; Lopez, Rodrigo

2013-01-01

The EMBL-European Bioinformatics Institute (EMBL-EBI) offers public access to patent sequence data, providing a valuable service to the intellectual property and scientific communities. The non-redundant (NR) patent sequence databases comprise two-level nucleotide and protein sequence clusters (NRNL1, NRNL2, NRPL1 and NRPL2) based on sequence identity (level-1) and patent family (level-2). Annotation from the source entries in these databases is merged and enhanced with additional information from the patent literature and biological context. Corrections in patent publication numbers, kind-codes and patent equivalents significantly improve the data quality. Data are available through various user interfaces including web browser, downloads via FTP, SRS, Dbfetch and EBI-Search. Sequence similarity/homology searches against the databases are available using BLAST, FASTA and PSI-Search. In this article, we describe the data collection and annotation and also outline major changes and improvements introduced since 2009. Apart from data growth, these changes include additional annotation for singleton clusters, the identifier versioning for tracking entry change and the entry mappings between the two-level databases. Database URL: http://www.ebi.ac.uk/patentdata/nr/

The Annotation-enriched non-redundant patent sequence databases

PubMed Central

Li, Weizhong; Kondratowicz, Bartosz; McWilliam, Hamish; Nauche, Stephane; Lopez, Rodrigo

2013-01-01

The EMBL-European Bioinformatics Institute (EMBL-EBI) offers public access to patent sequence data, providing a valuable service to the intellectual property and scientific communities. The non-redundant (NR) patent sequence databases comprise two-level nucleotide and protein sequence clusters (NRNL1, NRNL2, NRPL1 and NRPL2) based on sequence identity (level-1) and patent family (level-2). Annotation from the source entries in these databases is merged and enhanced with additional information from the patent literature and biological context. Corrections in patent publication numbers, kind-codes and patent equivalents significantly improve the data quality. Data are available through various user interfaces including web browser, downloads via FTP, SRS, Dbfetch and EBI-Search. Sequence similarity/homology searches against the databases are available using BLAST, FASTA and PSI-Search. In this article, we describe the data collection and annotation and also outline major changes and improvements introduced since 2009. Apart from data growth, these changes include additional annotation for singleton clusters, the identifier versioning for tracking entry change and the entry mappings between the two-level databases. Database URL: http://www.ebi.ac.uk/patentdata/nr/ PMID:23396323

Mixed-method study of a conceptual model of evidence-based intervention sustainment across multiple public-sector service settings.

PubMed

Aarons, Gregory A; Green, Amy E; Willging, Cathleen E; Ehrhart, Mark G; Roesch, Scott C; Hecht, Debra B; Chaffin, Mark J

2014-12-10

This study examines sustainment of an EBI implemented in 11 United States service systems across two states, and delivered in 87 counties. The aims are to 1) determine the impact of state and county policies and contracting on EBI provision and sustainment; 2) investigate the role of public, private, and academic relationships and collaboration in long-term EBI sustainment; 3) assess organizational and provider factors that affect EBI reach/penetration, fidelity, and organizational sustainment climate; and 4) integrate findings through a collaborative process involving the investigative team, consultants, and system and community-based organization (CBO) stakeholders in order to further develop and refine a conceptual model of sustainment to guide future research and provide a resource for service systems to prepare for sustainment as the ultimate goal of the implementation process. A mixed-method prospective and retrospective design will be used. Semi-structured individual and group interviews will be used to collect information regarding influences on EBI sustainment including policies, attitudes, and practices; organizational factors and external policies affecting model implementation; involvement of or collaboration with other stakeholders; and outer- and inner-contextual supports that facilitate ongoing EBI sustainment. Document review (e.g., legislation, executive orders, regulations, monitoring data, annual reports, agendas and meeting minutes) will be used to examine the roles of state, county, and local policies in EBI sustainment. Quantitative measures will be collected via administrative data and web surveys to assess EBI reach/penetration, staff turnover, EBI model fidelity, organizational culture and climate, work attitudes, implementation leadership, sustainment climate, attitudes toward EBIs, program sustainment, and level of institutionalization. Hierarchical linear modeling will be used for quantitative analyses. Qualitative analyses will be tailored to each of the qualitative methods (e.g., document review, interviews). Qualitative and quantitative approaches will be integrated through an inclusive process that values stakeholder perspectives. The study of sustainment is critical to capitalizing on and benefiting from the time and fiscal investments in EBI implementation. Sustainment is also critical to realizing broad public health impact of EBI implementation. The present study takes a comprehensive mixed-method approach to understanding sustainment and refining a conceptual model of sustainment.

The dynamics of de-adoption: a case study of policy change, de-adoption, and replacement of an evidence-based HIV intervention.

PubMed

McKay, Virginia R; Margaret Dolcini, M; Hoffer, Lee D

2017-12-01

Evidence-based intervention (EBI) de-adoption and its influence on public health organizations are largely unexplored within public health implementation research. However, a recent shift in support for HIV prevention EBIs by the Centers for Disease Control and Prevention provides an opportunity to explore EBI de-adoption. The current mixed-method study examines EBI de-adoption and the subsequent impact on a community-based organization (CBO) dedicated to HIV prevention. We conducted a case study with a CBO implementing RESPECT, an HIV prevention EBI, over 5 years (2010-2014), but then de-adopted the intervention. We collected archival data documenting RESPECT implementation and conducted two semi-structured interviews with RESPECT staff (N = 5). Using Fixsen and colleagues' implementation framework, we developed a narrative of RESPECT implementation, delivery, and de-adoption and a thematic analysis to understand additional consequences of RESPECT de-adoption. Discontinuation of RESPECT activities unfolded in a process over time, requiring effort by RESPECT staff. RESPECT de-adoption had wide-reaching influences on individual staff, interactions between the staff and the community, the agency overall, and for implementation of future EBIs. We propose a revision of the implementation framework, incorporating EBI de-adoption as a phase of the implementation cycle. Furthermore, EBI de-adoption may have important, unintended consequences and can inform future HIV prevention strategies and guide research focusing on EBI de-adoption.

Low dose elective brain irradiation in small cell carcinoma of the lung

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

Beiler, D.D.; Kane, R.C.; Bernath, A.M.

Elective brain irradiation (EBI) in a dosage of 3000 rad (midplane) in 2 weeks (nominal standard dose (NSD) = 1314 ret) has proven highly effective in preventing initial brain relapse in small cell lung carcinoma. However, the optimal radiation dose for EBI is unknown. 55 patients (31 with regional disease, 24 with extensive disease) without brain metastases were treated with a 4 drug chemotherapy program, (lomustine (CCNU), methotrexate, cyclophosphamide, vincristine) plus radiotherapy (R.T.), 3000 rad in 2 weeks to the primary chest lesion and were randomized to EBI or a control group. The EBI consisted of 2400 rad whole brain,more » midplane, in 8 fractions, 10 days (NSD = 1130 ret) given at the same time as the R.T. to the primary (3 weeks post-initial chemotherapy). Though all 54 evaluable patients received CCNU 50 mg/M/sup 2/q. 6 weeks, there were 5 initial brain relapses among 31 control patients (16%) vs none in the 23 EBI patients. The time at risk for recurrence was similar in the two groups, i.e. 31 weeks median in the EBI and 32 weeks in the no-EBI patients. Brain relapses occurred in 2/17 with limited disease and 3/14 with extensive disease. It appears that 2400 rad in 8 fractions is as effective for EBI as larger doses. Toxicity was limited to alopecia. Survival was not significantly affected by EBI, though there is a suggestion of improvement in the regional group.« less

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

PubMed

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.

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

PubMed Central

Highfield, Linda; Hartman, Marieke A.; Mullen, Patricia Dolan; 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. PMID:26587531

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

PubMed

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.

The EBI search engine: EBI search as a service—making biological data accessible for all

PubMed Central

Park, Young M.; Squizzato, Silvano; Buso, Nicola; Gur, Tamer

2017-01-01

Abstract We present an update of the EBI Search engine, an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities. The interconnectivity that exists between data resources at EMBL–EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types that include nucleotide and protein sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, as well as the life science literature. EBI Search provides a powerful RESTful API that enables its integration into third-party portals, thus providing ‘Search as a Service’ capabilities, which are the main topic of this article. PMID:28472374

Colorectal Cancer Control Program Grantees’ Use of Evidence-Based Interventions

PubMed Central

Hannon, Peggy A.; Maxwell, Annette E.; Escoffery, Cam; Vu, Thuy; Kohn, Marlana; Leeman, Jennifer; Carvalho, Michelle L.; Pfeiffer, Debbie J.; Dwyer, Andrea; Fernandez, Maria E.; Vernon, Sally W.; Liang, Lily; DeGroff, Amy

2015-01-01

Background Colorectal cancer (CRC) screening is recommended for adults aged 50–75 years, yet screening rates are low, especially among the uninsured. The CDC initiated the Colorectal Cancer Control Program (CRCCP) in 2009 with the goal of increasing CRC screening rates to 80% by 2014. A total of 29 grantees (states and tribal organizations) receive CRCCP funding to (1) screen uninsured adults and (2) promote CRC screening at the population level. Purpose CRCCP encourages grantees to use one or more of five evidence-based interventions (EBIs) recommended by the Guide to Community Preventive Services. The purpose of the study was to evaluate grantees’ EBI use. Methods A web-based survey was conducted in 2011 measuring grantees’ use of CRC screening EBIs and identifying their implementation partners. Data were analyzed in 2012. Results Twenty-eight grantees (97%) completed the survey. Most respondents (96%) used small media. Fewer used client reminders (75%); reduction of structural barriers (50%); provider reminders (32%); or provider assessment and feedback (50%). Provider-oriented EBIs were rated as harder to implement than client-oriented EBIs. Grantees partnered with several types of organizations to implement EBIs, many with county- or state-wide reach. Conclusions Almost all grantees implement EBIs to promote CRC screening, but the EBIs that may have the greatest impact with CRC screening are implemented by fewer grantees in the first 2 years of the CRCCP. PMID:24139779

Reducing Our Carbon Footprint: Converting Plants to Fuel (LBNL Science at the Theater)

ScienceCinema

Somerville, Chris [Univ. of California, Berkeley, CA (United States)

2018-05-23

Berkeley Lab's Chris Somerville is a leading authority on the structure and function of plant cell walls, which comprise most of the body mass of higher plants. He views the knowledge of cell wall structure and function as furthering the development of plants with improved usefulness: these plants are strong potential sources of renewable materials and biofuel feedstocks. His scientific expertise defines an ideal match of his interest - in the development of cellulosic and other solar-to-fuel science - with his recent appointment as Director of the Energy Biosciences Institute (EBI). With colleagues in biology, physical sciences, engineering, and environmental and the social sciences, he now leads the EBI multidisciplinary teams' research efforts to develop next-generation, carbon-neutral transportation fuels.

The Ensembl REST API: Ensembl Data for Any Language

PubMed Central

Yates, Andrew; Beal, Kathryn; Keenan, Stephen; McLaren, William; Pignatelli, Miguel; Ritchie, Graham R. S.; Ruffier, Magali; Taylor, Kieron; Vullo, Alessandro; Flicek, Paul

2015-01-01

Motivation: We present a Web service to access Ensembl data using Representational State Transfer (REST). The Ensembl REST server enables the easy retrieval of a wide range of Ensembl data by most programming languages, using standard formats such as JSON and FASTA while minimizing client work. We also introduce bindings to the popular Ensembl Variant Effect Predictor tool permitting large-scale programmatic variant analysis independent of any specific programming language. Availability and implementation: The Ensembl REST API can be accessed at http://rest.ensembl.org and source code is freely available under an Apache 2.0 license from http://github.com/Ensembl/ensembl-rest. Contact: ayates@ebi.ac.uk or flicek@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25236461

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

PubMed

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 population outcomes. Furthermore, this model demonstrates how ABMs may be leveraged to inform research design and assess the impact of EBI sustainability in practice.

Converting the Conducting Behavior of Graphene Oxides from n-Type to p-Type via Electron-Beam Irradiation.

PubMed

Mirzaei, Ali; Kwon, Yong Jung; Wu, Ping; Kim, Sang Sub; Kim, Hyoun Woo

2018-02-28

We studied the effects of electron-beam irradiation (EBI) on the structural and gas-sensing properties of graphene oxide (GO). To understand the effects of EBI on the structure and gas-sensing behavior of irradiated GO, the treated GO was compared with nonirradiated GO. Characterization results indicated an enhancement in the number of oxygen functional groups that occurs with EBI exposure at 100 kGy and then decreases with doses in the range of 100-500 kGy. Data from Raman spectra indicated that EBI could generate defects, and NO 2 -sensing results at room temperature showed a decreased NO 2 response after exposure to EBI at 100 kGy; further increasing the dose to 500 kGy resulted in p-type semiconducting conductivity. The conversion of GO from n-type to p-type via EBI is explained not only through the generation of holes but also the variation in the amount of residual functional groups, including carboxyl (COOH) and hydroxyl groups (C-OH). The obtained results suggest that EBI can be a useful tool to convert GO into a diverse range of sensing devices.

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

PubMed

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.

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

PubMed

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.

Moderate Effects of Same-Sex Legislation on Dependent Employer-Based Insurance Coverage among Sexual Minorities

PubMed Central

Tran, Linda Diem

2016-01-01

A difference-in-difference approach was used to compare the effects of same-sex domestic partnership, civil union, and marriage policies on same- and different-sex partners who could have benefitted from their partners’ employer-based insurance (EBI) coverage. Same-sex partners had 78% lower odds (ME=-21%) of having EBI compared to different-sex partners, adjusting for socioeconomic and health-related factors. Same-sex partners living in states that recognized same-sex marriage or domestic partnership had 89% greater odds of having EBI compared to those in states that did not recognize same-sex unions (ME=5%). The impact of same-sex legislation on increasing take-up of dependent EBI coverage among lesbians, gay men, and bisexual individuals (LGBs) was modest, and domestic partnership legislation was equally as effective as same-sex marriage in increasing same-sex partner EBI coverage. Extending dependent EBI coverage to same-sex partners can mitigate gaps in coverage for a segment of the LGB population but will not eliminate them. PMID:26762647

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

PubMed

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 http://cmapper.ewostech.net Readers can download the development manual from the website http://cmapper.ewostech.net/docs/cMapperDocumentation.pdf. Source Code is available at https://github.com/muhammadshoaib/cmapperContact:smahn@gachon.ac.krSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Predictive Toxicology: Current Status and Future Outlook (EBI ...

EPA Pesticide Factsheets

Slide presentation at the EBI-EMBL Industry Programme Workshop on Predictive Toxicology and the currently status of Computational Toxicology activities at the US EPA. Slide presentation at the EBI-EMBL Industry Programme Workshop on Predictive Toxicology and the currently status of Computational Toxicology activities at the US EPA.

The EBI search engine: EBI search as a service-making biological data accessible for all.

PubMed

Park, Young M; Squizzato, Silvano; Buso, Nicola; Gur, Tamer; Lopez, Rodrigo

2017-07-03

We present an update of the EBI Search engine, an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities. The interconnectivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types that include nucleotide and protein sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, as well as the life science literature. EBI Search provides a powerful RESTful API that enables its integration into third-party portals, thus providing 'Search as a Service' capabilities, which are the main topic of this article. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

PubMed

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.

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

ERIC Educational Resources Information Center

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…

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

PubMed

Tran, Linda Diem

2016-12-01

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

easyDAS: Automatic creation of DAS servers

PubMed Central

2011-01-01

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. PMID:21244646

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

PubMed Central

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

Early Brain Injury Associated with Systemic Inflammation After Subarachnoid Hemorrhage.

PubMed

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.

Extreme Algal Bloom Detection with MERIS

NASA Astrophysics Data System (ADS)

Amin, R.; Gilerson, A.; Gould, R.; Arnone, R.; Ahmed, S.

2009-05-01

Harmful Algal Blooms (HAB's) are a major concern all over the world due to their negative impacts on the marine environment, human health, and the economy. Their detection from space still remains a challenge particularly in turbid coastal waters. In this study we propose a simple reflectance band difference approach for use with Medium Resolution Imaging Spectrometer (MERIS) data to detect intense plankton blooms. For convenience we label this approach as the Extreme Bloom Index (EBI) which is defined as EBI = Rrs (709) - Rrs (665). Our initial analysis shows that this band difference approach has some advantages over the band ratio approaches, particularly in reducing errors due to imperfect atmospheric corrections. We also do a comparison between the proposed EBI technique and the Maximum Chlorophyll Index (MCI) Gower technique. Our preliminary result shows that both the EBI and MCI indeces detect intense plankton blooms, however, MCI is more vulnerable in highly scattering waters, giving more positive false alarms than EBI.

Adapting an evidence-based intervention for homeless women: engaging the community in shared decision-making.

PubMed

Cederbaum, Julie A; Song, Ahyoung; Hsu, Hsun-Ta; Tucker, Joan S; Wenzel, Suzanne L

2014-11-01

As interest grows in the diffusion of evidence-based interventions (EBIs), there is increasing concern about how to mitigate implementation challenges; this paper concerns adapting an EBI for homeless women. Complementing earlier focus groups with homeless women, homeless service providers (n = 32) were engaged in focus groups to assess capacity, needs, and barriers with implementation of EBIs. Deductive analyses of data led to the selection of four EBIs. Six consensus groups were then undertaken; three each with homeless women (n = 24) and homeless service providers (n = 21). The selected EBI was adapted and pretested with homeless women (n = 9) and service providers (n = 6). The structured consensus group process provided great utility and affirmed the expertise of homeless women and service providers as experts in their domain. Engaging providers in the selection process reduced the structural barriers within agencies as obstacles to diffusion.

Laboratory Directed Research and Development Program

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

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

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 onmore » 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.« less

Laboratory Directed Research and Development Program. Annual report

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

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

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 onmore » 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.« less

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

ERIC Educational Resources Information Center

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

2010-01-01

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

The European Bioinformatics Institute in 2017: data coordination and integration

PubMed Central

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

Electrical bioimpedance enabling prompt intervention in traumatic brain injury

NASA Astrophysics Data System (ADS)

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.

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

ERIC Educational Resources Information Center

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

2009-01-01

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

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

PubMed Central

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

Signaling Pathway in Early Brain Injury after Subarachnoid Hemorrhage: News Update.

PubMed

Ji, Chengyuan; Chen, Gang

2016-01-01

The annual incidence of subarachnoid hemorrhage (SAH) caused by intracranial aneurysm rupture is approximately 10.5/10 million people in China, making SAH the third most frequently occurring hemorrhage of the intracranial type after cerebral embolism and hypertensive intracerebral hemorrhage. SAH caused by ruptured aneurysm leads to a mortality rate as high as 67 %, and, because of the sudden onset of this disease, approximately 12-15 % of patients die before they can receive effective treatment. Early brain injury (EBI) is the brain damage occurring within the first 72 h after SAH. Two-thirds of mortality caused by SAH occurs within 48 h, mainly as a result of EBI. With the development of molecular biology and medicine microscopy techniques, various signaling pathways involved in EBI after SAH have been revealed. Understanding these signaling pathways may help clinicians treat EBI after SAH and improve long-term prognosis of SAH patients. This chapter summarizes several important signaling pathways implicated in EBI caused by SAH.

Portfolio Management

NASA Technical Reports Server (NTRS)

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

Decreased interleukin 35 and CD4+EBI3+ T cells in patients with active systemic lupus erythematosus.

PubMed

Ouyang, Han; Shi, Yong-Bing; Liu, Zhi-Chun; Wang, Zhi; Feng, Sheng; Kong, Shu-Min; Lu, Ying

2014-08-01

Interleukin 35 (IL-35) is likely to contribute to the development of autoimmune diseases, as the Epstein-Barr virus-induced gene protein 3 (EBI3) is the specificity subunit of IL-35. Nevertheless, until recently, no studies have evaluated its role in systemic lupus erythematosus (SLE) in humans. The objective of this study was to investigate the serum IL-35 level and the percentage of CD4EBI3 T cells in the peripheral blood of patients with SLE and explore the roles of double-positive T cells and IL-35 in the pathogenesis of SLE and the effects of glucocorticoid on these roles. Fifty-five hospitalized patients with SLE were recruited, and 20 volunteers were enrolled as healthy controls. Serum IL-35 levels were measured by enzyme-linked immunosorbent assay, and the percentage of CD4EBI3 T cells was analyzed by flow cytometry. The serum IL-35 level and the percentage of CD4EBI3 T cells were significantly decreased in patients with active SLE compared with healthy controls and patients with inactive SLE. The serum IL-35 level and the percentage of CD4EBI3 T cells were negatively correlated with the SLE disease activity index. The percentages of CD4EBI3 T cells and serum IL-35 levels in 10 untreated patients with active SLE were increased at days l, 3, and 7 after the treatment with methylprednisolone (0.8 mg·kg·d) compared with the percentages before the treatment. These results demonstrate that abnormalities in IL-35 and CD4EBI3 T cells may play important roles in the pathogenesis of SLE; the percentage of double-positive T cells and the level of IL-35 are parameters for the evaluation of SLE activity and severity.

Chondrocyte channel transcriptomics

PubMed Central

Lewis, Rebecca; May, Hannah; Mobasheri, Ali; Barrett-Jolley, Richard

2013-01-01

To date, a range of ion channels have been identified in chondrocytes using a number of different techniques, predominantly electrophysiological and/or biomolecular; each of these has its advantages and disadvantages. Here we aim to compare and contrast the data available from biophysical and microarray experiments. This letter analyses recent transcriptomics datasets from chondrocytes, accessible from the European Bioinformatics Institute (EBI). We discuss whether such bioinformatic analysis of microarray datasets can potentially accelerate identification and discovery of ion channels in chondrocytes. The ion channels which appear most frequently across these microarray datasets are discussed, along with their possible functions. We discuss whether functional or protein data exist which support the microarray data. A microarray experiment comparing gene expression in osteoarthritis and healthy cartilage is also discussed and we verify the differential expression of 2 of these genes, namely the genes encoding large calcium-activated potassium (BK) and aquaporin channels. PMID:23995703

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

PubMed Central

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

2015-01-01

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. PMID:25883136

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

PubMed Central

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

2017-01-01

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

Electrical bioimpedance and other techniques for gastric emptying and motility evaluation

PubMed Central

Huerta-Franco, María Raquel; Vargas-Luna, Miguel; Montes-Frausto, Juana Berenice; Flores-Hernández, Corina; Morales-Mata, Ismael

2012-01-01

The aim of this article is to identify non-invasive, inexpensive, highly sensitive and accurate techniques for evaluating and diagnosing gastric diseases. In the case of the stomach, there are highly sensitive and specific methods for assessing gastric motility and emptying (GME). However, these methods are invasive, expensive and/or not technically feasible for all clinicians and patients. We present a summary of the most relevant international information on non-invasive methods and techniques for clinically evaluating GME. We particularly emphasize the potential of gastric electrical bioimpedance (EBI). EBI was initially used mainly in gastric emptying studies and was essentially abandoned in favor of techniques such as electrogastrography and the gold standard, scintigraphy. The current research evaluating the utility of gastric EBI either combines this technique with other frequently used techniques or uses new methods for gastric EBI signal analysis. In this context, we discuss our results and those of other researchers who have worked with gastric EBI. In this review article, we present the following topics: (1) a description of the oldest methods and procedures for evaluating GME; (2) an explanation of the methods currently used to evaluate gastric activity; and (3) a perspective on the newest trends and techniques in clinical and research GME methods. We conclude that gastric EBI is a highly effective non-invasive, easy to use and inexpensive technique for assessing GME. PMID:22368782

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

PubMed Central

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

2016-01-01

ChEBI is a database and ontology containing information about chemical entities of biological interest. It currently includes over 46 000 entries, each of which is classified within the ontology and assigned multiple annotations including (where relevant) a chemical structure, database cross-references, synonyms and literature citations. All content is freely available and can be accessed online at http://www.ebi.ac.uk/chebi. In this update paper, we describe recent improvements and additions to the ChEBI offering. We have substantially extended our collection of endogenous metabolites for several organisms including human, mouse, Escherichia coli and yeast. Our front-end has also been reworked and updated, improving the user experience, removing our dependency on Java applets in favour of embedded JavaScript components and moving from a monthly release update to a ‘live’ website. Programmatic access has been improved by the introduction of a library, libChEBI, in Java, Python and Matlab. Furthermore, we have added two new tools, namely an analysis tool, BiNChE, and a query tool for the ontology, OntoQuery. PMID:26467479

The synthesis method for design of electron flow sources

NASA Astrophysics Data System (ADS)

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.

Electron beam induced etching of carbon nanotubes enhanced by secondary electrons in oxygen.

PubMed

Yoshida, Hideto; Tomita, Yuto; Soma, Kentaro; Takeda, Seiji

2017-05-12

Multi-walled carbon nanotubes (CNTs) are subjected to electron-beam-induced etching (EBIE) in oxygen. The EBIE process is observed in situ by environmental transmission electron microscopy. The partial pressure of oxygen (10 and 100 Pa), energy of the primary electrons (80 and 200 keV), and environment of the CNTs (suspended or supported on a silicon nitride membrane) are investigated as factors affecting the etching rate. The EBIE rate of CNTs was markedly promoted by the effects of secondary electrons that were emitted from a silicon nitride membrane under irradiation by primary electrons. Membrane supported CNTs can be cut by EBIE with a spatial accuracy better than 3 nm, and a nanogap of 2 nm can be successfully achieved between the ends of two suspended CNTs.

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

PubMed

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 describe a novel regulatory mechanism where Ebi3 dampens cardiac inflammation by modulating the overproduction of IFN-γ, the bona fide culprit of Chagas disease cardiomyopathy.

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

PubMed Central

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 describe a novel regulatory mechanism where Ebi3 dampens cardiac inflammation by modulating the overproduction of IFN-γ, the bona fide culprit of Chagas disease cardiomyopathy. PMID:29033934

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

NASA Astrophysics Data System (ADS)

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.

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

PubMed Central

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

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

PubMed

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

2017-01-04

The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation interface. These developments have improved the data release frequency by increasing automation of curation and providing scaling improvements. The range of available Catalog data has also been extended with structured ancestry and recruitment information added for all studies. The infrastructure improvements also support scaling for larger arrays, exome and sequencing studies, allowing the Catalog to adapt to the needs of evolving study design, genotyping technologies and user needs in the future. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Use of Evidence-Based Interventions and Implementation Strategies to Increase Colorectal Cancer Screening in Federally Qualified Health Centers.

PubMed

Adams, Swann Arp; Rohweder, Catherine L; Leeman, Jennifer; Friedman, Daniela B; Gizlice, Ziya; Vanderpool, Robin C; Askelson, Natoshia; Best, Alicia; Flocke, Susan A; Glanz, Karen; Ko, Linda K; Kegler, Michelle

2018-05-16

While colorectal cancer (CRC) screening rates have been increasing in the general population, rates are considerably lower in Federally Qualified Health Centers (FQHCs), which serve a large proportion of uninsured and medically vulnerable patients. Efforts to screen eligible patients must be accelerated if we are to reach the national screening goal of 80% by 2018 and beyond. To inform this work, we conducted a survey of key informants at FQHCs in eight states to determine which evidence-based interventions (EBIs) to promote CRC screening are currently being used, and which implementation strategies are being employed to ensure that the interventions are executed as intended. One hundred and forty-eight FQHCs were invited to participate in the study, and 56 completed surveys were received for a response rate of 38%. Results demonstrated that provider reminder and recall systems were the most commonly used EBIs (44.6%) while the most commonly used implementation strategy was the identification of barriers (84.0%). The mean number of EBIs that were fully implemented at the centers was 2.4 (range 0-7) out of seven. Almost one-quarter of respondents indicated that their FQHCs were not using any EBIs to increase CRC screening. Full implementation of EBIs was correlated with higher CRC screening rates. These findings identify gaps as well as the preferences and needs of FQHCs in selecting and implementing EBIs for CRC screening.

Comparison of dry-textile electrodes for electrical bioimpedance spectroscopy measurements

NASA Astrophysics Data System (ADS)

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

2010-04-01

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

Building a drug ontology based on RxNorm and other sources

PubMed Central

2013-01-01

Background 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. Results 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. Conclusions 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. PMID:24345026

Building a drug ontology based on RxNorm and other sources.

PubMed

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.

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

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

PubMed

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.

Selective intestinal decontamination with fluoroquinolones for the prevention of early bacterial infections after liver transplantation.

PubMed

San-Juan, Rafael; Aguado, Jose M; Lumbreras, Carlos; Fortun, Jesus; Len, Oscar; Munoz, Patricia; Montejo, Miguel; Moreno, Asunción; Cordero, Elisa; Blanes, Marino; Ramos, Antonio; Torre-Cisneros, Julian; López-Medrano, Francisco; Carratala, Jordi; Moreno, Enrique

2011-08-01

The role of selective intestinal decontamination with fluoroquinolones (FQ-SID) in the prevention of early bacterial infections (EBIs) in liver transplant recipients (LTRs) is unknown. We used the online database of the Spanish Network of Infection in Transplantation/Spanish Network for Research in Infectious Diseases, which prospectively analyzed 1010 LTRs from 12 Spanish hospitals from September 2003 to February 2005. We compared the incidence and etiology of EBIs (30 days after transplantation) in 415 LTRs from 4 centers that used FQ-SID (>7 days) and in 595 LTRs from 8 hospitals that did not use FQ-SID. A multivariate logistic regression analysis (including an adjustment for the transplant center factor) was performed to evaluate the potential protective factor of FQ-SID in the development of EBIs. We reported 266 EBI episodes in 252 LTRs (incidence = 24.9%). There were no differences in the incidence of EBIs between patients in the FQ-SID group and patients not in the FQ-SID group [109/415 (26.3%) versus 143/595 (24%), P = 0.9]. Although LTRs who received FQ-SID had a lower incidence of infections due to enteric bacteria (2.7% versus 6.5%, P = 0.007) and a higher incidence of infections due to nonfermenting gram-negative bacilli (6.6% versus 2.6%, P = 0.004), these findings could not be confirmed after an adjustment by the center factor in the multivariate models. We found no significant differences in the incidence of enterococcal infections (3.4% with FQ-SID versus 3.9% without FQ-SID, P = 0.5). Multivariate analysis did not confirm any protective effect of FQ-SID against the development of EBIs by enteric bacteria. In conclusion, FQ-SID does not reduce the incidence of EBIs in LTRs and could be withheld from this group of patients. Copyright © 2011 American Association for the Study of Liver Diseases.

Issues and Challenges in the Design of Culturally Adapted Evidence-Based Interventions

PubMed Central

Castro, Felipe González; Barrera, Manuel; Holleran Steiker, Lori K.

2014-01-01

This article examines issues and challenges in the design of cultural adaptations that are developed from an original evidence-based intervention (EBI). Recently emerging multistep frameworks or stage models are examined, as these can systematically guide the development of culturally adapted EBIs. Critical issues are also presented regarding whether and how such adaptations may be conducted, and empirical evidence is presented regarding the effectiveness of such cultural adaptations. Recent evidence suggests that these cultural adaptations are effective when applied with certain subcultural groups, although they are less effective when applied with other subcultural groups. Generally, current evidence regarding the effectiveness of cultural adaptations is promising but mixed. Further research is needed to obtain more definitive conclusions regarding the efficacy and effectiveness of culturally adapted EBIs. Directions for future research and recommendations are presented to guide the development of a new generation of culturally adapted EBIs. PMID:20192800

Update and expansion of the HIV/AIDS prevention program archive (HAPPA)

PubMed Central

Card, Josefina J.; Cunningham, Shayna D.; Newman, Emily N.; Golden, Rachel E.

2017-01-01

Established in 1996 with funding from CDC and NIH, the HIV/AIDS Prevention Program Archive (HAPPA) is now the biggest private sector collection of HIV-related evidence-based behavioral interventions (EBIs). Each EBI in HAPPA has been determined by a distinguished Scientist Expert Panel to have demonstrated efficacy in preventing HIV or its risk-related behaviors in the United States. The multimedia replications kits contain everything that a new site would need to implement an EBI such as a user guide that gives an overview of the program and the evidence of its effectiveness; a facilitator’s manual that gives step-by-step implementation protocols for each session; and session implementation materials referenced in the facilitator's manual such as slides, video clips, participant handouts, activity masters, checklists, and homework assignments for the next session. The program packages also contain evaluation materials such as surveys and questionnaires that were used in the original demonstration of effectiveness and that may be used to re-evaluate the program as implemented in a new setting. Recently, we have expanded HAPPA’s scope to include HIV EBIs developed globally and to include evidence-based structural interventions (effective in modifying the physical, social, cultural, political, economic, legal, and/or policy aspects of the HIV risk environment). This paper describes HAPPA’s procedures for identifying, selecting, acquiring and packaging HIV EBIs. It also provides comprehensive lists of evidence-based HIV behavioral and structural interventions and gives information on how to access EBI program packages for implementation in new settings. PMID:28781971

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

PubMed

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.

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

PubMed

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

2013-01-01

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

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

PubMed

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

2016-11-01

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

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

PubMed Central

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

2017-01-01

If evidence-based interventions (EBIs) are not sustained, investments are wasted and public health impact is limited. Leadership has been suggested as a key determinant of implementation and sustainment; however, little empirical work has examined this factor. This mixed-methods study framed using the Exploration, Preparation, Implementation, Sustainment (EPIS) conceptual framework examines leadership in both the outer service system context and inner organizational context in eleven system-wide implementations of the same EBI across two U.S. states and 87 counties. Quantitative data at the outer context (i.e., system) and inner context (i.e., team) levels demonstrated that leadership predicted future sustainment and differentiated between sites with full, partial, or no sustainment. In the outer context positive sustainment leadership was characterized as establishing a project’s mission and vision, early and continued planning for sustainment, realistic project plans, and having alternative strategies for project survival. Inner context frontline transformational leadership predicted sustainment while passive-avoidant leadership predicted non-sustainment. Qualitative results found that sustainment was associated with outer context leadership characterized by engagement in ongoing supportive EBI championing, marketing to stakeholders; persevering in these activities; taking action to institutionalize the EBI with funding, contracting, and system improvement plans; and fostering ongoing collaboration between stakeholders at state and county, and community stakeholder levels. For frontline leadership the most important activities included championing the EBI and providing practical support for service providers. There was both convergence and expansion that identified unique contributions of the quantitative and qualitative methods. Greater attention to leadership in both the outer system and inner organizational contexts is warranted to enhance EBI implementation and sustainment. PMID:27439504

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

PubMed Central

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

2014-01-01

Evidence-based interventions (EBIs) are used in public health to prevent HIV infection among youth and other groups. EBIs include core elements, features that are thought to be responsible for the efficacy of interventions. The authors evaluate experiences of organizations that adopted an HIV-prevention EBI, Focus on Kids (FOK), and their fidelity to the intervention’s eight core elements. A cross-sectional telephone survey was administered to 34 staff members from organizations that had previously implemented FOK. Questions assessed how the organization adhered to, adapted, dropped, or altered the intervention. None of the organizations implemented all eight core elements. This study underscores the importance for HIV intervention researchers to clearly identify and describe core elements. More effort is needed to reflect the constraints practitioners face in nonresearch settings. To ensure intervention effectiveness, additional research and technical assistance are needed to help organizations implement HIV prevention EBIs with fidelity. PMID:18445739

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

PubMed

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.

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

PubMed

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

2016-09-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

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

PubMed Central

Highfield, Linda; Hartman, Marieke A.; Bartholomew, L. Kay; Balihe, Philomene; Ausborn, Valerie A.

2015-01-01

Breast cancer mortality disparities continue, particularly for uninsured and minority women. A number of effective evidence-based interventions (EBIs) exist for addressing barriers to mammography screening; however, their uptake and use in community has been limited. Few cancer-specific studies have evaluated adapted EBIs in new contexts, and fewer still have considered implementation. This study sought to (1) evaluate the effectiveness of an adapted mammography EBI in improving appointment keeping in African American women and (2) describe processes of implementation in a new practice setting. We used the type 1 hybrid design to test effectiveness and implementation using a quasi-experimental design. Logistic regression and intent-to-treat analysis were used to evaluate mammography appointment attendance. The no-show rate was 44% (comparison) versus 19% (intervention). The adjusted odds of a woman in the intervention group attending her appointment were 3.88 (p < 0.001). The adjusted odds of a woman attending her appointment in the intent-to-treat analysis were 2.31 (p < 0.05). Adapted EBI effectiveness was 3.88 (adjusted OR) versus 2.10 (OR) for the original program, indicating enhanced program effect. A number of implementation barriers and facilitators were identified. Our findings support previous studies noting that sequentially measuring EBI efficacy and effectiveness, followed by implementation, may be missing important contextual information. PMID:26504790

Dynamic Pattern Formation in Electron-Beam-Induced Etching [Emergent formation of dynamic topographic patterns in electron beam induced etching

DOE PAGES

Martin, Aiden A.; Bahm, Alan; Bishop, James; ...

2015-12-15

Here, we report highly ordered topographic patterns that form on the surface of diamond, span multiple length scales, and have a symmetry controlled by the precursor gas species used in electron-beam-induced etching (EBIE). The pattern formation dynamics reveals an etch rate anisotropy and an electron energy transfer pathway that is overlooked by existing EBIE models. Therefore, we, modify established theory such that it explains our results and remains universally applicable to EBIE. Furthermore, the patterns can be exploited in controlled wetting, optical structuring, and other emerging applications that require nano- and microscale surface texturing of a wide band-gap material.

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

PubMed Central

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

2016-01-01

Sustainment of evidence-based interventions (EBIs) in human services depends on the inner context of community-based organizations (CBOs) that provide services and the outer context of their broader environment. Increasingly, public officials are experimenting with contracting models from for-profit industries to procure human services. In this case study, we conducted qualitative interviews with key government and CBO stakeholders to examine implementation of the Best Value-Performance Information Procurement System to contract for EBIs in a child welfare system. Findings suggest that stakeholder relationships may be compromised when procurement disregards local knowledge, communication, collaboration, and other factors supporting EBIs and public health initiatives. PMID:26386977

Is Personalized Learning the Future of School?

ERIC Educational Resources Information Center

Paz-Albo, Jesús

2017-01-01

This article describes an innovative teaching approach that can offer the changes needed for school improvement. When entering an Education: Basic and Interactive (EBI) classroom, one will see students focused on accomplishing self-guided tasks and eager to move on to the next challenge in their self-paced learning. The EBI Project described here…

The European Bioinformatics Institute's data resources: towards systems biology.

PubMed

Brooksbank, Catherine; Cameron, Graham; Thornton, Janet

2005-01-01

Genomic and post-genomic biological research has provided fine-grain insights into the molecular processes of life, but also threatens to drown biomedical researchers in data. Moreover, as new high-throughput technologies are developed, the types of data that are gathered en masse are diversifying. The need to collect, store and curate all this information in ways that allow its efficient retrieval and exploitation is greater than ever. The European Bioinformatics Institute's (EBI's) databases and tools have evolved to meet the changing needs of molecular biologists: since we last wrote about our services in the 2003 issue of Nucleic Acids Research, we have launched new databases covering protein-protein interactions (IntAct), pathways (Reactome) and small molecules (ChEBI). Our existing core databases have continued to evolve to meet the changing needs of biomedical researchers, and we have developed new data-access tools that help biologists to move intuitively through the different data types, thereby helping them to put the parts together to understand biology at the systems level. The EBI's data resources are all available on our website at http://www.ebi.ac.uk.

The European Bioinformatics Institute's data resources: towards systems biology

PubMed Central

Brooksbank, Catherine; Cameron, Graham; Thornton, Janet

2005-01-01

Genomic and post-genomic biological research has provided fine-grain insights into the molecular processes of life, but also threatens to drown biomedical researchers in data. Moreover, as new high-throughput technologies are developed, the types of data that are gathered en masse are diversifying. The need to collect, store and curate all this information in ways that allow its efficient retrieval and exploitation is greater than ever. The European Bioinformatics Institute's (EBI's) databases and tools have evolved to meet the changing needs of molecular biologists: since we last wrote about our services in the 2003 issue of Nucleic Acids Research, we have launched new databases covering protein–protein interactions (IntAct), pathways (Reactome) and small molecules (ChEBI). Our existing core databases have continued to evolve to meet the changing needs of biomedical researchers, and we have developed new data-access tools that help biologists to move intuitively through the different data types, thereby helping them to put the parts together to understand biology at the systems level. The EBI's data resources are all available on our website at http://www.ebi.ac.uk. PMID:15608238

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

PubMed

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.

Developing a Policy Flight Simulator to Facilitate the Adoption of an Evidence-Based Intervention

PubMed Central

Yu, Zhongyuan; Hirschman, Karen B.; Pepe, Kara; Pauly, Mark V.; Naylor, Mary D.; Rouse, William B.

2018-01-01

While the use of evidence-based interventions (EBIs) has been advocated by the medical research community for quite some time, uptake of these interventions by healthcare providers has been slow. One possible explanation is that it is challenging for providers to estimate impacts of a specific EBI on their particular organization. To address that concern, we developed and evaluated a type of simulation called a policy flight simulator to determine if it could improve the adoption decision about a specific EBI, the transitional care model (TCM). The TCM uses an advanced practice nurse-led model of care to transition older adults with multiple chronic conditions from a hospitalization to home. An evaluation by a National Advisory Committee, made up of senior representatives from various stakeholders in the U.S. healthcare system, found the policy flight simulator to be a useful tool that has the potential to better inform adoption decisions. This paper describes the simulation development effort and documents lessons learned that may be useful to the healthcare modeling community and those interested in using simulation to support decisions based on EBIs. PMID:29805921

DNA sequence chromatogram browsing using JAVA and CORBA.

PubMed

Parsons, J D; Buehler, E; Hillier, L

1999-03-01

DNA sequence chromatograms (traces) are the primary data source for all large-scale genomic and expressed sequence tags (ESTs) sequencing projects. Access to the sequencing trace assists many later analyses, for example contig assembly and polymorphism detection, but obtaining and using traces is problematic. Traces are not collected and published centrally, they are much larger than the base calls derived from them, and viewing them requires the interactivity of a local graphical client with local data. To provide efficient global access to DNA traces, we developed a client/server system based on flexible Java components integrated into other applications including an applet for use in a WWW browser and a stand-alone trace viewer. Client/server interaction is facilitated by CORBA middleware which provides a well-defined interface, a naming service, and location independence. [The software is packaged as a Jar file available from the following URL: http://www.ebi.ac.uk/jparsons. Links to working examples of the trace viewers can be found at http://corba.ebi.ac.uk/EST. All the Washington University mouse EST traces are available for browsing at the same URL.

