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.

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

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.

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.

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.

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.

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…

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

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.

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.

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.

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.

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

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).

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

PubMed

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

2016-02-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

Design 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.

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

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.

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

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.

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.

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.

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

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.

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.

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

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.

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.

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.

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.

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.

Electron beam simulation from gun to collector: Towards a complete solution

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

Mertzig, R., E-mail: robert.mertzig@cern.ch; Shornikov, A., E-mail: robert.mertzig@cern.ch; Wenander, F.

An electron-beam simulation technique for high-resolution complete EBIS/T modelling is presented. The technique was benchmarked on the high compression HEC{sup 2} test-stand with an electron beam current, current density and energy of 10 A, 10 kA/cm{sup 2} and 49.2 keV, and on the immersed electron beam at REXEBIS for electron beam characteristics of 0.4 A, 200 A/cm{sup 2} and 4.5 keV. In both Brillouin-like and immersed beams the electron-beam radius varies from several millimeters at the gun, through some hundreds of micrometers in the ionization region to a few centimeters at the collector over a total length of several meters.more » We report on our approach for finding optimal meshing parameters, based on the local beam properties such as magnetic field-strength, electron energy and beam radius. This approach combined with dividing the problem domain into sub-domains, and subsequent splicing of the local solutions allowed us to simulate the beam propagation in EBISes from the gun to the collector using a conventional PC in about 24–36 h. Brillouin-like electron beams propagated through the complete EBIS were used to analyze the beam behavior within the collector region. We checked whether elastically reflected paraxial electrons from a Brillouin-like beam will escape from the collector region and add to the loss current. We have also studied the power deposition profiles as function of applied potentials using two electrode geometries for a Brillouin-like beam including the effects of backscattered electrons.« 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…

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.

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.

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.

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…

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.

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.

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…

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

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.

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.

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.

Ionization of polarized 3He+ ions in EBIS trap with slanted electrostatic mirror.

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

Pikin,A.; Zelenski, A.; Kponou, A.

2007-09-10

Methods of producing the nuclear polarized {sup 3}He{sup +} ions and their ionization to {sup 3}H{sup ++} in ion trap of the electron Beam Ion Source (EBIS) are discussed. Computer simulations show that injection and accumulation of {sup 3}He{sup +} ions in the EBIS trap with slanted electrostatic mirror can be very effective for injection times longer than the ion traversal time through the trap.

Ionization of polarized {sup 3}He{sup +} ions in EBIS trap with slanted electrostatic mirror

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

Pikin, A.; Zelenski, A.; Kponou, A.

2008-02-06

Methods of producing the nuclear polarized {sup 3}He{sup +} ions and their ionization to {sup 3}He{sup ++} in ion trap of the electron Beam Ion Source (EBIS) are discussed. Computer simulations show that injection and accumulation of {sup 3}He{sup +} ions in the EBIS trap with slanted electrostatic mirror can be very effective for injection times longer than the ion traversal time through the trap.

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

Numerical simulation of ion charge breeding in electron beam ion source

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

Zhao, L., E-mail: zhao@far-tech.com; Kim, Jin-Soo

2014-02-15

The Electron Beam Ion Source particle-in-cell code (EBIS-PIC) tracks ions in an EBIS electron beam while updating electric potential self-consistently and atomic processes by the Monte Carlo method. Recent improvements to the code are reported in this paper. The ionization module has been improved by using experimental ionization energies and shell effects. The acceptance of injected ions and the emittance of extracted ion beam are calculated by extending EBIS-PIC to the beam line transport region. An EBIS-PIC simulation is performed for a Cs charge-breeding experiment at BNL. The charge state distribution agrees well with experiments, and additional simulation results ofmore » radial profiles and velocity space distributions of the trapped ions are presented.« less

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

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

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

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

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.

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.

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.

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.

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.

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…

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.

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.

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

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.

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

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.

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…

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

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

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.

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.

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.

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.

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.

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

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.

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

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).

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

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

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.

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

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.

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…

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.

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

PubMed

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

2012-09-28

To evaluate gastric motility using electrical bio-impedance (EBI) and gastric changes as a result of stress induced by psychological tests. A group of 57 healthy women, aged 40-60 years, was recruited, and a clinical history and physical examination were performed. The women were free from severe anxiety, chronic or acute stress, severe depression, mental diseases and conditions that affect gastric activity. The women were evaluated under fasting conditions, and using a four-electrode configuration, the gastric signals were obtained through a BIOPAC MP-150 system. The volunteers were evaluated using the following paradigm: basal state, recording during the Stroop Test, intermediate resting period, recording during the Raven Test, and a final resting period. We analyzed the relative areas of the frequency spectrum: A1 (1-2 cpm), A2 (2-4 cpm), A3 (4-8 cpm), and A4 (8-12 cpm), as well as the median of area A2 + A3. The data were analyzed by an autoregressive method using a Butterworth filter with MatLab and Origin. Analysis of variance (ANOVA) and Friedman ANOVA (for nonparametric variables) were performed; in addition, pairs of groups were compared using the T dependent and Wilcoxon T tests. The results of the main values of area A2 were not significantly different comparing the five steps of the experimental paradigm. Nevertheless, there was a tendency of this A2 region to decrease during the stress tests, with recuperation at the final resting step. When an extended gastric region was considered (1-4 cpm), significant differences with the psychological stress tests were present (F = 3.85, P = 0.005). The A3 region also showed significant changes when the stress psychological tests were administered (F = 7.25, P < 0.001). These differences were influenced by the changes in the adjacent gastric region of A2. The parameter that we proposed in previous studies for the evaluation of gastric motility by electrical bio-impedance (EBI) was the median of the area under the region from 2 to 8 cpm (A2 + A3). The mean values of these frequencies (median of the A2 + A3 area) with the stress test showed significant changes (F = 5.5, P < 0.001). The results of the Wilcoxon T test for the A4 area parameter, which is influenced by the breathing response, changed significantly during the Raven stress test (P < 0.05). We confirm that the gastric response to acute psychological stress can be evaluated by short-term EBI.

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

PubMed

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

2015-01-01

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

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/

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.

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.

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.

"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.

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

Intracranial hemorrhage alters scalp potential distribution in bioimpedance cerebral monitoring: Preliminary results from FEM simulation on a realistic head model and human subjects

PubMed Central

Atefi, Seyed Reza; Seoane, Fernando; Kamalian, Shervin; Rosenthal, Eric S.; Lev, Michael H.; Bonmassar, Giorgio

2016-01-01

Purpose: Current diagnostic neuroimaging for detection of intracranial hemorrhage (ICH) is limited to fixed scanners requiring patient transport and extensive infrastructure support. ICH diagnosis would therefore benefit from a portable diagnostic technology, such as electrical bioimpedance (EBI). Through simulations and patient observation, the authors assessed the influence of unilateral ICH hematomas on quasisymmetric scalp potential distributions in order to establish the feasibility of EBI technology as a potential tool for early diagnosis. Methods: Finite element method (FEM) simulations and experimental left–right hemispheric scalp potential differences of healthy and damaged brains were compared with respect to the asymmetry caused by ICH lesions on quasisymmetric scalp potential distributions. In numerical simulations, this asymmetry was measured at 25 kHz and visualized on the scalp as the normalized potential difference between the healthy and ICH damaged models. Proof-of-concept simulations were extended in a pilot study of experimental scalp potential measurements recorded between 0 and 50 kHz with the authors’ custom-made bioimpedance spectrometer. Mean left–right scalp potential differences recorded from the frontal, central, and parietal brain regions of ten healthy control and six patients suffering from acute/subacute ICH were compared. The observed differences were measured at the 5% level of significance using the two-sample Welch t-test. Results: The 3D-anatomically accurate FEM simulations showed that the normalized scalp potential difference between the damaged and healthy brain models is zero everywhere on the head surface, except in the vicinity of the lesion, where it can vary up to 5%. The authors’ preliminary experimental results also confirmed that the left–right scalp potential difference in patients with ICH (e.g., 64 mV) is significantly larger than in healthy subjects (e.g., 20.8 mV; P < 0.05). Conclusions: Realistic, proof-of-concept simulations confirmed that ICH affects quasisymmetric scalp potential distributions. Pilot clinical observations with the authors’ custom-made bioimpedance spectrometer also showed higher left–right potential differences in the presence of ICH, similar to those of their simulations, that may help to distinguish healthy subjects from ICH patients. Although these pilot clinical observations are in agreement with the computer simulations, the small sample size of this study lacks statistical power to exclude the influence of other possible confounders such as age, sex, and electrode positioning. The agreement with previously published simulation-based and clinical results, however, suggests that EBI technology may be potentially useful for ICH detection. PMID:26843231

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

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.