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

PubMed Central

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

Implementing referral to an electronic alcohol brief advice website in primary healthcare: results from the ODHIN implementation trial

PubMed Central

Bendtsen, Preben; Müssener, Ulrika; Karlsson, Nadine; López-Pelayo, Hugo; Palacio-Vieira, Jorge; Colom, Joan; Gual, Antoni; Reynolds, Jillian; Wallace, Paul; Segura, Lidia; Anderson, Peter

2016-01-01

Objectives The objective of the present study was to explore whether the possibility of offering facilitated access to an alcohol electronic brief intervention (eBI) instead of delivering brief face-to-face advice increased the proportion of consulting adults who were screened and given brief advice. Design The study was a 12-week implementation study. Sixty primary healthcare units (PHCUs) in 5 jurisdictions (Catalonia, England, the Netherlands, Poland and Sweden) were asked to screen adults who attended the PHCU for risky drinking. Setting A total of 120 primary healthcare centres from 5 jurisdictions in Europe. Participants 746 individual providers (general practitioners, nurses or other professionals) participated in the study. Primary outcome Change in the proportion of patients screened and referred to eBI comparing a baseline 4-week preimplementation period with a 12-week implementation period. Results The possibility of referring patients to the eBI was not found to be associated with any increase in the proportion of patients screened. However, it was associated with an increase in the proportion of screen-positive patients receiving brief advice from 70% to 80% for the screen-positive sample as a whole (p<0.05), mainly driven by a significant increase in brief intervention rates in England from 87% to 96% (p<0.01). The study indicated that staff displayed a low level of engagement in this new technology. Staff continued to offer face-to-face advice to a larger proportion of patients (54%) than referral to eBI (38%). In addition, low engagement was seen among the referred patients; on average, 18% of the patients logged on to the website with a mean log-on rate across the different countries between 0.58% and 36.95%. Conclusions Referral to eBI takes nearly as much time as brief oral advice and might require more introduction and training before staff are comfortable with referring to eBI. Trial registration number NCT01501552; Post-results. PMID:27311902

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.

PubMed

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.

Validation of the Chinese Version of the Epistemic Beliefs Inventory Using Confirmatory Factor Analysis

ERIC Educational Resources Information Center

Wang, Xihui; Zhang, Zhidong; Zhang, Xiuying; Hou, Dadong

2013-01-01

The Epistemic Beliefs Inventory (EBI), as a theory-based and empirically validated instrument, was originally developed and widely used in the North American context. Through a strict translation procedure the authors translated the EBI into Chinese, and then administered it to 451 students in 7 universities in mainland China. The construct…

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

ERIC Educational Resources Information Center

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 Conceptualization, Integration, and Support of Evidence-Based Interventions in the Schools

ERIC Educational Resources Information Center

Becker, Kimberly D.; Domitrovich, Celene E.

2011-01-01

The studies in this issue break the mold of the traditional stage model of the development and testing of evidence-based interventions (EBIs) within the confines of highly controlled studies (Onken, Blaine, & Battjes, 1997). Although this approach has merits, the need for EBIs in school settings has outpaced their deployment. The authors of these…

Evidence Based Interventions: An Examination of Pre-Service Training, Professional Development, and Classroom Implementation

ERIC Educational Resources Information Center

Hoover, Kristin Nicole

2013-01-01

The purpose of the study was to examine the relationship between EBI training for special education teachers and their practice of classroom interventions for children with an autism spectrum disorder (ASD). Evaluating the usage of EBIs in the classroom is imperative because of the many obligations educators have to uphold federal compliances…

The Sophomore RA Experience: An Examination of Job Satisfaction, Turnover Intentions, and RA Self-Efficacy

ERIC Educational Resources Information Center

Brandt Brecheisen, Shannon M.

2014-01-01

The purpose of this national, quantitative study was to (1) provide psychometrics for the ACUHO-I/EBI RA Survey, a joint project between between Educational Benchmarking, Inc (EBI) and The Association of College and University Housing Officers--International (ACUHO-I), and (2) explore the sophomore resident assistant (RA) experience. This study…

The European Bioinformatics Institute's data resources 2014.

PubMed

Brooksbank, Catherine; Bergman, Mary Todd; Apweiler, Rolf; Birney, Ewan; Thornton, Janet

2014-01-01

Molecular Biology has been at the heart of the 'big data' revolution from its very beginning, and the need for access to biological data is a common thread running from the 1965 publication of Dayhoff's 'Atlas of Protein Sequence and Structure' through the Human Genome Project in the late 1990s and early 2000s to today's population-scale sequencing initiatives. The European Bioinformatics Institute (EMBL-EBI; http://www.ebi.ac.uk) is one of three organizations worldwide that provides free access to comprehensive, integrated molecular data sets. Here, we summarize the principles underpinning the development of these public resources and provide an overview of EMBL-EBI's database collection to complement the reviews of individual databases provided elsewhere in this issue.

The Role of Collaborations in Sustaining an Evidence-Based Intervention to Reduce Child Neglect

PubMed Central

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

2016-01-01

Child neglect is the most prevalent form of child maltreatment and represents 79.5% of open child-welfare cases. A recent study found the evidence-based intervention (EBI) SafeCare® (SC) to significantly reduce child neglect recidivism rates. To fully capitalize on the effectiveness of such EBIs, service systems must engage in successful implementation and sustainment; however, little is known regarding what factors influence EBI sustainment. Collaborations among stakeholders are suggested as a means for facilitating EBI implementation and sustainment. This study combines descriptive quantitative survey data with qualitative interview and focus group findings to examine the role of collaboration within the context of public-private partnerships in 11 child welfare systems implementing SC. Participants included administrators of government child welfare systems and community-based organizations, as well as supervisors, coaches, and home visitors of the SC program. Sites were classified as fully-, partially-, and non-sustaining based on implementation fidelity. One-way analysis of variance was used to examine differences in stakeholder reported Effective Collaboration scores across fully-sustaining, partially-sustaining, and non-sustaining sites. Qualitative transcripts were analyzed via open and focused coding to identify the commonality, diversity, and complexity of collaborations involved in implementing and sustaining SC. Fully-sustaining sites reported significantly greater levels of effective collaboration than non-sustaining sites. Key themes described by SC stakeholders included shared vision, building on existing relationships, academic support, problem solving and resource sharing, and maintaining collaborations over time. Both quantitative and qualitative results converge in highlighting the importance of effective collaboration in EBI sustainment in child welfare service systems. PMID:26712422

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

ERIC Educational Resources Information Center

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

2013-01-01

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

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

PubMed

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

2017-02-01

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

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

PubMed

Collins, Charles B; Sapiano, Tobey N

2016-10-01

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

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

PubMed

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.

Implementing referral to an electronic alcohol brief advice website in primary healthcare: results from the ODHIN implementation trial.

PubMed

Bendtsen, Preben; Müssener, Ulrika; Karlsson, Nadine; López-Pelayo, Hugo; Palacio-Vieira, Jorge; Colom, Joan; Gual, Antoni; Reynolds, Jillian; Wallace, Paul; Segura, Lidia; Anderson, Peter

2016-06-16

The objective of the present study was to explore whether the possibility of offering facilitated access to an alcohol electronic brief intervention (eBI) instead of delivering brief face-to-face advice increased the proportion of consulting adults who were screened and given brief advice. The study was a 12-week implementation study. Sixty primary healthcare units (PHCUs) in 5 jurisdictions (Catalonia, England, the Netherlands, Poland and Sweden) were asked to screen adults who attended the PHCU for risky drinking. A total of 120 primary healthcare centres from 5 jurisdictions in Europe. 746 individual providers (general practitioners, nurses or other professionals) participated in the study. Change in the proportion of patients screened and referred to eBI comparing a baseline 4-week preimplementation period with a 12-week implementation period. The possibility of referring patients to the eBI was not found to be associated with any increase in the proportion of patients screened. However, it was associated with an increase in the proportion of screen-positive patients receiving brief advice from 70% to 80% for the screen-positive sample as a whole (p<0.05), mainly driven by a significant increase in brief intervention rates in England from 87% to 96% (p<0.01). The study indicated that staff displayed a low level of engagement in this new technology. Staff continued to offer face-to-face advice to a larger proportion of patients (54%) than referral to eBI (38%). In addition, low engagement was seen among the referred patients; on average, 18% of the patients logged on to the website with a mean log-on rate across the different countries between 0.58% and 36.95%. Referral to eBI takes nearly as much time as brief oral advice and might require more introduction and training before staff are comfortable with referring to eBI. NCT01501552; Post-results. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

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

PubMed

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.

EBI1/CCR7 is a new member of dendritic cell chemokine receptor that is up-regulated upon maturation.

PubMed

Yanagihara, S; Komura, E; Nagafune, J; Watarai, H; Yamaguchi, Y

1998-09-15

Dendritic cells (DC) that are stimulated with inflammatory mediators can maturate and migrate from nonlymphoid tissues to lymphoid organs to initiate T cell-mediated immune responses. This migratory step is closely related to the maturation of the DC. In an attempt to identify chemokine receptors that might influence migration and are selectively expressed in mature DC, we have discovered that the chemokine receptor, EBI1/CCR7, is strikingly up-regulated upon maturation in three distinct culture systems: 1) mouse bone marrow-derived DC, 2) mouse epidermal Langerhans cells, and 3) human monocyte-derived DC. The EBI1/CCR7 expressed in mature DC is functional because ELC/MIP-3beta, recently identified as a ligand of EBI1/CCR7, induces a rise in intracellular free calcium concentrations and directional migration of human monocyte-derived mature DC (HLA-DRhigh, CD1a(low), CD14-, CD25+, CD83+, and CD86high) in a dose-dependent manner, but not of immature DC (HLA-DRlow, CD1a(high), CD14-, CD25-, CD83-, and CD86-). In contrast, macrophage inflammatory protein-1alpha (MIP-1alpha), monocyte chemotactic protein-3 (MCP-3), and RANTES are active on immature DC but not on mature DC. Thus, it seems likely that MIP-1alpha, MCP-3, and RANTES can mediate the migration of immature DC located in peripheral sites, whereas ELC/MIP-3beta can direct the migration of Ag-carrying DC from peripheral inflammatory sites, where DC are stimulated to up-regulate the expression of EBI1/CCR7, to lymphoid organs. It is postulated that different chemokines and chemokine receptors are involved in DC migration in vivo, depending on the maturation state of DC.

Wearable Vector Electrical Bioimpedance System to Assess Knee Joint Health

PubMed Central

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

2017-01-01

Objective We designed and validated a portable electrical bioimpedance (EBI) system to quantify knee joint health. Methods Five separate experiments were performed to demonstrate the: (1) ability of the EBI system to assess knee injury and recovery; (2) inter-day 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; (5) use of the system with dry electrodes integrated to a wearable knee wrap. Results (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<0.05); the absolute difference in R decreased significantly (p<0.05) in injured subjects following rehabilitation. (2) The average inter-day variability (standard deviation) of the absolute difference in knee R was 2.5Ω, and for X was, 1.2 Ω. (3) Local heating/cooling resulted in a significant decrease/increase in knee R (p<0.01). (4) The proposed subject position detection algorithm achieved 97.4% leave-one subject out cross-validated accuracy and 98.2% precision in detecting when the subject is in the correct position to take measurements. (5) Linear regression between the knee R and X measured using the wet electrodes and the designed wearable knee wrap were highly correlated (r2 = 0.8 and 0.9, respectively). Conclusion This work demonstrates the use of wearable EBI measurements in monitoring knee joint health. Significance The proposed wearable system has the potential for assessing knee joint health outside the clinic/lab and help guide rehabilitation. PMID:28026745

Wearable Vector Electrical Bioimpedance System to Assess Knee Joint Health.

PubMed

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 < 0.05); the absolute difference in R decreased significantly (p < 0.05) in injured subjects following rehabilitation. 2) The average interday variability (standard deviation) of the absolute difference in 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 < 0.01). 4) The proposed subject position detection algorithm achieved 97.4% leave-one subject out cross-validated accuracy and 98.2% precision in detecting when the subject is in the correct position to take measurements. 5) Linear regression between the 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.

Deterministic Nanopatterning of Diamond Using Electron Beams.

PubMed

Bishop, James; Fronzi, Marco; Elbadawi, Christopher; Nikam, Vikram; Pritchard, Joshua; Fröch, Johannes E; Duong, Ngoc My Hanh; Ford, Michael J; Aharonovich, Igor; Lobo, Charlene J; Toth, Milos

2018-03-27

Diamond is an ideal material for a broad range of current and emerging applications in tribology, quantum photonics, high-power electronics, and sensing. However, top-down processing is very challenging due to its extreme chemical and physical properties. Gas-mediated electron beam-induced etching (EBIE) has recently emerged as a minimally invasive, facile means to dry etch and pattern diamond at the nanoscale using oxidizing precursor gases such as O 2 and H 2 O. Here we explain the roles of oxygen and hydrogen in the etch process and show that oxygen gives rise to rapid, isotropic etching, while the addition of hydrogen gives rise to anisotropic etching and the formation of topographic surface patterns. We identify the etch reaction pathways and show that the anisotropy is caused by preferential passivation of specific crystal planes. The anisotropy can be controlled by the partial pressure of hydrogen and by using a remote RF plasma source to radicalize the precursor gas. It can be used to manipulate the geometries of topographic surface patterns as well as nano- and microstructures fabricated by EBIE. Our findings constitute a comprehensive explanation of the anisotropic etch process and advance present understanding of electron-surface interactions.

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

PubMed

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.

Analysis Tool Web Services from the EMBL-EBI.

PubMed

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.

Analysis Tool Web Services from the EMBL-EBI

PubMed Central

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

2013-01-01

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. PMID:23671338

Possible Role of Inflammation and Galectin-3 in Brain Injury after Subarachnoid Hemorrhage

PubMed Central

2018-01-01

Aneurysmal subarachnoid hemorrhage (SAH) is known as one of the most devastating diseases in the central nervous system. In the past few decades, research on SAH has focused on cerebral vasospasm to prevent post-SAH delayed cerebral ischemia (DCI) and to improve outcomes. However, increasing evidence has suggested that early brain injury (EBI) is an important mechanism contributing to DCI, cerebral vasospasm as well as poor outcomes. Though the mechanism of EBI is very complex, inflammation is thought to play a pivotal role in EBI. Galectin-3 is a unique chimera type in the galectin family characterized by its β-galactoside-binding lectin, which mediates various pathologies, such as fibrosis, cell adhesion, and inflammation. Recently, two clinical studies revealed galectin-3 to be a possible prognostic biomarker in SAH patients. In addition, our recent report suggested that higher acute-stage plasma galectin-3 levels correlated with subsequent development of delayed cerebral infarction that was not associated with vasospasm in SAH patients. We review the possible role and molecular mechanisms of inflammation as well as galectin-3 in brain injuries, especially focusing on EBI after SAH, and discuss galectin-3 as a potential new therapeutic or research target in post-SAH brain injuries. PMID:29414883

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

PubMed

Hao, Shuangying; Song, Chuanhui; Shang, Longcheng; Yu, Jiang; Qiao, Tong; Li, Kuanyu

2016-03-10

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.

Water Quality Vocabulary Development and Deployment

NASA Astrophysics Data System (ADS)

Simons, B. A.; Yu, J.; Cox, S. J.

2013-12-01

Semantic descriptions of observed properties and associated units of measure are fundamental to understanding of environmental observations, including groundwater, surface water and marine water quality. Semantic descriptions can be captured in machine-readable ontologies and vocabularies, thus providing support for the annotation of observation values from the disparate data sources with appropriate and accurate metadata, which is critical for achieving semantic interoperability. However, current stand-alone water quality vocabularies provide limited support for cross-system comparisons or data fusion. To enhance semantic interoperability, the alignment of water-quality properties with definitions of chemical entities and units of measure in existing widely-used vocabularies is required. Modern ontologies and vocabularies are expressed, organized and deployed using Semantic Web technologies. We developed an ontology for observed properties (i.e. a model for expressing appropriate controlled vocabularies) which extends the NASA/TopQuadrant QUDT ontology for Unit and QuantityKind with two additional classes and two properties (see accompanying paper by Cox, Simons and Yu). We use our ontology to populate the Water Quality vocabulary with a set of individuals of each of the four key classes (and their subclasses), and add appropriate relationships between these individuals. This ontology is aligned with other relevant stand-alone Water Quality vocabularies and domain ontologies. Developing the Water Quality vocabulary involved two main steps. First, the Water Quality vocabulary was populated with individuals of the ObservedProperty class, which was determined from a census of existing datasets and services. Each ObservedProperty individual relates to other individuals of Unit and QuantityKind (taken from QUDT where possible), and to IdentifiedObject individuals. As a large fraction of observed water quality data are classified by the chemical substance involved, the 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

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

PubMed

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

2013-06-01

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

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

PubMed Central

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

2016-01-01

EBI metagenomics (https://www.ebi.ac.uk/metagenomics/) is a freely available hub for the analysis and archiving of metagenomic and metatranscriptomic data. Over the last 2 years, the resource has undergone rapid growth, with an increase of over five-fold in the number of processed samples and consequently represents one of the largest resources of analysed shotgun metagenomes. Here, we report the status of the resource in 2016 and give an overview of new developments. In particular, we describe updates to data content, a complete overhaul of the analysis pipeline, streamlining of data presentation via the website and the development of a new web based tool to compare functional analyses of sequence runs within a study. We also highlight two of the higher profile projects that have been analysed using the resource in the last year: the oceanographic projects Ocean Sampling Day and Tara Oceans. PMID:26582919

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

PubMed

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.

Inhibition of mammalian target of rapamycin attenuates early brain injury through modulating microglial polarization after experimental subarachnoid hemorrhage in rats.

PubMed

You, Wanchun; Wang, Zhong; Li, Haiying; Shen, Haitao; Xu, Xiang; Jia, Genlai; Chen, Gang

2016-08-15

Here, we aimed to study the role and underlying mechanism of mTOR in early brain injury (EBI) after subarachnoid hemorrhage (SAH). Experiment 1, the time course of mTOR activation in the cortex following SAH. Experiment 2, the role of mTOR in SAH-induced EBI. Adult SD rats were divided into four groups: sham group (n=18), SAH+vehicle group (n=18), SAH+rapamycin group (n=18), SAH+AZD8055 group (n=18). Experiment 3, we incubated enriched microglia with OxyHb. Rapamycin and AZD8055 were also used to demonstrate the mTOR's role on microglial polarization in vitro. The phosphorylation levels of mTOR and its substrates were significantly increased and peaked at 24h after SAH. Rapamycin or AZD8055 markedly decreased the phosphorylation levels of mTOR and its substrates and the activation of microglia in vivo, and promoted the microglial polarization from M1 phenotype to M2 phenotype. In addition, administration of rapamycin and AZD8055 following SAH significantly ameliorated EBI, including neuronal apoptosis, neuronal necrosis, brain edema and blood-brain barrier permeability. Our findings suggested that the rapamycin and AZD8055 could attenuate the development of EBI in this SAH model, possibly through inhibiting the activation of microglia by mTOR pathway. Copyright © 2016 Elsevier B.V. All rights reserved.

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

PubMed

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.

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

PubMed Central

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

Non-redundant patent sequence databases with value-added annotations at two levels

PubMed Central

Li, Weizhong; McWilliam, Hamish; de la Torre, Ana Richart; Grodowski, Adam; Benediktovich, Irina; Goujon, Mickael; Nauche, Stephane; Lopez, Rodrigo

2010-01-01

The European Bioinformatics Institute (EMBL-EBI) provides public access to patent data, including abstracts, chemical compounds and sequences. Sequences can appear multiple times due to the filing of the same invention with multiple patent offices, or the use of the same sequence by different inventors in different contexts. Information relating to the source invention may be incomplete, and biological information available in patent documents elsewhere may not be reflected in the annotation of the sequence. Search and analysis of these data have become increasingly challenging for both the scientific and intellectual-property communities. Here, we report a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents. The databases were created at two levels by the use of sequence MD5 checksums. Sequences within a level-1 cluster are 100% identical over their whole length. Level-2 clusters were defined by sub-grouping level-1 clusters based on patent family information. Value-added annotations, such as publication number corrections, earliest publication dates and feature collations, significantly enhance the quality of the data, allowing for better tracking and cross-referencing. The databases are available format: http://www.ebi.ac.uk/patentdata/nr/. PMID:19884134

Non-redundant patent sequence databases with value-added annotations at two levels.

PubMed

Li, Weizhong; McWilliam, Hamish; de la Torre, Ana Richart; Grodowski, Adam; Benediktovich, Irina; Goujon, Mickael; Nauche, Stephane; Lopez, Rodrigo

2010-01-01

The European Bioinformatics Institute (EMBL-EBI) provides public access to patent data, including abstracts, chemical compounds and sequences. Sequences can appear multiple times due to the filing of the same invention with multiple patent offices, or the use of the same sequence by different inventors in different contexts. Information relating to the source invention may be incomplete, and biological information available in patent documents elsewhere may not be reflected in the annotation of the sequence. Search and analysis of these data have become increasingly challenging for both the scientific and intellectual-property communities. Here, we report a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents. The databases were created at two levels by the use of sequence MD5 checksums. Sequences within a level-1 cluster are 100% identical over their whole length. Level-2 clusters were defined by sub-grouping level-1 clusters based on patent family information. Value-added annotations, such as publication number corrections, earliest publication dates and feature collations, significantly enhance the quality of the data, allowing for better tracking and cross-referencing. The databases are available format: http://www.ebi.ac.uk/patentdata/nr/.

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

PubMed

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.

Capability for change at community health centers serving Asian Pacific Islanders: an exploratory study of a cancer screening evidence-based intervention.

PubMed

Sohng, Hee Yon; Kuniyuki, Alan; Edelson, Jane; Weir, Rosy Chang; Song, Hui; Tu, Shin-Ping

2013-01-01

Understanding and enhancing change capabilities, including Practice Adaptive Reserve (PAR), of Community Health Centers (CHCs) may mitigate cancer-related health disparities. Using stratified random sampling, we recruited 232 staff from seven CHCs serving Asian Pacific Islander communities to complete a self-administered survey. We performed multilevel regression analyses to examine PAR composite scores by CHC, position type, and number of years worked at their clinic. The mean PAR score was 0.7 (s.d. 0.14). Higher scores were associated with a greater perceived likelihood that clinic staff would participate in an evidence-based intervention (EBI). Constructs such as communication, clinic flow, sensemaking, change valence, and resource availability were positively associated with EBI implementation or trended toward significance. PAR scores are positively associated with perceived likelihood of clinic staff participation in cancer screening EBI. Future research is needed to determine PAR levels most conducive to implementing change and to developing interventions that enhance Adaptive Reserve.

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

NASA Astrophysics Data System (ADS)

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

2013-04-01

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

Health Ministry and Activities in African American Faith-Based Organizations: A Qualitative Examination of Facilitators, Barriers, and Use of Technology.

PubMed

Holt, Cheryl L; Graham-Phillips, Anita L; Daniel Mullins, C; Slade, Jimmie L; Savoy, Alma; Carter, Roxanne

2017-01-01

African American faith-based organizations (FBOs) play an important role in addressing health disparities. Increasingly, churches offer health fairs, screenings, or education through health ministries. However, little is known about linking these organizations with evidence-based interventions (EBIs) developed by research. This study explored 1) factors that facilitate or impede health ministry activities, including the adoption of EBIs, and 2) opportunities to use technology to support/enhance the capacity of FBOs to sustain health-related activities. We conducted 18 key informant interviews with African American pastors and FBO leaders and six focus groups with members. A popular health ministry strategy was distribution of print materials. There was limited awareness of EBIs and how to access them. Challenges included maintaining qualified volunteers, financial resources, and technical assistance needs. Participants used technology and social media but older adults did so less often. Findings have implications for dissemination/implementation research in FBOs, in relation to the translational continuum.

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

PubMed

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

2015-09-01

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

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

PubMed

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.

Gene Ontology annotations at SGD: new data sources and annotation methods

PubMed Central

Hong, Eurie L.; Balakrishnan, Rama; Dong, Qing; Christie, Karen R.; Park, Julie; Binkley, Gail; Costanzo, Maria C.; Dwight, Selina S.; Engel, Stacia R.; Fisk, Dianna G.; Hirschman, Jodi E.; Hitz, Benjamin C.; Krieger, Cynthia J.; Livstone, Michael S.; Miyasato, Stuart R.; Nash, Robert S.; Oughtred, Rose; Skrzypek, Marek S.; Weng, Shuai; Wong, Edith D.; Zhu, Kathy K.; Dolinski, Kara; Botstein, David; Cherry, J. Michael

2008-01-01

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature. Therefore, GO annotations available at SGD now include high-throughput data as well as computational predictions provided by the GO Annotation Project (GOA UniProt; http://www.ebi.ac.uk/GOA/). Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods. In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current. PMID:17982175

I. Direct observation of zirconocene-catalyzed alkene polymerization via NMR and the role of an aluminum alkyl during polymerization. II. Design and evaluation of an online nanoscience course for teachers

NASA Astrophysics Data System (ADS)

Tomasik, Janice Hall

The plastics industry has been revolutionalized by development of group 4 metallocene polymerization catalysts. These catalysts have higher activities and stereoselectivities than traditional heterogeneous Ziegler-Natta polymerization catalysts, and produce polymers with narrower molecular weight distributions and with better control of the polymer stereochemistry. The reaction kinetics of catalytic alkene polymerizations are complicated and difficult to resolve macroscopically. To overcome these difficulties, research has used NMR spectroscopy to directly observe catalytic reaction intermediates; many advances in our understanding of the complex mechanisms behind these polymerization reactions have resulted. In this work, the direct observation of alkene insertion into zirconocene-polymeryls via NMR spectroscopy is presented. Alkenes studied are 3-methylpentene, styrene, and 1,4-pentadiene. Kinetic measurements are reported for the polymerization of 3-methylpentene by rac-(EBI)Zr(Me)(MeB(C6F 5)3) (EBI = C2H4(1-indenyl)2) and rac-(EBI)Zr(polyhexenyl)(MeB(C6F5) 3). Also presented are NMR spectroscopic characterizations of rac-(EBI)Zr(styrenyl)(MeB(C6F5)3) and rac-(EBI)Zr(1,4-pentadienyl)(MeB(C6F 5)3). In addition, NMR spectroscopy is used to directly monitor the behavior of an aluminum alkyl during the polymerization of 1-hexene by rac -(EBI)2Zr(Me)(MeB(C6F5)3). The rates of polymerization are not inhibited by Al(iBu) 2(BHT), Al(Me)(BHT)2, or Al(iBu)3 (BHT = 2,6-di- tert-butyl-4-methylphenyl). Detailed measurement of polymerization rate and catalyst speciation demonstrate that BHT modified aluminum alkyls protect active sites from decomposition in the presence of protic impurities such as methanol. Also presented in this work is the design and evaluation of an online course for teachers about nanoscience. Nanotechnology is an important emerging field that is estimated to need about 2 million workers worldwide by 2015. Therefore the educational system is being encouraged to incorporate major nanoscience concepts into curricula. In order to facilitate the integration of nanoscience, an online professional development course for teachers has been developed and offered at the University of Wisconsin-Madison. Evaluation results from the first three versions of the course indicate the online learning environment was very close to ideal. Comparisons of pre-instruction to post-instruction quiz responses indicate significant learning gains by participants. Importantly, survey results show the online course helped teachers to successfully incorporate nanoscience into their curricula.

Improving the delivery of brief interventions for heavy drinking in primary health care: outcome results of the Optimizing Delivery of Health Care Intervention (ODHIN) five-country cluster randomized factorial trial.

PubMed

Anderson, Peter; Bendtsen, Preben; Spak, Fredrik; Reynolds, Jillian; Drummond, Colin; Segura, Lidia; Keurhorst, Myrna N; Palacio-Vieira, Jorge; Wojnar, Marcin; Parkinson, Kathryn; Colom, Joan; Kłoda, Karolina; Deluca, Paolo; Baena, Begoña; Newbury-Birch, Dorothy; Wallace, Paul; Heinen, Maud; Wolstenholme, Amy; van Steenkiste, Ben; Mierzecki, Artur; Okulicz-Kozaryn, Katarzyna; Ronda, Gaby; Kaner, Eileen; Laurant, Miranda G H; Coulton, Simon; Gual, Toni

2016-11-01

To test if training and support, financial reimbursement and option of referring screen-positive patients to an internet-based method of giving advice (eBI) can increase primary health-care providers' delivery of Alcohol Use Disorders Identification Test (AUDIT)-C-based screening and advice to heavy drinkers. Cluster randomized factorial trial with 12-week implementation and measurement period. Primary health-care units (PHCU) in different locations throughout Catalonia, England, the Netherlands, Poland and Sweden. A total of 120 PHCU, 24 in each of Catalonia, England, the Netherlands, Poland and Sweden. PHCUs were randomized to one of eight groups: care as usual, training and support (TS), financial reimbursement (FR) and eBI; paired combinations of TS, FR and eBI, and all of FR, TS and eBI. The primary outcome measure was the proportion of eligible adult (age 18+ years) patients screened during a 12-week implementation period. Secondary outcome measures were proportion of screen-positive patients advised; and proportion of consulting adult patients given an intervention (screening and advice to screen-positives) during the same 12-week implementation period. During a 4-week baseline measurement period, the proportion of consulting adult patients who were screened for their alcohol consumption was 0.059 per PHCU (95% CI 0.034 to 0.084). Based on the factorial design, the ratio of the logged proportion screened during the 12-week implementation period was 1.48 (95% CI = 1.13-1.95) in PHCU that received TS versus PHCU that did not receive TS; for FR, the ratio was 2.00 (95% CI = 1.56-2.56). The option of referral to eBI did not lead to a higher proportion of patients screened. The ratio for TS plus FR was 2.34 (95% CI = 1.77-3.10), and the ratio for TS plus FR plus eBI was1.68 (95% CI = 1.11-2.53). Providing primary health-care units with training, support and financial reimbursement for delivering Alcohol Use Disorders Identification Test-C-based screening and advice to heavy drinkers increases screening for alcohol consumption. Providing primary health-care units with the option of referring screen-positive patients to an internet-based method of giving advice does not appear to increase screening for alcohol consumption. © 2016 Society for the Study of Addiction.

Using EMBL-EBI services via Web interface and programmatically via Web Services

PubMed Central

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

2015-01-01

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. PMID:25501941

Facilitators and barriers to effective scale-up of an evidence-based multilevel HIV prevention intervention.

PubMed

Kegeles, Susan M; Rebchook, Gregory; Tebbetts, Scott; Arnold, Emily

2015-04-17

Since the scale-up of HIV/AIDS prevention evidence-based interventions (EBIs) has not been simple, it is important to examine processes that occur in the translation of the EBIs into practice that affect successful implementation. The goal of this paper is to examine facilitators and barriers to effective implementation that arose among 72 community-based organizations as they moved into practice a multilevel HIV prevention intervention EBI, the Mpowerment Project, for young gay and bisexual men. CBOs that were implementing the Mpowerment Project participated in this study and were assessed at baseline, and 6-months, 1 year, and 2 years post-baseline. Semi-structured telephone interviews were conducted separately with individuals at each CBO. Study data came from 647 semi-structured interviews and extensive notes and commentaries from technical assistance providers. Framework Analysis guided the analytic process. Barriers and facilitators to implementation was the overarching thematic framework used across all the cases in our analysis. Thirteen themes emerged regarding factors that influence the successful implementation of the MP. These were organized into three overarching themes: HIV Prevention System Factors, Community Factors, and Intervention Factors. The entire HIV Prevention System, including coordinators, supervisors, executive directors, funders, and national HIV prevention policies, all influenced implementation success. Other Prevention System Factors that affected the effective translation of the EBI into practice include Knowledge About Intervention, Belief in the Efficacy of the Intervention, Desire to Change Existing Prevention Approach, Planning for Intervention Before Implementation, Accountability, Appropriateness of Individuals for Coordinator Positions, Evaluation of Intervention, and Organizational Stability. Community Factors included Geography and Sociopolitical Climate. Intervention Factors included Intervention Characteristics and Adaptation Issues. The entire ecological system in which an EBI occurs affects implementation. It is imperative to focus capacity-building efforts on getting individuals at different levels of the HIV Prevention System into alignment regarding understanding and believing in the program's goals and methods. For a Prevention Support System to be maximally useful, it must address facilitators or barriers to implementation, address the right people, and use modalities to convey information that are acceptable for users of the system.

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

PubMed Central

2012-01-01

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 research. These preliminary results help fill this gap by describing the reliability and measurement properties of a theory-based tool; the short, user-friendly instrument may be useful to researchers and practitioners seeking to assess organizational readiness for EBIs across a variety of chronic disease prevention programs and settings. PMID:22800294

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

PubMed

Stamatakis, Katherine A; McQueen, Amy; Filler, Carl; Boland, Elizabeth; Dreisinger, Mariah; Brownson, Ross C; Luke, Douglas A

2012-07-16

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. 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. 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. The lack of adequate measurement tools hinders progress in dissemination and implementation research. These preliminary results help fill this gap by describing the reliability and measurement properties of a theory-based tool; the short, user-friendly instrument may be useful to researchers and practitioners seeking to assess organizational readiness for EBIs across a variety of chronic disease prevention programs and settings.

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

PubMed Central

2016-01-01

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

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

PubMed

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.

Non-invasive method for the aortic blood pressure waveform estimation using the measured radial EBI

NASA Astrophysics Data System (ADS)

Krivoshei, Andrei; Lamp, Jürgen; Min, Mart; Uuetoa, Tiina; Uuetoa, Hasso; Annus, Paul

2013-04-01

The paper presents a method for the Central Aortic Pressure (CAP) waveform estimation from the measured radial Electrical Bio-Impedance (EBI). The method proposed here is a non-invasive and health-safe approach to estimate the cardiovascular system parameters, such as the Augmentation Index (AI). Reconstruction of the CAP curve from the EBI data is provided by spectral domain transfer functions (TF), found on the bases of data analysis. Clinical experiments were carried out on 30 patients in the Center of Cardiology of East-Tallinn Central Hospital during coronary angiography on patients in age of 43 to 80 years. The quality and reliability of the method was tested by comparing the evaluated augmentation indices obtained from the invasively measured CAP data and from the reconstructed curve. The correlation coefficient r = 0.89 was calculated in the range of AICAP values from 5 to 28. Comparing to the traditional tonometry based method, the developed one is more convenient to use and it allows long-term monitoring of the AI, what is not possible with tonometry probes.

Modulation of inflammation by interleukin-27

PubMed Central

Bosmann, Markus; Ward, Peter A.

2013-01-01

A growing body of evidence suggests an essential role of the heterodimeric cytokine, IL-27, for regulating immunity. IL-27 is composed of two subunits (p28 and EBI3) and is classified as a member of the IL-12 family of cytokines. APCs have been recognized as a major cellular source of IL-27 following activation with microbial products or IFNs (types I and II). In this review, we describe the current knowledge of the implications of IL-27 during the pathogenesis of infectious and autoimmune diseases. Experimental studies have used genetically targeted IL-27RA−/− mice, EBI3−/− mice, and p28−/− mice or involved study designs with administration of bioengineered IL-27/IL-27RA homologs. Whereas many reports have described that IL-27 suppresses inflammation, we also review the current literature, suggesting promotion of inflammation by IL-27 in some settings. Recent advances have also been made in understanding the cross-talk of cleavage products of the complement system with IL-27-mediated immune responses. Additional data on IL-27 have been obtained recently by observational studies in human patients with acute and chronic inflammatory diseases. Collectively, the findings from the past decade identify IL-27 as a critical immunoregulatory cytokine, especially for T cells, whereas some controversy is fueled by results challenging the view of IL-27 as a classical silencer of inflammation. PMID:23904441

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

PubMed

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.

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

PubMed

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.g., eugenol), which may explain the formation of some TCD AEs. The OCMR could be efficiently queried for useful information using SPARQL scripts. The OCMR ontology was developed to systematically represent 26 traditional anti-rheumatism Chinese drugs and their related information. The OCMR analysis identified possible anti-rheumatism and AE mechanisms of these drugs. Our novel ontology-based approach can also be applied to systematic representation and analysis of other traditional Chinese drugs.

A System for Information Management in BioMedical Studies—SIMBioMS

PubMed Central

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

The IntAct molecular interaction database in 2012

PubMed Central

Kerrien, Samuel; Aranda, Bruno; Breuza, Lionel; Bridge, Alan; Broackes-Carter, Fiona; Chen, Carol; Duesbury, Margaret; Dumousseau, Marine; Feuermann, Marc; Hinz, Ursula; Jandrasits, Christine; Jimenez, Rafael C.; Khadake, Jyoti; Mahadevan, Usha; Masson, Patrick; Pedruzzi, Ivo; Pfeiffenberger, Eric; Porras, Pablo; Raghunath, Arathi; Roechert, Bernd; Orchard, Sandra; Hermjakob, Henning

2012-01-01

IntAct is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. Two levels of curation are now available within the database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported. As from September 2011, IntAct contains approximately 275 000 curated binary interaction evidences from over 5000 publications. The IntAct website has been improved to enhance the search process and in particular the graphical display of the results. New data download formats are also available, which will facilitate the inclusion of IntAct's data in the Semantic Web. IntAct is an active contributor to the IMEx consortium (http://www.imexconsortium.org). IntAct source code and data are freely available at http://www.ebi.ac.uk/intact. PMID:22121220

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

PubMed

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.

Toward Non-Invasive and Automatic Intravenous Infiltration Detection: Evaluation of Bioimpedance and Skin Strain in a Pig Model.

PubMed

Bicen, A Ozan; West, Leanne L; Cesar, Liliana; Inan, Omer T

2018-01-01

Intravenous (IV) therapy is prevalent in hospital settings, where fluids are typically delivered with an IV into a peripheral vein of the patient. IV infiltration is the inadvertent delivery of fluids into the extravascular space rather than into the vein (and requires urgent treatment to avoid scarring and severe tissue damage), for which medical staff currently needs to check patients periodically. In this paper, the performance of two non-invasive sensing modalities, electrical bioimpedance (EBI), and skin strain sensing, for the automatic detection of IV infiltration was investigated in an animal model. Infiltrations were physically simulated on the hind limb of anesthetized pigs, where the sensors for EBI and skin strain sensing were co-located. The obtained data were used to examine the ability to distinguish between infusion into the vein and an infiltration event using bioresistance and bioreactance (derived from EBI), as well as skin strain. Skin strain and bioresistance sensing could achieve detection rates greater than 0.9 for infiltration fluid volumes of 2 and 10 mL, respectively, for a given false positive, i.e., false alarm rate of 0.05. Furthermore, the fusion of multiple sensing modalities could achieve a detection rate of 0.97 with a false alarm rate of 0.096 for 5mL fluid volume of infiltration. EBI and skin strain sensing can enable non-invasive and real-time IV infiltration detection systems. Fusion of multiple sensing modalities can help to detect expanded range of leaking fluid volumes. The provided performance results and comparisons in this paper are an important step towards clinical translation of sensing technologies for detecting IV infiltration.

Toward Non-Invasive and Automatic Intravenous Infiltration Detection: Evaluation of Bioimpedance and Skin Strain in a Pig Model

PubMed Central

Bicen, A. Ozan; West, Leanne L.; Cesar, Liliana

2018-01-01

Intravenous (IV) therapy is prevalent in hospital settings, where fluids are typically delivered with an IV into a peripheral vein of the patient. IV infiltration is the inadvertent delivery of fluids into the extravascular space rather than into the vein (and requires urgent treatment to avoid scarring and severe tissue damage), for which medical staff currently needs to check patients periodically. In this paper, the performance of two non-invasive sensing modalities, electrical bioimpedance (EBI), and skin strain sensing, for the automatic detection of IV infiltration was investigated in an animal model. Infiltrations were physically simulated on the hind limb of anesthetized pigs, where the sensors for EBI and skin strain sensing were co-located. The obtained data were used to examine the ability to distinguish between infusion into the vein and an infiltration event using bioresistance and bioreactance (derived from EBI), as well as skin strain. Skin strain and bioresistance sensing could achieve detection rates greater than 0.9 for infiltration fluid volumes of 2 and 10 mL, respectively, for a given false positive, i.e., false alarm rate of 0.05. Furthermore, the fusion of multiple sensing modalities could achieve a detection rate of 0.97 with a false alarm rate of 0.096 for 5mL fluid volume of infiltration. EBI and skin strain sensing can enable non-invasive and real-time IV infiltration detection systems. Fusion of multiple sensing modalities can help to detect expanded range of leaking fluid volumes. The provided performance results and comparisons in this paper are an important step towards clinical translation of sensing technologies for detecting IV infiltration. PMID:29692956

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

PubMed

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.

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

PubMed Central

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

2016-01-01

The adoption and implementation of evidence-based interventions (EBIs) are end goals of translational research, however, potential end-users’ perceptions of an EBI’s 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. PMID:26244479

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

PubMed

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

2017-04-01

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

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

PubMed Central

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

2011-01-01

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

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

PubMed

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.

SPARQL-enabled identifier conversion with Identifiers.org

PubMed Central

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

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

PubMed

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

2014-01-01

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

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

PubMed

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.

EBI metagenomics—a new resource for the analysis and archiving of metagenomic data

PubMed Central

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

2014-01-01

Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil, tundra, plants and body sites). Metagenomics brings with it a number of challenges, including the management, analysis, storage and sharing of data. In response to these challenges, we have developed a new metagenomics resource (http://www.ebi.ac.uk/metagenomics/) that allows users to easily submit raw nucleotide reads for functional and taxonomic analysis by a state-of-the-art pipeline, and have them automatically stored (together with descriptive, standards-compliant metadata) in the European Nucleotide Archive. PMID:24165880

E-MSD: an integrated data resource for bioinformatics.

PubMed

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.

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

PubMed

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.

Overexpression of Epstein-Barr virus-induced gene 3 protein (EBI3) in MRL/lpr mice suppresses their lupus nephritis by activating regulatory T cells.

PubMed

Shinsuke, Nishimura; Hiroshi, Inoue

2013-11-01

To identify the effect of an imbalance of Th1/Th2 cytokines on the development of autoimmune glomerulonephritis (lupus nephritis), we studied the modification of pathological changes in diffuse proliferative glomerulonephritis (DPGN) and membranous glomerulonephritis (MGN) in MRL/lpr mice, which are animal models of systemic lupus erythematosus (SLE). Transgenic MRL/lpr mice (Tg) that overexpressed Epstein--Barr virus-induced gene 3 (EBI3) showed almost normal renal function, which was demonstrated by healing of glomerulonephritis upon renal histology, as compared to the wild-type MRL/lpr (Wt) mice. The levels of anti-dsDNA antibodies and IgE decreased in the Tg mice compared to Wt mice. Quantitative real-time PCR indicated an increase in the mRNA levels of FoxP3, and a decrease in that of IFNγ in the splenocytes of Tg mice as compared to Wt mice. In addition, flow cytometric analysis showed an increase in CD4(+)CD25(+)FoxP3(+)-T cells in the former, as compared to the latter. Our findings suggest that EBI3-overexpression in MRL/lpr mice induces generation of regulatory T cells, which causes suppression of autoimmune and inflammatory reactions by affecting the Th1/Th2 cytokine balance.