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

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

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.

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

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.

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

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

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

PubMed

Becker, Reinard; Kester, Oliver

2010-02-01

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

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.

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.

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

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

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

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.

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

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.

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

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

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.

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

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.

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.

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

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

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

PubMed

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

2016-06-01

Omega-3 fatty acids have been reported to improve neuron functions during aging and in patients affected by mild cognitive impairment, and mediate potent anti-inflammatory via G protein-coupled receptor 120 (GPR120) signal pathway. Neuron dysfunction and inflammatory response also contributed to the progression of subarachnoid hemorrhage (SAH)-induced early brain injury (EBI). This study was to examine the effects of omega-3 fatty acids on SAH-induced EBI. Two weeks before SAH, 30% Omega-3 fatty acids was administered by oral gavage at 1g/kg body weight once every 24h. Specific siRNA for GPR120 was exploited. Terminal deoxynucleotidyl transferase dUTP nick end labeling, fluoro-Jade B staining, and neurobehavioral scores and brain water content test showed that omega-3 fatty acids effectively suppressed SAH-induced brain cell apoptosis and neuronal degradation, behavioral impairment, and brain edema. Western blot, immunoprecipitation, and electrophoretic mobility shift assays results showed that omega-3 fatty acids effectively suppressed SAH-induced elevation of inflammatory factors, including cyclooxygenase-2, monocyte chemoattractant protein-1, and inducible nitric oxide synthase. In addition, omega-3 fatty acids could inhibit phosphorylation of transforming growth factor β activated kinase-1 (TAK1), MEK4, c-Jun N-terminal kinase, and IkappaB kinase as well as activation of nuclear factor kappa B through regulating GPR120/β-arrestin2/TAK1 binding protein-1 pathway. Furthermore, siRNA-induced GPR120 silencing blocked the protective effects of omega-3 fatty acids. Here, we show that stimulation of GPR120 with omega-3 fatty acids pretreatment causes anti-apoptosis and anti-inflammatory effects via β-arrestin2/TAK1 binding protein-1/TAK1 pathway in the brains of SAH rats. Fish omega-3 fatty acids as part of a daily diet may reduce EBI in an experimental rat model of SAH. Copyright © 2016 Elsevier Ltd. All rights reserved.

Theoretical and Experimental Research on a Millimeter-Wavelength Free-Electron Laser

DTIC Science & Technology

1989-09-01

Plauma Sci. vol. PS-3, pp. 1-5, 1975. off (Fig. 7); this may be due to the TEo2 cutoff of the 5 cm [5] A. Grossman and T. C. Marshall, "Orbits of a test...from maycor (a machineable glass ), in the form of a N ihin-walled cone. Thermistors attached to the cone de-N 1- v/ " liver a signal which unbalances a...0.7; this is given by using a calorimeter cone fabricated of "Macor." a ma- eBI, nc chineable glass with high absorption at millimeter wave- vl = (eB

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

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.

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.

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

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

PubMed

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

2010-02-01

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

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

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.

CAP waveform estimation from the measured electrical bioimpedance values: Patient's heart rate variability analysis.

PubMed

Krivoshei, A; Uuetoa, H; Min, M; Annus, P; Uuetoa, T; Lamp, J

2015-08-01

The paper presents analysis of the generic transfer function (TF) between Electrical Bioimpedance (EBI) measured non-invasively on the wrist and Central Aortic Pressure (CAP) invasively measured at the aortic root. Influence of the Heart Rate (HR) variations on the generic TF and on reconstructed CAP waveforms is investigated. The HR variation analysis is provided on a single patient data to exclude inter-patient influences at the current research stage. A new approach for the generic TF estimating from a data ensemble is presented as well. Moreover, an influence of the cardiac period beginning point selection is analyzed and empirically optimal solution for its selection is proposed.