A rule-based ontological framework for the classification of molecules

PubMed Central

2014-01-01

Background A variety of key activities within life sciences research involves integrating and intelligently managing large amounts of biochemical information. Semantic technologies provide an intuitive way to organise and sift through these rapidly growing datasets via the design and maintenance of ontology-supported knowledge bases. To this end, OWL—a W3C standard declarative language— has been extensively used in the deployment of biochemical ontologies that can be conveniently organised using the classification facilities of OWL-based tools. One of the most established ontologies for the chemical domain is ChEBI, an open-access dictionary of molecular entities that supplies high quality annotation and taxonomical information for biologically relevant compounds. However, ChEBI is being manually expanded which hinders its potential to grow due to the limited availability of human resources. Results In this work, we describe a prototype that performs automatic classification of chemical compounds. The software we present implements a sound and complete reasoning procedure of a formalism that extends datalog and builds upon an off-the-shelf deductive database system. We capture a wide range of chemical classes that are not expressible with OWL-based formalisms such as cyclic molecules, saturated molecules and alkanes. Furthermore, we describe a surface ‘less-logician-like’ syntax that allows application experts to create ontological descriptions of complex biochemical objects without prior knowledge of logic. In terms of performance, a noticeable improvement is observed in comparison with previous approaches. Our evaluation has discovered subsumptions that are missing from the manually curated ChEBI ontology as well as discrepancies with respect to existing subclass relations. We illustrate thus the potential of an ontology language suitable for the life sciences domain that exhibits a favourable balance between expressive power and practical feasibility. Conclusions Our proposed methodology can form the basis of an ontology-mediated application to assist biocurators in the production of complete and error-free taxonomies. Moreover, such a tool could contribute to a more rapid development of the ChEBI ontology and to the efforts of the ChEBI team to make annotated chemical datasets available to the public. From a modelling point of view, our approach could stimulate the adoption of a different and expressive reasoning paradigm based on rules for which state-of-the-art and highly optimised reasoners are available; it could thus pave the way for the representation of a broader spectrum of life sciences and biomedical knowledge. PMID:24735706

A rule-based ontological framework for the classification of molecules.

PubMed

Magka, Despoina; Krötzsch, Markus; Horrocks, Ian

2014-01-01

A variety of key activities within life sciences research involves integrating and intelligently managing large amounts of biochemical information. Semantic technologies provide an intuitive way to organise and sift through these rapidly growing datasets via the design and maintenance of ontology-supported knowledge bases. To this end, OWL-a W3C standard declarative language- has been extensively used in the deployment of biochemical ontologies that can be conveniently organised using the classification facilities of OWL-based tools. One of the most established ontologies for the chemical domain is ChEBI, an open-access dictionary of molecular entities that supplies high quality annotation and taxonomical information for biologically relevant compounds. However, ChEBI is being manually expanded which hinders its potential to grow due to the limited availability of human resources. In this work, we describe a prototype that performs automatic classification of chemical compounds. The software we present implements a sound and complete reasoning procedure of a formalism that extends datalog and builds upon an off-the-shelf deductive database system. We capture a wide range of chemical classes that are not expressible with OWL-based formalisms such as cyclic molecules, saturated molecules and alkanes. Furthermore, we describe a surface 'less-logician-like' syntax that allows application experts to create ontological descriptions of complex biochemical objects without prior knowledge of logic. In terms of performance, a noticeable improvement is observed in comparison with previous approaches. Our evaluation has discovered subsumptions that are missing from the manually curated ChEBI ontology as well as discrepancies with respect to existing subclass relations. We illustrate thus the potential of an ontology language suitable for the life sciences domain that exhibits a favourable balance between expressive power and practical feasibility. Our proposed methodology can form the basis of an ontology-mediated application to assist biocurators in the production of complete and error-free taxonomies. Moreover, such a tool could contribute to a more rapid development of the ChEBI ontology and to the efforts of the ChEBI team to make annotated chemical datasets available to the public. From a modelling point of view, our approach could stimulate the adoption of a different and expressive reasoning paradigm based on rules for which state-of-the-art and highly optimised reasoners are available; it could thus pave the way for the representation of a broader spectrum of life sciences and biomedical knowledge.

Toward community standards in the quest for orthologs

PubMed Central

Dessimoz, Christophe; Gabaldón, Toni; Roos, David S.; Sonnhammer, Erik L. L.; Herrero, Javier; Altenhoff, Adrian; Apweiler, Rolf; Ashburner, Michael; Blake, Judith; Boeckmann, Brigitte; Bridge, Alan; Bruford, Elspeth; Cherry, Mike; Conte, Matthieu; Dannie, Durand; Datta, Ruchira; Dessimoz, Christophe; Domelevo Entfellner, Jean-Baka; Ebersberger, Ingo; Gabaldón, Toni; Galperin, Michael; Herrero, Javier; Joseph, Jacob; Koestler, Tina; Kriventseva, Evgenia; Lecompte, Odile; Leunissen, Jack; Lewis, Suzanna; Linard, Benjamin; Livstone, Michael S.; Lu, Hui-Chun; Martin, Maria; Mazumder, Raja; Messina, David; Miele, Vincent; Muffato, Matthieu; Perrière, Guy; Punta, Marco; Roos, David; Rouard, Mathieu; Schmitt, Thomas; Schreiber, Fabian; Silva, Alan; Sjölander, Kimmen; Škunca, Nives; Sonnhammer, Erik; Stanley, Eleanor; Szklarczyk, Radek; Thomas, Paul; Uchiyama, Ikuo; Van Bel, Michiel; Vandepoele, Klaas; Vilella, Albert J.; Yates, Andrew; Zdobnov, Evgeny

2012-01-01

The identification of orthologs—genes pairs descended from a common ancestor through speciation, rather than duplication—has emerged as an essential component of many bioinformatics applications, ranging from the annotation of new genomes to experimental target prioritization. Yet, the development and application of orthology inference methods is hampered by the lack of consensus on source proteomes, file formats and benchmarks. The second ‘Quest for Orthologs’ meeting brought together stakeholders from various communities to address these challenges. We report on achievements and outcomes of this meeting, focusing on topics of particular relevance to the research community at large. The Quest for Orthologs consortium is an open community that welcomes contributions from all researchers interested in orthology research and applications. Contact: dessimoz@ebi.ac.uk PMID:22332236

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

PubMed

Preveena, Jagadesan; Bhore, Subhash J

2013-01-01

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

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

PubMed Central

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

2013-01-01

Effective HIV prevention programs for people living with HIV/AIDS (PLWH) are important to reduce new infections and to ensure PLWH remain healthy. This paper describes the systematic adaptation of a U.S.-developed Evidence Based Intervention (EBI) using the Centers for Disease Control and Prevention (CDC) Map of Adaption Process for use at a Pediatric Hospital in Kinshasa, Democratic Republic of the Congo (DRC). The adapted intervention, Supporting Youth and Motivating Positive Action or SYMPA, a six-session risk reduction intervention targeted for youth living with HIV/AIDS (YLWH) in Kinshasa was adapted from the Healthy Living Project and guided by the Social Action Theory. This paper describes the process of implementing the first four steps of the ADAPT framework (Assess, Select, Prepare, and Pilot). Our study has shown that an EBI developed and implemented in the U.S. can be adapted successfully for a different target population in a low-resource context through an iterative process following the CDC ADAPT framework. This process included reviewing existing literature, adapting and adding components, and focusing on increasing staff capacity. This paper provides a rare, detailed description of the adaptation process and may aid organizations seeking to adapt and implement HIV prevention EBIs in sub-Saharan Africa and beyond. PMID:23063699

Measurement equivalence: A non-technical primer on categorical multi-group confirmatory factor analysis in school psychology.

PubMed

Pendergast, Laura L; von der Embse, Nathaniel; Kilgus, Stephen P; Eklund, Katie R

2017-02-01

Evidence-based interventions (EBIs) have become a central component of school psychology research and practice, but EBIs are dependent upon the availability and use of evidence-based assessments (EBAs) with diverse student populations. Multi-group confirmatory factor analysis (MG-CFA) is an analytical tool that can be used to examine the validity and measurement equivalence/invariance of scores across diverse groups. The objective of this article is to provide a conceptual and procedural overview of categorical MG-CFA, as well as an illustrated example based on data from the Social and Academic Behavior Risk Screener (SABRS) - a tool designed for use in school-based interventions. This article serves as a non-technical primer on the topic of MG-CFA with ordinal (rating scale) data and does so through the framework of examining equivalence of measures used for EBIs within multi-tiered models - an understudied topic. To go along with the illustrated example, we have provided supplementary files that include sample data, Mplus input code, and an annotated guide for understanding the input code (http://dx.doi.org/10.1016/j.jsp.2016.11.002). Data needed to reproduce analyses in this article are available as supplemental materials (online only) in the Appendix of this article. Copyright © 2016 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

Characterization of photocathode dark current vs. temperature in image intensifier tube modules and intensified televisions

NASA Astrophysics Data System (ADS)

Bender, Edward J.; Wood, Michael V.; Hart, Steve; Heim, Gerald B.; Torgerson, John A.

2004-10-01

Image intensifiers (I2) have gained wide acceptance throughout the Army as the premier nighttime mobility sensor for the individual soldier, with over 200,000 fielded systems. There is increasing need, however, for such a sensor with a video output, so that it can be utilized in remote vehicle platforms, and/or can be electronically fused with other sensors. The image-intensified television (I2TV), typically consisting of an image intensifier tube coupled via fiber optic to a solid-state imaging array, has been the primary solution to this need. I2TV platforms in vehicles, however, can generate high internal heat loads and must operate in high-temperature environments. Intensifier tube dark current, called "Equivalent Background Input" or "EBI", is not a significant factor at room temperature, but can seriously degrade image contrast and intra-scene dynamic range at such high temperatures. Cooling of the intensifier's photocathode is the only practical solution to this problem. The US Army RDECOM CERDEC Night Vision & Electronic Sensors Directorate (NVESD) and Ball Aerospace have collaborated in the reported effort to more rigorously characterize intensifier EBI versus temperature. NVESD performed non-imaging EBI measurements of Generation 2 and 3 tube modules over a large range of ambient temperature, while Ball performed an imaging evaluation of Generation 3 I2TVs over a similar temperature range. The findings and conclusions of this effort are presented.

E-MSD: an integrated data resource for bioinformatics

PubMed Central

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. PMID:15608192

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

PubMed

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.

Using equivalence-based instruction to teach piano skills to college students.

PubMed

Griffith, Kristin R; Ramos, Amber L; Hill, Kelli E; Miguel, Caio F

2018-04-01

The purpose of the current study was to evaluate the effects of equivalence-based instruction (EBI) on the emergence of basic music reading and piano playing skills. Six female college students learned to identify three musical chord notations given their respective dictated names. Participants also learned to play chords on the piano following the dictated name of the chord, and to play the chords to a song on a keyboard. Results are consistent with past research, in that stimuli became substitutable for each other and acquired a common behavioral function. Data suggest that EBI was an effective and efficient procedure to teach adults to read musical notation, as well as play chords and a song on a piano keyboard. © 2018 Society for the Experimental Analysis of Behavior.

The European Bioinformatics Institute’s data resources 2014

PubMed Central

Brooksbank, Catherine; Bergman, Mary Todd; Apweiler, Rolf; Birney, Ewan; Thornton, Janet

2014-01-01

Molecular Biology has been at the heart of the ‘big data’ revolution from its very beginning, and the need for access to biological data is a common thread running from the 1965 publication of Dayhoff’s ‘Atlas of Protein Sequence and Structure’ through the Human Genome Project in the late 1990s and early 2000s to today’s population-scale sequencing initiatives. The European Bioinformatics Institute (EMBL-EBI; http://www.ebi.ac.uk) is one of three organizations worldwide that provides free access to comprehensive, integrated molecular data sets. Here, we summarize the principles underpinning the development of these public resources and provide an overview of EMBL-EBI’s database collection to complement the reviews of individual databases provided elsewhere in this issue. PMID:24271396

Proceedings of the 10th international workshop on ECR ion sources

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

Meyer, F W; Kirkpatrick, M I

This report contains papers on the following topics: Recent Developments and Future Projects on ECR Ion Sources; Operation of the New KVI ECR Ion Source at 10 GHz; Operational Experience and Status of the INS SF-ECR Ion Source; Results of the New ECR4'' 14.5 GHz ECRIS; Preliminary Performance of the AECR; Experimental Study of the Parallel and Perpendicular Particle Losses from an ECRIS Plasma; Plasma Instability in Electron Cyclotron Resonance Heated Ion Sources; The Hyperbolic Energy Analyzer; Status of ECR Source Development; The New 10 GHz CAPRICE Source; First Operation of the Texas A M ECR Ion Source; Recent Developmentsmore » of the RIKEN ECR Ion Sources; The 14 GHz CAPRICE Source; Characteristics and Potential Applications of an ORNL Microwave ECR Multicusp Plasma Ion Source; ECRIPAC: The Production and Acceleration of Multiply Charged Ions Using an ECR Plasma; ECR Source for the HHIRF Tandem Accelerator; Feasibility Studies for an ECR-Generated Plasma Stripper; Production of Ion Beams by using the ECR Plasmas Cathode; A Single Stage ECR Source for Efficient Production of Radioactive Ion Beams; The Single Staged ECR Source at the TRIUMF Isotope Separator TISOL; The Continuous Wave, Optically Pumped H{sup {minus}} Source; The H{sup +} ECR Source for the LAMPF Optically Pumped Polarized Ion Source; Present Status of the Warsaw CUSP ECR Ion Source; An ECR Source for Negative Ion Production; GYRAC-D: A Device for a 200 keV ECR Plasma Production and Accumulation; Status Report of the 14.4 GHZ ECR in Legnaro; Status of JYFL-ECRIS; Report on the Uppsala ECRIS Facility and Its Planned Use for Atomic Physics; A 10 GHz ECR Ion Source for Ion-Electron and Ion-Atom Collision Studies; and Status of the ORNL ECR Source Facility for Multicharged Ion Collision Research.« less

Three or Four Fractions of 4-5 Gy per Week in Postoperative High-Dose-Rate Brachytherapy for Endometrial Carcinoma

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

Rovirosa, Angeles, E-mail: rovirosa@clinic.ub.es; Ascaso, Carlos; Sanchez-Reyes, Alberto

2011-10-01

Purpose: To evaluate the results of high-dose-rate brachytherapy (HDRBT) using a schedule of three or four fractions per week, when possible, in 89 patients on local control and toxicity in postoperative treatment of endometrial carcinoma. The effect of the overall HDRBT treatment time (OTT) on toxicity was also evaluated. Patients and Methods: Federation Internationale de Gynecologie Obstetrique Stage: 24 IB, 45 IC, 4 IIA, 6 IIB, 4 IIIA, 2 IIIB, and 4 IIIC. Radiotherapy: Group 1-67 of 89 patients received external beam irradiation (EBI; 44-50 Gy) plus HDRBT (3 fractions of 4-6 Gy); Group 2-22 of 89 patients received HDRBTmore » alone (6 fractions of 4-5 Gy). OTT: Group 1-HDRBT was completed in a median of 5 days in 32 patients and in >5 days in 35; Group 2-HDRBT was completed in <15 days in 11 patients and in {>=}16 days in 11. Toxicity was evaluated using Radiation Therapy Oncology Group scores and the bioequivalent dose (BED) study was performed in vaginal mucosa surface. Statistics included Student's t test, chi-square test, and receiving operator curves. Results: With a mean follow-up of 31 months (range, 6-70), 1 of 89 patients had vaginal relapse. Early toxicity appeared in 8 of 89 (9%) patients and was resolved. Late toxicity appeared in 13/89 (14%): vaginal nine Grade 1, three Grade 2, one Grade 4; bladder two Grade 2; rectal three Grade 1, one Grade 2. No differences were found in relation to OTT in Groups 1 and 2. Mean BED was 88.48 Gy in Group 1 and 165.28 Gy in Group 2. Cases with Grade 2 late vaginal toxicity received >75 Gy after EBI and >165 Gy in Group 2. Conclusions: Three fractions of 4-5 Gy in 3-5 days after EBI or 6 fractions in <15 days in patients receiving HDRBT alone was a safe treatment in relation to toxicity and local control. Vaginal surface BED less than 75 Gy after EBI and less than 160 Gy in HDRBT alone may be safe to avoid G2 toxicity.« less

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

PubMed

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.

Chemical Entity Recognition and Resolution to ChEBI

PubMed Central

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

Nanojoint Formation between Ceramic Titanate Nanowires and Spot Melting of Metal Nanowires with Electron Beam.

PubMed

Bo, Arixin; Alarco, Jose; Zhu, Huaiyong; Waclawik, Eric R; Zhan, Haifei; Gu, YuanTong

2017-03-15

Construction of nanoarchitectures requires techniques like joint formation and trimming. For ceramic materials, however, it is extremely difficult to form nanojoints by conventional methods like merging. In this work, we demonstrate that ceramic titanate nanowires (NWs) can be joined by spot melting under electron beam (e-beam) irradiation (EBI). The irradiation fuses the contacted spot of titanate NWs yielding an intact nanojoint. Nanojoints with different morphologies can be produced. The joint structures consist of titanium dioxide (TiO 2 ) rutile, anatase, and titanate phases in the direction away from the e-beam melting spot. The titanate binds to anatase via a crystallographic matching coherent interface (the oxygen atoms at the interface are shared by the two phases) and the anatase solidly binds to the rutile joint. The resulting rutile joint is stable at high temperatures. Additionally, it is demonstrated that the heat production from EBI treated rutile can be utilized to break metal NWs (Ag, Cu, and Ni) apart by spot melting. The required e-beam intensity is considerably mild (75 pA/cm 2 ) which allows visual access and control over the NW melting. Direct melting of Ag and Cu is not applicable under EBI due to their high thermal conductivity even with high current density (500 pA/cm 2 ). Our findings reveal that ceramic nanojoint formation and spot melting at nanoscale are applicable if the properties of nanomaterials are understood and properly utilized.

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

PubMed Central

Preveena, Jagadesan; Bhore, Subhash J.

2013-01-01

Background: In traditional medicine, Tridax procumbens Linn. is used in the treatment of injuries and wounds. The bacterial endophytes (BEs) of medicinal plants could produce medicinally important metabolites found in their hosts; and hence, the involvement of BEs in conferring wound healing properties to T. Procumbens cannot be ruled out. But, we do not know which types of BEs are associated with T. Procumbens. Objective: The objective of this study was to investigate the fast growing and cultivable BEs associated with T. procumbens. Materials and Methods: Leaves and stems of healthy T. Procumbens plants were collected and cultivable BEs were isolated from surface-sterilized leaf and stem tissue samples using Luria-Bertani (LB) agar (medium) at standard conditions. A polymerase chain reaction was employed to amplify 16S rRNA coding gene fragments from the isolates. Cultivable endophytic bacterial isolates (EBIs) were identified using 16S rRNA gene nucleotide sequence similarity based method of bacterial identification. Results: Altogether, 50 culturable EBIs were isolated. 16S rRNA gene nucleotide sequences analysis using the Basic Local Alignment Search Tool (BLAST) revealed identities of the EBIs. Analysis reveals that cultivable Bacillus spp., Cronobacter sakazakii, Enterobacter spp., Lysinibacillus sphaericus, Pantoea spp., Pseudomonas spp. and Terribacillus saccharophilus are associated with T. Procumbens. Conclusion: Based on the results, we conclude that 24 different types of culturable BEs are associated with traditionally used medicinal plant, T. Procumbens, and require further study. PMID:24501447

Novel view synthesis by interpolation over sparse examples

NASA Astrophysics Data System (ADS)

Liang, Bodong; Chung, Ronald C.

2006-01-01

Novel view synthesis (NVS) is an important problem in image rendering. It involves synthesizing an image of a scene at any specified (novel) viewpoint, given some images of the scene at a few sample viewpoints. The general understanding is that the solution should bypass explicit 3-D reconstruction of the scene. As it is, the problem has a natural tie to interpolation, despite that mainstream efforts on the problem have been adopting formulations otherwise. Interpolation is about finding the output of a function f(x) for any specified input x, given a few input-output pairs {(xi,fi):i=1,2,3,...,n} of the function. If the input x is the viewpoint, and f(x) is the image, the interpolation problem becomes exactly NVS. We treat the NVS problem using the interpolation formulation. In particular, we adopt the example-based everything or interpolation (EBI) mechanism-an established mechanism for interpolating or learning functions from examples. EBI has all the desirable properties of a good interpolation: all given input-output examples are satisfied exactly, and the interpolation is smooth with minimum oscillations between the examples. We point out that EBI, however, has difficulty in interpolating certain classes of functions, including the image function in the NVS problem. We propose an extension of the mechanism for overcoming the limitation. We also present how the extended interpolation mechanism could be used to synthesize images at novel viewpoints. Real image results show that the mechanism has promising performance, even with very few example images.

Forward-backward multiplicity fluctuation and longitudinal harmonics in high-energy nuclear collisions

DOE PAGES

Jia, Jiangyong; Radhakrishnan, Sooraj; Zhou, Mingliang

2016-04-18

In this paper, an analysis method is proposed to study the forward-backward (FB) multiplicity fluctuation in high-energy nuclear collisions, built on the earlier work of Bzdak and Teaney [Phys. Rev. C 87, 024906 (2013)]. The method allows the decomposition of the centrality dependence of average multiplicity from the dynamical event-by-event (EbyE) fluctuation of multiplicity in pseudorapidity. Application of the method to AMPT (A Multi-Phase Transport model) and HIJING (Heavy Ion Jet INteraction Generator) models shows that the long-range component of the FB correlation is captured by a few longitudinal harmonics, with the first component driven by the asymmetry in themore » number of participating nucleons in the two colliding nuclei. The higher-order longitudinal harmonics are found to be strongly damped in AMPT compared to HIJING, due to weaker short-range correlations as well as the final-state effects present in the AMPT model. Two-particle pseudorapidity correlation reveals interesting charge-dependent short-range structures that are absent in HIJING model. Lastly, the proposed method opens an avenue to elucidate the particle production mechanism and early time dynamics in heavy-ion collisions. Future analysis directions and prospects of using the pseudorapidity correlation function to understand the centrality bias in p + p, p + A, and A + A collisions are discussed.« less

An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge

PubMed Central

Onwubiko, J.; Zaru, R.; Rosanoff, S.; Antunes, R.; Bingley, M.; Watkins, X.; O'Donovan, C.; Martin, M. J.

2017-01-01

Abstract Enzymes are a key part of life processes and are increasingly important for various areas of research such as medicine, biotechnology, bioprocessing and drug research. The goal of the Enzyme Portal is to provide an interface to all European Bioinformatics Institute (EMBL-EBI) data about enzymes (de Matos, P., et al., (2013), BMC Bioinformatics, 14 (1), 103). These data include enzyme function, sequence features and family classification, protein structure, reactions, pathways, small molecules, diseases and the associated literature. The sources of enzyme data are: the UniProt Knowledgebase (UniProtKB) (UniProt Consortium, 2015), the Protein Data Bank in Europe (PDBe), (Valenkar, S., et al., Nucleic Acids Res.2016; 44, D385–D395) Rhea—a database of enzyme-catalysed reactions (Morgat, A., et al., Nucleic Acids Res. 2015; 43, D459-D464), Reactome—a database of biochemical pathways (Fabregat, A., et al., Nucleic Acids Res. 2016; 44, D481–D487), IntEnz—a resource with enzyme nomenclature information (Fleischmann, A., et al., Nucleic Acids Res. 2004 32, D434–D437) and ChEBI (Hastings, J., et al., Nucleic Acids Res. 2013) and ChEMBL (Bento, A. P., et al., Nucleic Acids Res. 201442, 1083–1090)—resources which contain information about small-molecule chemistry and bioactivity. This article describes the redesign of Enzyme Portal and the increased functionality added to maximise integration and interpretation of these data. Use case examples of the Enzyme Portal and the versatile workflows its supports are illustrated. We welcome the suggestion of new resources for integration. PMID:28158609

An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge.

PubMed

Pundir, S; Onwubiko, J; Zaru, R; Rosanoff, S; Antunes, R; Bingley, M; Watkins, X; O'Donovan, C; Martin, M J

2017-03-01

Enzymes are a key part of life processes and are increasingly important for various areas of research such as medicine, biotechnology, bioprocessing and drug research. The goal of the Enzyme Portal is to provide an interface to all European Bioinformatics Institute (EMBL-EBI) data about enzymes (de Matos, P., et al. , (2013), BMC Bioinformatics , (1), 103). These data include enzyme function, sequence features and family classification, protein structure, reactions, pathways, small molecules, diseases and the associated literature. The sources of enzyme data are: the UniProt Knowledgebase (UniProtKB) (UniProt Consortium, 2015), the Protein Data Bank in Europe (PDBe), (Valenkar, S., et al ., Nucleic Acids Res. 2016; , D385-D395) Rhea-a database of enzyme-catalysed reactions (Morgat, A., et al .,  Nucleic Acids Res.  2015; , D459-D464), Reactome-a database of biochemical pathways (Fabregat, A., et al ., Nucleic Acids Res. 2016;  , D481-D487), IntEnz-a resource with enzyme nomenclature information (Fleischmann, A., et al ., Nucleic Acids Res.  2004 , D434-D437) and ChEBI (Hastings, J., et al .,  Nucleic Acids Res. 2013) and ChEMBL (Bento, A. P., et al ., Nucleic Acids Res.  2014 , 1083-1090)-resources which contain information about small-molecule chemistry and bioactivity. This article describes the redesign of Enzyme Portal and the increased functionality added to maximise integration and interpretation of these data. Use case examples of the Enzyme Portal and the versatile workflows its supports are illustrated. We welcome the suggestion of new resources for integration. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Invited commentary: broadening the evidence for adolescent sexual and reproductive health and education in the United States.

PubMed

Schalet, Amy T; Santelli, John S; Russell, Stephen T; Halpern, Carolyn T; Miller, Sarah A; Pickering, Sarah S; Goldberg, Shoshana K; Hoenig, Jennifer M

2014-10-01

Scientific research has made major contributions to adolescent health by providing insights into factors that influence it and by defining ways to improve it. However, US adolescent sexual and reproductive health policies-particularly sexuality health education policies and programs-have not benefited from the full scope of scientific understanding. From 1998 to 2009, federal funding for sexuality education focused almost exclusively on ineffective and scientifically inaccurate abstinence-only-until-marriage (AOUM) programs. Since 2010, the largest source of federal funding for sexual health education has been the "tier 1" funding of the Office of Adolescent Health's Teen Pregnancy Prevention Initiative. To be eligible for such funds, public and private entities must choose from a list of 35 programs that have been designated as "evidence-based" interventions (EBIs), determined based on their effectiveness at preventing teen pregnancies, reducing sexually transmitted infections, or reducing rates of sexual risk behaviors (i.e., sexual activity, contraceptive use, or number of partners). Although the transition from primarily AOUM to EBI is important progress, this definition of evidence is narrow and ignores factors known to play key roles in adolescent sexual and reproductive health. Important bodies of evidence are not treated as part of the essential evidence base, including research on lesbian, gay, bisexual, transgender, queer, and questioning (LGBTQ) youth; gender; and economic inequalities and health. These bodies of evidence underscore the need for sexual health education to approach adolescent sexuality holistically, to be inclusive of all youth, and to address and mitigate the impact of structural inequities. We provide recommendations to improve US sexual health education and to strengthen the translation of science into programs and policy.

Plasma-surface interaction in negative hydrogen ion sources

NASA Astrophysics Data System (ADS)

Wada, Motoi

2018-05-01

A negative hydrogen ion source delivers more beam current when Cs is introduced to the discharge, but a continuous operation of the source reduces the beam current until more Cs is added to the source. This behavior can be explained by adsorption and ion induced desorption of Cs atoms on the plasma grid surface of the ion source. The interaction between the ion source plasma and the plasma grid surface of a negative hydrogen ion source is discussed in correlation to the Cs consumption of the ion source. The results show that operation with deuterium instead of hydrogen should require more Cs consumption and the presence of medium mass impurities as well as ions of the source wall materials in the arc discharge enlarges the Cs removal rate during an ion source discharge.

A singly charged ion source for radioactive {sup 11}C ion acceleration

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

Katagiri, K.; Noda, A.; Nagatsu, K.

2016-02-15

A new singly charged ion source using electron impact ionization has been developed to realize an isotope separation on-line system for simultaneous positron emission tomography imaging and heavy-ion cancer therapy using radioactive {sup 11}C ion beams. Low-energy electron beams are used in the electron impact ion source to produce singly charged ions. Ionization efficiency was calculated in order to decide the geometric parameters of the ion source and to determine the required electron emission current for obtaining high ionization efficiency. Based on these considerations, the singly charged ion source was designed and fabricated. In testing, the fabricated ion source wasmore » found to have favorable performance as a singly charged ion source.« less

Comparison of reactant and analyte ions for ⁶³Nickel, corona discharge, and secondary electrospray ionization sources with ion mobility-mass spectrometry.

PubMed

Crawford, C L; Hill, H H

2013-03-30

(63)Nickel radioactive ionization ((63)Ni) is the most common and widely used ion source for ion mobility spectrometry (IMS). Regulatory, financial, and operational concerns with this source have promoted recent development of non-radioactive sources, such as corona discharge ionization (CD), for stand-alone IMS systems. However, there has been no comparison of the negative ion species produced by all three sources in the literature. This study compares the negative reactant and analyte ions produced by three sources on an ion mobility-mass spectrometer: conventional (63)Ni, CD, and secondary electrospray ionization (SESI). Results showed that (63)Ni and SESI produced the same reactant ion species while CD produced only the nitrate monomer and dimer ions. The analyte ions produced by each ion source were the same except for the CD source which produced a different ion species for the explosive RDX than either the (63)Ni or SESI source. Accurate and reproducible reduced mobility (K0) values, including several values reported here for the first time, were found for each explosive with each ion source. Overall, the SESI source most closely reproduced the reactant ion species and analyte ion species profiles for (63)Ni. This source may serve as a non-radioactive, robust, and flexible alternative for (63)Ni. Copyright © 2013 Elsevier B.V. All rights reserved.

The design of an electron gun switchable between immersed and Brillouin flowa)

NASA Astrophysics Data System (ADS)

Becker, R.; Kester, O.

2012-02-01

An electron gun, which can be switched from immersed flow to Brillouin flow during operation, may have advantages for charge breeders as well as for electron beam ion sources and traps (EBISTs). For EBISTs this allows to change the current density according to the repetition frequency and charge state, for charge breeders and EBISTs a lower current density in immersed flow provides higher acceptance for injected ions, while the higher current density in Brillouin flow results in shorter breeding times and a lower emittance for the extracted beam. Therefore, we have designed such a gun for an EBIS with 5 T central magnetic field and without the use of iron and moving the gun. The gun was placed in the axial fringing field of the 5 T solenoid in such a position that a gate valve can be placed between the gun and the cryostat to allow for simple maintenance. The field at the cathode surface turned out to be only 0.05 T, which is not enough to focus 50 A/cm2 at a few kV. However, if a small normal conducting solenoid is placed over the vacuum tube in position of the gun, a field of 0.1 T may be obtained. With this the use of LaB6 as cathode material results in a magnetic compression of 44 and therewith in a focused current density in the trap region of more than 2000 A/cm2. By reversing the current in the gun solenoid the cathode field can easily compensated to zero. By proper design of the electrodes and the compression region, the gun will be able to deliver a beam in Brillouin flow. While this is interesting by itself - remember the "super-compression" reported on CRYEBIS-I - any magnetic field between zero and the value for immersed flow will result in an electron beam with a wide range of adjustable high current densities. The design tools used have been INTMAG(C) for the calculation of magnetic fields, EGN2(C) for the simulation of the gun and ANALYSE(C) for detailed analysis of the results (for more information see www.egun-igun.com).

The design of an electron gun switchable between immersed and Brillouin flow.

PubMed

Becker, R; Kester, O

2012-02-01

An electron gun, which can be switched from immersed flow to Brillouin flow during operation, may have advantages for charge breeders as well as for electron beam ion sources and traps (EBISTs). For EBISTs this allows to change the current density according to the repetition frequency and charge state, for charge breeders and EBISTs a lower current density in immersed flow provides higher acceptance for injected ions, while the higher current density in Brillouin flow results in shorter breeding times and a lower emittance for the extracted beam. Therefore, we have designed such a gun for an EBIS with 5 T central magnetic field and without the use of iron and moving the gun. The gun was placed in the axial fringing field of the 5 T solenoid in such a position that a gate valve can be placed between the gun and the cryostat to allow for simple maintenance. The field at the cathode surface turned out to be only 0.05 T, which is not enough to focus 50 A∕cm(2) at a few kV. However, if a small normal conducting solenoid is placed over the vacuum tube in position of the gun, a field of 0.1 T may be obtained. With this the use of LaB(6) as cathode material results in a magnetic compression of 44 and therewith in a focused current density in the trap region of more than 2000 A∕cm(2). By reversing the current in the gun solenoid the cathode field can easily compensated to zero. By proper design of the electrodes and the compression region, the gun will be able to deliver a beam in Brillouin flow. While this is interesting by itself--remember the "super-compression" reported on CRYEBIS-I--any magnetic field between zero and the value for immersed flow will result in an electron beam with a wide range of adjustable high current densities. The design tools used have been INTMAG(C) for the calculation of magnetic fields, EGN2(C) for the simulation of the gun and ANALYSE(C) for detailed analysis of the results (for more information see www.egun-igun.com).

Laser ion source for high brightness heavy ion beam

DOE PAGES

Okamura, M.

2016-09-01

A laser ion source is known as a high current high charge state heavy ion source. But, we place great emphasis on the capability to realize a high brightness ion source. A laser ion source has a pinpoint small volume where materials are ionized and can achieve quite uniform low temperature ion beam. Those features may enable us to realize very small emittance beams. Furthermore, a low charge state high brightness laser ion source was successfully commissioned in Brookhaven National Laboratory in 2014. Now most of all the solid based heavy ions are being provided from the laser ion sourcemore » for regular operation.« less

Design and simulation of ion optics for ion sources for production of singly charged ions

NASA Astrophysics Data System (ADS)

Zelenak, A.; Bogomolov, S. L.

2004-05-01

During the last 2 years different types of the singly charged ion sources were developed for FLNR (JINR) new projects such as Dubna radioactive ion beams, (Phase I and Phase II), the production of the tritium ion beam and the MASHA mass separator. The ion optics simulations for 2.45 GHz electron cyclotron resonance source, rf source, and the plasma ion source were performed. In this article the design and simulation results of the optics of new ion sources are presented. The results of simulation are compared with measurements obtained during the experiments.

Ultra-short ion and neutron pulse production

DOEpatents

Leung, Ka-Ngo; Barletta, William A.; Kwan, Joe W.

2006-01-10

An ion source has an extraction system configured to produce ultra-short ion pulses, i.e. pulses with pulse width of about 1 .mu.s or less, and a neutron source based on the ion source produces correspondingly ultra-short neutron pulses. To form a neutron source, a neutron generating target is positioned to receive an accelerated extracted ion beam from the ion source. To produce the ultra-short ion or neutron pulses, the apertures in the extraction system of the ion source are suitably sized to prevent ion leakage, the electrodes are suitably spaced, and the extraction voltage is controlled. The ion beam current leaving the source is regulated by applying ultra-short voltage pulses of a suitable voltage on the extraction electrode.

Improved ion source

DOEpatents

Leung, K.N.; Ehlers, K.W.

1982-05-04

A magnetic filter for an ion source reduces the production of undesired ion species and improves the ion beam quality. High-energy ionizing electrons are confined by the magnetic filter to an ion source region, where the high-energy electrons ionize gas molecules. One embodiment of the magnetic filter uses permanent magnets oriented to establish a magnetic field transverse to the direction of travel of ions from the ion source region to the ion extraction region. In another embodiment, low energy 16 eV electrons are injected into the ion source to dissociate gas molecules and undesired ion species into desired ion species,

Ion source

DOEpatents

Leung, Ka-Ngo; Ehlers, Kenneth W.

1984-01-01

A magnetic filter for an ion source reduces the production of undesired ion species and improves the ion beam quality. High-energy ionizing electrons are confined by the magnetic filter to an ion source region, where the high-energy electrons ionize gas molecules. One embodiment of the magnetic filter uses permanent magnets oriented to establish a magnetic field transverse to the direction of travel of ions from the ion source region to the ion extraction region. In another embodiment, low energy 16 eV electrons are injected into the ion source to dissociate gas molecules and undesired ion species into desired ion species.

DUAL HEATED ION SOURCE STRUCTURE HAVING ARC SHIFTING MEANS

DOEpatents

Lawrence, E.O.

1959-04-14

An ion source is presented for calutrons, particularly an electrode arrangement for the ion generator of a calutron ion source. The ion source arc chamber is heated and an exit opening with thermally conductive plates defines the margins of the opening. These plates are electrically insulated from the body of the ion source and are connected to a suitable source of voltage to serve as electrodes for shaping the ion beam egressing from the arc chamber.

Positive and negative ion beam merging system for neutral beam production

DOEpatents

Leung, Ka-Ngo; Reijonen, Jani

2005-12-13

The positive and negative ion beam merging system extracts positive and negative ions of the same species and of the same energy from two separate ion sources. The positive and negative ions from both sources pass through a bending magnetic field region between the pole faces of an electromagnet. Since the positive and negative ions come from mirror image positions on opposite sides of a beam axis, and the positive and negative ions are identical, the trajectories will be symmetrical and the positive and negative ion beams will merge into a single neutral beam as they leave the pole face of the electromagnet. The ion sources are preferably multicusp plasma ion sources. The ion sources may include a multi-aperture extraction system for increasing ion current from the sources.

Aether: leveraging linear programming for optimal cloud computing in genomics

PubMed Central

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

2018-01-01

Abstract Motivation Across biology, we are seeing rapid developments in scale of data production without a corresponding increase in data analysis capabilities. Results 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. Availability and implementation 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. Contact chirag_patel@hms.harvard.edu or aleksandar.kostic@joslin.harvard.edu Supplementary information Supplementary data are available at Bioinformatics online. PMID:29228186

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

PubMed

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.

Very-low-energy-spread ion sources

NASA Astrophysics Data System (ADS)

Lee, Y.

1997-05-01

Ion beams with low axial energy spread are required in many applications such as ion projection lithography, isobaric separation in radioactive ion beam experiments, and ion beam deposition processes. In an ion source, the spread of the axial ion energy is caused by the nonuniformity of the plasma potential distribution along the source axis. Multicusp ion sources are capable of production positive and negative ions with good beam quality and relatively low energy spread. By intorducing a magnetic filter inside the multicusp source chamber, the axial plasma potential distribution is modified and the energy spread of positive hydrogen ions can be reduced to as low as 1 eV. The energy spread measurements of multicusp sources have been conducted by employing three different techniques: an electrostatic energy analyzer at the source exit; a magnetic deflection spectrometer; and a retarding-field energy analyzer for the accelerated beam. These different measurements confirmed tha! t ! the axial energy spread of positive and negative ions generated in the filter-equipped multicusp sources are small. New ion source configurations are now being investigated at LBNL with the purpose of achieving enen lower energy spread (<1eV) and of maximizing source performance such as reliability and lifetime.

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

PubMed

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.

Synthesis of Carbon Foam from Waste Artificial Marble Powder and Carboxymethyl Cellulose via Electron Beam Irradiation and Its Characterization

PubMed Central

Kim, Hong Gun; Kim, Yong Sun; Kwac, Lee Ku; Chae, Su-Hyeong; Shin, Hye Kyoung

2018-01-01

Carbon foams were prepared by carbonization of carboxymethyl cellulose (CMC)/waste artificial marble powder (WAMP) composites obtained via electron beam irradiation (EBI); these composites were prepared by mixing eco-friendly CMC with WAMP as the fillers for improved their poor mechanical strength. Gel fractions of the CMC/WAMP composites obtained at various EBI doses were investigated, and it was found that the CMC/WAMP composites obtained at an EBI dose of 80 kGy showed the highest gel fraction (95%); hence, the composite prepared at this dose was selected for preparing the carbon foam. The thermogravimetric analysis of the CMC/WAMP composites obtained at 80 kGy; showed that the addition of WAMP increased the thermal stability and carbon residues of the CMC/WAMP composites at 900 °C. SEM images showed that the cell walls of the CMC/WAMP carbon foams were thicker more than those of the CMC carbon foam. In addition, energy dispersive X-ray spectroscopy showed that the CMC/WAMP carbon foams contained small amounts of aluminum, derived from WAMP. The results confirmed that the increased WAMP content and hence increased aluminum content improved the thermal conductivity of the composites and their corresponding carbon foams. Moreover, the addition of WAMP increased the compressive strength of CMC/WAMP composites and hence the strength of their corresponding carbon foams. In conclusion, this synthesis method is encouraging, as it produces carbon foams of pore structure with good mechanical properties and thermal conductivity. PMID:29565300

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

PubMed

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.

Protective immune response against Toxoplasma gondii elicited by a novel yeast-based vaccine with microneme protein 16.

PubMed

Wang, Long-Jiang; Xiao, Ting; Xu, Chao; Li, Jin; Liu, Gong-Zhen; Yin, Kun; Cui, Yong; Wei, Qing-Kuan; Huang, Bing-Cheng; Sun, Hui

2018-06-22

Toxoplasma gondii is an obligate intracellular protozoan that can invade all eukaryotic cells and infect all warm-blood animals, causing the important zoonosis toxoplasmosis. Invasion of host cells is the key step necessary for T. gondii to complete its life cycle and microneme proteins play an important role in attachment and invasion of host cells. Microneme protein 16 (TgMIC16) is a new protective protein in T. gondii and belongs to transmembrane microneme proteins (TM-MIC). The TM-MICs are released onto the parasite's surface as complexes capable of interacting with host cell receptors. In the present study, we expressed the TgMIC16 protein on the surface of Saccharomyce cerevisiae (pCTCON2-TgMIC16/EBY100) and evaluated it as a potential vaccine for BALB/c mice against challenge infection with the RH strain of T. gondii. We immunized BALB/c mice both orally and intraperitoneally. After three immunizations, the immune response was evaluated by measuring antibody levels, lymphocyte proliferative responses, percentages of CD4 + and CD8 + T lymphocytes, cytokine production, and the survival times of challenged mice. The results showed that the pCTCON2-TgMIC16/EBY100 vaccine stimulated humoral and cellular immune responses. In addition, mice immunized with the pCTCON2-TgMIC16/EBY100 vaccine showed increased survival times compared with non-immunized controls. In summary, TgMIC16 displayed on the cell surface of S. cerevisiae could be used as potential vaccine against toxoplasmosis. Copyright © 2018 Elsevier Ltd. All rights reserved.

Three or four fractions of 4-5 Gy per week in postoperative high-dose-rate brachytherapy for endometrial carcinoma.

PubMed

Rovirosa, Angeles; Ascaso, Carlos; Sánchez-Reyes, Alberto; Herreros, Antonio; Abellana, Rosa; Pahisa, Jaume; Lejarcegui, Jose Antonio; Biete, Albert

2011-10-01

To evaluate the results of high-dose-rate brachytherapy (HDRBT) using a schedule of three or four fractions per week, when possible, in 89 patients on local control and toxicity in postoperative treatment of endometrial carcinoma. The effect of the overall HDRBT treatment time (OTT) on toxicity was also evaluated. Fédération Internationale de Gynécologie Obstétrique Stage: 24 IB, 45 IC, 4 IIA, 6 IIB, 4 IIIA, 2 IIIB, and 4 IIIC. Radiotherapy: Group 1-67 of 89 patients received external beam irradiation (EBI; 44-50 Gy) plus HDRBT (3 fractions of 4-6 Gy); Group 2-22 of 89 patients received HDRBT alone (6 fractions of 4-5 Gy). OTT: Group 1-HDRBT was completed in a median of 5 days in 32 patients and in >5 days in 35; Group 2-HDRBT was completed in <15 days in 11 patients and in ≥16 days in 11. Toxicity was evaluated using Radiation Therapy Oncology Group scores and the bioequivalent dose (BED) study was performed in vaginal mucosa surface. Statistics included Student's t test, chi-square test, and receiving operator curves. With a mean follow-up of 31 months (range, 6-70), 1 of 89 patients had vaginal relapse. Early toxicity appeared in 8 of 89 (9%) patients and was resolved. Late toxicity appeared in 13/89 (14%): vaginal nine Grade 1, three Grade 2, one Grade 4; bladder two Grade 2; rectal three Grade 1, one Grade 2. No differences were found in relation to OTT in Groups 1 and 2. Mean BED was 88.48 Gy in Group 1 and 165.28 Gy in Group 2. Cases with Grade 2 late vaginal toxicity received >75 Gy after EBI and >165 Gy in Group 2. Three fractions of 4-5 Gy in 3-5 days after EBI or 6 fractions in <15 days in patients receiving HDRBT alone was a safe treatment in relation to toxicity and local control. Vaginal surface BED less than 75 Gy after EBI and less than 160 Gy in HDRBT alone may be safe to avoid G2 toxicity. Copyright © 2011 Elsevier Inc. All rights reserved.

A Multicusp Ion Source for Radioactive Ion Beams

NASA Astrophysics Data System (ADS)

Wutte, D.; Freedman, S.; Gough, R.; Lee, Y.; Leitner, M.; Leung, K. N.; Lyneis, C.; Picard, D. S.; Sun, L.; Williams, M. D.; Xie, Z. Q.

1997-05-01

In order to produce a radioactive ion beam of (14)O+, a 10-cm-diameter, 13.56 MHz radio frequency (rf) driven multicusp ion source is now being developed at Lawrence Berkeley National Laboratory. In this paper we describe the specific ion source design and the basic ion source characteristics using Ar, Xe and a 90types of measurements have been performed: extractable ion current, ion species distributions, gas efficiency, axial energy spread and ion beam emittance measurements. The source can generate ion current densities of approximately 60 mA/cm2 . In addition the design of the ion beam extraction/transport system for the actual experimental setup for the radioactive beam line will be presented.

Focused electron and ion beam systems

DOEpatents

Leung, Ka-Ngo; Reijonen, Jani; Persaud, Arun; Ji, Qing; Jiang, Ximan

2004-07-27

An electron beam system is based on a plasma generator in a plasma ion source with an accelerator column. The electrons are extracted from a plasma cathode in a plasma ion source, e.g. a multicusp plasma ion source. The beam can be scanned in both the x and y directions, and the system can be operated with multiple beamlets. A compact focused ion or electron beam system has a plasma ion source and an all-electrostatic beam acceleration and focusing column. The ion source is a small chamber with the plasma produced by radio-frequency (RF) induction discharge. The RF antenna is wound outside the chamber and connected to an RF supply. Ions or electrons can be extracted from the source. A multi-beam system has several sources of different species and an electron beam source.

Microfabricated ion frequency standard

DOEpatents

Schwindt, Peter; Biedermann, Grant; Blain, Matthew G.; Stick, Daniel L.; Serkland, Darwin K.; Olsson, III, Roy H.

2010-12-28

A microfabricated ion frequency standard (i.e. an ion clock) is disclosed with a permanently-sealed vacuum package containing a source of ytterbium (Yb) ions and an octupole ion trap. The source of Yb ions is a micro-hotplate which generates Yb atoms which are then ionized by a ultraviolet light-emitting diode or a field-emission electron source. The octupole ion trap, which confines the Yb ions, is formed from suspended electrodes on a number of stacked-up substrates. A microwave source excites a ground-state transition frequency of the Yb ions, with a frequency-doubled vertical-external-cavity laser (VECSEL) then exciting the Yb ions up to an excited state to produce fluorescent light which is used to tune the microwave source to the ground-state transition frequency, with the microwave source providing a precise frequency output for the ion clock.

An ion source module for the Beijing Radioactive Ion-beam Facility

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

Cui, B., E-mail: cui@ciae.ac.cn; Huang, Q.; Tang, B.

2014-02-15

An ion source module is developed for Beijing Radioactive Ion-beam Facility. The ion source module is designed to meet the requirements of remote handling. The connection and disconnection of the electricity, cooling and vacuum between the module and peripheral units can be executed without on-site manual work. The primary test of the target ion source has been carried out and a Li{sup +} beam has been extracted. Details of the ion source module and its primary test results are described.

Ion source research and development at University of Jyväskylä: Studies of different plasma processes and towards the higher beam intensities.

PubMed

Koivisto, H; Kalvas, T; Tarvainen, O; Komppula, J; Laulainen, J; Kronholm, R; Ranttila, K; Tuunanen, J; Thuillier, T; Xie, D; Machicoane, G

2016-02-01

Several ion source related research and development projects are in progress at the Department of Physics, University of Jyväskylä (JYFL). The work can be divided into investigation of the ion source plasma and development of ion sources, ion beams, and diagnostics. The investigation covers the Electron Cyclotron Resonance Ion Source (ECRIS) plasma instabilities, vacuum ultraviolet (VUV) and visible light emission, photon induced electron emission, and the development of plasma diagnostics. The ion source development covers the work performed for radiofrequency-driven negative ion source, RADIS, beam line upgrade of the JYFL 14 GHz ECRIS, and the development of a new room-temperature-magnet 18 GHz ECRIS, HIISI.

Improved Multiple-Species Cyclotron Ion Source

NASA Technical Reports Server (NTRS)

Soli, George A.; Nichols, Donald K.

1990-01-01

Use of pure isotope 86Kr instead of natural krypton in multiple-species ion source enables source to produce krypton ions separated from argon ions by tuning cylcotron with which source used. Addition of capability to produce and separate krypton ions at kinetic energies of 150 to 400 MeV necessary for simulation of worst-case ions occurring in outer space.

Uniform resolution of compact identifiers for biomedical data

PubMed Central

Wimalaratne, Sarala M.; Juty, Nick; Kunze, John; Janée, Greg; McMurry, Julie A.; Beard, Niall; Jimenez, Rafael; Grethe, Jeffrey S.; Hermjakob, Henning; Martone, Maryann E.; Clark, Tim

2018-01-01

Most biomedical data repositories issue locally-unique accessions numbers, but do not provide globally unique, machine-resolvable, persistent identifiers for their datasets, as required by publishers wishing to implement data citation in accordance with widely accepted principles. Local accessions may however be prefixed with a namespace identifier, providing global uniqueness. Such “compact identifiers” have been widely used in biomedical informatics to support global resource identification with local identifier assignment. We report here on our project to provide robust support for machine-resolvable, persistent compact identifiers in biomedical data citation, by harmonizing the Identifiers.org and N2T.net (Name-To-Thing) meta-resolvers and extending their capabilities. Identifiers.org services hosted at the European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), and N2T.net services hosted at the California Digital Library (CDL), can now resolve any given identifier from over 600 source databases to its original source on the Web, using a common registry of prefix-based redirection rules. We believe these services will be of significant help to publishers and others implementing persistent, machine-resolvable citation of research data. PMID:29737976

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.

PubMed

McCarthy, Davis J; Campbell, Kieran R; Lun, Aaron T L; Wills, Quin F

2017-04-15

Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of individual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) and normalization. We have developed the R/Bioconductor package scater to facilitate rigorous pre-processing, quality control, normalization and visualization of scRNA-seq data. The package provides a convenient, flexible workflow to process raw sequencing reads into a high-quality expression dataset ready for downstream analysis. scater provides a rich suite of plotting tools for single-cell data and a flexible data structure that is compatible with existing tools and can be used as infrastructure for future software development. The open-source code, along with installation instructions, vignettes and case studies, is available through Bioconductor at http://bioconductor.org/packages/scater . davis@ebi.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Liquid metal ion source and alloy

DOEpatents

Clark, Jr., William M.; Utlaut, Mark W.; Behrens, Robert G.; Szklarz, Eugene G.; Storms, Edmund K.; Santandrea, Robert P.; Swanson, Lynwood W.

1988-10-04

A liquid metal ion source and alloy, wherein the species to be emitted from the ion source is contained in a congruently vaporizing alloy. In one embodiment, the liquid metal ion source acts as a source of arsenic, and in a source alloy the arsenic is combined with palladium, preferably in a liquid alloy having a range of compositions from about 24 to about 33 atomic percent arsenic. Such an alloy may be readily prepared by a combustion synthesis technique. Liquid metal ion sources thus prepared produce arsenic ions for implantation, have long lifetimes, and are highly stable in operation.

Ion Beam Propulsion Study

NASA Technical Reports Server (NTRS)

2008-01-01

The Ion Beam Propulsion Study was a joint high-level study between the Applied Physics Laboratory operated by NASA and ASRC Aerospace at Kennedy Space Center, Florida, and Berkeley Scientific, Berkeley, California. The results were promising and suggested that work should continue if future funding becomes available. The application of ion thrusters for spacecraft propulsion is limited to quite modest ion sources with similarly modest ion beam parameters because of the mass penalty associated with the ion source and its power supply system. Also, the ion source technology has not been able to provide very high-power ion beams. Small ion beam propulsion systems were used with considerable success. Ion propulsion systems brought into practice use an onboard ion source to form an energetic ion beam, typically Xe+ ions, as the propellant. Such systems were used for steering and correction of telecommunication satellites and as the main thruster for the Deep Space 1 demonstration mission. In recent years, "giant" ion sources were developed for the controlled-fusion research effort worldwide, with beam parameters many orders of magnitude greater than the tiny ones of conventional space thruster application. The advent of such huge ion beam sources and the need for advanced propulsion systems for exploration of the solar system suggest a fresh look at ion beam propulsion, now with the giant fusion sources in mind.

Development of the ion source for cluster implantation

NASA Astrophysics Data System (ADS)

Kulevoy, T. V.; Seleznev, D. N.; Kozlov, A. V.; Kuibeda, R. P.; Kropachev, G. N.; Alexeyenko, O. V.; Dugin, S. N.; Oks, E. M.; Gushenets, V. I.; Hershcovitch, A.; Jonson, B.; Poole, H. J.

2014-02-01

Bernas ion source development to meet needs of 100s of electron-volt ion implanters for shallow junction production is in progress in Institute for Theoretical and Experimental Physics. The ion sources provides high intensity ion beam of boron clusters under self-cleaning operation mode. The last progress with ion source operation is presented. The mechanism of self-cleaning procedure is described.

Air ion concentrations in various urban outdoor environments

NASA Astrophysics Data System (ADS)

Ling, Xuan; Jayaratne, Rohan; Morawska, Lidia

2010-06-01

Atmospheric ions are produced by many natural and anthropogenic sources and their concentrations vary widely between different environments. There is very little information on their concentrations in different types of urban environments, how they compare across these environments and their dominant sources. In this study, we measured airborne concentrations of small ions, particles and net particle charge at 32 different outdoor sites in and around a major city in Australia and identified the main ion sources. Sites were classified into seven groups as follows: park, woodland, city centre, residential, freeway, power lines and power substation. Generally, parks were situated away from ion sources and represented the urban background value of about 270 ions cm -3. Median concentrations at all other groups were significantly higher than in the parks. We show that motor vehicles and power transmission systems are two major ion sources in urban areas. Power lines and substations constituted strong unipolar sources, while motor vehicle exhaust constituted strong bipolar sources. The small ion concentration in urban residential areas was about 960 cm -3. At sites where ion sources were co-located with particle sources, ion concentrations were inhibited due to the ion-particle attachment process. These results improved our understanding on air ion distribution and its interaction with particles in the urban outdoor environment.

Negative ion source with low temperature transverse divergence optical system

DOEpatents

Whealton, John H.; Stirling, William L.

1986-01-01

A negative ion source is provided which has extremely low transverse divergence as a result of a unique ion focusing system in which the focal line of an ion beam emanating from an elongated, concave converter surface is outside of the ion exit slit of the source and the path of the exiting ions. The beam source operates with a minimum ion temperature which makes possible a sharply focused (extremely low transverse divergence) ribbon like negative ion beam.

Negative ion source with low temperature transverse divergence optical system

DOEpatents

Whealton, J.H.; Stirling, W.L.

1985-03-04

A negative ion source is provided which has extremely low transverse divergence as a result of a unique ion focusing system in which the focal line of an ion beam emanating from an elongated, concave converter surface is outside of the ion exit slit of the source and the path of the exiting ions. The beam source operates with a minimum ion temperature which makes possible a sharply focused (extremely low transverse divergence) ribbon like negative ion beam.

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

Koivisto, H., E-mail: hannu.koivisto@phys.jyu.fi; Kalvas, T.; Tarvainen, O.

Several ion source related research and development projects are in progress at the Department of Physics, University of Jyväskylä (JYFL). The work can be divided into investigation of the ion source plasma and development of ion sources, ion beams, and diagnostics. The investigation covers the Electron Cyclotron Resonance Ion Source (ECRIS) plasma instabilities, vacuum ultraviolet (VUV) and visible light emission, photon induced electron emission, and the development of plasma diagnostics. The ion source development covers the work performed for radiofrequency-driven negative ion source, RADIS, beam line upgrade of the JYFL 14 GHz ECRIS, and the development of a new room-temperature-magnetmore » 18 GHz ECRIS, HIISI.« less

ION SOURCE

DOEpatents

Martina, E.F.

1958-04-22

An improved ion source particularly adapted to provide an intense beam of ions with minimum neutral molecule egress from the source is described. The ion source structure includes means for establishing an oscillating electron discharge, including an apertured cathode at one end of the discharge. The egress of ions from the source is in a pencil like beam. This desirable form of withdrawal of the ions from the plasma created by the discharge is achieved by shaping the field at the aperture of the cathode. A tubular insulator is extended into the plasma from the aperture and in cooperation with the electric fields at the cathode end of the discharge focuses the ions from the source,

Magnetic field design for a Penning ion source for a 200 keV electrostatic accelerator

NASA Astrophysics Data System (ADS)

Fathi, A.; Feghhi, S. A. H.; Sadati, S. M.; Ebrahimibasabi, E.

2017-04-01

In this study, the structure of magnetic field for a Penning ion source has been designed and constructed with the use of permanent magnets. The ion source has been designed and constructed for a 200 keV electrostatic accelerator. With using CST Studio Suite, the magnetic field profile inside the ion source was simulated and an appropriate magnetic system was designed to improve particle confinement. Designed system consists of two ring magnets with 9 mm distance from each other around the anode. The ion source was constructed and the cylindrical magnet and designed magnetic system were tested on the ion source. The results showed that the ignition voltage for ion source with the designed magnetic system is almost 300 V lower than the ion source with the cylindrical magnet. Better particle confinement causes lower voltage discharge to occur.

Versatile plasma ion source with an internal evaporator

NASA Astrophysics Data System (ADS)

Turek, M.; Prucnal, S.; Drozdziel, A.; Pyszniak, K.

2011-04-01

A novel construction of an ion source with an evaporator placed inside a plasma chamber is presented. The crucible is heated to high temperatures directly by arc discharge, which makes the ion source suitable for substances with high melting points. The compact ion source enables production of intense ion beams for wide spectrum of solid elements with typical separated beam currents of ˜100-150 μA for Al +, Mn +, As + (which corresponds to emission current densities of 15-25 mA/cm 2) for the extraction voltage of 25 kV. The ion source works for approximately 50-70 h at 100% duty cycle, which enables high ion dose implantation. The typical power consumption of the ion source is 350-400 W. The paper presents detailed experimental data (e.g. dependences of ion currents and anode voltages on discharge and filament currents and magnetic flux densities) for Cr, Fe, Al, As, Mn and In. The discussion is supported by results of Monte Carlo method based numerical simulation of ionisation in the ion source.

Industrial ion source technology

NASA Technical Reports Server (NTRS)

Kaufman, H. R.

1976-01-01

A 30 cm electron bombardment ion source was designed and fabricated for micromachining and sputtering applications. This source has a multipole magnetic field that employs permanent magnets between permeable pole pieces. An average ion current density of 1 ma/sq cm with 500 eV argon ions was selected as a design operating condition. The ion beam at this operating condition was uniform and well collimated, with an average variation of plus or minus 5 percent over the center 20 cm of the beam at distances up to 30 cm from the ion source. A variety of sputtering applications were undertaken with a small 10 cm ion source to better understand the ion source requirements in these applications. The results of these experimental studies are also included.

Neutralization of an ion beam from the end-Hall ion source by a plasma electron source based on a discharge in crossed E × H fields

NASA Astrophysics Data System (ADS)

Dostanko, A. P.; Golosov, D. A.

2009-10-01

The possibility of using a plasma electron source (PES) with a discharge in crossed E × H field for compensating the ion beam from an end-Hall ion source (EHIS) is analyzed. The PES used as a neutralizer is mounted in the immediate vicinity of the EHIS ion generation and acceleration region at 90° to the source axis. The behavior of the discharge and emission parameters of the EHIS is determined for operation with a filament neutralizer and a plasma electron source. It is found that the maximal discharge current from the ion source attains a value of 3.8 A for operation with a PES and 4 A for operation with a filament compensator. It is established that the maximal discharge current for the ion source strongly depends on the working gas flow rate for low flow rates (up to 10 ml/min) in the EHIS; for higher flow rates, the maximum discharge current in the EHIS depends only on the emissivity of the PES. Analysis of the emission parameters of EHISs with filament and plasma neutralizers shows that the ion beam current and the ion current density distribution profile are independent of the type of the electron source and the ion current density can be as high as 0.2 mA/cm2 at a distance of 25 cm from the EHIS anode. The balance of currents in the ion source-electron source system is considered on the basis of analysis of operation of EHISs with various sources of electrons. It is concluded that the neutralization current required for operation of an ion source in the discharge compensation mode must be equal to or larger than the discharge current of the ion source. The use of PES for compensating the ion beam from an end-Hall ion source proved to be effective in processes of ion-assisted deposition of thin films using reactive gases like O2 or N2. The application of the PES technique makes it possible to increase the lifetime of the ion-assisted deposition system by an order of magnitude (the lifetime with a Ti cathode is at least 60 h and is limited by the replacement life of the deposited cathode insertion).

Development progresses of radio frequency ion source for neutral beam injector in fusion devices.

PubMed

Chang, D H; Jeong, S H; Kim, T S; Park, M; Lee, K W; In, S R

2014-02-01

A large-area RF (radio frequency)-driven ion source is being developed in Germany for the heating and current drive of an ITER device. Negative hydrogen ion sources are the major components of neutral beam injection systems in future large-scale fusion experiments such as ITER and DEMO. RF ion sources for the production of positive hydrogen (deuterium) ions have been successfully developed for the neutral beam heating systems at IPP (Max-Planck-Institute for Plasma Physics) in Germany. The first long-pulse ion source has been developed successfully with a magnetic bucket plasma generator including a filament heating structure for the first NBI system of the KSTAR tokamak. There is a development plan for an RF ion source at KAERI to extract the positive ions, which can be applied for the KSTAR NBI system and to extract the negative ions for future fusion devices such as the Fusion Neutron Source and Korea-DEMO. The characteristics of RF-driven plasmas and the uniformity of the plasma parameters in the test-RF ion source were investigated initially using an electrostatic probe.

Low energy spread ion source with a coaxial magnetic filter

DOEpatents

Leung, Ka-Ngo; Lee, Yung-Hee Yvette

2000-01-01

Multicusp ion sources are capable of producing ions with low axial energy spread which are necessary in applications such as ion projection lithography (IPL) and radioactive ion beam production. The addition of a radially extending magnetic filter consisting of a pair of permanent magnets to the multicusp source reduces the energy spread considerably due to the improvement in the uniformity of the axial plasma potential distribution in the discharge region. A coaxial multicusp ion source designed to further reduce the energy spread utilizes a cylindrical magnetic filter to achieve a more uniform axial plasma potential distribution. The coaxial magnetic filter divides the source chamber into an outer annular discharge region in which the plasma is produced and a coaxial inner ion extraction region into which the ions radially diffuse but from which ionizing electrons are excluded. The energy spread in the coaxial source has been measured to be 0.6 eV. Unlike other ion sources, the coaxial source has the capability of adjusting the radial plasma potential distribution and therefore the transverse ion temperature (or beam emittance).

Laser ion source for isobaric heavy ion collider experiment.

PubMed

Kanesue, T; Kumaki, M; Ikeda, S; Okamura, M

2016-02-01

Heavy-ion collider experiment in isobaric system is under investigation at Relativistic Heavy Ion Collider. For this experiment, ion source is required to maximize the abundance of the intended isotope. The candidate of the experiment is (96)Ru + (96)Zr. Since the natural abundance of particular isotope is low and composition of isotope from ion source depends on the composites of the target, an isotope enriched material may be needed as a target. We studied the performance of the laser ion source required for the experiment for Zr ions.

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

NASA Astrophysics Data System (ADS)

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.

Identification of OBO nonalignments and its implications for OBO enrichment.

PubMed

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.

SAIL—a software system for sample and phenotype availability across biobanks and cohorts

PubMed Central

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

The software architecture of climate models: a graphical comparison of CMIP5 and EMICAR5 configurations

NASA Astrophysics Data System (ADS)

Alexander, K.; Easterbrook, S. M.

2015-01-01

We analyse the source code of eight coupled climate models, selected from those that participated in the CMIP5 (Taylor et al., 2012) or EMICAR5 (Eby et al., 2013; Zickfeld et al., 2013) intercomparison projects. For each model, we sort the preprocessed code into components and subcomponents based on dependency structure. We then create software architecture diagrams which show the relative sizes of these components/subcomponents and the flow of data between them. The diagrams also illustrate several major classes of climate model design; the distribution of complexity between components, which depends on historical development paths as well as the conscious goals of each institution; and the sharing of components between different modelling groups. These diagrams offer insights into the similarities and differences between models, and have the potential to be useful tools for communication between scientists, scientific institutions, and the public.

The software architecture of climate models: a graphical comparison of CMIP5 and EMICAR5 configurations

NASA Astrophysics Data System (ADS)

Alexander, K.; Easterbrook, S. M.

2015-04-01

We analyze the source code of eight coupled climate models, selected from those that participated in the CMIP5 (Taylor et al., 2012) or EMICAR5 (Eby et al., 2013; Zickfeld et al., 2013) intercomparison projects. For each model, we sort the preprocessed code into components and subcomponents based on dependency structure. We then create software architecture diagrams that show the relative sizes of these components/subcomponents and the flow of data between them. The diagrams also illustrate several major classes of climate model design; the distribution of complexity between components, which depends on historical development paths as well as the conscious goals of each institution; and the sharing of components between different modeling groups. These diagrams offer insights into the similarities and differences in structure between climate models, and have the potential to be useful tools for communication between scientists, scientific institutions, and the public.

Liquid metal ion source and alloy for ion emission of multiple ionic species

DOEpatents

Clark, Jr., William M.; Utlaut, Mark W.; Wysocki, Joseph A.; Storms, Edmund K.; Szklarz, Eugene G.; Behrens, Robert G.; Swanson, Lynwood W.; Bell, Anthony E.

1987-06-02

A liquid metal ion source and alloy for the simultaneous ion evaporation of arsenic and boron, arsenic and phosphorus, or arsenic, boron and phosphorus. The ionic species to be evaporated are contained in palladium-arsenic-boron and palladium-arsenic-boron-phosphorus alloys. The ion source, including an emitter means such as a needle emitter and a source means such as U-shaped heater element, is preferably constructed of rhenium and tungsten, both of which are readily fabricated. The ion sources emit continuous beams of ions having sufficiently high currents of the desired species to be useful in ion implantation of semiconductor wafers for preparing integrated circuit devices. The sources are stable in operation, experience little corrosion during operation, and have long operating lifetimes.

Improvement of a plasma uniformity of the 2nd ion source of KSTAR neutral beam injector.

PubMed

Jeong, S H; Kim, T S; Lee, K W; Chang, D H; In, S R; Bae, Y S

2014-02-01

The 2nd ion source of KSTAR (Korea Superconducting Tokamak Advanced Research) NBI (Neutral Beam Injector) had been developed and operated since last year. A calorimetric analysis revealed that the heat load of the back plate of the ion source is relatively higher than that of the 1st ion source of KSTAR NBI. The spatial plasma uniformity of the ion source is not good. Therefore, we intended to identify factors affecting the uniformity of a plasma density and improve it. We estimated the effects of a direction of filament current and a magnetic field configuration of the plasma generator on the plasma uniformity. We also verified that the operation conditions of an ion source could change a uniformity of the plasma density of an ion source.

Adjustable ECR Ion Source Control System: Ion Source Hydrogen Positive Project

NASA Astrophysics Data System (ADS)

Arredondo, I.; Eguiraun, M.; Jugo, J.; Piso, D.; del Campo, M.; Poggi, T.; Varnasseri, S.; Feuchtwanger, J.; Bilbao, J.; Gonzalez, X.; Harper, G.; Muguira, L.; Miracoli, R.; Corres, J.; Belver, D.; Echevarria, P.; Garmendia, N.; Gonzalez, P.; Etxebarria, V.

2015-06-01

ISHP (Ion Source Hydrogen Positive) project consists of a highly versatile ECR type ion source. It has been built for several purposes, on the one hand, to serve as a workbench to test accelerator related technologies and validate in-house made developments, at the first stages. On the other hand, to design an ion source valid as the first step in an actual LINAC. Since this paper is focused on the control system of ISHP, besides the ion source, all the hardware and its control architecture is presented. Nowadays the ion source is able to generate a pulse of positive ions of Hydrogen from 2 μs to a few ms range with a repetition rate ranging from 1 Hz to 50 Hz with a maximum of 45 mA of current. Furthermore, the first experiments with White Rabbit (WR) synchronization system are presented.

Naringin alleviates early brain injury after experimental subarachnoid hemorrhage by reducing oxidative stress and inhibiting apoptosis.

PubMed

Han, Yuwei; Su, Jingyuan; Liu, Xiujuan; Zhao, Yuan; Wang, Chenchen; Li, Xiaoming

2017-07-01

This study aims to clarify the neuroprotective effect of naringin on early brain injury (EBI) following subarachnoid hemorrhage (SAH) and the possible mechanisms of naringin in the treatment of SAH. The endovascular puncture model was performed to induce SAH model in rats and the efficacy of 40mg/kg and 80mg/kg naringin were tested by intraperitoneally administration. SAH grade, neurological score, brain edema, blood-brain barrier permeability, the changes of oxidative stress related factors, apoptosis-related proteins, mitogen-activated protein kinase (MAPK) signaling pathway and neuronal morphology were detected to analyze the potential effect of naringin against SAH. The results demonstrated that naringin significantly ameliorated EBI, including SAH severity, neurologic deficits, brain edema and blood-brain barrier integrity by attenuating SAH-induced oxidative stress and apoptosis, and reduced the oxidant damage and apoptosis by inhibiting the activation of MAPK signaling pathway, which suggested a therapeutic potential of naringin in providing neuroprotection after SAH. Copyright © 2016 Elsevier Inc. All rights reserved.

Retaining clients in an outcome monitoring evaluation study: HIV prevention efforts in community settings.

PubMed

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.

Laser ion source with solenoid field

NASA Astrophysics Data System (ADS)

Kanesue, Takeshi; Fuwa, Yasuhiro; Kondo, Kotaro; Okamura, Masahiro

2014-11-01

Pulse length extension of highly charged ion beam generated from a laser ion source is experimentally demonstrated. The laser ion source (LIS) has been recognized as one of the most powerful heavy ion source. However, it was difficult to provide long pulse beams. By applying a solenoid field (90 mT, 1 m) at plasma drifting section, a pulse length of carbon ion beam reached 3.2 μs which was 4.4 times longer than the width from a conventional LIS. The particle number of carbon ions accelerated by a radio frequency quadrupole linear accelerator was 1.2 × 1011, which was provided by a single 1 J Nd-YAG laser shot. A laser ion source with solenoid field could be used in a next generation heavy ion accelerator.

Ion-source modeling and improved performance of the CAMS high-intensity Cs-sputter ion source

NASA Astrophysics Data System (ADS)

Brown, T. A.; Roberts, M. L.; Southon, J. R.

2000-10-01

The interior of the high-intensity Cs-sputter source used in routine operations at the Center for Accelerator Mass Spectrometry (CAMS) has been computer modeled using the program NEDLab, with the aim of improving negative ion output. Space charge effects on ion trajectories within the source were modeled through a successive iteration process involving the calculation of ion trajectories through Poisson-equation-determined electric fields, followed by calculation of modified electric fields incorporating the charge distribution from the previously calculated ion trajectories. The program has several additional features that are useful in ion source modeling: (1) averaging of space charge distributions over successive iterations to suppress instabilities, (2) Child's Law modeling of space charge limited ion emission from surfaces, and (3) emission of particular ion groups with a thermal energy distribution and at randomized angles. The results of the modeling effort indicated that significant modification of the interior geometry of the source would double Cs + ion production from our spherical ionizer and produce a significant increase in negative ion output from the source. The results of the implementation of the new geometry were found to be consistent with the model results.

DUHOCAMIS: a dual hollow cathode ion source for metal ion beams.

PubMed

Zhao, W J; Müller, M W O; Janik, J; Liu, K X; Ren, X T

2008-02-01

In this paper we describe a novel ion source named DUHOCAMIS for multiply charged metal ion beams. This ion source is derived from the hot cathode Penning ion gauge ion source (JINR, Dubna, 1957). A notable characteristic is the modified Penning geometry in the form of a hollow sputter electrode, coaxially positioned in a compact bottle-magnetic field along the central magnetic line of force. The interaction of the discharge geometry with the inhomogeneous but symmetrical magnetic field enables this device to be operated as hollow cathode discharge and Penning discharge as well. The main features of the ion source are the very high metal ion efficiency (up to 25%), good operational reproducibility, flexible and efficient operations for low charged as well as highly charged ions, compact setup, and easy maintenance. For light ions, e.g., up to titanium, well-collimated beams in the range of several tens of milliamperes of pulsed ion current (1 ms, 10/s) have been reliably performed in long time runs.

Investigation of ISIS and Brookhaven National Laboratory ion source electrodes after extended operation

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

Lettry J.; Alessi J.; Faircloth, D.

2012-02-23

Linac4 accelerator of Centre Europeen de Recherches Nucleaires is under construction and a RF-driven H{sup -} ion source is being developed. The beam current requirement for Linac4 is very challenging: 80 mA must be provided. Cesiated plasma discharge ion sources such as Penning or magnetron sources are also potential candidates. Accelerator ion sources must achieve typical reliability figures of 95% and above. Investigating and understanding the underlying mechanisms involved with source failure or ageing is critical when selecting the ion source technology. Plasma discharge driven surface ion sources rely on molybdenum cathodes. Deformation of the cathode surfaces is visible aftermore » extended operation periods. A metallurgical investigation of an ISIS ion source is presented. The origin of the deformation is twofold: Molybdenum sputtering by cesium ions digs few tenths of mm cavities while a growth of molybdenum is observed in the immediate vicinity. The molybdenum growth under hydrogen atmosphere is hard and loosely bound to the bulk. It is, therefore, likely to peel off and be transported within the plasma volume. The observation of the cathode, anode, and extraction electrodes of the magnetron source operated at BNL for two years are presented. A beam simulation of H{sup -}, electrons, and Cs{sup -} ions was performed with the IBSimu code package to qualitatively explain the observations. This paper describes the operation conditions of the ion sources and discusses the metallurgical analysis and beam simulation results.« less

Investigation of ISIS and Brookhaven National Laboratory ion source electrodes after extended operation

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

Lettry, J.; Gerardin, A.; Pereira, H.

2012-02-15

Linac4 accelerator of Centre Europeen de Recherches Nucleaires is under construction and a RF-driven H{sup -} ion source is being developed. The beam current requirement for Linac4 is very challenging: 80 mA must be provided. Cesiated plasma discharge ion sources such as Penning or magnetron sources are also potential candidates. Accelerator ion sources must achieve typical reliability figures of 95% and above. Investigating and understanding the underlying mechanisms involved with source failure or ageing is critical when selecting the ion source technology. Plasma discharge driven surface ion sources rely on molybdenum cathodes. Deformation of the cathode surfaces is visible aftermore » extended operation periods. A metallurgical investigation of an ISIS ion source is presented. The origin of the deformation is twofold: Molybdenum sputtering by cesium ions digs few tenths of mm cavities while a growth of molybdenum is observed in the immediate vicinity. The molybdenum growth under hydrogen atmosphere is hard and loosely bound to the bulk. It is, therefore, likely to peel off and be transported within the plasma volume. The observation of the cathode, anode, and extraction electrodes of the magnetron source operated at BNL for two years are presented. A beam simulation of H{sup -}, electrons, and Cs{sup -} ions was performed with the IBSimu code package to qualitatively explain the observations. This paper describes the operation conditions of the ion sources and discusses the metallurgical analysis and beam simulation results.« less

Effects of Solvent and Ion Source Pressure on the Analysis of Anabolic Steroids by Low Pressure Photoionization Mass Spectrometry.

PubMed

Liu, Chengyuan; Zhu, Yanan; Yang, Jiuzhong; Zhao, Wan; Lu, Deen; Pan, Yang

2017-04-01

Solvent and ion source pressure were two important factors relating to the photon induced ion-molecule reactions in low pressure photoionization (LPPI). In this work, four anabolic steroids were analyzed by LPPI mass spectrometry. Both the ion species present and their relative abundances could be controlled by switching the solvent and adjusting the ion source pressure. Whereas M •+ , MH + , [M - H 2 O] + , and solvent adducts were observed in positive LPPI, [M - H] - and various oxidation products were abundant in negative LPPI. Changing the solvent greatly affected formation of the ion species in both positive and negative ion modes. The ion intensities of the solvent adduct and oxygen adduct were selectively enhanced when the ion source pressure was elevated from 68 to 800 Pa. The limit of detection could be decreased by increasing the ion source pressure. Graphical Abstract ᅟ.

Effects of Solvent and Ion Source Pressure on the Analysis of Anabolic Steroids by Low Pressure Photoionization Mass Spectrometry

NASA Astrophysics Data System (ADS)

Liu, Chengyuan; Zhu, Yanan; Yang, Jiuzhong; Zhao, Wan; Lu, Deen; Pan, Yang

2017-04-01

Solvent and ion source pressure were two important factors relating to the photon induced ion-molecule reactions in low pressure photoionization (LPPI). In this work, four anabolic steroids were analyzed by LPPI mass spectrometry. Both the ion species present and their relative abundances could be controlled by switching the solvent and adjusting the ion source pressure. Whereas M•+, MH+, [M - H2O]+, and solvent adducts were observed in positive LPPI, [M - H]- and various oxidation products were abundant in negative LPPI. Changing the solvent greatly affected formation of the ion species in both positive and negative ion modes. The ion intensities of the solvent adduct and oxygen adduct were selectively enhanced when the ion source pressure was elevated from 68 to 800 Pa. The limit of detection could be decreased by increasing the ion source pressure.

Ion sources for electric propulsion

NASA Technical Reports Server (NTRS)

Stuhlinger, E.

1971-01-01

Ion systems, which accelerate ions of Cs, Hg, or colloid particles by electrostatic fields, are furthest advanced and ready for application. Four kinds of ion sources have been developed: The contact ionization source for Cs as propellants, the electron bombardment source for Cs or Hg, the RF ionization source for Hg, and the hollow needle spray nozzle for colloidal glycerol particles. In each case, the ion beam must be neutralized by injection of electrons shortly behind the exit orifice to avoid adverse space charge effects.

Linked randomised controlled trials of face-to-face and electronic brief intervention methods to prevent alcohol related harm in young people aged 14-17 years presenting to Emergency Departments (SIPS junior).

PubMed

Deluca, Paolo; Coulton, Simon; Alam, M Fasihul; Cohen, David; Donoghue, Kim; Gilvarry, Eilish; Kaner, Eileen; Maconochie, Ian; McArdle, Paul; McGovern, Ruth; Newbury-Birch, Dorothy; Patton, Robert; Phillips, Ceri; Phillips, Thomas; Russell, Ian; Strang, John; Drummond, Colin

2015-04-10

Alcohol is a major global threat to public health. Although the main burden of chronic alcohol-related disease is in adults, its foundations often lie in adolescence. Alcohol consumption and related harm increase steeply from the age of 12 until 20 years. Several trials focusing upon young people have reported significant positive effects of brief interventions on a range of alcohol consumption outcomes. A recent review of reviews also suggests that electronic brief interventions (eBIs) using internet and smartphone technologies may markedly reduce alcohol consumption compared with minimal or no intervention controls. Interventions that target non-drinking youth are known to delay the onset of drinking behaviours. Web based alcohol interventions for adolescents also demonstrate significantly greater reductions in consumption and harm among 'high-risk' drinkers; however changes in risk status at follow-up for non-drinkers or low-risk drinkers have not been assessed in controlled trials of brief alcohol interventions. The study design comprises two linked randomised controlled trials to evaluate the effectiveness and cost-effectiveness of two intervention strategies compared with screening alone. One trial will focus on high-risk adolescent drinkers attending Emergency Departments (Eds) and the other will focus on those identified as low-risk drinkers or abstinent from alcohol but attending the same ED. Our primary (null) hypothesis is similar for both trials: Personalised Feedback and Brief Advice (PFBA) and Personalised Feedback plus electronic Brief Intervention (eBI) are no more effective than screening alone in alcohol consumed at 12 months after randomisation as measured by the Time-Line Follow-Back 28-day version. Our secondary (null) hypothesis relating to economics states that PFBA and eBI are no more cost-effective than screening alone. In total 1,500 participants will be recruited into the trials, 750 high-risk drinkers and 750 low-risk drinkers or abstainers. Participants will be randomised with equal probability, stratified by centre, to either a screening only control group or one of the two interventions: single session of PFBA or eBI. All participants will be eligible to receive treatment as usual in addition to any trial intervention. Individual participants will be followed up at 6 and 12 months after randomisation. The protocol represents an ambitious innovative programme of work addressing alcohol use in the adolescent population. ISRCTN45300218. Registered 5th July 2014.

Preliminary Tests of a Paul ion Trap as an Ion Source

NASA Astrophysics Data System (ADS)

Sadat Kiai, S. M.; Zirak, A. R.; Elahi, M.; Adlparvar, S.; Mortazavi, B. N.; Safarien, A.; Farhangi, S.; Sheibani, S.; Alhooie, S.; Khalaj, M. M. A.; Dabirzadeh, A. A.; Ruzbehani, M.; Zahedi, F.

2010-10-01

The paper reports on the design and construction of a Paul ion trap as an ion source by using an impact electron ionization technique. Ions are produced in the trap and confined for the specific time which is then extracted and detected by a Faraday cup. Especial electronic configurations are employed between the end caps, ring electrodes, electron gun and a negative voltage for the detector. This configuration allows a constant low level of pure ion source between the pulsed confined ion sources. The present experimental results are based on the production and confinement of Argon ions with good stability and repeatability, but in principle, the technique can be used for various Argon like ions.

Laser ion source with solenoid field

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

Kanesue, Takeshi, E-mail: tkanesue@bnl.gov; Okamura, Masahiro; Fuwa, Yasuhiro

2014-11-10

Pulse length extension of highly charged ion beam generated from a laser ion source is experimentally demonstrated. The laser ion source (LIS) has been recognized as one of the most powerful heavy ion source. However, it was difficult to provide long pulse beams. By applying a solenoid field (90 mT, 1 m) at plasma drifting section, a pulse length of carbon ion beam reached 3.2 μs which was 4.4 times longer than the width from a conventional LIS. The particle number of carbon ions accelerated by a radio frequency quadrupole linear accelerator was 1.2 × 10{sup 11}, which was provided by a single 1 J Nd-YAGmore » laser shot. A laser ion source with solenoid field could be used in a next generation heavy ion accelerator.« less

Laser ion source with solenoid field

DOE PAGES

Kanesue, Takeshi; Fuwa, Yasuhiro; Kondo, Kotaro; ...

2014-11-12

Pulse length extension of highly charged ion beam generated from a laser ion source is experimentally demonstrated. In this study, the laser ion source (LIS) has been recognized as one of the most powerful heavy ion source. However, it was difficult to provide long pulse beams. By applying a solenoid field (90 mT, 1 m) at plasma drifting section, a pulse length of carbon ion beam reached 3.2 μs which was 4.4 times longer than the width from a conventional LIS. The particle number of carbon ions accelerated by a radio frequency quadrupole linear accelerator was 1.2 × 10 11,more » which was provided by a single 1 J Nd-YAG laser shot. A laser ion source with solenoid field could be used in a next generation heavy ion accelerator.« less

Recent Development of IMP LECR3 Ion Source

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

Zhang, Z.M.; Zhao, H.W.; Li, J.Y.

2005-03-15

18GHz microwave has been fed to the LECR3 ion source to produce intense highly charged ion beams although this ion source was designed for 14.5GHz. Then 1.1 emA Ar8+ and 325 e{mu}A Ar11+ were obtained at 18GHz. During the source running for atomic physics experiment, some higher charge state ion beams such as Ar17+ and Ar18+ were detected and have been validated by atomic physics method. Furthermore, a few special gases, e.g. SiH4 and SF6, were tested on LECR3 ion source to produce required ion beams to satisfy the requirements of atomic physics experiments.

Liquid metal ion source assembly for external ion injection into an electron string ion source (ESIS)

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

Segal, M. J., E-mail: mattiti@gmail.com; University of Cape Town, Rondebosch, Cape Town 7700; Bark, R. A.

An assembly for a commercial Ga{sup +} liquid metal ion source in combination with an ion transportation and focusing system, a pulse high-voltage quadrupole deflector, and a beam diagnostics system has been constructed in the framework of the iThemba LABS (Cape Town, South Africa)—JINR (Dubna, Russia) collaboration. First, results on Ga{sup +} ion beam commissioning will be presented. Outlook of further experiments for measurements of charge breeding efficiency in the electron string ion source with the use of external injection of Ga{sup +} and Au{sup +} ion beams will be reported as well.

A 1D ion species model for an RF driven negative ion source

NASA Astrophysics Data System (ADS)

Turner, I.; Holmes, A. J. T.

2017-08-01

A one-dimensional model for an RF driven negative ion source has been developed based on an inductive discharge. The RF source differs from traditional filament and arc ion sources because there are no primary electrons present, and is simply composed of an antenna region (driver) and a main plasma discharge region. However the model does still make use of the classical plasma transport equations for particle energy and flow, which have previously worked well for modelling DC driven sources. The model has been developed primarily to model the Small Negative Ion Facility (SNIF) ion source at CCFE, but may be easily adapted to model other RF sources. Currently the model considers the hydrogen ion species, and provides a detailed description of the plasma parameters along the source axis, i.e. plasma temperature, density and potential, as well as current densities and species fluxes. The inputs to the model are currently the RF power, the magnetic filter field and the source gas pressure. Results from the model are presented and where possible compared to existing experimental data from SNIF, with varying RF power, source pressure.