IPD—the Immuno Polymorphism Database

PubMed Central

Robinson, James; Halliwell, Jason A.; McWilliam, Hamish; Lopez, Rodrigo; Marsh, Steven G. E.

2013-01-01

The Immuno Polymorphism Database (IPD), http://www.ebi.ac.uk/ipd/ is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer-cell immunoglobulin-like receptors, IPD-MHC, a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The data is currently available online from the website and FTP directory. This article describes the latest updates and additional tools added to the IPD project. PMID:23180793

Self-organizing ontology of biochemically relevant small molecules

PubMed Central

2012-01-01

Background The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. Results To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. Conclusions We conclude that the proposed methodology can ease the burden of chemical data annotators and dramatically increase their productivity. We anticipate that the use of formal logic in our proposed framework will make chemical classification criteria more transparent to humans and machines alike and will thus facilitate predictive and integrative bioactivity model development. PMID:22221313

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.

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

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.

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.

A new rabbit model for the study of early brain injury after subarachnoid hemorrhage.

PubMed

Marbacher, Serge; Andereggen, Lukas; Neuschmelting, Volker; Widmer, Hans Rudolf; von Gunten, Michael; Takala, Jukka; Jakob, Stephan M; Fandino, Javier

2012-07-15

Pathophysiological disturbances during subarachnoid hemorrhage (SAH) and within the first few days thereafter are responsible for significant brain damage. Early brain injury (EBI) after SAH has become the focus of current research activities. The purpose of the present study was to evaluate whether a novel rabbit SAH model provokes EBI by means of neuronal degeneration, brain tissue death, and apoptosis in cerebral vascular endothelial cells. SAH was performed using an extra-intracranial blood shunt. Intracranial pressure (ICP), cerebral perfusion pressure (CPP), and bilateral regional cerebral blood flow (rCBF) were continuously measured. Apoptosis and neurodegeneration were detected 24h post-SAH in basilar artery endothelial cells, bilateral basal cortex, and hippocampus (CA1 and CA3) using terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) and Fluoro-jade B (FJB), respectively. ICP increase caused a CPP decrease to almost zero (8±5mmHg) and decreases in left and right rCBF to 23±8% and 19±9% of their baseline values. TUNEL- and FJB-stained sections revealed significant apoptosis and neurodegeneration in both basal cortex and hippocampal regions compared to sham-operated animals. The apoptotic index in basilar artery endothelial cells was 74%±11%. The blood shunt rabbit SAH model elicits acute physiological dearrangements and provokes marked and consistent early damage to the hippocampus, basal cortex, and cerebral vasculature 24h thereafter. These findings make the model a valid tool for investigation of pre-vasospasm pathophysiological mechanisms and novel treatment modalities. Copyright © 2012 Elsevier B.V. All rights reserved.

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.

Bioinformatics training: selecting an appropriate learning content management system--an example from the European Bioinformatics Institute.

PubMed

Wright, Victoria Ann; Vaughan, Brendan W; Laurent, Thomas; Lopez, Rodrigo; Brooksbank, Cath; Schneider, Maria Victoria

2010-11-01

Today's molecular life scientists are well educated in the emerging experimental tools of their trade, but when it comes to training on the myriad of resources and tools for dealing with biological data, a less ideal situation emerges. Often bioinformatics users receive no formal training on how to make the most of the bioinformatics resources and tools available in the public domain. The European Bioinformatics Institute, which is part of the European Molecular Biology Laboratory (EMBL-EBI), holds the world's most comprehensive collection of molecular data, and training the research community to exploit this information is embedded in the EBI's mission. We have evaluated eLearning, in parallel with face-to-face courses, as a means of training users of our data resources and tools. We anticipate that eLearning will become an increasingly important vehicle for delivering training to our growing user base, so we have undertaken an extensive review of Learning Content Management Systems (LCMSs). Here, we describe the process that we used, which considered the requirements of trainees, trainers and systems administrators, as well as taking into account our organizational values and needs. This review describes the literature survey, user discussions and scripted platform testing that we performed to narrow down our choice of platform from 36 to a single platform. We hope that it will serve as guidance for others who are seeking to incorporate eLearning into their bioinformatics training programmes.