Detection of explosives using negative ion mobility spectrometry in air based on dopant-assisted thermal ionization.

PubMed

Shahraki, Hassan; Tabrizchi, Mahmoud; Farrokhpor, Hossein

2018-05-26

The ionization source is an essential component of most explosive detectors based on negative ion mobility spectrometry. Conventional ion sources suffer from such inherent limitations as special safety regulations on radioactive sources or generating interfering ions (for non-radioactive sources) such as corona discharge operating in the air. In this study, a new negative ion source is introduced for ion mobility spectrometry that is based on thermal ionization and operates in the air, applicable to explosives detection. Our system consists of a heating filament powered by an isolated power supply connected to negative high voltage. The ionization is assisted by doping chlorinated compounds in the gas phase using chlorinated hydrocarbons in contact with the heating element to yield Cl - reactant ions. Several chlorinated hydrocarbons are evaluated as the reagent chemicals for providing Cl- reactant ions, of which CCl 4 is identified as the best ionizing reagent. The ion source is evaluated by recording the ion mobility spectra of common explosives, including TNT, RDX, and PETN in the air. A detection limit of 150 pg is obtained for TNT. Compared to other ionization sources, the new source is found to be low-cost, simple, and long-lived, making it suited to portable explosives detection devices. Copyright © 2018 Elsevier B.V. All rights reserved.

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

Cuomo, J.J.; Rossnagel, S.M.; Kaufman, H.R.

The work presented in this book deals with ion beam processing for basic sputter etching of samples, for sputter deposition of thin films, for the synthesis of material in thin form, and for the modification of the properties of thin films. The ion energy range covered is from a few tens of eV to about 10,000 eV, with primary interest in the range of about 20 to 1-2 keV, where implantation of the incident ion is a minor effect. Of the types of ion sources and devices available, this book examines principally broad beam ion sources, characterized by high fluxesmore » and large work areas. These sources include the ECR ion source, the Kaufman-type single- and multiple-grid sources, gridless sources such as the Hall effect or closed-drift source, and hydrid sources such as the ionized cluster beam system.« less

Numerical Simulation of Ion Transport in a Nano-Electrospray Ion Source at Atmospheric Pressure

NASA Astrophysics Data System (ADS)

Wang, Wei; Bajic, Steve; John, Benzi; Emerson, David R.

2018-03-01

Understanding ion transport properties from the ion source to the mass spectrometer (MS) is essential for optimizing device performance. Numerical simulation helps in understanding of ion transport properties and, furthermore, facilitates instrument design. In contrast to previously reported numerical studies, ion transport simulations in a continuous injection mode whilst considering realistic space-charge effects have been carried out. The flow field was solved using Reynolds-averaged Navier-Stokes (RANS) equations, and a particle-in-cell (PIC) method was applied to solve a time-dependent electric field with local charge density. A series of ion transport simulations were carried out at different cone gas flow rates, ion source currents, and capillary voltages. A force evaluation analysis reveals that the electric force, the drag force, and the Brownian force are the three dominant forces acting on the ions. Both the experimental and simulation results indicate that cone gas flow rates of ≤250 slph (standard liter per hour) are important for high ion transmission efficiency, as higher cone gas flow rates reduce the ion signal significantly. The simulation results also show that the ion transmission efficiency reduces exponentially with an increased ion source current. Additionally, the ion loss due to space-charge effects has been found to be predominant at a higher ion source current, a lower capillary voltage, and a stronger cone gas counterflow. The interaction of the ion driving force, ion opposing force, and ion dispersion is discussed to illustrate ion transport mechanism in the ion source at atmospheric pressure. [Figure not available: see fulltext.

Numerical Simulation of Ion Transport in a Nano-Electrospray Ion Source at Atmospheric Pressure.

PubMed

Wang, Wei; Bajic, Steve; John, Benzi; Emerson, David R

2018-03-01

Understanding ion transport properties from the ion source to the mass spectrometer (MS) is essential for optimizing device performance. Numerical simulation helps in understanding of ion transport properties and, furthermore, facilitates instrument design. In contrast to previously reported numerical studies, ion transport simulations in a continuous injection mode whilst considering realistic space-charge effects have been carried out. The flow field was solved using Reynolds-averaged Navier-Stokes (RANS) equations, and a particle-in-cell (PIC) method was applied to solve a time-dependent electric field with local charge density. A series of ion transport simulations were carried out at different cone gas flow rates, ion source currents, and capillary voltages. A force evaluation analysis reveals that the electric force, the drag force, and the Brownian force are the three dominant forces acting on the ions. Both the experimental and simulation results indicate that cone gas flow rates of ≤250 slph (standard liter per hour) are important for high ion transmission efficiency, as higher cone gas flow rates reduce the ion signal significantly. The simulation results also show that the ion transmission efficiency reduces exponentially with an increased ion source current. Additionally, the ion loss due to space-charge effects has been found to be predominant at a higher ion source current, a lower capillary voltage, and a stronger cone gas counterflow. The interaction of the ion driving force, ion opposing force, and ion dispersion is discussed to illustrate ion transport mechanism in the ion source at atmospheric pressure. Graphical Abstract.

New ion source for KSTAR neutral beam injection system.

PubMed

Kim, Tae-Seong; Jeong, Seung Ho; In, Sang-Ryul

2012-02-01

The neutral beam injection system (NBI-1) of the KSTAR tokamak can accommodate three ion sources; however, it is currently equipped with only one prototype ion source. In the 2010 and 2011 KSTAR campaigns, this ion source supplied deuterium neutral beam power of 0.7-1.6 MW to the KSTAR plasma with a beam energy of 70-100 keV. A new ion source will be prepared for the 2012 KSTAR campaign with a much advanced performance compared with the previous one. The newly designed ion source has a very large transparency (∼56%) without deteriorating the beam optics, which is designed to deliver a 2 MW injection power of deuterium beams at 100 keV. The plasma generator of the ion source is of a horizontally cusped bucket type, and the whole inner wall, except the cathode filaments and plasma grid side, functions as an anode. The accelerator assembly consists of four multi-circular aperture grids made of copper and four electrode flanges made of aluminum alloy. The electrodes are insulated using PEEK. The ion source will be completed and tested in 2011.

An all permanent magnet electron cyclotron resonance ion source for heavy ion therapy.

PubMed

Cao, Yun; Li, Jia Qing; Sun, Liang Ting; Zhang, Xue Zhen; Feng, Yu Cheng; Wang, Hui; Ma, Bao Hua; Li, Xi Xia

2014-02-01

A high charge state all permanent Electron Cyclotron Resonance ion source, Lanzhou All Permanent ECR ion source no. 3-LAPECR3, has been successfully built at IMP in 2012, which will serve as the ion injector of the Heavy Ion Medical Machine (HIMM) project. As a commercial device, LAPECR3 features a compact structure, small size, and low cost. According to HIMM scenario more than 100 eμA of C(5+) ion beam should be extracted from the ion source, and the beam emittance better than 75 π*mm*mrad. In recent commissioning, about 120 eμA of C(5+) ion beam was got when work gas was CH4 while about 262 eμA of C(5+) ion beam was obtained when work gas was C2H2 gas. The design and construction of the ion source and its low-energy transportation beam line, and the preliminary commissioning results will be presented in detail in this paper.

The negative hydrogen Penning ion gauge ion source for KIRAMS-13 cyclotron

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

An, D. H.; Jung, I. S.; Kang, J.

2008-02-15

The cold-cathode-type Penning ion gauge (PIG) ion source for the internal ion source of KIRAMS-13 cyclotron has been used for generation of negative hydrogen ions. The dc H-beam current of 650 {mu}A from the PIG ion source with the Dee voltage of 40 kV and arc current of 1.0 A is extrapolated from the measured dc extraction beam currents at the low extraction dc voltages. The output optimization of PIG ion source in the cyclotron has been carried out by using various chimneys with different sizes of the expansion gap between the plasma boundary and the chimney wall. This papermore » presents the results of the dc H-extraction measurement and the expansion gap experiment.« less

The direct injection of intense ion beams from a high field electron cyclotron resonance ion source into a radio frequency quadrupole

NASA Astrophysics Data System (ADS)

Rodrigues, G.; Becker, R.; Hamm, R. W.; Baskaran, R.; Kanjilal, D.; Roy, A.

2014-02-01

The ion current achievable from high intensity ECR sources for highly charged ions is limited by the high space charge. This makes classical extraction systems for the transport and subsequent matching to a radio frequency quadrupole (RFQ) accelerator less efficient. The direct plasma injection (DPI) method developed originally for the laser ion source avoids these problems and uses the combined focusing of the gap between the ion source and the RFQ vanes (or rods) and the focusing of the rf fields from the RFQ penetrating into this gap. For high performance ECR sources that use superconducting solenoids, the stray magnetic field of the source in addition to the DPI scheme provides focusing against the space charge blow-up of the beam. A combined extraction/matching system has been designed for a high performance ECR ion source injecting into an RFQ, allowing a total beam current of 10 mA from the ion source for the production of highly charged 238U40+ (1.33 mA) to be injected at an ion source voltage of 60 kV. In this design, the features of IGUN have been used to take into account the rf-focusing of an RFQ channel (without modulation), the electrostatic field between ion source extraction and the RFQ vanes, the magnetic stray field of the ECR superconducting solenoid, and the defocusing space charge of an ion beam. The stray magnetic field is shown to be critical in the case of a matched beam.

The direct injection of intense ion beams from a high field electron cyclotron resonance ion source into a radio frequency quadrupole.

PubMed

Rodrigues, G; Becker, R; Hamm, R W; Baskaran, R; Kanjilal, D; Roy, A

2014-02-01

The ion current achievable from high intensity ECR sources for highly charged ions is limited by the high space charge. This makes classical extraction systems for the transport and subsequent matching to a radio frequency quadrupole (RFQ) accelerator less efficient. The direct plasma injection (DPI) method developed originally for the laser ion source avoids these problems and uses the combined focusing of the gap between the ion source and the RFQ vanes (or rods) and the focusing of the rf fields from the RFQ penetrating into this gap. For high performance ECR sources that use superconducting solenoids, the stray magnetic field of the source in addition to the DPI scheme provides focusing against the space charge blow-up of the beam. A combined extraction/matching system has been designed for a high performance ECR ion source injecting into an RFQ, allowing a total beam current of 10 mA from the ion source for the production of highly charged (238)U(40+) (1.33 mA) to be injected at an ion source voltage of 60 kV. In this design, the features of IGUN have been used to take into account the rf-focusing of an RFQ channel (without modulation), the electrostatic field between ion source extraction and the RFQ vanes, the magnetic stray field of the ECR superconducting solenoid, and the defocusing space charge of an ion beam. The stray magnetic field is shown to be critical in the case of a matched beam.

Inner Source Pickup Ions Observed by Ulysses

NASA Astrophysics Data System (ADS)

Gloeckler, G.

2016-12-01

The existence of an inner source of pickup ions close to the Sun was proposed in order to explain the unexpected discovery of C+ in the high-speed polar solar wind. Here I report on detailed analyses of the composition and the radial and latitudinal variations of inner source pickup ions measured with the Solar Wind Ion Composition Spectrometer on Ulysses from 1991 to 1998, approaching and during solar minimum. We find that the C+ intensity drops off with radial distance R as R-1.53, peaks at mid latitudes and drops to its lowest value in the ecliptic. Not only was C+ observed, but also N+, O+, Ne+, Na+, Mg+, Ar+, S+, K+, CH+, NH+, OH+, H2O+, H3O+, MgH+, HCN+, C2H4+, SO+ and many other singly-charged heavy ions and molecular ions. The measured velocity distributions of inner source pickup C+ and O+ indicate that these inner source pickup ions are most likely produced by charge exchange, photoionization and electron impact ionization of neutrals close to the Sun (within 10 to 30 solar radii). Possible causes for the unexpected latitudinal variations and the neutral source(s) producing the inner source pickup ions as well as plausible production mechanisms for inner source pickup ions will be discussed.

Application of ion thruster technology to a 30-cm multipole sputtering ion source

NASA Technical Reports Server (NTRS)

Robinson, R. S.; Kaufman, H. R.

1976-01-01

A 30-cm electron-bombardment ion source has been designed and fabricated for micromachining and sputtering applications. This source has a multipole magnetic field that employs permanent magnets between permeable pole pieces. An average ion current density of 1 ma/sq cm with 500-eV argon ions was selected as a design operating condition. The ion beam at this operating condition was uniform and well collimated, with an average variation of + or -5 percent over the center 20 cm of the beam at a distance up to 30 cm from the ion source.

Simulation of RF power and multi-cusp magnetic field requirement for H- ion sources

NASA Astrophysics Data System (ADS)

Pathak, Manish; Senecha, V. K.; Kumar, Rajnish; Ghodke, Dharmraj. V.

2016-12-01

A computer simulation study for multi-cusp RF based H- ion source has been carried out using energy and particle balance equation for inductively coupled uniformly dense plasma considering sheath formation near the boundary wall of the plasma chamber for RF ion source used as high current injector for 1 Gev H- Linac project for SNS applications. The average reaction rates for different reactions responsible for H- ion production and destruction have been considered in the simulation model. The RF power requirement for the caesium free H- ion source for a maximum possible H- ion beam current has been derived by evaluating the required current and RF voltage fed to the coil antenna using transformer model for Inductively Coupled Plasma (ICP). Different parameters of RF based H- ion source like excited hydrogen molecular density, H- ion density, RF voltage and current of RF antenna have been calculated through simulations in the presence and absence of multicusp magnetic field to distinctly observe the effect of multicusp field. The RF power evaluated for different H- ion current values have been compared with the experimental reported results showing reasonably good agreement considering the fact that some RF power will be reflected from the plasma medium. The results obtained have helped in understanding the optimum field strength and field free regions suitable for volume emission based H- ion sources. The compact RF ion source exhibits nearly 6 times better efficiency compare to large diameter ion source.

Polyatomic ions from a high current ion implanter driven by a liquid metal ion source.

PubMed

Pilz, W; Laufer, P; Tajmar, M; Böttger, R; Bischoff, L

2017-12-01

High current liquid metal ion sources are well known and found their first application as field emission electric propulsion thrusters in space technology. The aim of this work is the adaption of such kind of sources in broad ion beam technology. Surface patterning based on self-organized nano-structures on, e.g., semiconductor materials formed by heavy mono- or polyatomic ion irradiation from liquid metal (alloy) ion sources (LMAISs) is a very promising technique. LMAISs are nearly the only type of sources delivering polyatomic ions from about half of the periodic table elements. To overcome the lack of only very small treated areas by applying a focused ion beam equipped with such sources, the technology taken from space propulsion systems was transferred into a large single-end ion implanter. The main component is an ion beam injector based on high current LMAISs combined with suited ion optics allocating ion currents in the μA range in a nearly parallel beam of a few mm in diameter. Different types of LMAIS (needle, porous emitter, and capillary) are presented and characterized. The ion beam injector design is specified as well as the implementation of this module into a 200 kV high current ion implanter operating at the HZDR Ion Beam Center. Finally, the obtained results of large area surface modification of Ge using polyatomic Bi 2 + ions at room temperature from a GaBi capillary LMAIS will be presented and discussed.

Polyatomic ions from a high current ion implanter driven by a liquid metal ion source

NASA Astrophysics Data System (ADS)

Pilz, W.; Laufer, P.; Tajmar, M.; Böttger, R.; Bischoff, L.

2017-12-01

High current liquid metal ion sources are well known and found their first application as field emission electric propulsion thrusters in space technology. The aim of this work is the adaption of such kind of sources in broad ion beam technology. Surface patterning based on self-organized nano-structures on, e.g., semiconductor materials formed by heavy mono- or polyatomic ion irradiation from liquid metal (alloy) ion sources (LMAISs) is a very promising technique. LMAISs are nearly the only type of sources delivering polyatomic ions from about half of the periodic table elements. To overcome the lack of only very small treated areas by applying a focused ion beam equipped with such sources, the technology taken from space propulsion systems was transferred into a large single-end ion implanter. The main component is an ion beam injector based on high current LMAISs combined with suited ion optics allocating ion currents in the μA range in a nearly parallel beam of a few mm in diameter. Different types of LMAIS (needle, porous emitter, and capillary) are presented and characterized. The ion beam injector design is specified as well as the implementation of this module into a 200 kV high current ion implanter operating at the HZDR Ion Beam Center. Finally, the obtained results of large area surface modification of Ge using polyatomic Bi2+ ions at room temperature from a GaBi capillary LMAIS will be presented and discussed.

Combined corona discharge and UV photoionization source for ion mobility spectrometry.

PubMed

Bahrami, Hamed; Tabrizchi, Mahmoud

2012-08-15

An ion mobility spectrometer is described which is equipped with two non-radioactive ion sources, namely an atmospheric pressure photoionization and a corona discharge ionization source. The two sources cannot only run individually but are additionally capable of operating simultaneously. For photoionization, a UV lamp was mounted parallel to the axis of the ion mobility cell. The corona discharge electrode was mounted perpendicular to the UV radiation. The total ion current from the photoionization source was verified as a function of lamp current, sample flow rate, and drift field. Simultaneous operation of the two ionization sources was investigated by recording ion mobility spectra of selected samples. The design allows one to observe peaks from either the corona discharge or photoionization individually or simultaneously. This makes it possible to accurately compare peaks in the ion mobility spectra from each individual source. Finally, the instrument's capability for discriminating two peaks appearing in approximately identical drift times using each individual ionization source is demonstrated. Copyright © 2012 Elsevier B.V. All rights reserved.

New Cs sputter ion source with polyatomic ion beams for secondary ion mass spectrometry applications

NASA Astrophysics Data System (ADS)

Belykh, S. F.; Palitsin, V. V.; Veryovkin, I. V.; Kovarsky, A. P.; Chang, R. J. H.; Adriaens, A.; Dowsett, M. G.; Adams, F.

2007-08-01

A simple design for a cesium sputter ion source compatible with vacuum and ion-optical systems as well as with electronics of the commercially available Cameca IMS-4f instrument is reported. This ion source has been tested with the cluster primary ions of Sin- and Cun-. Our experiments with surface characterization and depth profiling conducted to date demonstrate improvements of the analytical capabilities of the secondary ion mass spectrometry instrument due to the nonadditive enhancement of secondary ion emission and shorter ion ranges of polyatomic projectiles compared to atomic ones with the same impact energy.

Capacity Building: Evidence-Based Practice and Adolescents on the Autism Spectrum

ERIC Educational Resources Information Center

Rue, Hanna C.; Knox, Maria

2013-01-01

Empirical research in the treatment of autism spectrum disorders (ASDs) has resulted in the identification of numerous evidence-based interventions (EBIs). Adolescents with an ASD are faced with unique academic challenges, complex social environments, and physiological changes. They often require interventions to aid in acclimating to their…

76 FR 18553 - Agency Forms Undergoing Paperwork Reduction Act Review

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-04

.... Women Involved in Life Learning from Other Women (WILLOW) is an EBI that focuses on health education and.... Proposed Project Community-based Organization (CBO) Monitoring and Evaluation Project (CMEP) of Women Involved in Life Learning from Other Women (WILLOW)--New--National Center for HIV/AIDS, Viral Hepatitis...

Characterization and Performance of a High-Current-Density Ion Implanter with Magnetized Hollow-Cathode Plasma Source

NASA Astrophysics Data System (ADS)

Falkenstein, Zoran; Rej, Donald; Gavrilov, Nikolai

1998-10-01

In a collaboration between the Institute of Electrophysics (IEP) and the Los Alamos National Laboratory (LANL), the IEP has developed an industrial scalable, high-power, large-area ion source for the surface modification of materials. The plasma source of the ion beam source can be described as a pulsed glow discharge with a cold, hollow-cathode in a weak magnetic field. Extraction and focusing of positive ions by an acceleration and ion-optical plate system renders the generation of a homogeneous, large-area ion beam with an averaged total ion current of up to 50 mA at acceleration voltages of up to 50 kV. The principle set-up of the ion beam source as well as some electrical characteristics (gas discharge current and the extracted ion beam current) are presented for a lab-scale prototype. Measurements of the radial ion current density profiles within the ion beam for various discharge parameters, as well as results on surface modification by ion implantation of nitrogen into aluminum and chromium are presented. Finally, a comparison of the applied ion dose with the retained ion doses is given.

Electron cyclotron resonance ion sources in use for heavy ion cancer therapy.

PubMed

Tinschert, K; Iannucci, R; Lang, R

2008-02-01

The use of electron cyclotron resonance (ECR) ion sources for producing ion beams for heavy ion cancer therapy has been established for more than ten years. After the Heavy Ion Medical Accelerator (HIMAC) at Chiba, Japan started therapy of patients with carbon ions in 1994 the first carbon ion beam for patient treatment at the accelerator facility of GSI was delivered in 1997. ECR ion sources are the perfect tool for providing the required ion beams with good stability, high reliability, and easy maintenance after long operating periods. Various investigations were performed at GSI with different combinations of working gas and auxiliary gas to define the optimal beam conditions for an extended use of further ion species for the dedicated Heidelberg Ion Beam Therapy (HIT) facility installed at the Radiological University Hospital Heidelberg, Germany. Commercially available compact all permanent magnet ECR ion sources operated at 14.5 GHz were chosen for this facility. Besides for (12)C(4+) these ion sources are used to provide beams of (1)H(3)(1+), (3)He(1+), and (16)O(6+). The final commissioning at the HIT facility could be finished at the end of 2006.

Characterization of the ITER model negative ion source during long pulse operation

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

Hemsworth, R.S.; Boilson, D.; Crowley, B.

2006-03-15

It is foreseen to operate the neutral beam system of the International Thermonuclear Experimental Reactor (ITER) for pulse lengths extending up to 1 h. The performance of the KAMABOKO III negative ion source, which is a model of the source designed for ITER, is being studied on the MANTIS test bed at Cadarache. This article reports the latest results from the characterization of the ion source, in particular electron energy distribution measurements and the comparison between positive ion and negative ion extraction from the source.

Radio frequency multicusp ion source development (invited)

NASA Astrophysics Data System (ADS)

Leung, K. N.

1996-03-01

The radio-frequency (rf) driven multicusp source was originally developed for use in the Superconducting Super Collider injector. It has been demonstrated that the source can meet the H- beam current and emittance requirements for this application. By employing a porcelain-coated antenna, a clean plasma discharge with very long-life operation can be achieved. Today, the rf source is used to generate both positive and negative hydrogen ion beams and has been tested in various particle accelerator laboratories throughout the world. Applications of this ion source have been extended to other fields such as ion beam lithography, oil-well logging, ion implantation, accelerator mass spectrometry and medical therapy machines. This paper summarizes the latest rf ion source technology and development at the Lawrence Berkeley National Laboratory.

PULSED ION SOURCE

DOEpatents

Ford, F.C.; Ruff, J.W.; Zizzo, S.G.; Cook, B.

1958-11-11

An ion source is described adapted for pulsed operation and producing copious quantities of ions with a particular ion egress geometry. The particular source construction comprises a conical member having a conducting surface formed of a metal with a gas occladed therein and narrow non-conducting portions hereon dividing the conducting surface. A high voltage pulse is applied across the conducting surface or producing a discharge across the surface. After the gas ions have been produced by the discharge, the ions are drawn from the source in a diverging conical beam by a specially constructed accelerating electrode.

Simulation study on ion extraction from electron cyclotron resonance ion sources

NASA Astrophysics Data System (ADS)

Fu, S.; Kitagawa, A.; Yamada, S.

1994-04-01

In order to study beam optics of NIRS-ECR ion source used in the HIMAC project, the EGUN code has been modified to make it capable of modeling ion extraction from a plasma. Two versions of the modified code are worked out with two different methods in which 1D and 2D sheath theories are used, respectively. Convergence problem of the strong nonlinear self-consistent equations is investigated. Simulations on NIRS-ECR ion source and HYPER-ECR ion source are presented in this paper, exhibiting an agreement with the experiment results.

RF synchronized short pulse laser ion source

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

Fuwa, Yasuhiro, E-mail: fuwa@kyticr.kuicr.kyoto-u.ac.jp; Iwashita, Yoshihisa; Tongu, Hiromu

A laser ion source that produces shortly bunched ion beam is proposed. In this ion source, ions are extracted immediately after the generation of laser plasma by an ultra-short pulse laser before its diffusion. The ions can be injected into radio frequency (RF) accelerating bucket of a subsequent accelerator. As a proof-of-principle experiment of the ion source, a RF resonator is prepared and H{sub 2} gas was ionized by a short pulse laser in the RF electric field in the resonator. As a result, bunched ions with 1.2 mA peak current and 5 ns pulse length were observed at themore » exit of RF resonator by a probe.« less

PULSED ION SOURCE

DOEpatents

Martina, E.F.

1958-10-14

An improved pulsed ion source of the type where the gas to be ionized is released within the source by momentary heating of an electrode occluded with the gas is presented. The other details of the ion source construction include an electron emitting filament and a positive reference grid, between which an electron discharge is set up, and electrode means for withdrawing the ions from the source. Due to the location of the gas source behind the electrode discharge region, and the positioning of the vacuum exhaust system on the opposite side of the discharge, the released gas is drawn into the electron discharge and ionized in accurately controlled amounts. Consequently, the output pulses of the ion source may be accurately controlled.

Timeframe Dependent Fragment Ions Observed in In-Source Decay Experiments with β-Casein Using MALDI MS.

PubMed

Sekiya, Sadanori; Nagoshi, Keishiro; Iwamoto, Shinichi; Tanaka, Koichi; Takayama, Mitsuo

2015-09-01

The fragment ions observed with time-of-flight (TOF) and quadrupole ion trap (QIT) TOF mass spectrometers (MS) combined with matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) experiments of phosphorylated analytes β-casein and its model peptide were compared from the standpoint of the residence timeframe of analyte and fragment ions in the MALDI ion source and QIT cell. The QIT-TOF MS gave fragment c-, z'-, z-ANL, y-, and b-ions, and further degraded fragments originating from the loss of neutrals such as H(2)O, NH(3), CH(2)O (from serine), C2H4O (from threonine), and H(3)PO(4), whereas the TOF MS merely showed MALDI source-generated fragment c-, z'-, z-ANL, y-, and w-ions. The fragment ions observed in the QIT-TOF MS could be explained by the injection of the source-generated ions into the QIT cell or a cooperative effect of a little internal energy deposition, a long residence timeframe (140 ms) in the QIT cell, and specific amino acid effects on low-energy CID, whereas the source-generated fragments (c-, z'-, z-ANL, y-, and w-ions) could be a result of prompt radical-initiated fragmentation of hydrogen-abundant radical ions [M + H + H](+) and [M + H - H](-) within the 53 ns timeframe, which corresponds to the delayed extraction time. The further degraded fragment b/y-ions produced in the QIT cell were confirmed by positive- and negative-ion low-energy CID experiments performed on the source-generated ions (c-, z'-, and y-ions). The loss of phosphoric acid (98 u) from analyte and fragment ions can be explained by a slow ergodic fragmentation independent of positive and negative charges.

Timeframe Dependent Fragment Ions Observed in In-Source Decay Experiments with β-Casein Using MALDI MS

NASA Astrophysics Data System (ADS)

Sekiya, Sadanori; Nagoshi, Keishiro; Iwamoto, Shinichi; Tanaka, Koichi; Takayama, Mitsuo

2015-09-01

The fragment ions observed with time-of-flight (TOF) and quadrupole ion trap (QIT) TOF mass spectrometers (MS) combined with matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) experiments of phosphorylated analytes β-casein and its model peptide were compared from the standpoint of the residence timeframe of analyte and fragment ions in the MALDI ion source and QIT cell. The QIT-TOF MS gave fragment c-, z'-, z-ANL, y-, and b-ions, and further degraded fragments originating from the loss of neutrals such as H2O, NH3, CH2O (from serine), C2H4O (from threonine), and H3PO4, whereas the TOF MS merely showed MALDI source-generated fragment c-, z'-, z-ANL, y-, and w-ions. The fragment ions observed in the QIT-TOF MS could be explained by the injection of the source-generated ions into the QIT cell or a cooperative effect of a little internal energy deposition, a long residence timeframe (140 ms) in the QIT cell, and specific amino acid effects on low-energy CID, whereas the source-generated fragments (c-, z'-, z-ANL, y-, and w-ions) could be a result of prompt radical-initiated fragmentation of hydrogen-abundant radical ions [M + H + H]+ and [M + H - H]- within the 53 ns timeframe, which corresponds to the delayed extraction time. The further degraded fragment b/y-ions produced in the QIT cell were confirmed by positive- and negative-ion low-energy CID experiments performed on the source-generated ions (c-, z'-, and y-ions). The loss of phosphoric acid (98 u) from analyte and fragment ions can be explained by a slow ergodic fragmentation independent of positive and negative charges.

Compact 2.45 GHz ECR Ion Source for generation of singly-charged ions

NASA Astrophysics Data System (ADS)

Fatkullin, Riyaz; Bogomolov, Sergey; Kuzmenkov, Konstantin; Efremov, Andrey

2018-04-01

2.45 GHz ECR ion sources are widely used for production of protons, single charged heavy ions and secondary radioactive ion beams. This paper describes the development of a compact ECR ion source based on 2.45 GHz coaxial resonator. The first results of extracted current measurements at different resonator configuration as a function of UHF frequency, power and gas flow are presented.

Tandem-Mirror Ion Source

NASA Technical Reports Server (NTRS)

Biddle, A.; Stone, N.; Reasoner, D.; Chisholm, W.; Reynolds, J.

1986-01-01

Improved ion source produces beam of ions at any kinetic energy from 1 to 1,000 eV, with little spread in energy or angle. Such ion beams useful in studies of surface properties of materials, surface etching, deposition, and development of plasma-diagnostic instrumentation. Tandemmirror ion source uses electrostatic and magnetic fields to keep electrons in ionization chamber and assure uniform output ion beam having low divergence in energy and angle.

System integration of RF based negative ion experimental facility at IPR

NASA Astrophysics Data System (ADS)

Bansal, G.; Bandyopadhyay, M.; Singh, M. J.; Gahlaut, A.; Soni, J.; Pandya, K.; Parmar, K. G.; Sonara, J.; Chakraborty, A.

2010-02-01

The setting up of RF based negative ion experimental facility shall witness the beginning of experiments on the negative ion source fusion applications in India. A 1 MHz RF generator shall launch 100 kW RF power into a single driver on the plasma source to produce a plasma of density ~5 × 1012 cm-3. The source can deliver a negative ion beam of ~10 A with a current density of ~30 mA/cm2 and accelerated to 35 kV through an electrostatic ion accelerator. The experimental system is similar to a RF based negative ion source, BATMAN, presently operating at IPP. The subsystems for source operation are designed and procured principally from indigenous resources, keeping the IPP configuration as a base line. The operation of negative ion source is supported by many subsystems e.g. vacuum pumping system with gate valves, cooling water system, gas feed system, cesium delivery system, RF generator, high voltage power supplies, data acquisition and control system, and different diagnostics. The first experiments of negative ion source are expected to start at IPR from the middle of 2009.

Laser-ablation-based ion source characterization and manipulation for laser-driven ion acceleration

NASA Astrophysics Data System (ADS)

Sommer, P.; Metzkes-Ng, J.; Brack, F.-E.; Cowan, T. E.; Kraft, S. D.; Obst, L.; Rehwald, M.; Schlenvoigt, H.-P.; Schramm, U.; Zeil, K.

2018-05-01

For laser-driven ion acceleration from thin foils (∼10 μm–100 nm) in the target normal sheath acceleration regime, the hydro-carbon contaminant layer at the target surface generally serves as the ion source and hence determines the accelerated ion species, i.e. mainly protons, carbon and oxygen ions. The specific characteristics of the source layer—thickness and relevant lateral extent—as well as its manipulation have both been investigated since the first experiments on laser-driven ion acceleration using a variety of techniques from direct source imaging to knife-edge or mesh imaging. In this publication, we present an experimental study in which laser ablation in two fluence regimes (low: F ∼ 0.6 J cm‑2, high: F ∼ 4 J cm‑2) was applied to characterize and manipulate the hydro-carbon source layer. The high-fluence ablation in combination with a timed laser pulse for particle acceleration allowed for an estimation of the relevant source layer thickness for proton acceleration. Moreover, from these data and independently from the low-fluence regime, the lateral extent of the ion source layer became accessible.

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

He, W.; Zhao, H.W.; Liu, Zh.W.

To study the injection of additional electrons from an external electron gun into the plasma of a Penning ionization gauge (PIG) ion source, a test bench for the external electron-beam enhancement of the PIG (E-PIG) ion source was set up. A source magnet assembly was built to satisfy the request for magnetic field configuration of the E-PIG ion source. Numerical calculations have been done to optimize the magnetic field configuration so as to fit the primary electrons to be fed into the PIG discharge chamber along the spreading magnetic field lines. Many possible methods for improving the performance and stabilitymore » of the PIG ion source have been used in the E-PIG ion source, including the use of multicrystal LaB{sub 6} cathode and optimized axial magnetic field. This article presents a detailed design of the E-PIG ion source. Substantial enhancement of ion charge state is expected to be observed which demonstrates that the E-PIG is a viable alternative to other much more costly and difficult to operate devices for the production of intense ion beams of higher charge state.« less

Review on heavy ion radiotherapy facilities and related ion sources (invited)a)

NASA Astrophysics Data System (ADS)

Kitagawa, A.; Fujita, T.; Muramatsu, M.; Biri, S.; Drentje, A. G.

2010-02-01

Heavy ion radiotherapy awakens worldwide interest recently. The clinical results obtained by the Heavy Ion Medical Accelerator in Chiba at the National Institute of Radiological Sciences in Japan have clearly demonstrated the advantages of carbon ion radiotherapy. Presently, there are four facilities for heavy ion radiotherapy in operation, and several new facilities are under construction or being planned. The most common requests for ion sources are a long lifetime and good stability and reproducibility. Sufficient intensity has been achieved by electron cyclotron resonance ion sources at the present facilities.

Development of Compact Electron Cyclotron Resonance Ion Source with Permanent Magnets for High-Energy Carbon-Ion Therapy

NASA Astrophysics Data System (ADS)

Muramatsu, M.; Kitagawa, A.; Iwata, Y.; Hojo, S.; Sakamoto, Y.; Sato, S.; Ogawa, Hirotsugu; Yamada, S.; Ogawa, Hiroyuki; Yoshida, Y.; Ueda, T.; Miyazaki, H.; Drentje, A. G.

2008-11-01

Heavy-ion cancer treatment is being carried out at the Heavy Ion Medical Accelerator in Chiba (HIMAC) with 140 to 400 MeV/n carbon ions at National Institute of Radiological Sciences (NIRS) since 1994. At NIRS, more than 4,000 patients have been treated, and the clinical efficiency of carbon ion radiotherapy has been demonstrated for many diseases. A more compact accelerator facility for cancer therapy is now being constricted at the Gunma University. In order to reduce the size of the injector (consists of ion source, low-energy beam transport and post-accelerator Linac include these power supply and cooling system), an ion source requires production of highly charged carbon ions, lower electric power for easy installation of the source on a high-voltage platform, long lifetime and easy operation. A compact Electron Cyclotron Resonance Ion Source (ECRIS) with all permanent magnets is one of the best types for this purpose. An ECRIS has advantage for production of highly charged ions. A permanent magnet is suitable for reduce the electric power and cooling system. For this, a 10 GHz compact ECRIS with all permanent magnets (Kei2-source) was developed. The maximum mirror magnetic fields on the beam axis are 0.59 T at the extraction side and 0.87 T at the gas-injection side, while the minimum B strength is 0.25 T. These parameters have been optimized for the production of C4+ based on experience at the 10 GHz NIRS-ECR ion source. The Kei2-source has a diameter of 320 mm and a length of 295 mm. The beam intensity of C4+ was obtained to be 618 eμA under an extraction voltage of 30 kV. Outline of the heavy ion therapy and development of the compact ion source for new facility are described in this paper.

RCNP Project on Polarized {sup 3}He Ion Sources - From Optical Pumping to Cryogenic Method

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

Tanaka, M.; Inomata, T.; Takahashi, Y.

2009-08-04

A polarized {sup 3}He ion source has been developed at RCNP for intermediate and high energy spin physics. Though we started with an OPPIS (Optical Pumping Polarized Ion Source), it could not provide highly polarized {sup 3}He beam because of fundamental difficulties. Subsequently to this unhappy result, we examined novel types of the polarized {sup 3}He ion source, i.e., EPPIS (Electron Pumping Polarized Ion Source), and ECRPIS (ECR Polarized Ion Source) experimentally or theoretically, respectively. However, attainable {sup 3}He polarization degrees and beam intensities were still insufficient for practical use. A few years later, we proposed a new idea formore » the polarized {sup 3}He ion source, SEPIS (Spin Exchange Polarized Ion Source) which is based on enhanced spin-exchange cross sections at low incident energies for {sup 3}He{sup +}+Rb, and its feasibility was experimentally examined.Recently, we started a project on polarized {sup 3}He gas generated by the brute force method with low temperature (approx4 mK) and strong magnetic field (approx17 T), and rapid melting of highly polarized solid {sup 3}He followed by gasification. When this project will be successful, highly polarized {sup 3}He gas will hopefully be used for a new type of the polarized {sup 3}He ion source.« less

Emittance studies of the 2.45 GHz permanent magnet ECR ion source

NASA Astrophysics Data System (ADS)

Zelenak, A.; Bogomolov, S. L.; Yazvitsky, N. Yu.

2004-05-01

During the past several years different types of permanent magnet 2.45 GHz (electron cyclotron resonance) ion sources were developed for production of singly charged ions. Ion sources of this type are used in the first stage of DRIBs project, and are planned to be used in the MASHA mass separator. The emittance of the beam provided by the source is one of the important parameters for these applications. An emittance scanner composed from a set of parallel slits and rotary wire beam profile monitor was used for the studying of the beam emittance characteristics. The emittance of helium and argon ion beams was measured with different shapes of the plasma electrode for several ion source parameters: microwave power, source potential, plasma aperture-puller aperture gap distance, gas pressure. The results of measurements are compared with previous simulations of ion optics.

Ion source and injection line for high intensity medical cyclotron

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

Jia, XianLu, E-mail: jiaxl@ciae.ac.cn; Guan, Fengping; Yao, Hongjuan

2014-02-15

A 14 MeV high intensity compact cyclotron, CYCIAE-14, was built at China Institute of Atomic Energy (CIAE). An injection system based on the external H− ion source was used on CYCIAE-14 so as to provide high intensity beam, while most positron emission tomography cyclotrons adopt internal ion source. A beam intensity of 100 μA/14 MeV was extracted from the cyclotron with a small multi-cusp H− ion source (CIAE-CH-I type) and a short injection line, which the H− ion source of 3 mA/25 keV H− beam with emittance of 0.3π mm mrad and the injection line of with only 1.2 m from themore » extraction of ion source to the medial plane of the cyclotron. To increase the extracted beam intensity of the cyclotron, a new ion source (CIAE-CH-II type) of 9.1 mA was used, with maximum of 500 μA was achieved from the cyclotron. The design and test results of the ion source and injection line optimized for high intensity acceleration will be given in this paper.« less

Negative ion source with external RF antenna

DOEpatents

Leung, Ka-Ngo; Hahto, Sami K.; Hahto, Sari T.

2007-02-13

A radio frequency (RF) driven plasma ion source has an external RF antenna, i.e. the RF antenna is positioned outside the plasma generating chamber rather than inside. The RF antenna is typically formed of a small diameter metal tube coated with an insulator. An external RF antenna assembly is used to mount the external RF antenna to the ion source. The RF antenna tubing is wound around the external RF antenna assembly to form a coil. The external RF antenna assembly is formed of a material, e.g. quartz, which is essentially transparent to the RF waves. The external RF antenna assembly is attached to and forms a part of the plasma source chamber so that the RF waves emitted by the RF antenna enter into the inside of the plasma chamber and ionize a gas contained therein. The plasma ion source is typically a multi-cusp ion source. A converter can be included in the ion source to produce negative ions.

An all permanent magnet electron cyclotron resonance ion source for heavy ion therapy

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

Cao, Yun, E-mail: caoyun@impcas.ac.cn; Li, Jia Qing; Sun, Liang Ting

2014-02-15

A high charge state all permanent Electron Cyclotron Resonance ion source, Lanzhou All Permanent ECR ion source no. 3-LAPECR3, has been successfully built at IMP in 2012, which will serve as the ion injector of the Heavy Ion Medical Machine (HIMM) project. As a commercial device, LAPECR3 features a compact structure, small size, and low cost. According to HIMM scenario more than 100 eμA of C{sup 5+} ion beam should be extracted from the ion source, and the beam emittance better than 75 π*mm*mrad. In recent commissioning, about 120 eμA of C{sup 5+} ion beam was got when work gasmore » was CH{sub 4} while about 262 eμA of C{sup 5+} ion beam was obtained when work gas was C{sub 2}H{sub 2} gas. The design and construction of the ion source and its low-energy transportation beam line, and the preliminary commissioning results will be presented in detail in this paper.« less

Ion source for high-precision mass spectrometry

DOEpatents

Todd, Peter J.; McKown, Henry S.; Smith, David H.

1984-01-01

The invention is directed to a method for increasing the precision of positive-ion relative abundance measurements conducted in a sector mass spectrometer having an ion source for directing a beam of positive ions onto a collimating slit. The method comprises incorporating in the source an electrostatic lens assembly for providing a positive-ion beam of circular cross section for collimation by the slit.

Compact RF ion source for industrial electrostatic ion accelerator

NASA Astrophysics Data System (ADS)

Kwon, Hyeok-Jung; Park, Sae-Hoon; Kim, Dae-Il; Cho, Yong-Sub

2016-02-01

Korea Multi-purpose Accelerator Complex is developing a single-ended electrostatic ion accelerator to irradiate gaseous ions, such as hydrogen and nitrogen, on materials for industrial applications. ELV type high voltage power supply has been selected. Because of the limited space, electrical power, and robust operation, a 200 MHz RF ion source has been developed. In this paper, the accelerator system, test stand of the ion source, and its test results are described.

Compact RF ion source for industrial electrostatic ion accelerator.

PubMed

Kwon, Hyeok-Jung; Park, Sae-Hoon; Kim, Dae-Il; Cho, Yong-Sub

2016-02-01

Korea Multi-purpose Accelerator Complex is developing a single-ended electrostatic ion accelerator to irradiate gaseous ions, such as hydrogen and nitrogen, on materials for industrial applications. ELV type high voltage power supply has been selected. Because of the limited space, electrical power, and robust operation, a 200 MHz RF ion source has been developed. In this paper, the accelerator system, test stand of the ion source, and its test results are described.

A vacuum spark ion source: High charge state metal ion beams

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

Yushkov, G. Yu., E-mail: gyushkov@mail.ru; Nikolaev, A. G.; Frolova, V. P.

2016-02-15

High ion charge state is often important in ion beam physics, among other reasons for the very practical purpose that it leads to proportionately higher ion beam energy for fixed accelerating voltage. The ion charge state of metal ion beams can be increased by replacing a vacuum arc ion source by a vacuum spark ion source. Since the voltage between anode and cathode remains high in a spark discharge compared to the vacuum arc, higher metal ion charge states are generated which can then be extracted as an ion beam. The use of a spark of pulse duration less thanmore » 10 μs and with current up to 10 kA allows the production of ion beams with current of several amperes at a pulse repetition rate of up to 5 pps. We have demonstrated the formation of high charge state heavy ions (bismuth) of up to 15 + and a mean ion charge state of more than 10 +. The physics and techniques of our vacuum spark ion source are described.« less

The modification at CSNS ion source

NASA Astrophysics Data System (ADS)

Liu, S.; Ouyang, H.; Huang, T.; Xiao, Y.; Cao, X.; Lv, Y.; Xue, K.; Chen, W.

2017-08-01

The commissioning of CSNS front end has been finished. Above 15 mA beam intensity is obtained at the end of RFQ. For CSNS ion source, it is a type of penning surface plasma ion source, similar to ISIS ion source. To improve the operation stability and reduce spark rate, some modifications have been performed, including Penning field, extraction optics and post acceleration. PBGUNS is applied to optimize beam extraction. The co-extraction electrons are considered at PBGUNS simulation and various extracted structure are simulated aiming to make the beam through the extracted electrode without loss. The stability of ion source is improved further.

The ionization length in plasmas with finite temperature ion sources

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

Jelic, N.; Kos, L.; Duhovnik, J.

2009-12-15

The ionization length is an important quantity which up to now has been precisely determined only in plasmas which assume that the ions are born at rest, i.e., in discharges known as 'cold ion-source' plasmas. Presented here are the results of our calculations of the ionization lengths in plasmas with an arbitrary ion source temperature. Harrison and Thompson (H and T) [Proc. Phys. Soc. 74, 145 (1959)] found the values of this quantity for the cases of several ion strength potential profiles in the well-known Tonks-Langmuir [Phys. Rev. 34, 876 (1929)] discharge, which is characterized by 'cold' ion temperature. Thismore » scenario is also known as the 'singular' ion-source discharge. The H and T analytic result covers cases of ion sources proportional to exp(betaPHI) with PHI the normalized plasma potential and beta=0,1,2 values, which correspond to particular physical scenarios. Many years following H and T's work, Bissell and Johnson (B and J) [Phys. Fluids 30, 779 (1987)] developed a model with the so-called 'warm' ion-source temperature, i.e., 'regular' ion source, under B and J's particular assumption that the ionization strength is proportional to the local electron density. However, it appears that B and J were not interested in determining the ionization length at all. The importance of this quantity to theoretical modeling was recognized by Riemann, who recently answered all the questions of the most advanced up-to-date plasma-sheath boundary theory with cold ions [K.-U. Riemann, Phys. Plasmas 13, 063508 (2006)] but still without the stiff warm ion-source case solution, which is highly resistant to solution via any available analytic method. The present article is an extension of H and T's results obtained for a single point only with ion source temperature T{sub n}=0 to arbitrary finite ion source temperatures. The approach applied in this work is based on the method recently developed by Kos et al. [Phys. Plasmas 16, 093503 (2009)].« less

Inductively generated streaming plasma ion source

DOEpatents

Glidden, Steven C.; Sanders, Howard D.; Greenly, John B.

2006-07-25

A novel pulsed, neutralized ion beam source is provided. The source uses pulsed inductive breakdown of neutral gas, and magnetic acceleration and control of the resulting plasma, to form a beam. The beam supplies ions for applications requiring excellent control of ion species, low remittance, high current density, and spatial uniformity.

Use of predissociation to enhance the atomic hydrogen ion fraction in ion sources

DOEpatents

Kim, Jinchoon

1979-01-01

A duopigatron ion source is modified by replacing the normal oxide-coated wire filament cathode of the ion source with a hot tungsten oven through which hydrogen gas is fed into the arc chamber. The hydrogen gas is predissociated in the hot oven prior to the arc discharge, and the recombination rate is minimized by hot walls inside of the arc chamber. With the use of the above modifications, the atomic H.sub.1.sup.+ ion fraction output can be increased from the normal 50% to greater than 70% with a corresponding decrease in the H.sub.2.sup.+ and H.sub.3.sup.+ molecular ion fraction outputs from the ion source.

Ion energy spread and current measurements of the rf-driven multicusp ion source

NASA Astrophysics Data System (ADS)

Lee, Y.; Gough, R. A.; Kunkel, W. B.; Leung, K. N.; Perkins, L. T.; Pickard, D. S.; Sun, L.; Vujic, J.; Williams, M. D.; Wutte, D.

1997-03-01

Axial energy spread and useful beam current of positive ion beams have been carried out using a radio frequency (rf)-driven multicusp ion source. Operating the source with a 13.56 MHz induction discharge, the axial energy spread is found to be approximately 3.2 eV. The extractable beam current of the rf-driven source is found to be comparable to that of filament-discharge sources. With a 0.6 mm diameter extraction aperture, a positive hydrogen ion beam current density of 80 mA/cm2 can be obtained at a rf input power of 2.5 kW. The expected source lifetime is much longer than that of filament discharges.

Axial energy spread measurements of an accelerated positive ion beam

NASA Astrophysics Data System (ADS)

Lee, Y.; Gough, R. A.; Kunkel, W. B.; Leung, K. N.; Perkins, L. T.; Pickard, D. S.; Sun, L.; Vujic, J.; Williams, M. D.; Wutte, D.; Mondelli, Alfred A.; Stengl, Gerhard

1997-01-01

A multicusp ion source has been designed for use in ion projection lithography. Longitudinal energy spreads of the extracted positive hydrogen ion beam have been studied using a retarding field energy analyzer. It has been found that the filament-discharge multicusp ion source can deliver a beam with an energy spread less than 3 eV which is required for the ALG-1000 machine. The multicusp ion source can also deliver the current required for the application.

Means for obtaining a metal ion beam from a heavy-ion cyclotron source

DOEpatents

Hudson, E.D.; Mallory, M.L.

1975-08-01

A description is given of a modification to a cyclotron ion source used in producing a high intensity metal ion beam. A small amount of an inert support gas maintains the usual plasma arc, except that it is necessary for the support gas to have a heavy mass, e.g., xenon or krypton as opposed to neon. A plate, fabricated from the metal (or anything that can be sputtered) to be ionized, is mounted on the back wall of the ion source arc chamber and is bombarded by returning energetic low-charged gas ions that fail to cross the initial accelerating gap between the ion source and the accelerating electrode. Some of the atoms that are dislodged from the plate by the returning gas ions become ionized and are extracted as a useful beam of heavy ions. (auth)

Ion source for high-precision mass spectrometry

DOEpatents

Todd, P.J.; McKown, H.S.; Smith, D.H.

1982-04-26

The invention is directed to a method for increasing the precision of positive-ion relative abundance measurements conducted in a sector mass spectrometer having an ion source for directing a beam of positive ions onto a collimating slit. The method comprises incorporating in the source an electrostatic lens assembly for providing a positive-ion beam of circular cross section for collimation by the slit. 2 figures, 3 tables.

Implementation of Design Changes Towards a More Reliable, Hands-off Magnetron Ion Source

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

Sosa, A.; Bollinger, D. S.; Karns, P. R.

As the main H- ion source for the accelerator complex, magnetron ion sources have been used at Fermilab since the 1970’s. At the offline test stand, new R&D is carried out to develop and upgrade the present magnetron-type sources of H- ions of up to 80 mA and 35 keV beam energy in the context of the Proton Improvement Plan. The aim of this plan is to provide high-power proton beams for the experiments at FNAL. In order to reduce the amount of tuning and monitoring of these ion sources, a new electronic system consisting of a current-regulated arc dischargemore » modulator allow the ion source to run at a constant arc current for improved beam output and operation. A solenoid-type gas valve feeds H2 gas into the source precisely and independently of ambient temperature. This summary will cover several studies and design changes that have been tested and will eventually be implemented on the operational magnetron sources at Fermilab. Innovative results for this type of ion source include cathode geometries, solenoid gas valves, current controlled arc pulser, cesium boiler redesign, gas mixtures of hydrogen and nitrogen, and duty factor reduction, with the aim to improve source lifetime, stability, and reducing the amount of tuning needed. In this summary, I will highlight the advances made in ion sources at Fermilab and will outline the directions of the continuing R&D effort.« less

Sample inlet tube for ion source

DOEpatents

Prior, David [Hermiston, OR; Price, John [Richland, WA; Bruce, Jim [Oceanside, CA

2002-09-24

An improved inlet tube is positioned within an aperture through the device to allow the passage of ions from the ion source, through the improved inlet tube, and into the interior of the device. The inlet tube is designed with a larger end and a smaller end wherein the larger end has a larger interior diameter than the interior diameter of the smaller end. The inlet tube is positioned within the aperture such that the larger end is pointed towards the ion source, to receive ions therefrom, and the smaller end is directed towards the interior of the device, to deliver the ions thereto. Preferably, the ion source utilized in the operation of the present invention is a standard electrospray ionization source. Similarly, the present invention finds particular utility in conjunction with analytical devices such as mass spectrometers.

A 5 x 40 cm rectangular-beam multipole ion source

NASA Technical Reports Server (NTRS)

Robinson, R. S.; Kaufman, H. R.; Haynes, C. M.

1981-01-01

A rectangular ion source particularly suited for the continuous sputter processing of materials over a wide area is discussed. A multipole magnetic field configuration was used to design an ion source with a 5 x 40 cm beam area, while a three-grid ion optics system was used to maximize ion current density at the design ion energy of 500 eV. An average extracted current density of about 4 mA/sq cm could be obtained from 500 eV Ar ions. The difference between the experimental performance and the design value of 6 mA/sq cm is attributed to grid misalignment due to thermal expansion. The discharge losses at typical operating conditions ranged from about 600 to 1000 eV/ion, in reasonable agreement with the design value of 800 eV/ion. The use of multiple rectangular-beam ion sources to process wider areas than would be possible with a single source was also studied, and the most uniform coverage was found to be obtainable with a 0 to 2 cm overlap.

Static time-of-flight secondary ion mass spectrometry analysis of microelectronics related substrates using a polyatomic ion source

NASA Astrophysics Data System (ADS)

Ravanel, X.; Trouiller, C.; Juhel, M.; Wyon, C.; Kwakman, L. F. Tz.; Léonard, D.

2008-12-01

Recent time-of-flight secondary ion mass spectrometry studies using primary ion cluster sources such as Au n+, SF 5+, Bi n+ or C 60+ have shown the great advantages in terms of secondary ion yield enhancement and ion formation efficiency of polyatomic ion sources as compared to monoatomic ion sources like the commonly used Ga +. In this work, the effective gains provided by such a source in the static ToF-SIMS analysis of microelectronics devices were investigated. Firstly, the influence of the number of atoms in the primary cluster ion on secondary ion formation was studied for physically adsorbed di-isononyl phthalate (DNP) (plasticizer) and perfluoropolyether (PFPE). A drastic increase in secondary ion formation efficiency and a much lower detection limit were observed when using a polyatomic primary ion. Moreover, the yield of the higher mass species was much enhanced indicating a lower degree of fragmentation that can be explained by the fact that the primary ion energy is spread out more widely, or that there is a lower energy per incoming ion. Secondly, the influence of the number of Bi atoms in the Bi n primary ion on the information depth was studied using reference thermally grown silicon oxide samples. The information depth provided by a Bi n cluster was shown to be lowered when the number of atoms in the aggregate was increased.

Operation Status of the J-PARC Negative Hydrogen Ion Source

NASA Astrophysics Data System (ADS)

Oguri, H.; Ikegami, K.; Ohkoshi, K.; Namekawa, Y.; Ueno, A.

2011-09-01

A cesium-free negative hydrogen ion source driven with a lanthanum hexaboride (LaB6) filament is being operated without any serious trouble for approximately four years in J-PARC. Although the ion source is capable of producing an H- ion current of more than 30 mA, the current is routinely restricted to approximately 16 mA at present for the stable operation of the RFQ linac which has serious discharge problem from September 2008. The beam run is performed during 1 month cycle, which consisted of a 4-5 weeks beam operation and a few days down-period interval. At the recent beam run, approximately 700 h continuous operation was achieved. At every runs, the beam interruption time due to the ion source failure is a few hours, which correspond to the ion source availability of more than 99%. The R&D work is being performed in parallel with the operation in order to enhance the further beam current. As a result, the H- ion current of 61 mA with normalized rms emittance of 0.26 πmm.mrad was obtained by adding a cesium seeding system to a J-PARC test ion source which has the almost same structure with the present J-PARC ion source.

A Collison nebulizer as an ion source for mass spectrometry analysis

NASA Astrophysics Data System (ADS)

Pervukhin, V. V.; Sheven', D. G.; Kolomiets, Yu. N.

2014-12-01

It is proposed to use a Collison nebulizer as a source of ionization for mass-spectrometry with ionization at atmospheric pressure. This source does not require an electric voltage, radioactive sources, heaters, or liquid pumps. It is shown that the number of ions produced by the Collison nebulizer is ten times greater than the quantity of ions produced by the 63Ni radioactive source and three to four times greater than the number of ions produced with sonic ionization devices.

Measurement of Epistemological Beliefs: Psychometric Properties of the EQEBI Test Scores

ERIC Educational Resources Information Center

Ordonez, Xavier G.; Ponsoda, Vicente; Abad, Francisco J.; Romero, Sonia J.

2009-01-01

This article proposes a new test (called the EQEBI) for the measurement of epistemological beliefs, integrating and extending the Epistemological Questionnaire (EQ) and the Epistemic Beliefs Inventory (EBI). In Study 1, the two tests were translated and applied to a Spanish-speaking sample. A detailed dimensionality exploration, by means of the…

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

ERIC Educational Resources Information Center

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.…

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

ERIC Educational Resources Information Center

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…

Sound Speed and Attenuation in Multiphase Media

DTIC Science & Technology

2009-01-01

100 to 300 m/s for sandy sediments with porosities of 40-50%. Hastrup [13:121-127] reports empirical relationships that relative speed ratios 1.0 ≤ cb...Eby, "Acoustic attenuation in a liquid layer over a "slow" viscoelastic solid", J. Acoust. Soc. Amer. 3496), 836-843, 1962 [13] O. F. Hastrup

HMMER web server: 2018 update.

PubMed

Potter, Simon C; Luciani, Aurélien; Eddy, Sean R; Park, Youngmi; Lopez, Rodrigo; Finn, Robert D

2018-06-14

The HMMER webserver [http://www.ebi.ac.uk/Tools/hmmer] is a free-to-use service which provides fast searches against widely used sequence databases and profile hidden Markov model (HMM) libraries using the HMMER software suite (http://hmmer.org). The results of a sequence search may be summarized in a number of ways, allowing users to view and filter the significant hits by domain architecture or taxonomy. For large scale usage, we provide an application programmatic interface (API) which has been expanded in scope, such that all result presentations are available via both HTML and API. Furthermore, we have refactored our JavaScript visualization library to provide standalone components for different result representations. These consume the aforementioned API and can be integrated into third-party websites. The range of databases that can be searched against has been expanded, adding four sequence datasets (12 in total) and one profile HMM library (6 in total). To help users explore the biological context of their results, and to discover new data resources, search results are now supplemented with cross references to other EMBL-EBI databases.

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

PubMed

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.

Text processing through Web services: calling Whatizit.

PubMed

Rebholz-Schuhmann, Dietrich; Arregui, Miguel; Gaudan, Sylvain; Kirsch, Harald; Jimeno, Antonio

2008-01-15

Text-mining (TM) solutions are developing into efficient services to researchers in the biomedical research community. Such solutions have to scale with the growing number and size of resources (e.g. available controlled vocabularies), with the amount of literature to be processed (e.g. about 17 million documents in PubMed) and with the demands of the user community (e.g. different methods for fact extraction). These demands motivated the development of a server-based solution for literature analysis. Whatizit is a suite of modules that analyse text for contained information, e.g. any scientific publication or Medline abstracts. Special modules identify terms and then link them to the corresponding entries in bioinformatics databases such as UniProtKb/Swiss-Prot data entries and gene ontology concepts. Other modules identify a set of selected annotation types like the set produced by the EBIMed analysis pipeline for proteins. In the case of Medline abstracts, Whatizit offers access to EBI's in-house installation via PMID or term query. For large quantities of the user's own text, the server can be operated in a streaming mode (http://www.ebi.ac.uk/webservices/whatizit).

Evaluating and optimizing horticultural regimes in space plant growth facilities

NASA Technical Reports Server (NTRS)

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

2004-01-01

In designing innovative space plant growth facilities (SPGF) for long duration space flight, various limitations must be addressed including onboard resources: volume, energy consumption, heat transfer and crew labor expenditure. The required accuracy in evaluating on board resources by using the equivalent mass methodology and applying it to the design of such facilities is not precise. This is due to the uncertainty of the structure and not completely understanding the properties of all associated hardware, including the technology in these systems. We present a simple criteria of optimization for horticultural regimes in SPGF: Qmax = max [M x (EBI)2/(V x E x T], where M is the crop harvest in terms of total dry biomass in the plant growth system; EBI is the edible biomass index (harvest index), V is volume occupied by the crop; E is the crop light energy supply during growth; T is the crop growth duration. The criterion reflects directly on the consumption of onboard resources for crop production. c2004 COSPAR. Published by Elsevier Ltd. All rights reserved.

E-MSD: an integrated data resource for bioinformatics.

PubMed

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

2004-01-01

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 Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD 'atlas pages' show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins. We have also implemented a novel search interface that begins to integrate separate MSD search services in a single graphical tool. We have worked closely with collaborators to build a new visualization tool that can present both structure and sequence data in a unified interface, and this data viewer is now used throughout the MSD services for the visualization and presentation of search results. Examples showcasing the functionality and power of these tools are available from tutorial webpages (http://www. ebi.ac.uk/msd-srv/docs/roadshow_tutorial/).

E-MSD: an integrated data resource for bioinformatics

PubMed Central

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

2004-01-01

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 Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD ‘atlas pages’ show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins. We have also implemented a novel search interface that begins to integrate separate MSD search services in a single graphical tool. We have worked closely with collaborators to build a new visualization tool that can present both structure and sequence data in a unified interface, and this data viewer is now used throughout the MSD services for the visualization and presentation of search results. Examples showcasing the functionality and power of these tools are available from tutorial webpages (http://www.ebi.ac.uk/msd-srv/docs/roadshow_tutorial/). PMID:14681397

A Call to Develop Evidence-based Interventions to Reduce Sexually Transmitted Infections in Juvenile Justice Populations.

PubMed

Gates, Madison L; Staples-Horne, Michelle; Cartier, Jeanne; Best, Candace; Stone, Rebecca; Walker, Veronica; Hastings, Beverly; Yoo, Wonsuk; Webb, Nancy C; Braithwaite, Ronald L

2016-01-01

Sexually transmitted infections (STIs), including human immunodeficiency virus (HIV) risk, are a significant health issue for young women (ages 16-21), especially African Americans with a juvenile justice history. Studies have found that 44% of young African American women have had at least one STI compared to 24.1% for all young women. The rate of STIs among young women with juvenile justice histories, particularly African Americans, is likely much higher than their non-detained peers. Yet, there are few evidence-based interventions (EBIs) designed specifically for the detained population. In 2014, the Centers for Disease Control and Prevention's Compendium of Evidence-Based Interventions and Best Practices for HIV Prevention listed few programs that comprehensively included components related to mental health, intimate relationships and high risk sexual behaviors that would be salient for a detained population. Further, many EBIs have had limited or no long-term protective effect. We propose that interrelated factors (mental health, substance use, trauma and intimate relationships) can effectively decrease risk and increase protective behaviors for the detained population most at risk.

The EMBL nucleotide sequence database

PubMed Central

Stoesser, Guenter; Baker, Wendy; van den Broek, Alexandra; Camon, Evelyn; Garcia-Pastor, Maria; Kanz, Carola; Kulikova, Tamara; Lombard, Vincent; Lopez, Rodrigo; Parkinson, Helen; Redaschi, Nicole; Sterk, Peter; Stoehr, Peter; Tuli, Mary Ann

2001-01-01

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via ftp, email and World Wide Web interfaces. EBI’s Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many specialized databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. PMID:11125039

"Boring" family routines reduce non-communicable diseases: a commentary and call for action.

PubMed

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.

Provider Perspectives on Evidence-Based HIV Prevention Interventions: Barriers and Facilitators to Implementation

PubMed Central

Dickson-Gomez, Julia

2011-01-01

Abstract Since the beginning of the HIV/AIDS epidemic, community-based organizations (CBOs) have been key players in combating this disease through grassroots prevention programs and close ties to at-risk populations. Increasingly, both funding agencies and public health institutions require that CBOs implement evidence-based HIV prevention interventions, most of which are researcher developed. However, after completing training for these evidence-based interventions (EBIs), agencies may either abandon plans to implement them or significantly modify the intervention. Based on 22 semistructured interviews with HIV prevention service providers, this article explores the barriers and facilitators to dissemination and implementation of EBIs included in the Centers for Disease Control and Prevention's (CDC) Diffusion of Effective Behavioral Interventions (DEBI) program. Results suggest that there is a tension between the need to implement interventions with fidelity and the lack of guidance on how to adapt the interventions for their constituencies and organizational contexts. Findings suggest the need for HIV prevention intervention development and dissemination that integrate community partners in all phases of research and dissemination. PMID:21323564

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

PubMed Central

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

Method and source for producing a high concentration of positively charged molecular hydrogen or deuterium ions

DOEpatents

Ehlers, Kenneth W.; Leung, Ka-Ngo

1988-01-01

A high concentration of positive molecular ions of hydrogen or deuterium gas is extracted from a positive ion source having a short path length of extracted ions, relative to the mean free path of the gas molecules, to minimize the production of other ion species by collision between the positive ions and gas molecules. The ion source has arrays of permanent magnets to produce a multi-cusp magnetic field in regions remote from the plasma grid and the electron emitters, for largely confining the plasma to the space therebetween. The ion source has a chamber which is short in length, relative to its transverse dimensions, and the electron emitters are at an even shorter distance from the plasma grid, which contains one or more extraction apertures.

Intense beam production of highly charged heavy ions by the superconducting electron cyclotron resonance ion source SECRAL.

PubMed

Zhao, H W; Sun, L T; Zhang, X Z; Guo, X H; Cao, Y; Lu, W; Zhang, Z M; Yuan, P; Song, M T; Zhao, H Y; Jin, T; Shang, Y; Zhan, W L; Wei, B W; Xie, D Z

2008-02-01

There has been increasing demand to provide higher beam intensity and high enough beam energy for heavy ion accelerator and some other applications, which has driven electron cyclotron resonance (ECR) ion source to produce higher charge state ions with higher beam intensity. One of development trends for highly charged ECR ion source is to build new generation ECR sources by utilization of superconducting magnet technology. SECRAL (superconducting ECR ion source with advanced design in Lanzhou) was successfully built to produce intense beams of highly charged ion for Heavy Ion Research Facility in Lanzhou (HIRFL). The ion source has been optimized to be operated at 28 GHz for its maximum performance. The superconducting magnet confinement configuration of the ion source consists of three axial solenoid coils and six sextupole coils with a cold iron structure as field booster and clamping. An innovative design of SECRAL is that the three axial solenoid coils are located inside of the sextupole bore in order to reduce the interaction forces between the sextupole coils and the solenoid coils. For 28 GHz operation, the magnet assembly can produce peak mirror fields on axis of 3.6 T at injection, 2.2 T at extraction, and a radial sextupole field of 2.0 T at plasma chamber wall. During the commissioning phase at 18 GHz with a stainless steel chamber, tests with various gases and some metals have been conducted with microwave power less than 3.5 kW by two 18 GHz rf generators. It demonstrates the performance is very promising. Some record ion beam intensities have been produced, for instance, 810 e microA of O(7+), 505 e microA of Xe(20+), 306 e microA of Xe(27+), and so on. The effect of the magnetic field configuration on the ion source performance has been studied experimentally. SECRAL has been put into operation to provide highly charged ion beams for HIRFL facility since May 2007.

Intense beam production of highly charged heavy ions by the superconducting electron cyclotron resonance ion source SECRAL (invited)a)

NASA Astrophysics Data System (ADS)

Zhao, H. W.; Sun, L. T.; Zhang, X. Z.; Guo, X. H.; Cao, Y.; Lu, W.; Zhang, Z. M.; Yuan, P.; Song, M. T.; Zhao, H. Y.; Jin, T.; Shang, Y.; Zhan, W. L.; Wei, B. W.; Xie, D. Z.

2008-02-01

There has been increasing demand to provide higher beam intensity and high enough beam energy for heavy ion accelerator and some other applications, which has driven electron cyclotron resonance (ECR) ion source to produce higher charge state ions with higher beam intensity. One of development trends for highly charged ECR ion source is to build new generation ECR sources by utilization of superconducting magnet technology. SECRAL (superconducting ECR ion source with advanced design in Lanzhou) was successfully built to produce intense beams of highly charged ion for Heavy Ion Research Facility in Lanzhou (HIRFL). The ion source has been optimized to be operated at 28GHz for its maximum performance. The superconducting magnet confinement configuration of the ion source consists of three axial solenoid coils and six sextupole coils with a cold iron structure as field booster and clamping. An innovative design of SECRAL is that the three axial solenoid coils are located inside of the sextupole bore in order to reduce the interaction forces between the sextupole coils and the solenoid coils. For 28GHz operation, the magnet assembly can produce peak mirror fields on axis of 3.6T at injection, 2.2T at extraction, and a radial sextupole field of 2.0T at plasma chamber wall. During the commissioning phase at 18GHz with a stainless steel chamber, tests with various gases and some metals have been conducted with microwave power less than 3.5kW by two 18GHz rf generators. It demonstrates the performance is very promising. Some record ion beam intensities have been produced, for instance, 810eμA of O7+, 505eμA of Xe20+, 306eμA of Xe27+, and so on. The effect of the magnetic field configuration on the ion source performance has been studied experimentally. SECRAL has been put into operation to provide highly charged ion beams for HIRFL facility since May 2007.

Composition of inner-source heavy pickup ions at 1 AU: SOHO/CELIAS/CTOF observations. Implications for the production mechanisms

NASA Astrophysics Data System (ADS)

Taut, A.; Berger, L.; Drews, C.; Wimmer-Schweingruber, R. F.

2015-04-01

Context. Pickup ions in the inner heliosphere mainly originate in two sources, one interstellar and one in the inner solar system. In contrast to the interstellar source that is comparatively well understood, the nature of the inner source has not been clearly identified. Former results obtained with the Solar Wind Ion Composition Spectrometer on-board the Ulysses spacecraft revealed that the composition of inner-source pickup ions is similar, but not equal, to the elemental solar-wind composition. These observations suffered from very low counting statistics of roughly one C+ count per day. Aims: Because the composition of inner-source pickup ions could lead to identifying their origin, we used data from the Charge-Time-Of-Flight sensor on-board the Solar and Heliospheric Observatory. It offers a large geometry factor that results in about 100 C+ counts per day combined with an excellent mass-per-charge resolution. These features enable a precise determination of the inner-source heavy pickup ion composition at 1 AU. To address the production mechanisms of inner-source pickup ions, we set up a toy model based on the production scenario involving the passage of solar-wind ions through thin dust grains to explain the observed deviations of the inner-source PUI and the elemental solar-wind composition. Methods: An in-flight calibration of the sensor allows identification of heavy pickup ions from pulse height analysis data by their mass-per-charge. A statistical analysis was performed to derive the inner-source heavy pickup ion relative abundances of N+, O+, Ne+, Mg+, Mg2+, and Si+ compared to C+. Results: Our results for the inner-source pickup ion composition are in good agreement with previous studies and confirm the deviations from the solar-wind composition. The large geometry factor of the Charge-Time-of-Flight sensor even allowed the abundance ratios of the two most prominent pickup ions, C+ and O+, to be investigated at varying solar-wind speeds. We found that the O+/C+ ratio increases systematically with higher solar-wind speeds. This observation is an unprecedented feature characterising the production of inner-source pickup ions. Comparing our observations to the toy model results, we find that both the deviation from the solar-wind composition and the solar-wind-speed dependent O+/C+ ratio can be explained.

Simulation of cesium injection and distribution in rf-driven ion sources for negative hydrogen ion generation.

PubMed

Gutser, R; Fantz, U; Wünderlich, D

2010-02-01

Cesium seeded sources for surface generated negative hydrogen ions are major components of neutral beam injection systems in future large-scale fusion experiments such as ITER. Stability and delivered current density depend highly on the cesium conditions during plasma-on and plasma-off phases of the ion source. The Monte Carlo code CSFLOW3D was used to study the transport of neutral and ionic cesium in both phases. Homogeneous and intense flows were obtained from two cesium sources in the expansion region of the ion source and from a dispenser array, which is located 10 cm in front of the converter surface.

Evolution of Instrumentation for the Study of Gas-Phase Ion/Ion Chemistry via Mass Spectrometry

PubMed Central

Xia, Yu; McLuckey, Scott A.

2008-01-01

The scope of gas phase ion/ion chemistry accessible to mass spectrometry is largely defined by the available tools. Due to the development of novel instrumentation, a wide range of reaction phenomenologies have been noted, many of which have been studied extensively and exploited for analytical applications. This perspective presents the development of mass spectrometry-based instrumentation for the study of the gas phase ion/ion chemistry in which at least one of the reactants is multiply-charged. The instrument evolution is presented within the context of three essential elements required for any ion/ion reaction study: the ionization source(s), the reaction vessel or environment, and the mass analyzer. Ionization source arrangements have included source combinations that allow for reactions between multiply charged ions of one polarity and singly charged ions of opposite polarity, arrangements that enable the study of reactions of multiply charged ions of opposite polarity, and most recently, arrangements that allow for ion formation from more than two ion sources. Gas phase ion/ion reaction studies have been performed at near atmospheric pressure in flow reactor designs and within electrodynamic ion traps operated in the mTorr range. With ion trap as a reaction vessel, ionization and reaction processes can be independently optimized and ion/ion reactions can be implemented within the context of MSn experiments. Spatial separation of the reaction vessel from the mass analyzer allows for the use of any form of mass analysis in conjunction with ion/ion reactions. Time-of-flight mass analysis, for example, has provided significant improvements in mass analysis figures of merit relative to mass filters and ion traps. PMID:18083527

Recent operation of the FNAL magnetron H- ion source

NASA Astrophysics Data System (ADS)

Karns, P. R.; Bollinger, D. S.; Sosa, A.

2017-08-01

This paper will detail changes in the operational paradigm of the Fermi National Accelerator Laboratory (FNAL) magnetron H- ion source due to upgrades in the accelerator system. Prior to November of 2012 the H- ions for High Energy Physics (HEP) experiments were extracted at ˜18 keV vertically downward into a 90 degree bending magnet and accelerated through a Cockcroft-Walton accelerating column to 750 keV. Following the upgrade in the fall of 2012 the H- ions are now directly extracted from a magnetron at 35 keV and accelerated to 750 keV by a Radio Frequency Quadrupole (RFQ). This change in extraction energy as well as the orientation of the ion source required not only a redesign of the ion source, but an updated understanding of its operation at these new values. Discussed in detail are the changes to the ion source timing, arc discharge current, hydrogen gas pressure, and cesium delivery system that were needed to maintain consistent operation at >99% uptime for HEP, with an increased ion source lifetime of over 9 months.

Development and characterization of a high-reliability, extended-lifetime H- ion source

NASA Astrophysics Data System (ADS)

Becerra, Gabriel; Barrows, Preston; Sherman, Joseph

2015-11-01

Phoenix Nuclear Labs (PNL) has designed and constructed a long-lifetime, negative hydrogen (H-) ion source, in partnership with Fermilab for an ion beam injector servicing future Intensity Frontier particle accelerators. The specifications for the low-energy beam transport (LEBT) section are 5-10 mA of continuous H- ion current at 30 keV with <0.2 π-mm-mrad emittance. Existing ion sources at Fermilab rely on plasma-facing electrodes, limiting their lifetime to a few hundred hours, while requiring relatively high gas loads on downstream components. PNL's design features an electron cyclotron resonance (ECR) microwave plasma driver which has been extensively developed in positive ion source systems, having demonstrated 1000+ hours of operation and >99% continuous uptime at PNL. Positive ions and hyperthermal neutrals drift toward a low-work-function surface, where a fraction is converted into H- hydrogen ions, which are subsequently extracted into a low-energy beam using electrostatic lenses. A magnetic filter preferentially removes high-energy electrons emitted by the source plasma, in order to mitigate H- ion destruction via electron-impact detachment. The design of the source subsystems and preliminary diagnostic results will be presented.

Design of a compact all-permanent magnet ECR ion source injector for ReA at the MSU NSCL

NASA Astrophysics Data System (ADS)

Pham, Alfonse N.; Leitner, Daniela; Glennon, Patrick; Ottarson, Jack; Lawton, Don; Portillo, Mauricio; Machicoane, Guillaume; Wenstrom, John; Lajoie, Andrew

2016-06-01

The design of a compact all-permanent magnet electron cyclotron resonance (ECR) ion source injector for the ReAccelerator Facility (ReA) at the Michigan State University (MSU) National Superconducting Cyclotron Laboratory (NSCL) is currently being carried out. The ECR ion source injector will complement the electron beam ion trap (EBIT) charge breeder as an off-line stable ion beam injector for the ReA linac. The objective of the ECR ion source injector is to provide continuous-wave beams of heavy ions from hydrogen to masses up to 136Xe within the ReA charge-to-mass ratio (Q / A) operational range from 0.2 to 0.5. The ECR ion source will be mounted on a high-voltage platform that can be adjusted to obtain the required 12 keV/u injection energy into a room temperature radio-frequency quadrupole (RFQ) for further acceleration. The beam line consists of a 30 kV tetrode extraction system, mass analyzing section, and optical matching section for injection into the existing ReA low energy beam transport (LEBT) line. The design of the ECR ion source and the associated beam line are discussed.

Bright focused ion beam sources based on laser-cooled atoms

PubMed Central

McClelland, J. J.; Steele, A. V.; Knuffman, B.; Twedt, K. A.; Schwarzkopf, A.; Wilson, T. M.

2016-01-01

Nanoscale focused ion beams (FIBs) represent one of the most useful tools in nanotechnology, enabling nanofabrication via milling and gas-assisted deposition, microscopy and microanalysis, and selective, spatially resolved doping of materials. Recently, a new type of FIB source has emerged, which uses ionization of laser cooled neutral atoms to produce the ion beam. The extremely cold temperatures attainable with laser cooling (in the range of 100 μK or below) result in a beam of ions with a very small transverse velocity distribution. This corresponds to a source with extremely high brightness that rivals or may even exceed the brightness of the industry standard Ga+ liquid metal ion source. In this review we discuss the context of ion beam technology in which these new ion sources can play a role, their principles of operation, and some examples of recent demonstrations. The field is relatively new, so only a few applications have been demonstrated, most notably low energy ion microscopy with Li ions. Nevertheless, a number of promising new approaches have been proposed and/or demonstrated, suggesting that a rapid evolution of this type of source is likely in the near future. PMID:27239245

Bright focused ion beam sources based on laser-cooled atoms

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

McClelland, J. J.; Wilson, T. M.; Steele, A. V.

2016-03-15

Nanoscale focused ion beams (FIBs) represent one of the most useful tools in nanotechnology, enabling nanofabrication via milling and gas-assisted deposition, microscopy and microanalysis, and selective, spatially resolved doping of materials. Recently, a new type of FIB source has emerged, which uses ionization of laser cooled neutral atoms to produce the ion beam. The extremely cold temperatures attainable with laser cooling (in the range of 100 μK or below) result in a beam of ions with a very small transverse velocity distribution. This corresponds to a source with extremely high brightness that rivals or may even exceed the brightness of themore » industry standard Ga{sup +} liquid metal ion source. In this review, we discuss the context of ion beam technology in which these new ion sources can play a role, their principles of operation, and some examples of recent demonstrations. The field is relatively new, so only a few applications have been demonstrated, most notably low energy ion microscopy with Li ions. Nevertheless, a number of promising new approaches have been proposed and/or demonstrated, suggesting that a rapid evolution of this type of source is likely in the near future.« less

Beam current enhancement of microwave plasma ion source utilizing double-port rectangular cavity resonator

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

Lee, Yuna; Park, Yeong-Shin; Jo, Jong-Gab

2012-02-15

Microwave plasma ion source with rectangular cavity resonator has been examined to improve ion beam current by changing wave launcher type from single-port to double-port. The cavity resonators with double-port and single-port wave launchers are designed to get resonance effect at TE-103 mode and TE-102 mode, respectively. In order to confirm that the cavities are acting as resonator, the microwave power for breakdown is measured and compared with the E-field strength estimated from the HFSS (High Frequency Structure Simulator) simulation. Langmuir probe measurements show that double-port cavity enhances central density of plasma ion source by modifying non-uniform plasma density profilemore » of the single-port cavity. Correspondingly, beam current from the plasma ion source utilizing the double-port resonator is measured to be higher than that utilizing single-port resonator. Moreover, the enhancement in plasma density and ion beam current utilizing the double-port resonator is more pronounced as higher microwave power applied to the plasma ion source. Therefore, the rectangular cavity resonator utilizing the double-port is expected to enhance the performance of plasma ion source in terms of ion beam extraction.« less

Beam current enhancement of microwave plasma ion source utilizing double-port rectangular cavity resonator.

PubMed

Lee, Yuna; Park, Yeong-Shin; Jo, Jong-Gab; Yang, J J; Hwang, Y S

2012-02-01

Microwave plasma ion source with rectangular cavity resonator has been examined to improve ion beam current by changing wave launcher type from single-port to double-port. The cavity resonators with double-port and single-port wave launchers are designed to get resonance effect at TE-103 mode and TE-102 mode, respectively. In order to confirm that the cavities are acting as resonator, the microwave power for breakdown is measured and compared with the E-field strength estimated from the HFSS (High Frequency Structure Simulator) simulation. Langmuir probe measurements show that double-port cavity enhances central density of plasma ion source by modifying non-uniform plasma density profile of the single-port cavity. Correspondingly, beam current from the plasma ion source utilizing the double-port resonator is measured to be higher than that utilizing single-port resonator. Moreover, the enhancement in plasma density and ion beam current utilizing the double-port resonator is more pronounced as higher microwave power applied to the plasma ion source. Therefore, the rectangular cavity resonator utilizing the double-port is expected to enhance the performance of plasma ion source in terms of ion beam extraction.

Comment on "Effects of Magnetic Field Gradient on Ion Beam Current in Cylindrical Hall Ion Source

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

Raitses, Y.; Smirnov A.; Fisch, N.J.

It is argued that the key difference of the cylindrical Hall thruster (CHT) as compared to the end-Hall ion source cannot be exclusively attributed to the magnetic field topology [Tang et al. J. Appl. Phys., 102, 123305 (2007)]. With a similar mirror-type topology, the CHT configuration provides the electric field with nearly equipotential magnetic field surfaces and a better suppression of the electron cross-field transport, as compared to both the end-Hall ion source and the cylindrical Hall ion source of Tang et al.

Interlaboratory study of the ion source memory effect in 36Cl accelerator mass spectrometry

NASA Astrophysics Data System (ADS)

Pavetich, Stefan; Akhmadaliev, Shavkat; Arnold, Maurice; Aumaître, Georges; Bourlès, Didier; Buchriegler, Josef; Golser, Robin; Keddadouche, Karim; Martschini, Martin; Merchel, Silke; Rugel, Georg; Steier, Peter

2014-06-01

Understanding and minimization of contaminations in the ion source due to cross-contamination and long-term memory effect is one of the key issues for accurate accelerator mass spectrometry (AMS) measurements of volatile elements. The focus of this work is on the investigation of the long-term memory effect for the volatile element chlorine, and the minimization of this effect in the ion source of the Dresden accelerator mass spectrometry facility (DREAMS). For this purpose, one of the two original HVE ion sources at the DREAMS facility was modified, allowing the use of larger sample holders having individual target apertures. Additionally, a more open geometry was used to improve the vacuum level. To evaluate this improvement in comparison to other up-to-date ion sources, an interlaboratory comparison had been initiated. The long-term memory effect of the four Cs sputter ion sources at DREAMS (two sources: original and modified), ASTER (Accélérateur pour les Sciences de la Terre, Environnement, Risques) and VERA (Vienna Environmental Research Accelerator) had been investigated by measuring samples of natural 35Cl/37Cl-ratio and samples highly-enriched in 35Cl (35Cl/37Cl ∼ 999). Besides investigating and comparing the individual levels of long-term memory, recovery time constants could be calculated. The tests show that all four sources suffer from long-term memory, but the modified DREAMS ion source showed the lowest level of contamination. The recovery times of the four ion sources were widely spread between 61 and 1390 s, where the modified DREAMS ion source with values between 156 and 262 s showed the fastest recovery in 80% of the measurements.

Large area multiarc ion beam source {open_quote}MAIS{close_quote}

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

Engelko, V.; Giese, H.; Schalk, S.

1996-12-31

A pulsed large area intense ion beam source is described, in which the ion emitting plasma is built up by an array of individual discharge units, homogeneously distributed over the surface of a common discharge electrode. A particularly advantageous feature of the source is that for plasma generation and subsequent acceleration of the ions only one common energy supply is necessary. This allows to simplify the source design and provides inherent synchronization of plasma production and ion extraction. The homogeneity of the plasma density was found to be superior to plasma sources using plasma expanders. Originally conceived for the productionmore » of proton beams, the source can easily be modified for the production of beams composed of carbon and metal ions or mixed ion species. Results of investigations of the source performance for the production of a proton beam are presented. The maximum beam current achieved to date is of the order of 100 A, with a particle kinetic energy of 15 - 30 keV and a pulse length in the range of 10 {mu}s.« less

Progress of superconducting electron cyclotron resonance ion sources at Institute of Modern Physics (IMP)

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

Sun, L., E-mail: sunlt@impcas.ac.cn; Feng, Y. C.; Zhang, W. H.

2014-02-15

Superconducting ECR ion sources can produce intense highly charged ion beams for the application in heavy ion accelerators. Superconducting Electron Resonance ion source with Advanced Design (SECRAL) is one of the few fully superconducting ECR ion sources that has been successfully built and put into routine operation for years. With enormous efforts and R and D work, promising results have been achieved with the ion source. Heated by the microwave power from a 7 kW/24 GHz gyrotron microwave generator, very intense highly charged gaseous ion beams have been produced, such as 455 eμA Xe{sup 27+}, 236 eμA Xe{sup 30+}, andmore » 64 eμA Xe{sup 35+}. Since heavy metallic ion beams are being more and more attractive and important for many accelerator projects globally, intensive studies have been made to produce highly charged heavy metal ion beams, such as those from bismuth and uranium. Recently, 420 eμA Bi{sup 30+} and 202 eμA U{sup 33+} have been produced with SECRAL source. This paper will present the latest results with SECRAL, and the operation status will be discussed as well. An introduction of recently started SECRAL II project will also be given in the presentation.« less

Progress of superconducting electron cyclotron resonance ion sources at Institute of Modern Physics (IMP).