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

The androgen receptor gene mutations database.

PubMed

Gottlieb, B; Trifiro, M; Lumbroso, R; Pinsky, L

1997-01-01

The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 212 to 272. We have expanded the database: (i) by adding a large amount of new data on somatic mutations in prostatic cancer tissue; (ii) by defining a new constitutional phenotype, mild androgen insensitivity (MAI); (iii) by placing additional relevant information on an internet site (http://www.mcgill.ca/androgendb/ ). The database has allowed us to examine the contribution of CpG sites to the multiplicity of reports of the same mutation in different families. The database is also available from EMBL (ftp.ebi.ac.uk/pub/databases/androgen) or as a Macintosh Filemaker Pro or Word file (MC33@musica,mcgill.ca)

The androgen receptor gene mutations database.

PubMed Central

Gottlieb, B; Trifiro, M; Lumbroso, R; Pinsky, L

1997-01-01

The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 212 to 272. We have expanded the database: (i) by adding a large amount of new data on somatic mutations in prostatic cancer tissue; (ii) by defining a new constitutional phenotype, mild androgen insensitivity (MAI); (iii) by placing additional relevant information on an internet site (http://www.mcgill.ca/androgendb/ ). The database has allowed us to examine the contribution of CpG sites to the multiplicity of reports of the same mutation in different families. The database is also available from EMBL (ftp.ebi.ac.uk/pub/databases/androgen) or as a Macintosh Filemaker Pro or Word file (MC33@musica,mcgill.ca) PMID:9016528

The androgen receptor gene mutations database.

PubMed

Gottlieb, B; Trifiro, M; Lumbroso, R; Vasiliou, D M; Pinsky, L

1996-01-01

The current version of the androgen receptor (AR) gene mutations database is described. We have added (if available) data on the androgen binding phenotype of the mutant AR, the clinical phenotype of the affected persons, the family history and whether the pathogenicity of a mutation has been proven. Exonic mutations are now listed in 5'-->3' sequence regardless of type and single base pair changes are presented in codon context. Splice site and intronic mutations are listed separately. The database has allowed us to substantiate and amplify the observation of mutational hot spots within exons encoding the AR androgen binding domain. The database is available from EML (ftp://www.ebi.ac.uk/pub/databases/androgen) or as a Macintosh Filemaker file (MC33@musica.mcgill.ca).

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

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.

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.

Expanding Diversity in Molecular Structures and Functions of the IL-6/IL-12 Heterodimeric Cytokine Family

PubMed Central

Hasegawa, Hideaki; Mizoguchi, Izuru; Chiba, Yukino; Ohashi, Mio; Xu, Mingli; Yoshimoto, Takayuki

2016-01-01

The interleukin (IL)-6/IL-12 family cytokines have pleiotropic functions and play critical roles in multiple immune responses. This cytokine family has very unique characteristics in that they comprise two distinct subunits forming a heterodimer and each cytokine and receptor subunit shares with each other. The members of this cytokine family are increasing; currently, there are more than six cytokines, including the tentatively named cytokines IL-Y (p28/p40), IL-12 (p35/p40), IL-23 (p19/p40), IL-27 [p28/Epstein–Barr virus-induced protein 3 (EBI3)], IL-35 (p35/EBI3), and IL-39 (p19/EBI3). This family of cytokines covers a very broad range of immune responses, including pro-inflammatory responses, such as helper T (Th)1, Th2, and Th17, to anti-inflammatory responses, such as regulatory T (Treg) cells and IL-10-producing Treg cells. IL-12 is the first member of this family, and IL-12, IL-23, and IL-27 are mainly produced by activated antigen-presenting cells, such as dendritic cells and macrophages. IL-12 plays a critical role in the promotion of Th1 immune responses by inducing interferon-γ production to combat pathogens and malignant tumors. IL-23 induces IL-17 production and is necessary to maintain pathogenic Th17 cells that cause inflammatory and autoimmune diseases. IL-27 was initially reported to play a critical role in promotion of Th1 differentiation; however, subsequent studies revealed that IL-27 has broader stimulatory and inhibitory roles by inducing IL-10-producing Treg cells. IL-35 is produced by forkhead box P3+ Treg cells and activated B cells and has immunosuppressive functions to maintain immune tolerance. The most recently identified cytokine, IL-39, is produced by activated B cells and has pro-inflammatory functions. The cytokine tentatively named IL-Y seems to have anti-inflammatory functions by inhibiting Th1 and Th17 differentiation. In addition, individual cytokine subunits were also shown to have self-standing activities. Thus, promiscuity within the IL-6/IL-12 family cytokines complicates structural and functional clarification and assignment of individual cytokines. A better understanding of the recent advances and expanding diversity in molecular structures and functions of the IL-6/IL-12 family cytokines could allow the creation of novel therapeutic strategies by using them as tools and targeted molecules. PMID:27867385