PubMed

Sun, L; Lu, W; Feng, Y C; Zhang, W H; Zhang, X Z; Cao, Y; Zhao, Y Y; Wu, W; Yang, T J; Zhao, B; Zhao, H W; Ma, L Z; Xia, J W; Xie, D

2014-02-01

Superconducting ECR ion sources can produce intense highly charged ion beams for the application in heavy ion accelerators. Superconducting Electron Resonance ion source with Advanced Design (SECRAL) is one of the few fully superconducting ECR ion sources that has been successfully built and put into routine operation for years. With enormous efforts and R&D work, promising results have been achieved with the ion source. Heated by the microwave power from a 7 kW/24 GHz gyrotron microwave generator, very intense highly charged gaseous ion beams have been produced, such as 455 eμA Xe(27+), 236 eμA Xe(30+), and 64 eμA Xe(35+). Since heavy metallic ion beams are being more and more attractive and important for many accelerator projects globally, intensive studies have been made to produce highly charged heavy metal ion beams, such as those from bismuth and uranium. Recently, 420 eμA Bi(30+) and 202 eμA U(33+) have been produced with SECRAL source. This paper will present the latest results with SECRAL, and the operation status will be discussed as well. An introduction of recently started SECRAL II project will also be given in the presentation.

Development of C⁶⁺ laser ion source and RFQ linac for carbon ion radiotherapy.

PubMed

Sako, T; Yamaguchi, A; Sato, K; Goto, A; Iwai, T; Nayuki, T; Nemoto, K; Kayama, T; Takeuchi, T

2016-02-01

A prototype C(6+) injector using a laser ion source has been developed for a compact synchrotron dedicated to carbon ion radiotherapy. The injector consists of a laser ion source and a 4-vane radio-frequency quadrupole (RFQ) linac. Ion beams are extracted from plasma and directly injected into the RFQ. A solenoid guides the low-energy beams into the RFQ. The RFQ is designed to accelerate high-intensity pulsed beams. A structure of monolithic vanes and cavities is adopted to reduce its power consumption. In beam acceleration tests, a solenoidal magnetic field set between the laser ion source and the RFQ helped increase both the peak currents before and after the RFQ by a factor of 4.

Development of C6+ laser ion source and RFQ linac for carbon ion radiotherapy

NASA Astrophysics Data System (ADS)

Sako, T.; Yamaguchi, A.; Sato, K.; Goto, A.; Iwai, T.; Nayuki, T.; Nemoto, K.; Kayama, T.; Takeuchi, T.

2016-02-01

A prototype C6+ injector using a laser ion source has been developed for a compact synchrotron dedicated to carbon ion radiotherapy. The injector consists of a laser ion source and a 4-vane radio-frequency quadrupole (RFQ) linac. Ion beams are extracted from plasma and directly injected into the RFQ. A solenoid guides the low-energy beams into the RFQ. The RFQ is designed to accelerate high-intensity pulsed beams. A structure of monolithic vanes and cavities is adopted to reduce its power consumption. In beam acceleration tests, a solenoidal magnetic field set between the laser ion source and the RFQ helped increase both the peak currents before and after the RFQ by a factor of 4.

IL-27 Production and STAT3-Dependent Upregulation of B7-H1 Mediate Immune Regulatory Functions of Liver Plasmacytoid DC1

PubMed Central

Matta, Benjamin M.; Raimondi, Giorgio; Rosborough, Brian R.; Sumpter, Tina L.; Thomson, Angus W.

2012-01-01

Plasmacytoid (p) dendritic cells (DC) are highly-specialized APC that, in addition to their well-recognized role in anti-viral immunity, also regulate immune responses. Liver-resident pDC are considerably less immunostimulatory than those from secondary lymphoid tissues and are equipped to promote immune tolerance/regulation through various mechanisms. IL-27 is an IL-12-family cytokine that regulates the function of both APC and T cells, although little is known about its role in pDC immunobiology. In this study, we show that mouse liver pDC express higher levels of IL-27p28 and EBV-induced protein (Ebi)3 compared to splenic pDC. Both populations of pDC express the IL-27Rα/WSX-1; however, only liver pDC significantly upregulate expression of the co-regulatory molecule B7 homolog-1 (B7-H1) in response to IL-27. Inhibition of STAT3 activation completely abrogates IL-27-induced upregulation of B7-H1 expression on liver pDC. Liver pDC treated with IL-27 increase the percentage of CD4+Foxp3+ T cells in MLR, which is dependent upon expression of B7-H1. pDC from Ebi3-deficient mice lacking functional IL-27, show increased capacity to stimulate allogeneic T cell proliferation and IFN-γ production in MLR. Liver but not spleen pDC suppress delayed-type hypersensitivity responses to OVA, an effect that is lost with Ebi3−/− and B7-H1−/− liver pDC compared to wild-type (WT) liver pDC. These data suggest that IL-27 signaling in pDC promotes their immunoregulatory function and that IL-27 produced by pDC contributes to their capacity to regulate immuneresponses in vitro and in vivo. PMID:22508931

SOX2 and SOX2-MYC Reprogramming Process of Fibroblasts to the Neural Stem Cells Compromised by Senescence

PubMed Central

Winiecka-Klimek, Marta; Smolarz, Maciej; Walczak, Maciej P.; Zieba, Jolanta; Hulas-Bigoszewska, Krystyna; Kmieciak, Blazej; Piaskowski, Sylwester; Rieske, Piotr; Grzela, Dawid P.; Stoczynska-Fidelus, Ewelina

2015-01-01

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 reprogrammed only into neuronal progenitors, mainly because of the inaccuracies of currently available protocols. PMID:26535892

Extended brief intervention to address alcohol misuse in people with mild to moderate intellectual disabilities living in the community (EBI-ID): study protocol for a randomised controlled trial.

PubMed

Kouimtsidis, Christos; Fodor-Wynne, Lucy; Scior, Katrina; Hunter, Rachael; Baio, Gianluca; Pezzoni, Vittoria; Hassiotis, Angela

2015-03-25

There is some evidence that people with intellectual disabilities who live in the community are exposed to the same risks of alcohol use as the rest of the population. Various interventions have been evaluated in the general population to tackle hazardous or harmful drinking and alcohol dependence, but the literature evaluating interventions is very limited regarding intellectual disabilities. The National Institute for Health and Clinical Excellence recommends that brief and extended brief interventions be used to help young persons and adults who have screened as positive for hazardous and harmful drinking. The objective of this trial is to investigate the feasibility of adapting and delivering an extended brief intervention (EBI) to persons with mild/moderate intellectual disability who live in the community and whose level of drinking is harmful or hazardous. The study has three stages, which include the adaptation of the Extended Brief Intervention (EBI) for people with intellectual disability, a single blind, randomised controlled trial of an individual Extended Brief Intervention to test the feasibility of the intervention, and a qualitative study that will assess the perceived acceptability and usefulness of the intervention. Fifty participants in total will be recruited from community intellectual disability services and social care or third sector organisations. The main outcome is a reduction in alcohol consumption measured by the Alcohol Use Disorders Identification Test. Alcohol misuse is a relatively under-researched mental health problem in people with intellectual disabilities. Therefore, the study addresses both diagnostic issues and the delivery of a simple first stage intervention, which is available to the population of average intelligence and young persons in particular. The findings from the study will guide the preparation of a large-scale study to test whether this treatment is clinically and cost-effective in this population. ISRCTN58783633 (19 December 2013).

Optimal Threshold Determination for Interpreting Semantic Similarity and Particularity: Application to the Comparison of Gene Sets and Metabolic Pathways Using GO and ChEBI

PubMed Central

Bettembourg, Charles; Diot, Christian; Dameron, Olivier

2015-01-01

Background The analysis of gene annotations referencing back to Gene Ontology plays an important role in the interpretation of high-throughput experiments results. This analysis typically involves semantic similarity and particularity measures that quantify the importance of the Gene Ontology annotations. However, there is currently no sound method supporting the interpretation of the similarity and particularity values in order to determine whether two genes are similar or whether one gene has some significant particular function. Interpretation is frequently based either on an implicit threshold, or an arbitrary one (typically 0.5). Here we investigate a method for determining thresholds supporting the interpretation of the results of a semantic comparison. Results We propose a method for determining the optimal similarity threshold by minimizing the proportions of false-positive and false-negative similarity matches. We compared the distributions of the similarity values of pairs of similar genes and pairs of non-similar genes. These comparisons were performed separately for all three branches of the Gene Ontology. In all situations, we found overlap between the similar and the non-similar distributions, indicating that some similar genes had a similarity value lower than the similarity value of some non-similar genes. We then extend this method to the semantic particularity measure and to a similarity measure applied to the ChEBI ontology. Thresholds were evaluated over the whole HomoloGene database. For each group of homologous genes, we computed all the similarity and particularity values between pairs of genes. Finally, we focused on the PPAR multigene family to show that the similarity and particularity patterns obtained with our thresholds were better at discriminating orthologs and paralogs than those obtained using default thresholds. Conclusion We developed a method for determining optimal semantic similarity and particularity thresholds. We applied this method on the GO and ChEBI ontologies. Qualitative analysis using the thresholds on the PPAR multigene family yielded biologically-relevant patterns. PMID:26230274

Numerical Analysis of Plasma Transport in Tandem Volume Magnetic Multicusp Ion Sources

DTIC Science & Technology

1992-03-01

the results of the model are qualitatively correct. Boltzmann Equation, Ion Sources, Plasma Simulation, Electron Temperature, Plasma Density, Ion Temperature, Hydrogen Ions, Magnetic Filters, Hydrogen Plasma Chemistry .

Computer Modeling of High-Intensity Cs-Sputter Ion Sources

NASA Astrophysics Data System (ADS)

Brown, T. A.; Roberts, M. L.; Southon, J. R.

The grid-point mesh program NEDLab has been used to computer model the interior of the high-intensity Cs-sputter source used in routine operations at the Center for Accelerator Mass Spectrometry (CAMS), with the goal of improving negative ion output. NEDLab has several features that are important to realistic modeling of such sources. First, space-charge effects are incorporated in the calculations through an automated ion-trajectories/Poissonelectric-fields successive-iteration process. Second, space charge distributions can be averaged over successive iterations to suppress model instabilities. Third, space charge constraints on ion emission from surfaces can be incorporate under Child's Law based algorithms. Fourth, the energy of ions emitted from a surface can be randomly chosen from within a thermal energy distribution. And finally, ions can be emitted from a surface at randomized angles The results of our modeling effort indicate that significant modification of the interior geometry of the source will double Cs+ ion production from our spherical ionizer and produce a significant increase in negative ion output from the source.

Performance test of electron cyclotron resonance ion sources for the Hyogo Ion Beam Medical Center

NASA Astrophysics Data System (ADS)

Sawada, K.; Sawada, J.; Sakata, T.; Uno, K.; Okanishi, K.; Harada, H.; Itano, A.; Higashi, A.; Akagi, T.; Yamada, S.; Noda, K.; Torikoshi, M.; Kitagawa, A.

2000-02-01

Two electron cyclotron resonance (ECR) ion sources were manufactured for the accelerator facility at the Hyogo Ion Beam Medical Center. H2+, He2+, and C4+ were chosen as the accelerating ions because they have the highest charge to mass ratio among ion states which satisfy the required intensity and quality. The sources have the same structure as the 10 GHz ECR source at the Heavy Ion Medical Accelerator in Chiba except for a few improvements in the magnetic structure. Their performance was investigated at the Sumitomo Heavy Industries factory before shipment. The maximum intensity was 1500 μA for H2+, 1320 μA for He2+, and 580 μA for C4+ at the end of the ion source beam transport line. These are several times higher than required. Sufficient performance was also observed in the flatness and long-term stability of the pulsed beams. These test results satisfy the requirements for medical use.

High-voltage terminal test of a test stand for a 1-MV electrostatic accelerator

NASA Astrophysics Data System (ADS)

Park, Sae-Hoon; Kim, Yu-Seok

2015-10-01

The Korea Multipurpose Accelerator Complex has been developing a 300-kV test stand for a 1-MV electrostatic accelerator ion source. The ion source and accelerating tube will be installed in a high-pressure vessel. The ion source in the high-pressure vessel is required to have a high reliability. The test stand has been proposed and developed to confirm the stable operating conditions of the ion source. The ion source will be tested at the test stand to verify the long-time operating conditions. The test stand comprises a 300-kV high-voltage terminal, a battery for the ion-source power, a 60-Hz inverter, 200-MHz radio-frequency power supply, a 5-kV extraction power supply, a 300-kV accelerating tube, and a vacuum system. The results of the 300-kV high-voltage terminal tests are presented in this paper.

Electron cyclotron resonance ion source for high currents of mono- and multicharged ion and general purpose unlimited lifetime application on implantation devices

NASA Astrophysics Data System (ADS)

Bieth, C.; Bouly, J. L.; Curdy, J. C.; Kantas, S.; Sortais, P.; Sole, P.; Vieux-Rochaz, J. L.

2000-02-01

The electron cyclotron resonance (ECR) ion sources were originally developed for high energy physic applications. They are used as injectors on linear accelerators and cyclotrons to further increase the particle energy via high charge state ions. This ECR technology is well suited for sources placed on a high voltage platform where ac power available is limited by insulated transformers. The PANTECHNIK family of ion source with its wide range of ion beam (various charge states with various beam currents) offers new possibilities and perspectives in the field of ion implantation. In addition to all these possibilities, the PANTECHNIK ion sources have many other advantages like: a very long lifetime without maintenance expense, good stability, efficiency of ionization close to 100% (this improves the lifetime of the pumping system and other equipment), the possibility of producing ion beams with different energies, and a very good reproducibility. The main characteristics of sources like Nanogan or SuperNanogan will be recalled. We will especially present the results obtained with the new Microgan 10 GHz source that can be optimized for the production of high currents of monocharged ion, including reactive gas like BF3 (2 mA e of B+) or medium currents of low charge state like 0.5 mA e of Ar4+. The latest results obtained with Microgan 10 GHz show that it is possible to drive the source up to 30 mA e of total current, with an emittance of 150 π mm mrad at 40 kV and also to maintain the production of multicharged ions like Ar8+.

A Penning sputter ion source with very low energy spread

NASA Astrophysics Data System (ADS)

Nouri, Z.; Li, R.; Holt, R. A.; Rosner, S. D.

2010-03-01

We have developed a version of the Frankfurt Penning ion source that produces ion beams with very low energy spreads of ˜3 eV, while operating in a new discharge mode characterized by very high pressure, low voltage, and high current. The extracted ions also comprise substantial metastable and doubly charged species. Detailed studies of the operating parameters of the source showed that careful adjustment of the magnetic field and gas pressure is critical to achieving optimum performance. We used a laser-fluorescence method of energy analysis to characterize the properties of the extracted ion beam with a resolving power of 1×10 4, and to measure the absolute ion beam energy to an accuracy of 4 eV in order to provide some insight into the distribution of plasma potential within the ion source. This characterization method is widely applicable to accelerator beams, though not universal. The low energy spread, coupled with the ability to produce intense ion beams from almost any gas or conducting solid, make this source very useful for high-resolution spectroscopic measurements on fast-ion beams.

Selective ion source

DOEpatents

Leung, K.N.

1996-05-14

A ion source is described wherein selected ions maybe extracted to the exclusion of unwanted ion species of higher ionization potential. Also described is a method of producing selected ions from a compound, such as P{sup +} from PH{sub 3}. The invention comprises a plasma chamber, an electron source, a means for introducing a gas to be ionized by electrons from the electron source, means for limiting electron energy from the electron source to a value between the ionization energy of the selected ion species and the greater ionization energy of an unwanted ion specie, and means for extracting the target ion specie from the plasma chamber. In one embodiment, the electrons are generated in a plasma cathode chamber immediately adjacent to the plasma chamber. A small extractor draws the electrons from the plasma cathode chamber into the relatively positive plasma chamber. The energy of the electrons extracted in this manner is easily controlled. The invention is particularly useful for doping silicon with P{sup +}, As{sup +}, and B{sup +} without the problematic presence of hydrogen, helium, water, or carbon oxide ions. Doped silicon is important for manufacture of semiconductors and semiconductor devices. 6 figs.

Selective ion source

DOEpatents

Leung, Ka-Ngo

1996-01-01

A ion source is described wherein selected ions maybe extracted to the exclusion of unwanted ion species of higher ionization potential. Also described is a method of producing selected ions from a compound, such as P.sup.+ from PH.sub.3. The invention comprises a plasma chamber, an electron source, a means for introducing a gas to be ionized by electrons from the electron source, means for limiting electron energy from the electron source to a value between the ionization energy of the selected ion species and the greater ionization energy of an unwanted ion specie, and means for extracting the target ion specie from the plasma chamber. In one embodiment, the electrons are generated in a plasma cathode chamber immediately adjacent to the plasma chamber. A small extractor draws the electrons from the plasma cathode chamber into the relatively positive plasma chamber. The energy of the electrons extracted in this manner is easily controlled. The invention is particularly useful for doping silicon with P.sup.+, AS.sup.+, and B.sup.+ without the problematic presence of hydrogen, helium, water, or carbon oxide ions. Doped silicon is important for manufacture of semiconductors and semiconductor devices.

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

PubMed Central

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 significant differences in participants' ability to respond to challenging or sensitive questions (P=.50) or their ability to help participants recognize how Latino culture supports safer sex (P=.32). There was a significant difference in their knowledge of core elements and modules (P<.001). A total of 74% (26/35) of the Second Life participants did agree/strongly agree that they had the skills to deliver the ¡Cuídate! program. Conclusions The results showed that participants found the Second Life environment to be acceptable to the learners and supported an experience in which learners were able to acquire the knowledge and skills needed to deliver the curriculum. PMID:26199045

A combined thermal dissociation and electron impact ionization source for radioactive ion beam generation{sup a}

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

Alton, G.D.; Williams, C.

1996-04-01

The probability for simultaneously dissociating and efficiently ionizing the individual atomic constituents of molecular feed materials with conventional, hot-cathode, electron-impact ion sources is low and consequently, the ion beams from these sources often appear as mixtures of several molecular sideband beams. This fragmentation process leads to dilution of the intensity of the species of interest for radioactive ion beam (RIB) applications where beam intensity is at a premium. We have conceived an ion source that combines the excellent molecular dissociation properties of a thermal dissociator and the high ionization efficiency characteristics of an electron impact ionization source that will, inmore » principle, overcome this handicap. The source concept will be evaluated as a potential candidate for use for RIB generation at the Holifield Radioactive Ion Beam Facility, now under construction at the Oak Ridge National Laboratory. The design features and principles of operation of the source are described in this article. {copyright} {ital 1996 American Institute of Physics.}« less

A combined thermal dissociation and electron impact ionization source for radioactive ion beam generation (abstract){sup a}

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

Alton, G.D.; Williams, C.

1996-03-01

The probability for simultaneously dissociating and efficiently ionizing the individual atomic constituents of molecular feed materials with conventional, hot-cathode, electron-impact ion sources is low and consequently, the ion beams from these sources often appear as mixtures of several molecular sideband beams. This fragmentation process leads to dilution of the intensity of the species of interest for radioactive ion beam (RIB) applications where beam intensity is at a premium. We have conceived an ion source that combines the excellent molecular dissociation properties of a thermal dissociator and the high ionization efficiency characteristics of an electron impact ionization source that will, inmore » principle, overcome this handicap. The source concept will be evaluated as a potential candidate for use for RIB generation at the Holifield Radioactive Ion Beam Facility, now under construction at the Oak Ridge National Laboratory. The design features and principles of operation of the source are described in this article. {copyright} {ital 1996 American Institute of Physics.}« less

RF H-minus ion source development in China spallation neutron source

NASA Astrophysics Data System (ADS)

Chen, W.; Ouyang, H.; Xiao, Y.; Liu, S.; Lü, Y.; Cao, X.; Huang, T.; Xue, K.

2017-08-01

China Spallation Neutron Source (CSNS) phase-I project currently uses a Penning surface plasma H- ion source, which has a life time of several weeks with occasional sparks between high voltage electrodes. To extend the life time of the ion source and prepare for the CSNS phase-II, we are trying to develop a RF negative hydrogen ion source with external antenna. The configuration of the source is similar to the DESY external antenna ion source and SNS ion source. However several changes are made to improve the stability and the life time. Firstly, Si3N4 ceramic with high thermal shock resistance, and high thermal conductivity is used for plasma chamber, which can endure an average power of 2000W. Secondly, the water-cooled antenna is brazed on the chamber to improve the energy efficiency. Thirdly, cesium is injected directly to the plasma chamber if necessary, to simplify the design of the converter and the extraction. Area of stainless steel exposed to plasma is minimized to reduce the sputtering and degassing. Instead Mo, Ta, and Pt coated materials are used to face the plasma, which makes the self-cleaning of the source possible.

A high repetition deterministic single ion source

NASA Astrophysics Data System (ADS)

Sahin, C.; Geppert, P.; Müllers, A.; Ott, H.

2017-12-01

We report on a deterministic single ion source with high repetition rate and high fidelity. The source employs a magneto-optical trap, where ultracold rubidium atoms are photoionized. The electrons herald the creation of a corresponding ion, whose timing information is used to manipulate its trajectory in flight. We demonstrate an ion rate of up to 4× {10}4 {{{s}}}-1 and achieve a fidelity for single ion operation of 98%. The technique can be used for all atomic species, which can be laser-cooled, and opens up new applications in ion microscopy, ion implantation and surface spectroscopy.

Negative ion source with hollow cathode discharge plasma

DOEpatents

Hershcovitch, Ady; Prelec, Krsto

1983-01-01

A negative ion source of the type where negative ions are formed by bombarding a low-work-function surface with positive ions and neutral particles from a plasma, wherein a highly ionized plasma is injected into an anode space containing the low-work-function surface. The plasma is formed by hollow cathode discharge and injected into the anode space along the magnetic field lines. Preferably, the negative ion source is of the magnetron type.

A high brightness source for nano-probe secondary ion mass spectrometry

NASA Astrophysics Data System (ADS)

Smith, N. S.; Tesch, P. P.; Martin, N. P.; Kinion, D. E.

2008-12-01

The two most prevalent ion source technologies in the field of surface analysis and surface machining are the Duoplasmatron and the liquid metal ion source (LMIS). There have been many efforts in this area of research to develop an alternative source [ S.K. Guharay, J. Orloff, M. Wada, IEEE Trans. Plasma Sci. 33 (6) (2005) 1911; N.S. Smith, W.P. Skoczylas, S.M. Kellogg, D.E. Kinion, P.P. Tesch, O. Sutherland, A. Aanesland, R.W. Boswell, J. Vac. Sci. Technol. B 24 (6) (2006) 2902-2906] with the brightness of a LMIS and yet the ability to produce secondary ion yield enhancing species such as oxygen. However, to date a viable alternative has not been realized. The high brightness and small virtual source size of the LMIS are advantageous for forming high resolution probes but a significant disadvantage when beam currents in excess of 100 nA are required, due to the effects of spherical aberration from the optical column. At these higher currents a source with a high angular intensity is optimal and in fact the relatively moderate brightness of today's plasma ion sources prevail in this operating regime. Both the LMIS and Duoplasmatron suffer from a large axial energy spread resulting in further limitations when forming focused beams at the chromatic limit where the figure-of-merit is inversely proportional to the square of the energy spread. Also, both of these ion sources operate with a very limited range of ion species. This article reviews some of the latest developments and some future potential in this area of instrument development. Here we present an approach to source development that could lead to oxygen ion beam SIMS imaging with 10 nm resolution, using a 'broad area' RF gas phase ion source.

Improving quantitative gas chromatography-electron ionization mass spectrometry results using a modified ion source: demonstration for a pharmaceutical application.

PubMed

D'Autry, Ward; Wolfs, Kris; Hoogmartens, Jos; Adams, Erwin; Van Schepdael, Ann

2011-07-01

Gas chromatography-mass spectrometry is a well established analytical technique. However, mass spectrometers with electron ionization sources may suffer from signal drifts, hereby negatively influencing quantitative performance. To demonstrate this phenomenon for a real application, a static headspace-gas chromatography method in combination with electron ionization-quadrupole mass spectrometry was optimized for the determination of residual dichloromethane in coronary stent coatings. Validating the method, the quantitative performance of an original stainless steel ion source was compared to that of a modified ion source. Ion source modification included the application of a gold coating on the repeller and exit plate. Several validation aspects such as limit of detection, limit of quantification, linearity and precision were evaluated using both ion sources. It was found that, as expected, the stainless steel ion source suffered from signal drift. As a consequence, non-linearity and high RSD values for repeated analyses were obtained. An additional experiment was performed to check whether an internal standard compound would lead to better results. It was found that the signal drift patterns of the analyte and internal standard were different, consequently leading to high RSD values for the response factor. With the modified ion source however, a more stable signal was observed resulting in acceptable linearity and precision. Moreover, it was also found that sensitivity improved compared to the stainless steel ion source. Finally, the optimized method with the modified ion source was applied to determine residual dichloromethane in the coating of coronary stents. The solvent was detected but found to be below the limit of quantification. Copyright © 2011 Elsevier B.V. All rights reserved.

Operation of Lanzhou all permanent electron cyclotron resonance ion source No. 2 on 320 kV platform with highly charged ions.

PubMed

Lu, W; Li, J Y; Kang, L; Liu, H P; Li, H; Li, J D; Sun, L T; Ma, X W

2014-02-01

The 320 kV platform for multi-discipline research with highly charged ions is a heavy ion beam acceleration instrument developed by Institute of Modern Physics, which is dedicated to basic scientific researches such as plasma, atom, material physics, and astrophysics, etc. The platform has delivered ion beams of 400 species for 36,000 h. The average operation time is around 5000 h/year. With the beams provided by the platform, lots of outstanding progresses were made in various research fields. The ion source of the platform is an all-permanent magnet electron cyclotron resonance ion source, LAPECR2 (Lanzhou All Permanent ECR ion source No. 2). The maximum axial magnetic fields are 1.28 T at injection and 1.07 T at extraction, and the radial magnetic field is up to 1.21 T at the inner wall of the plasma chamber. The ion source is capable to produce low, medium, and high charge state gaseous and metallic ion beams, such as H(+), (40)Ar(8+), (129)Xe(30+), (209)Bi(33+), etc. This paper will present the latest result of LAPECR2 and the routine operation status for the high voltage platform.

Nb3Sn superconducting magnets for electron cyclotron resonance ion sources.

PubMed

Ferracin, P; Caspi, S; Felice, H; Leitner, D; Lyneis, C M; Prestemon, S; Sabbi, G L; Todd, D S

2010-02-01

Electron cyclotron resonance (ECR) ion sources are an essential component of heavy-ion accelerators. Over the past few decades advances in magnet technology and an improved understanding of the ECR ion source plasma physics have led to remarkable performance improvements of ECR ion sources. Currently third generation high field superconducting ECR ion sources operating at frequencies around 28 GHz are the state of the art ion injectors and several devices are either under commissioning or under design around the world. At the same time, the demand for increased intensities of highly charged heavy ions continues to grow, which makes the development of even higher performance ECR ion sources a necessity. To extend ECR ion sources to frequencies well above 28 GHz, new magnet technology will be needed in order to operate at higher field and force levels. The superconducting magnet program at LBNL has been developing high field superconducting magnets for particle accelerators based on Nb(3)Sn superconducting technology for several years. At the moment, Nb(3)Sn is the only practical conductor capable of operating at the 15 T field level in the relevant configurations. Recent design studies have been focused on the possibility of using Nb(3)Sn in the next generation of ECR ion sources. In the past, LBNL has worked on the VENUS ECR, a 28 GHz source with solenoids and a sextupole made with NbTi operating at fields of 6-7 T. VENUS has now been operating since 2004. We present in this paper the design of a Nb(3)Sn ECR ion source optimized to operate at an rf frequency of 56 GHz with conductor peak fields of 13-15 T. Because of the brittleness and strain sensitivity of Nb(3)Sn, particular care is required in the design of the magnet support structure, which must be capable of providing support to the coils without overstressing the conductor. In this paper, we present the main features of the support structure, featuring an external aluminum shell pretensioned with water-pressurized bladders, and we analyze the expected coil stresses with a two-dimensional finite element mechanical model.

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

Kanesue, Takeshi; Ikeda, Shunsuke

A laser ion source is a promising candidate as an ion source for heavy ion inertial fusion (HIF), where a pulsed ultra-intense and low-charged heavy ion beam is required. It is a key development for a laser ion source to transport laser-produced plasma with a magnetic field to achieve a high current beam. The effect of a tapered magnetic field on laser produced plasma is demonstrated by comparing the results with a straight solenoid magnet. The magnetic field of interest is a wider aperture on a target side and narrower aperture on an extraction side. Furthermore, based on the experimentallymore » obtained results, the performance of a scaled laser ion source for HIF was estimated.« less

ION ACCELERATION SYSTEM

DOEpatents

Luce, J.S.; Martin, J.A.

1960-02-23

Well focused, intense ion beams are obtained by providing a multi- apertured source grid in front of an ion source chamber and an accelerating multi- apertured grid closely spaced from and in alignment with the source grid. The longest dimensions of the elongated apertures in the grids are normal to the direction of the magnetic field used with the device. Large ion currents may be withdrawn from the source, since they do not pass through any small focal region between the grids.

Scintillation screen applications in a vacuum arc ion source with composite hydride cathode

NASA Astrophysics Data System (ADS)

Wang, X. H.; Tuo, X. G.; Yang, Z.; Peng, Y. F.; Li, J.; Lv, H. Y.; Li, J. H.; Long, J. D.

2018-05-01

Vacuum arc ion source with composite hydride cathode was developed to produce intense ion beams which can be applied in particle accelerator injections. Beam profile and beam composition are two fundamental parameters of the beam for the vacuum arc ion source in such specific applications. An aluminum-coated scintillation screen with an ICCD camera readout was used to show the space-time distribution of the beam directly. A simple magnetic analysis assembly with the scintillation screen shows the beam composition information of this kind ion source. Some physical and technical issues are discussed and analyzed in the text.

Point-like neutron source based on high-current electron cyclotron resonance ion source with powerful millimeter wave plasma heating

NASA Astrophysics Data System (ADS)

Golubev, S. V.; Skalyga, V. A.; Izotov, I. V.; Sidorov, A. V.

2018-01-01

A possibility of an intense deuterium ion beam creation for a compact powerful point-like neutron source is discussed. The fusion takes place due to bombardment of deuterium (or tritium) loaded target by high-current focused deuterium ion beam with energy of 100 keV. The ways of high-current and low emittance ion beam formation from the plasma of quasi-gasdynamic ion source of a new generation based on an electron cyclotron resonance discharge in an open magnetic trap sustained by powerful microwave radiation are investigated.

Universal main magnetic focus ion source for production of highly charged ions

NASA Astrophysics Data System (ADS)

Ovsyannikov, V. P.; Nefiodov, A. V.; Levin, A. A.

2017-10-01

A novel room-temperature compact ion source has been developed for the efficient production of atomic ions by means of an electron beam with energy Ee and current density je controllable within wide ranges (100 eV ≲Ee ≲ 60 keV, 10 A/cm2 ≲je ≲ 20 kA/cm2). In the first experiments, the X-ray emission of Ir64+ ions has been measured. Based on a combination of two different techniques, the device can operate both as conventional Electron Beam Ion Source/Trap and novel Main Magnetic Focus Ion Source. The tunable electron-optical system allows for realizing laminar and turbulent electron flows in a single experimental setup. The device is intended primarily for fundamental and applied research at standard university laboratories.

Effect of tapered magnetic field on expanding laser-produced plasma for heavy-ion inertial fusion

DOE PAGES

Kanesue, Takeshi; Ikeda, Shunsuke

2016-12-20

A laser ion source is a promising candidate as an ion source for heavy ion inertial fusion (HIF), where a pulsed ultra-intense and low-charged heavy ion beam is required. It is a key development for a laser ion source to transport laser-produced plasma with a magnetic field to achieve a high current beam. The effect of a tapered magnetic field on laser produced plasma is demonstrated by comparing the results with a straight solenoid magnet. The magnetic field of interest is a wider aperture on a target side and narrower aperture on an extraction side. Furthermore, based on the experimentallymore » obtained results, the performance of a scaled laser ion source for HIF was estimated.« less

Thermal-electric numerical simulation of a surface ion source for the production of radioactive ion beams

NASA Astrophysics Data System (ADS)

Manzolaro, Mattia; Meneghetti, Giovanni; Andrighetto, Alberto

2010-11-01

In a facility for the production of radioactive ion beams (RIBs), the target system and the ion source are the most critical objects. In the context of the Selective Production of Exotic Species (SPES) project, a proton beam directly impinges a Uranium Carbide production target, generating approximately 10 13 fissions per second. The radioactive isotopes produced by the 238U fissions are then directed to the ion source to acquire a charge state. After that, the radioactive ions obtained are transported electrostatically to the subsequent areas of the facility. In this work the surface ion source at present adopted for the SPES project is studied by means of both analytical and numerical thermal-electric models. The theoretical results are compared with temperature and electric potential difference measurements.

Note: Ion source design for ion trap systems

NASA Astrophysics Data System (ADS)

Noriega, J. R.; Quevedo, M.; Gnade, B.; Vasselli, J.

2013-06-01

A small plasma (glow discharge) based ion source and circuit are described in this work. The ion source works by producing a high voltage pulsed discharge between two electrodes in a pressure range of 50-100 mTorr. A third mesh electrode is used for ion extraction. The electrodes are small stainless steel screws mounted in a MACOR ionization chamber in a linear arrangement. The electrode arrangement is driven by a circuit, design for low power operation. This design is a proof of concept intended for applications on small cylindrical ion traps.

Brightness measurement of an electron impact gas ion source for proton beam writing applications

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

Liu, N.; Santhana Raman, P.; Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583

We are developing a high brightness nano-aperture electron impact gas ion source, which can create ion beams from a miniature ionization chamber with relatively small virtual source sizes, typically around 100 nm. A prototype source of this kind was designed and successively micro-fabricated using integrated circuit technology. Experiments to measure source brightness were performed inside a field emission scanning electron microscope. The total output current was measured to be between 200 and 300 pA. The highest estimated reduced brightness was found to be comparable to the injecting focused electron beam reduced brightness. This translates into an ion reduced brightness thatmore » is significantly better than that of conventional radio frequency ion sources, currently used in single-ended MeV accelerators.« less

Brightness measurement of an electron impact gas ion source for proton beam writing applications.

PubMed

Liu, N; Xu, X; Pang, R; Raman, P Santhana; Khursheed, A; van Kan, J A

2016-02-01

We are developing a high brightness nano-aperture electron impact gas ion source, which can create ion beams from a miniature ionization chamber with relatively small virtual source sizes, typically around 100 nm. A prototype source of this kind was designed and successively micro-fabricated using integrated circuit technology. Experiments to measure source brightness were performed inside a field emission scanning electron microscope. The total output current was measured to be between 200 and 300 pA. The highest estimated reduced brightness was found to be comparable to the injecting focused electron beam reduced brightness. This translates into an ion reduced brightness that is significantly better than that of conventional radio frequency ion sources, currently used in single-ended MeV accelerators.

MetaboLights: An Open-Access Database Repository for Metabolomics Data.

PubMed

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.

Negative hydrogen ion sources for accelerators

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

Moehs, D.P.; /Fermilab; Peters, J.

2005-08-01

A variety of H{sup -} ion sources are in use at accelerator laboratories around the world. A list of these ion sources includes surface plasma sources with magnetron, Penning and surface converter geometries as well as magnetic-multipole volume sources with and without cesium. Just as varied is the means of igniting and maintaining magnetically confined plasmas. Hot and cold cathodes, radio frequency, and microwave power are all in use, as well as electron tandem source ignition. The extraction systems of accelerator H{sup -} ion sources are highly specialized utilizing magnetic and electric fields in their low energy beam transport systemsmore » to produce direct current, as well as pulsed and/or chopped beams with a variety of time structures. Within this paper, specific ion sources utilized at accelerator laboratories shall be reviewed along with the physics of surface and volume H{sup -} production in regard to source emittance. Current research trends including aperture modeling, thermal modeling, surface conditioning, and laser diagnostics will also be discussed.« less

Microwave ion source

DOEpatents

Leung, Ka-Ngo; Reijonen, Jani; Thomae, Rainer W.

2005-07-26

A compact microwave ion source has a permanent magnet dipole field, a microwave launcher, and an extractor parallel to the source axis. The dipole field is in the form of a ring. The microwaves are launched from the middle of the dipole ring using a coaxial waveguide. Electrons are heated using ECR in the magnetic field. The ions are extracted from the side of the source from the middle of the dipole perpendicular to the source axis. The plasma density can be increased by boosting the microwave ion source by the addition of an RF antenna. Higher charge states can be achieved by increasing the microwave frequency. A xenon source with a magnetic pinch can be used to produce intense EUV radiation.

Beam production of a laser ion source with a rotating hollow cylinder target for low energy positive and negative ions

NASA Astrophysics Data System (ADS)

Saquilayan, G. Q.; Wada, M.

2017-08-01

A laser ion source that utilizes a hollow cylinder target is being developed for the production of positive and negative ions. Continuous operation of the laser ion source is possible through the design of a rotating target. Ion extraction through a grounded circular aperture was tested for positive and negative ions up to 1 kV. Time-of-flight measurements for the mass separation of ions were made by placing a Faraday cup at locations 0 and 15 mm from the beam extraction axis. Signals corresponding to slow and massive ions were detected with mass at least 380 amu. Investigation on the beam profile suggests a geometrical optimization of the beam forming system is necessary.

Negative ion source with hollow cathode discharge plasma

DOEpatents

Hershcovitch, A.; Prelec, K.

1980-12-12

A negative ion source of the type where negative ions are formed by bombarding a low-work-function surface with positive ions and neutral particles from a plasma, wherein a highly ionized plasma is injected into an anode space containing the low-work-function surface is described. The plasma is formed by hollow cathode discharge and injected into the anode space along the magnetic field lines. Preferably, the negative ion source is of the magnetron type.

Beam Profile Studies for a One Eighth Betatron Wavelength Final Focusing Cell Following Phase Mixed Transport

DTIC Science & Technology

1988-10-26

concentrated into this off- axis peak is then considered. Estimates of the source brightness ( extraction ion diode source current density divided by the square...radioactive contamination of the accelerator. One possible scheme for avoiding this problem is to use extraction geometry ion diodes to focus the ion beams...annular region. These results will be coupled to two simple models of extraction ion diodes to determihe the ion source brightness requirements. These

Cleaning techniques for intense ion beam sources

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

Menge, P.R.; Cuneo, M.E.; Bailey, J.E.

Generation of high power lithium ion beams on the SABRE (1TW) and PBFA-X (20 TW) accelerators have been limited by the parallel acceleration of contaminant ions. during the beam pulse lithium is replaced by protons and carbon ions. This replacement is accompanied by rapid impedance decay of the diode. The contaminant hydrogen and carbon is believed to originate from impurity molecules on the surface and in the bulk of the lithium ion source and its substrate material. Cleaning techniques designed to remove hydrocarbons from the ion source have been employed with some success in test stand experiments and on SABRE.more » The test stand experiments have shown that a lithium fluoride (LiF) ion source film can accrue dozens of hydrocarbon monolayers on its surface while sitting in vacuum. Application of 13.5 MHz RF discharge cleaning with 90% Ar/10% O{sub 2} can significantly reduce the surface hydrocarbon layers on the LiF film. On SABRE, combinations of RF discharge cleaning, anode heating, layering gold between the source film (LiF) and its substrate, and cryogenic cathode cooling produced an increase by a factor of 1.5--2 in the quantity of high energy lithium in the ion beam. A corresponding decrease in protons and carbon ions was also observed. Cleaning experiments on PBFA-X are underway. New designs of contamination resistant films and Li ion sources are currently being investigated.« less

Improvements for extending the time between maintenance periods for the Heidelberg ion beam therapy center (HIT) ion sources.

PubMed

Winkelmann, Tim; Cee, Rainer; Haberer, Thomas; Naas, Bernd; Peters, Andreas; Schreiner, Jochen

2014-02-01

The clinical operation at the Heidelberg Ion Beam Therapy Center (HIT) started in November 2009; since then more than 1600 patients have been treated. In a 24/7 operation scheme two 14.5 GHz electron cyclotron resonance ion sources are routinely used to produce protons and carbon ions. The modification of the low energy beam transport line and the integration of a third ion source into the therapy facility will be shown. In the last year we implemented a new extraction system at all three sources to enhance the lifetime of extraction parts and reduce preventive and corrective maintenance. The new four-electrode-design provides electron suppression as well as lower beam emittance. Unwanted beam sputtering effects which typically lead to contamination of the insulator ceramics and subsequent high-voltage break-downs are minimized by the beam guidance of the new extraction system. By this measure the service interval can be increased significantly. As a side effect, the beam emittance can be reduced allowing a less challenging working point for the ion sources without reducing the effective beam performance. This paper gives also an outlook to further enhancements at the HIT ion source testbench.

VUV spectroscopic observations on the SABRE applied-B ion diode

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

Filuk, A.B.; Nash, T.J.; Noack, D.D.

We are using VUV spectroscopy to study the ion source region on the SABRE applied-B extraction ion diode. The VUV diagnostic views the anode-cathode gap perpendicular to the ion acceleration direction, and images a region 0--1 mm from the anode onto the entrance slit of a I m normal-incidence spectrometer. Time resolution is obtained by gating multiple striplines of a CuI- or MgF{sub 2} -coated micro-channel plate intensifier. We report on results with a passive proton/carbon ion source. Lines of carbon and oxygen are observed over 900--1600 {angstrom}. The optical depths of most of the lines are less than ormore » of order 1. Unfolding the Doppler broadening of the ion lines in the source plasma, we calculate the contribution of the source to the accelerated C IV ion micro-divergence as 4 mrad at peak power. Collisional-radiative modeling of oxygen line intensities provides the source plasma average electron density of 7{times}10{sup 16} cm{sup {minus}3} and temperature of 10 eV Measurements are planned with a lithium ion source and with VUV absorption spectroscopy.« less

The selective and efficient laser ion source and trap project LIST for on-line production of exotic nuclides

NASA Astrophysics Data System (ADS)

Wendt, Klaus; Gottwald, Tina; Hanstorp, Dag; Mattolat, Christoph; Raeder, Sebastian; Rothe, Sebastian; Schwellnus, Fabio; Havener, Charles; Lassen, Jens; Liu, Yuan

2010-02-01

Laser ion sources based on resonant excitation and ionization of atoms are well-established tools for selective and efficient production of radioactive ion beams. A recent trend is the complementary installation of reliable state-of-the-art all solid-state Ti:Sapphire laser systems. To date, 35 elements of the Periodic Table are available at laser ion sources by using these novel laser systems, which complements the overall accessibility to 54 elements including use of traditional dye lasers. Recent progress in the field concerns the identification of suitable optical excitation schemes for Ti:Sapphire laser excitation as well as technical developments of the source in respect to geometry, cavity material as well as by incorporation of an ion guide system in the form of the laser ion source trap LIST.

New development of laser ion source for highly charged ion beam production at Institute of Modern Physics (invited).

PubMed

Zhao, H Y; Zhang, J J; Jin, Q Y; Liu, W; Wang, G C; Sun, L T; Zhang, X Z; Zhao, H W

2016-02-01

A laser ion source based on Nd:YAG laser has been being studied at the Institute of Modern Physics for the production of high intensity high charge state heavy ion beams in the past ten years, for possible applications both in a future accelerator complex and in heavy ion cancer therapy facilities. Based on the previous results for the production of multiple-charged ions from a wide range of heavy elements with a 3 J/8 ns Nd:YAG laser [Zhao et al., Rev. Sci. Instrum. 85, 02B910 (2014)], higher laser energy and intensity in the focal spot are necessary for the production of highly charged ions from the elements heavier than aluminum. Therefore, the laser ion source was upgraded with a new Nd:YAG laser, the maximum energy of which is 8 J and the pulse duration can be adjusted from 8 to 18 ns. Since then, the charge state distributions of ions from various elements generated by the 8 J Nd:YAG laser were investigated for different experimental conditions, such as laser energy, pulse duration, power density in the focal spot, and incidence angle. It was shown that the incidence angle is one of the most important parameters for the production of highly charged ions. The capability of producing highly charged ions from the elements lighter than silver was demonstrated with the incidence angle of 10° and laser power density of 8 × 10(13) W cm(-2) in the focal spot, which makes a laser ion source complementary to the superconducting electron cyclotron resonance ion source for the future accelerator complex especially in terms of the ion beam production from some refractory elements. Nevertheless, great efforts with regard to the extraction of intense ion beams, modification of the ion beam pulse duration, and reliability of the ion source still need to be made for practical applications.

New development of laser ion source for highly charged ion beam production at Institute of Modern Physics (invited)

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

Zhao, H. Y., E-mail: zhaohy@impcas.ac.cn; Zhang, J. J.; Jin, Q. Y.

2016-02-15

A laser ion source based on Nd:YAG laser has been being studied at the Institute of Modern Physics for the production of high intensity high charge state heavy ion beams in the past ten years, for possible applications both in a future accelerator complex and in heavy ion cancer therapy facilities. Based on the previous results for the production of multiple-charged ions from a wide range of heavy elements with a 3 J/8 ns Nd:YAG laser [Zhao et al., Rev. Sci. Instrum. 85, 02B910 (2014)], higher laser energy and intensity in the focal spot are necessary for the production ofmore » highly charged ions from the elements heavier than aluminum. Therefore, the laser ion source was upgraded with a new Nd:YAG laser, the maximum energy of which is 8 J and the pulse duration can be adjusted from 8 to 18 ns. Since then, the charge state distributions of ions from various elements generated by the 8 J Nd:YAG laser were investigated for different experimental conditions, such as laser energy, pulse duration, power density in the focal spot, and incidence angle. It was shown that the incidence angle is one of the most important parameters for the production of highly charged ions. The capability of producing highly charged ions from the elements lighter than silver was demonstrated with the incidence angle of 10° and laser power density of 8 × 10{sup 13} W cm{sup −2} in the focal spot, which makes a laser ion source complementary to the superconducting electron cyclotron resonance ion source for the future accelerator complex especially in terms of the ion beam production from some refractory elements. Nevertheless, great efforts with regard to the extraction of intense ion beams, modification of the ion beam pulse duration, and reliability of the ion source still need to be made for practical applications.« less

Electron energy recovery system for negative ion sources

DOEpatents

Dagenhart, W.K.; Stirling, W.L.

1979-10-25

An electron energy recovery system for negative ion sources is provided. The system, employing crossed electric and magnetic fields, separates the electrons from the ions as they are extracted from the ion source plasma generator and before the ions are accelerated to their full energy. With the electric and magnetic fields oriented 90/sup 0/ to each other, the electrons remain at approximately the electrical potential at which they were generated. The electromagnetic forces cause the ions to be accelerated to the full accelerating supply voltage energy while being deflected through an angle of less than 90/sup 0/. The electrons precess out of the accelerating field region into an electron recovery region where they are collected at a small fraction of the full accelerating supply energy. It is possible, by this method, to collect > 90% of the electrons extracted along with the negative ions from a negative ion source beam at < 4% of full energy.

Caesium sputter ion source compatible with commercial SIMS instruments

NASA Astrophysics Data System (ADS)

Belykh, S. F.; Palitsin, V. V.; Veryovkin, I. V.; Kovarsky, A. P.; Chang, R. J. H.; Adriaens, A.; Dowsett, M.; Adams, F.

2006-07-01

A simple design for a caesium sputter cluster ion source compatible with commercially available secondary ion mass spectrometers is reported. This source has been tested with the Cameca IMS 4f instrument using the cluster Si n- and Cu n- ions, and will shortly be retrofitted to the floating low energy ion gun (FLIG) of the type used on the Cameca 4500/4550 quadruple instruments. Our experiments with surface characterization and depth profiling conducted to date demonstrate improvements of analytical capabilities of the SIMS instrument due to the non-additive enhancement of secondary ion emission and shorter ion ranges of polyatomic projectiles compared to atomic ions with the same impact energy.

Development of high intensity ion sources for a Tandem-Electrostatic-Quadrupole facility for Accelerator-Based Boron Neutron Capture Therapy.

PubMed

Bergueiro, J; Igarzabal, M; Sandin, J C Suarez; Somacal, H R; Vento, V Thatar; Huck, H; Valda, A A; Repetto, M; Kreiner, A J

2011-12-01

Several ion sources have been developed and an ion source test stand has been mounted for the first stage of a Tandem-Electrostatic-Quadrupole facility For Accelerator-Based Boron Neutron Capture Therapy. A first source, designed, fabricated and tested is a dual chamber, filament driven and magnetically compressed volume plasma proton ion source. A 4 mA beam has been accelerated and transported into the suppressed Faraday cup. Extensive simulations of the sources have been performed using both 2D and 3D self-consistent codes. Copyright © 2011 Elsevier Ltd. All rights reserved.

HIGH VOLTAGE ION SOURCE

DOEpatents

Luce, J.S.

1960-04-19

A device is described for providing a source of molecular ions having a large output current and with an accelerated energy of the order of 600 kv. Ions are produced in an ion source which is provided with a water-cooled source grid of metal to effect maximum recombination of atomic ions to molecular ions. A very high accelerating voltage is applied to withdraw and accelerate the molecular ions from the source, and means are provided for dumping the excess electrons at the lowest possible potentials. An accelerating grid is placed adjacent to the source grid and a slotted, grounded accelerating electrode is placed adjacent to the accelerating grid. A potential of about 35 kv is maintained between the source grid and accelerating grid, and a potential of about 600 kv is maintained between the accelerating grid and accelerating electrode. In order to keep at a minimum the large number of oscillating electrons which are created when such high voltages are employed in the vicinity of a strong magnetic field, a plurality of high voltage cascaded shields are employed with a conventional electron dumping system being employed between each shield so as to dump the electrons at the lowest possible potential rather than at 600 kv.

Development of the Long Pulse Negative Ion Source for ITER

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

Hemsworth, R.S.; Svensson, L.; Esch, H.P.L. de

2005-04-06

A model of the ion source designed for the neutral beam injectors of the International Thermonuclear Experimental Reactor (ITER), the KAMABOKO III ion source, is being tested on the MANTIS test stand at the DRFC Cadarache in collaboration with JAERI, Japan, who designed and supplied the ion source. The ion source is attached to a 3 grid 30 keV accelerator (also supplied by JAERI) and the accelerated negative ion current is determined from the energy deposited on a calorimeter located 1.6 m from the source.During experiments on MANTIS three adverse effects of long pulse operation were found: The negative ionmore » current to the calorimeter is {approx_equal}50% of that obtained from short pulse operation Increasing the plasma grid (PG) temperature results in {<=}40% enhancement in negative ion yield, substantially below that reported for short pulse operation, {>=}100%. The caesium 'consumption' is up to 1500 times that expected.Results presented here indicate that each of these is, at least partially, explained by thermal effects. Additionally presented are the results of a detailed characterisation of the source, which enable the most efficient mode of operation to be identified.« less

Increased Reliability for Single-Case Research Results: Is the Bootstrap the Answer?

ERIC Educational Resources Information Center

Parker, Richard I.

2006-01-01

There is need for objective and reliable single-case research (SCR) results in the movement toward evidence-based interventions (EBI), for inclusion in meta-analyses, and for funding accountability in clinical contexts. Yet SCR deals with data that often do not conform to parametric data assumptions and that yield results of low reliability. A…

Physiological and Growth Characteristics of Shewanella Species

DTIC Science & Technology

2016-05-01

AFCEC-CX-TY-TR-2016-0016 PHYSIOLOGICAL AND GROWTH CHARACTERISTICS OF SHEWANELLA SPECIES Karen Farrington, D. Matthew Eby, Susan Sizemore...Technical Report 01 March 2012 - 01 March 2014 Physiological and growth characteristics of Shewanella species FA4819-11-C-0003 Karen Farrington (1...unconventional operating temperatures. Secondly, the unusual growth characteristics of another Shewanella sp., Shewanella japonica, were investigated

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

ERIC Educational Resources Information Center

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…

Childhood Brain Insult: Can Age at Insult Help Us Predict Outcome?

ERIC Educational Resources Information Center

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

2009-01-01

Until recently, the impact of early brain insult (EBI) has been considered to be less significant than for later brain injuries, consistent with the notion that the young brain is more flexible and able to reorganize in the context of brain insult. This study aimed to evaluate this notion by comparing cognitive and behavioural outcomes for…

First operation and effect of a new tandem-type ion source based on electron cyclotron resonance

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

Kato, Yushi, E-mail: kato@eei.eng.osaka-u.ac.jp; Kimura, Daiju; Yano, Keisuke

A new tandem type source has been constructed on the basis of electron cyclotron resonance plasma for producing synthesized ion beams in Osaka University. Magnetic field in the first stage consists of all permanent magnets, i.e., cylindrically comb shaped one, and that of the second stage consists of a pair of mirror coil, a supplemental coil and the octupole magnets. Both stage plasmas can be individually operated, and produced ions in which is energy controlled by large bore extractor also can be transported from the first to the second stage. We investigate the basic operation and effects of the tandemmore » type electron cyclotron resonance ion source (ECRIS). Analysis of ion beams and investigation of plasma parameters are conducted on produced plasmas in dual plasmas operation as well as each single operation. We describe construction and initial experimental results of the new tandem type ion source based on ECRIS with wide operation window for aiming at producing synthesized ion beams as this new source can be a universal source in future.« less

High voltage holding in the negative ion sources with cesium deposition

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

Belchenko, Yu.; Abdrashitov, G.; Ivanov, A.

High voltage holding of the large surface-plasma negative ion source with cesium deposition was studied. It was found that heating of ion-optical system electrodes to temperature >100 °C facilitates the source conditioning by high voltage pulses in vacuum and by beam shots. The procedure of electrode conditioning and the data on high-voltage holding in the negative ion source with small cesium seed are described. The mechanism of high voltage holding improvement by depletion of cesium coverage is discussed.

Ionization source utilizing a jet disturber in combination with an ion funnel and method of operation

DOEpatents

Smith, Richard D.; Kim, Taeman; Tang, Keqi; Udseth, Harold R.

2003-06-24

A jet disturber used in combination with an ion funnel to focus ions and other charged particles generated at or near atmospheric pressure into a relatively low pressure region, which allows increased conductance of the ions and other charged particles. The jet disturber is positioned within an ion funnel and may be interfaced with a multi-capillary inlet juxtaposed between an ion source and the interior of an instrument maintained at near atmospheric pressure. The invention finds particular advantages when deployed to improve the ion transmission between an electrospray ionization source and the first vacuum stage of a mass spectrometer.

The study towards high intensity high charge state laser ion sources.

PubMed

Zhao, H Y; Jin, Q Y; Sha, S; Zhang, J J; Li, Z M; Liu, W; Sun, L T; Zhang, X Z; Zhao, H W

2014-02-01

As one of the candidate ion sources for a planned project, the High Intensity heavy-ion Accelerator Facility, a laser ion source has been being intensively studied at the Institute of Modern Physics in the past two years. The charge state distributions of ions produced by irradiating a pulsed 3 J/8 ns Nd:YAG laser on solid targets of a wide range of elements (C, Al, Ti, Ni, Ag, Ta, and Pb) were measured with an electrostatic ion analyzer spectrometer, which indicates that highly charged ions could be generated from low-to-medium mass elements with the present laser system, while the charge state distributions for high mass elements were relatively low. The shot-to-shot stability of ion pulses was monitored with a Faraday cup for carbon target. The fluctuations within ±2.5% for the peak current and total charge and ±6% for pulse duration were demonstrated with the present setup of the laser ion source, the suppression of which is still possible.

A 60 mA DC H- multi cusp ion source developed at TRIUMF

NASA Astrophysics Data System (ADS)

Jayamanna, K.; Ames, F.; Bylinskii, I.; Lovera, M.; Minato, B.

2018-07-01

This paper describes the latest high-current multi cusp type ion source developed at TRIUMF, which is capable of producing a negative hydrogen ion beam (H-) of 60 mA of direct current at 140V and 90A arc. The results achieved to date including emittance measurements and filament lifetime issues are presented. The low current version of this ion source is suitable for medical cyclotrons as well as accelerators and the high current version is intended for producing large neutral hydrogen beams for fusion research. The description of the source magnetic configuration, the electron filter profile and the differential pumping techniques given in the paper will allow the building of an arc discharge H- ion source with similar properties.

Very Large Area/Volume Microwave ECR Plasma and Ion Source

NASA Technical Reports Server (NTRS)

Foster, John E. (Inventor); Patterson, Michael J. (Inventor)

2009-01-01

The present invention is an apparatus and method for producing very large area and large volume plasmas. The invention utilizes electron cyclotron resonances in conjunction with permanent magnets to produce dense, uniform plasmas for long life ion thruster applications or for plasma processing applications such as etching, deposition, ion milling and ion implantation. The large area source is at least five times larger than the 12-inch wafers being processed to date. Its rectangular shape makes it easier to accommodate to materials processing than sources that are circular in shape. The source itself represents the largest ECR ion source built to date. It is electrodeless and does not utilize electromagnets to generate the ECR magnetic circuit, nor does it make use of windows.

Ion current detector for high pressure ion sources for monitoring separations

DOEpatents

Smith, R.D.; Wahl, J.H.; Hofstadler, S.A.

1996-08-13

The present invention relates generally to any application involving the monitoring of signal arising from ions produced by electrospray or other high pressure (>100 torr) ion sources. The present invention relates specifically to an apparatus and method for the detection of ions emitted from a capillary electrophoresis (CE) system, liquid chromatography, or other small-scale separation methods. And further, the invention provides a very simple diagnostic as to the quality of the separation and the operation of an electrospray source. 7 figs.

Ion current detector for high pressure ion sources for monitoring separations

DOEpatents

Smith, Richard D.; Wahl, Jon H.; Hofstadler, Steven A.

1996-01-01

The present invention relates generally to any application involving the monitoring of signal arising from ions produced by electrospray or other high pressure (>100 torr) ion sources. The present invention relates specifically to an apparatus and method for the detection of ions emitted from a capillary electrophoresis (CE) system, liquid chromatography, or other small-scale separation methods. And further, the invention provides a very simple diagnostic as to the quality of the separation and the operation of an electrospray source.

Kinetic modeling of particle dynamics in H- negative ion sources (invited)

NASA Astrophysics Data System (ADS)

Hatayama, A.; Shibata, T.; Nishioka, S.; Ohta, M.; Yasumoto, M.; Nishida, K.; Yamamoto, T.; Miyamoto, K.; Fukano, A.; Mizuno, T.

2014-02-01

Progress in the kinetic modeling of particle dynamics in H- negative ion source plasmas and their comparisons with experiments are reviewed, and discussed with some new results. Main focus is placed on the following two topics, which are important for the research and development of large negative ion sources and high power H- ion beams: (i) Effects of non-equilibrium features of EEDF (electron energy distribution function) on H- production, and (ii) extraction physics of H- ions and beam optics.

Ion source design for industrial applications

NASA Technical Reports Server (NTRS)

Kaufman, H. R.; Robinson, R. S.

1981-01-01

The design of broad-beam industrial ion sources is described. The approach used emphasizes refractory metal cathodes and permanent-magnet multipole discharge chambers. Design procedures and sample calculations are given for the discharge chamber, ion optics, cathodes, and magnetic circuit. Hardware designs are included for the isolator, cathode supports, anode supports, pole-piece assembly, and ion-optics supports. There are other ways of designing most ion source components, but the designs presented are representative of current technology and adaptable to a wide range of configurations.

Development of the negative ion beams relevant to ITER and JT-60SA at Japan Atomic Energy Agency.

PubMed

Hanada, M; Kojima, A; Tobari, H; Nishikiori, R; Hiratsuka, J; Kashiwagi, M; Umeda, N; Yoshida, M; Ichikawa, M; Watanabe, K; Yamano, Y; Grisham, L R

2016-02-01

In order to realize negative ion sources and accelerators to be applicable to International Thermonuclear Experimental Reactor and JT-60 Super Advanced, a large cesium (Cs)-seeded negative ion source and a multi-aperture and multi-stage electric acceleration have been developed at Japan Atomic Energy Agency (JAEA). Long pulse production and acceleration of the negative ion beams have been independently carried out. The long pulse production of the high current beams has achieved 100 s at the beam current of 15 A by modifying the JT-60 negative ion source. The pulse duration time is increased three times longer than that before the modification. As for the acceleration, a pulse duration time has been also extended two orders of magnitudes from 0.4 s to 60 s. The developments of the negative ion source and acceleration at JAEA are well in progress towards the realization of the negative ion sources and accelerators for fusion applications.

Electrical shielding box measurement of the negative hydrogen beam from Penning ion gauge ion source.

PubMed

Wang, T; Yang, Z; Dong, P; long, J D; He, X Z; Wang, X; Zhang, K Z; Zhang, L W

2012-06-01

The cold-cathode Penning ion gauge (PIG) type ion source has been used for generation of negative hydrogen (H(-)) ions as the internal ion source of a compact cyclotron. A novel method called electrical shielding box dc beam measurement is described in this paper, and the beam intensity was measured under dc extraction inside an electrical shielding box. The results of the trajectory simulation and dc H(-) beam extraction measurement were presented. The effect of gas flow rate, magnetic field strength, arc current, and extraction voltage were also discussed. In conclusion, the dc H(-) beam current of about 4 mA from the PIG ion source with the puller voltage of 40 kV and arc current of 1.31 A was extrapolated from the measurement at low extraction dc voltages.

Status of ion sources at National Institute of Radiological Sciences.

PubMed

Kitagawa, A; Fujita, T; Goto, A; Hattori, T; Hamano, T; Hojo, S; Honma, T; Imaseki, H; Katagiri, K; Muramatsu, M; Sakamoto, Y; Sekiguchi, M; Suda, M; Sugiura, A; Suya, N

2012-02-01

The National Institute of Radiological Sciences (NIRS) maintains various ion accelerators in order to study the effects of radiation of the human body and medical uses of radiation. Two electrostatic tandem accelerators and three cyclotrons delivered by commercial companies have offered various life science tools; these include proton-induced x-ray emission analysis (PIXE), micro beam irradiation, neutron exposure, and radioisotope tracers and probes. A duoplasmatron, a multicusp ion source, a penning ion source (PIG), and an electron cyclotron resonance ion source (ECRIS) are in operation for these purposes. The Heavy-Ion Medical Accelerator in Chiba (HIMAC) is an accelerator complex for heavy-ion radiotherapy, fully developed by NIRS. HIMAC is utilized not only for daily treatment with the carbon beam but also for fundamental experiments. Several ECRISs and a PIG at HIMAC satisfy various research and clinical requirements.

Ring current dynamics and plasma sheet sources. [magnetic storms

NASA Technical Reports Server (NTRS)

Lyons, L. R.

1984-01-01

The source of the energized plasma that forms in geomagnetic storm ring currents, and ring current decay are discussed. The dominant loss processes for ring current ions are identified as charge exchange and resonant interactions with ion-cyclotron waves. Ring current ions are not dominated by protons. At L4 and energies below a few tens of keV, O+ is the most abundant ion, He+ is second, and protons are third. The plasma sheet contributes directly or indirectly to the ring current particle population. An important source of plasma sheet ions is earthward streaming ions on the outer boundary of the plasma sheet. Ion interactions with the current across the geomagnetic tail can account for the formation of this boundary layer. Electron interactions with the current sheet are possibly an important source of plasma sheet electrons.

Status of ion sources at National Institute of Radiological Sciencesa)

NASA Astrophysics Data System (ADS)

Kitagawa, A.; Fujita, T.; Goto, A.; Hattori, T.; Hamano, T.; Hojo, S.; Honma, T.; Imaseki, H.; Katagiri, K.; Muramatsu, M.; Sakamoto, Y.; Sekiguchi, M.; Suda, M.; Sugiura, A.; Suya, N.

2012-02-01

The National Institute of Radiological Sciences (NIRS) maintains various ion accelerators in order to study the effects of radiation of the human body and medical uses of radiation. Two electrostatic tandem accelerators and three cyclotrons delivered by commercial companies have offered various life science tools; these include proton-induced x-ray emission analysis (PIXE), micro beam irradiation, neutron exposure, and radioisotope tracers and probes. A duoplasmatron, a multicusp ion source, a penning ion source (PIG), and an electron cyclotron resonance ion source (ECRIS) are in operation for these purposes. The Heavy-Ion Medical Accelerator in Chiba (HIMAC) is an accelerator complex for heavy-ion radiotherapy, fully developed by NIRS. HIMAC is utilized not only for daily treatment with the carbon beam but also for fundamental experiments. Several ECRISs and a PIG at HIMAC satisfy various research and clinical requirements.

Ion Outflow Observations

NASA Technical Reports Server (NTRS)

Mellot, Mary (Technical Monitor)

2002-01-01

The characteristics of out-flowing ions have been investigated under various circumstances. In particular the upwelling of ions from the cleft region has been studied to attempt to look at source characteristics (e.g., temperature, altitude). High altitude (6-8 Re) data tend to show ions species that have the same velocity and are adiabatically cooled. Such ions, while representative of their source, can not provide an accurate picture. Ion observations from the TIDE detector on the Polar spacecraft show an energy (or equivalently a velocity) spectrum of ions as they undo the geomagnetic mass spectrometer effect due to convection-gravity separation of the different species. Consolidation of this type of data into a complete representation of the source spectrum can be attempted by building a set of maximum-phase-space- density-velocity pairs and attributing the total to the source.

Super-atmospheric pressure chemical ionization mass spectrometry.

PubMed

Chen, Lee Chuin; Rahman, Md Matiur; Hiraoka, Kenzo

2013-03-01

Super-atmospheric pressure chemical ionization (APCI) mass spectrometry was performed using a commercial mass spectrometer by pressurizing the ion source with compressed air up to 7 atm. Similar to typical APCI source, reactant ions in the experiment were generated with corona discharge using a needle electrode. Although a higher needle potential was necessary to initiate the corona discharge, discharge current and detected ion signal were stable at all tested pressures. A Roots booster pump with variable pumping speed was installed between the evacuation port of the mass spectrometer and the original rough pumps to maintain a same pressure in the first pumping stage of the mass spectrometer regardless of ion source pressure. Measurement of gaseous methamphetamine and research department explosive showed an increase in ion intensity with the ion source pressure until an optimum pressure at around 4-5 atm. Beyond 5 atm, the ion intensity decreased with further increase of pressure, likely due to greater ion losses inside the ion transport capillary. For benzene, it was found that besides molecular ion and protonated species, ion due to [M + 2H](+) which was not so common in APCI, was also observed with high ion abundance under super-atmospheric pressure condition. Copyright © 2013 John Wiley & Sons, Ltd.

H- ion sources for CERN's Linac4

NASA Astrophysics Data System (ADS)

Lettry, J.; Aguglia, D.; Coutron, Y.; Chaudet, E.; Dallocchio, A.; Gil Flores, J.; Hansen, J.; Mahner, E.; Mathot, S.; Mattei, S.; Midttun, O.; Moyret, P.; Nisbet, D.; O'Neil, M.; Paoluzzi, M.; Pasquino, C.; Pereira, H.; Arias, J. Sanchez; Schmitzer, C.; Scrivens, R.; Steyaert, D.

2013-02-01

The specifications set to the Linac4 ion source are: H- ion pulses of 0.5 ms duration, 80 mA intensity and 45 keV energy within a normalized emittance of 0.25 mmmrad RMS at a repetition rate of 2 Hz. In 2010, during the commissioning of a prototype based on H- production from the plasma volume, it was observed that the powerful co-extracted electron beam inherent to this type of ion source could destroy its electron beam dump well before reaching nominal parameters. However, the same source was able to provide 80 mA of protons mixed with a small fraction of H2+ and H3+ molecular ions. The commissioning of the radio frequency quadrupole accelerator (RFQ), beam chopper and H- beam diagnostics of the Linac4 are scheduled for 2012 and its final installation in the underground building is to start in 2013. Therefore, a crash program was launched in 2010 and reviewed in 2011 aiming at keeping the original Linac4 schedule with the following deliverables: Design and production of a volume ion source prototype suitable for 20-30 mA H- and 80 mA proton pulses at 45 keV by mid-2012. This first prototype will be dedicated to the commissioning of the low energy components of the Linac4. Design and production of a second prototype suitable for 40-50 mA H- based on an external RF solenoid plasma heating and cesiated-surface production mechanism in 2013 and a third prototype based on BNL's Magnetron aiming at reliable 2 Hz and 80 mA H- operations in 2014. In order to ease the future maintenance and allow operation with Ion sources based on three different production principles, an ion source "front end" providing alignment features, pulsed gas injection, pumping units, beam tuning capabilities and pulsed bipolar high voltage acceleration was designed and is being produced. This paper describes the progress of the Linac4 ion source program, the design of the Front end and first ion source prototype. Preliminary results of the summer 2012 commissioning are presented. The outlook on the future prototype ion sources is sketched.

Comment on 'Effects of magnetic field gradient on ion beam current in cylindrical Hall ion source' [J. Appl. Phys. 102, 123305 (2007)

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

Raitses, Y.; Smirnov, A.; Fisch, N. J.

It is argued that the key difference in the cylindrical Hall thruster (CHT) as compared to the end-Hall ion source cannot be exclusively attributed to the magnetic field topology [Tang et al., J. Appl. Phys. 102, 123305 (2007)]. With a similar mirror-type topology, the CHT configuration provides the electric field with nearly equipotential magnetic field surfaces and a better suppression of the electron cross-field transport, as compared to both the end-Hall ion source and the cylindrical Hall ion source of [Tang et al., J. Appl. Phys. 102, 123305 (2007)].

Recent developments of ion sources for life-science studies at the Heavy Ion Medical Accelerator in Chiba (invited)

NASA Astrophysics Data System (ADS)

Kitagawa, A.; Drentje, A. G.; Fujita, T.; Muramatsu, M.; Fukushima, K.; Shiraishi, N.; Suzuki, T.; Takahashi, K.; Takasugi, W.; Biri, S.; Rácz, R.; Kato, Y.; Uchida, T.; Yoshida, Y.

2016-02-01

With about 1000-h of relativistic high-energy ion beams provided by Heavy Ion Medical Accelerator in Chiba, about 70 users are performing various biology experiments every year. A rich variety of ion species from hydrogen to xenon ions with a dose rate of several Gy/min is available. Carbon, iron, silicon, helium, neon, argon, hydrogen, and oxygen ions were utilized between 2012 and 2014. Presently, three electron cyclotron resonance ion sources (ECRISs) and one Penning ion source are available. Especially, the two frequency heating techniques have improved the performance of an 18 GHz ECRIS. The results have satisfied most requirements for life-science studies. In addition, this improved performance has realized a feasible solution for similar biology experiments with a hospital-specified accelerator complex.

Development of electron beam ion source for nanoprocess using highly charged ions

NASA Astrophysics Data System (ADS)

Sakurai, Makoto; Nakajima, Fumiharu; Fukumoto, Takunori; Nakamura, Nobuyuki; Ohtani, Shunsuke; Mashiko, Shinro; Sakaue, Hiroyuki

2005-07-01

Highly charged ion is useful to produce nanostructure on various materials, and is key tool to realize single ion implantation technique. On such demands for the application to nanotechnology, we have designed an electron bean ion source. The design stresses on the volume of drift tubes where highly charged ions are confined and the efficiency of ion extraction from the drift tube through collector electrode in order to obtain intense ion beam as much as possible. The ion source uses a discrete superconducting magnet cooled by a closed-cycle refrigerator in order to reduce the running costs and to simplify the operating procedures. The electrodes of electron gun, drift tubes, and collector are enclosed in ultrahigh vacuum tube that is inserted into the bore of the magnet system.

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

Hanada, M., E-mail: hanada.masaya@jaea.go.jp; Kojima, A.; Tobari, H.

In order to realize negative ion sources and accelerators to be applicable to International Thermonuclear Experimental Reactor and JT-60 Super Advanced, a large cesium (Cs)-seeded negative ion source and a multi-aperture and multi-stage electric acceleration have been developed at Japan Atomic Energy Agency (JAEA). Long pulse production and acceleration of the negative ion beams have been independently carried out. The long pulse production of the high current beams has achieved 100 s at the beam current of 15 A by modifying the JT-60 negative ion source. The pulse duration time is increased three times longer than that before the modification.more » As for the acceleration, a pulse duration time has been also extended two orders of magnitudes from 0.4 s to 60 s. The developments of the negative ion source and acceleration at JAEA are well in progress towards the realization of the negative ion sources and accelerators for fusion applications.« less

Development of a compact filament-discharge multi-cusp H- ion source.

PubMed

Jia, XianLu; Zhang, TianJue; Zheng, Xia; Qin, JiuChang

2012-02-01

A 14 MeV medical cyclotron with the external ion source has been designed and is being constructed at China Institute of Atomic Energy. The H(-) ion will be accelerated by this machine and the proton beam will be extracted by carbon strippers in dual opposite direction. The compact multi-cusp H(-) ion source has been developed for the cyclotron. The 79.5 mm long ion source is 48 mm in diameter, which is consisting of a special shape filament, ten columns of permanent magnets providing a multi-cusp field, and a three-electrode extraction system. So far, the 3 mA∕25 keV H(-) beam with an emittance of 0.3 π mm mrad has been obtained from the ion source. The paper gives the design details and the beam test results. Further experimental study is under way and an extracted beam of 5 mA is expected.

Thermal-electric coupled-field finite element modeling and experimental testing of high-temperature ion sources for the production of radioactive ion beams

NASA Astrophysics Data System (ADS)

Manzolaro, M.; Meneghetti, G.; Andrighetto, A.; Vivian, G.; D'Agostini, F.

2016-02-01

In isotope separation on line facilities the target system and the related ion source are two of the most critical components. In the context of the selective production of exotic species (SPES) project, a 40 MeV 200 μA proton beam directly impinges a uranium carbide target, generating approximately 1013 fissions per second. The radioactive isotopes produced in this way are then directed to the ion source, where they can be ionized and finally accelerated to the subsequent areas of the facility. In this work both the surface ion source and the plasma ion source adopted for the SPES facility are presented and studied by means of numerical thermal-electric models. Then, numerical results are compared with temperature and electric potential difference measurements, and finally the main advantages of the proposed simulation approach are discussed.

Negative ion-driven associated particle neutron generator

DOE PAGES

Antolak, A. J.; Leung, K. N.; Morse, D. H.; ...

2015-10-09

We describe an associated particle neutron generator that employs a negative ion source to produce high neutron flux from a small source size. Furthermore, negative ions produced in an rf-driven plasma source are extracted through a small aperture to form a beam which bombards a positively biased, high voltage target electrode. Electrons co-extracted with the negative ions are removed by a permanent magnet electron filter. The use of negative ions enables high neutron output (100% atomic ion beam), high quality imaging (small neutron source size), and reliable operation (no high voltage breakdowns). Finally, the neutron generator can operate in eithermore » pulsed or continuous-wave (cw) mode and has been demonstrated to produce 10 6 D-D n/s (equivalent to similar to 10 8 D-T n/s) from a 1 mm-diameter neutron source size to facilitate high fidelity associated particle imaging.« less

Operation of Lanzhou all permanent electron cyclotron resonance ion source No. 2 on 320 kV platform with highly charged ions

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

Lu, W., E-mail: luwang@impcas.ac.cn; University of Chinese Academy of Sciences, Beijing 100049; Li, J. Y.

2014-02-15

The 320 kV platform for multi-discipline research with highly charged ions is a heavy ion beam acceleration instrument developed by Institute of Modern Physics, which is dedicated to basic scientific researches such as plasma, atom, material physics, and astrophysics, etc. The platform has delivered ion beams of 400 species for 36 000 h. The average operation time is around 5000 h/year. With the beams provided by the platform, lots of outstanding progresses were made in various research fields. The ion source of the platform is an all-permanent magnet electron cyclotron resonance ion source, LAPECR2 (Lanzhou All Permanent ECR ion source No.more » 2). The maximum axial magnetic fields are 1.28 T at injection and 1.07 T at extraction, and the radial magnetic field is up to 1.21 T at the inner wall of the plasma chamber. The ion source is capable to produce low, medium, and high charge state gaseous and metallic ion beams, such as H{sup +}, {sup 40}Ar{sup 8+}, {sup 129}Xe{sup 30+}, {sup 209}Bi{sup 33+}, etc. This paper will present the latest result of LAPECR2 and the routine operation status for the high voltage platform.« less

Operation and development status of the J-PARC ion source

NASA Astrophysics Data System (ADS)

Yamazaki, S.; Ikegami, K.; Ohkoshi, K.; Ueno, A.; Koizumi, I.; Takagi, A.; Oguri, H.

2014-02-01

A cesium-free H- ion source driven with a LaB6 filament is being operated at the Japan Proton Accelerator Research Complex (J-PARC) without any serious trouble since the restoration from the March 2011 earthquake. The H- ion current from the ion source is routinely restricted approximately 19 mA for the lifetime of the filament. In order to increase the beam power at the linac beam operation (January to February 2013), the beam current from the ion source was increased to 22 mA. At this operation, the lifetime of the filament was estimated by the reduction in the filament current. According to the steep reduction in the filament current, the break of the filament was predicted. Although the filament has broken after approximately 10 h from the steep current reduction, the beam operation was restarted approximately 8 h later by the preparation for the exchange of new filament. At the study time for the 3 GeV rapid cycling synchrotron (April 2013), the ion source was operated at approximately 30 mA for 8 days. As a part of the beam current upgrade plan for the J-PARC, the front end test stand consisting of the ion source and the radio frequency quadrupole is under preparation. The RF-driven H- ion source developed for the J-PARC 2nd stage requirements will be tested at this test stand.

Plasma Ion Sources for Atmospheric Pressure Ionization Mass Spectrometry.

NASA Astrophysics Data System (ADS)

Zhao, Jian-Guo

1994-01-01

Atmospheric pressure ionization (API) sources using direct-current (DC) and radio-frequency (RF) plasma have been developed in this thesis work. These ion sources can provide stable discharge currents of ~ 1 mA, 2-3 orders of magnitude larger than that of the corona discharge, a widely used API source. The plasmas can be generated and maintained in 1 atm of various buffer gases by applying -500 to -1000 V (DC plasma) or 1-15 W with a frequency of 165 kHz (RF plasma) on the needle electrode. These ion sources have been used with liquid injection to detect various organic compounds of pharmaceutical, biotechnological and environmental interest. Key features of these ion sources include soft ionization with the protonated molecule as the largest peak, and superb sensitivity with detection limits in the low picogram or femtomole range and a linear dynamic range over ~4 orders of magnitude. The RF plasma has advantages over the DC plasma in its ability to operate in various buffer gases and to produce a more stable plasma. Factors influencing the performance of the ion sources have been studied, including RF power level, liquid flow rate, chamber temperature, solvent composition, and voltage affecting the collision induced dissociation (CID). Ionization of hydrocarbons by the RF plasma API source was also studied. Soft ionization is generally produced. To obtain high sensitivity, the ion source must be very dry and the needle-to-orifice distance must be small. Nitric oxide was used to enhance the sensitivity. The RF plasma source was then used for the analysis of hydrocarbons in auto emissions. Comparisons between the corona discharge and the RF plasma have been made in terms of discharge current, ion residence time, and the ion source model. The RF plasma source provides larger linear dynamic range and higher sensitivity than the corona discharge, due to its much larger discharge current. The RF plasma was also observed to provide longer ion residence times and was not limited by space-charge effect as in the corona source.

CALUTRON ION SOURCE

DOEpatents

Oppenheimer, F.F.

1959-06-01

A shielding arrangement for eliminating oscillating electrons in the ion source region of calutrons is offered. Metal plates are attached to the ion generator so as to intercept the magnetic field between ion generator and accelerating electrode. The oscillating electrons are discharged on the plates. (T.R.H.)

Intense highly charged ion beam production and operation with a superconducting electron cyclotron resonance ion source

NASA Astrophysics Data System (ADS)

Zhao, H. W.; Sun, L. T.; Guo, J. W.; Lu, W.; Xie, D. Z.; Hitz, D.; Zhang, X. Z.; Yang, Y.

2017-09-01

The superconducting electron cyclotron resonance ion source with advanced design in Lanzhou (SECRAL) is a superconducting-magnet-based electron cyclotron resonance ion source (ECRIS) for the production of intense highly charged heavy ion beams. It is one of the best performing ECRISs worldwide and the first superconducting ECRIS built with an innovative magnet to generate a high strength minimum-B field for operation with heating microwaves up to 24-28 GHz. Since its commissioning in 2005, SECRAL has so far produced a good number of continuous wave intensity records of highly charged ion beams, in which recently the beam intensities of 40Ar+ and 129Xe26+ have, for the first time, exceeded 1 emA produced by an ion source. Routine operations commenced in 2007 with the Heavy Ion accelerator Research Facility in Lanzhou (HIRFL), China. Up to June 2017, SECRAL has been providing more than 28,000 hours of highly charged heavy ion beams to the accelerator demonstrating its great capability and reliability. The great achievement of SECRAL is accumulation of numerous technical advancements, such as an innovative magnetic system and an efficient double-frequency (24 +18 GHz ) heating with improved plasma stability. This article reviews the development of SECRAL and production of intense highly charged ion beams by SECRAL focusing on its unique magnet design, source commissioning, performance studies and enhancements, beam quality and long-term operation. SECRAL development and its performance studies representatively reflect the achievements and status of the present ECR ion source, as well as the ECRIS impacts on HIRFL.

Charge exchange molecular ion source

DOEpatents

Vella, Michael C.

2003-06-03

Ions, particularly molecular ions with multiple dopant nucleons per ion, are produced by charge exchange. An ion source contains a minimum of two regions separated by a physical barrier and utilizes charge exchange to enhance production of a desired ion species. The essential elements are a plasma chamber for production of ions of a first species, a physical separator, and a charge transfer chamber where ions of the first species from the plasma chamber undergo charge exchange or transfer with the reactant atom or molecules to produce ions of a second species. Molecular ions may be produced which are useful for ion implantation.

A review of ion sources for medical accelerators (invited)

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

Muramatsu, M.; Kitagawa, A.

2012-02-15

There are two major medical applications of ion accelerators. One is a production of short-lived isotopes for radionuclide imaging with positron emission tomography and single photon emission computer tomography. Generally, a combination of a source for negative ions (usually H- and/or D-) and a cyclotron is used; this system is well established and distributed over the world. Other important medical application is charged-particle radiotherapy, where the accelerated ion beam itself is being used for patient treatment. Two distinctly different methods are being applied: either with protons or with heavy-ions (mostly carbon ions). Proton radiotherapy for deep-seated tumors has become widespreadmore » since the 1990s. The energy and intensity are typically over 200 MeV and several 10{sup 10} pps, respectively. Cyclotrons as well as synchrotrons are utilized. The ion source for the cyclotron is generally similar to the type for production of radioisotopes. For a synchrotron, one applies a positive ion source in combination with an injector linac. Carbon ion radiotherapy awakens a worldwide interest. About 6000 cancer patients have already been treated with carbon beams from the Heavy Ion Medical Accelerator in Chiba at the National Institute of Radiological Sciences in Japan. These clinical results have clearly verified the advantages of carbon ions. Heidelberg Ion Therapy Center and Gunma University Heavy Ion Medical Center have been successfully launched. Several new facilities are under commissioning or construction. The beam energy is adjusted to the depth of tumors. It is usually between 140 and 430 MeV/u. Although the beam intensity depends on the irradiation method, it is typically several 10{sup 8} or 10{sup 9} pps. Synchrotrons are only utilized for carbon ion radiotherapy. An ECR ion source supplies multi-charged carbon ions for this requirement. Some other medical applications with ion beams attract developer's interests. For example, the several types of accelerators are under development for the boron neutron capture therapy. This treatment is conventionally demonstrated by a nuclear reactor, but it is strongly expected to replace the reactor by the accelerator. We report status of ion source for medical application and such scope for further developments.« less

Polarized negative ions

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

Haeberli, W.

1981-04-01

This paper presents a survey of methods, commonly in use or under development, to produce beams of polarized negative ions for injection into accelerators. A short summary recalls how the hyperfine interaction is used to obtain nuclear polarization in beams of atoms. Atomic-beam sources for light ions are discussed. If the best presently known techniques are incorporated in all stages of the source, polarized H/sup -/ and D/sup -/ beams in excess of 10 ..mu..A can probably be achieved. Production of polarized ions from fast (keV) beams of polarized atoms is treated separately for atoms in the H(25) excited statemore » (Lamb-Shift source) and atoms in the H(1S) ground state. The negative ion beam from Lamb-Shift sources has reached a plateau just above 1 ..mu..A, but this beam current is adequate for many applications and the somewhat lower beam current is compensated by other desirable characteristics. Sources using fast polarized ground state atoms are in a stage of intense development. The next sections summarize production of polarized heavy ions by the atomic beam method, which is well established, and by optical pumping, which has recently been demonstrated to yield very large nuclear polarization. A short discussion of proposed ion sources for polarized /sup 3/He/sup -/ ions is followed by some concluding remarks.« less

High current H2(+) and H3(+) beam generation by pulsed 2.45 GHz electron cyclotron resonance ion source.

PubMed

Xu, Yuan; Peng, Shixiang; Ren, Haitao; Zhao, Jie; Chen, Jia; Zhang, Ailin; Zhang, Tao; Guo, Zhiyu; Chen, Jia'er

2014-02-01

The permanent magnet 2.45 GHz electron cyclotron resonance ion source at Peking University can produce more than 100 mA hydrogen ion beam working at pulsed mode. For the increasing requirements of cluster ions (H2(+) and H3(+)) in linac and cyclotron, experimental study was carried out to further understand the hydrogen plasma processes in the ion source for the generation of cluster ions. The constituents of extracted beam have been analyzed varying with the pulsed duration from 0.3 ms to 2.0 ms (repetition frequency 100 Hz) at different operation pressure. The fraction of cluster ions dramatically increased when the pulsed duration was lower than 0.6 ms, and more than 20 mA pure H3(+) ions with fraction 43.2% and 40 mA H2(+) ions with fraction 47.7% were obtained when the operation parameters were adequate. The dependence of extracted ion fraction on microwave power was also measured at different pressure as the energy absorbed by plasma will greatly influence electron temperature and electron density then the plasma processes in the ion source. More details will be presented in this paper.