Impact of pretransplant rifaximin therapy on early post-liver transplant infections.

PubMed

Esfeh, Jamak Modaresi; Hanouneh, Ibrahim A; Koval, Christine E; Kovacs, Christopher; Dalal, Deepan S; Ansari-Gilani, Kianoush; Confer, Bradley D; Eghtesad, Bijan; Zein, Nizar N; Menon, K V Narayanan

2014-05-01

Bacterial and fungal infections are major causes of morbidity and mortality after liver transplantation (LT). The role of intestinal decontamination in the prevention of post-LT infections is controversial. Rifaximin is widely used for the treatment of hepatic encephalopathy. The effect of rifaximin on post-LT infections is unknown. The aim of our study was to determine the effect of rifaximin therapy in the pretransplant period on early bacterial infections (EBIs) and fungal infections within the first 30 days after LT. All adult patients who underwent LT at our institution (January 2009 to July 2011) were included in this retrospective cohort study. Patients receiving antibiotics other than pretransplant protocol antibiotics were excluded. Patients were stratified into 2 groups based on the presence or absence of rifaximin therapy for at least 2 days before LT. Infections were defined by the isolation of any bacterial or fungal organisms within 30 days of LT. Multivariate regression analysis, Student t tests, and Pearson's chi-square tests were used to compare the 2 groups. Two hundred sixty-eight patients were included, and 71 of these patients (26.5%) were on rifaximin at the time of LT. The 2 groups were comparable with respect to age, sex, race, and Model for End-Stage Liver Disease score. There were no significant differences in the rates of EBIs (30% for the non-rifaximin group and 25% for the rifaximin group, P = 0.48) or fungal infections between the 2 groups. There was no increase in antimicrobial resistance among the infecting organisms. There was no difference in survival between the rifaximin and non-rifaximin groups (98% versus 97%, P = 0.36). In conclusion, the use of rifaximin in the pre-LT period was not associated with an increased risk of bacterial or fungal infections in the early post-LT period. © 2014 American Association for the Study of Liver Diseases.

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.

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.

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.

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

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.

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.

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

PubMed

Brookman-Frazee, Lauren; Stahmer, Aubyn C

2018-05-09

The Centers for Disease Control (2018) estimates that 1 in 59 children has autism spectrum disorder, and the annual cost of ASD in the U.S. is estimated to be $236 billion. Evidence-based interventions have been developed and demonstrate effectiveness in improving child outcomes. However, research on generalizable methods to scale up these practices in the multiple service systems caring for these children has been limited and is critical to meet this growing public health need. This project includes two, coordinated studies testing the effectiveness of the Translating Evidence-based Interventions (EBI) for ASD: Multi-Level Implementation Strategy (TEAMS) model. TEAMS focuses on improving implementation leadership, organizational climate, and provider attitudes and motivation in order to improve two key implementation outcomes-provider training completion and intervention fidelity and subsequent child outcomes. The TEAMS Leadership Institute applies implementation leadership strategies and TEAMS Individualized Provider Strategies for training applies motivational interviewing strategies to facilitate provider and organizational behavior change. A cluster randomized implementation/effectiveness Hybrid, type 3, trial with a dismantling design will be used to understand the effectiveness of TEAMS and the mechanisms of change across settings and participants. Study #1 will test the TEAMS model with AIM HI (An Individualized Mental Health Intervention for ASD) in publicly funded mental health services. Study #2 will test TEAMS with CPRT (Classroom Pivotal Response Teaching) in education settings. Thirty-seven mental health programs and 37 school districts will be randomized, stratified by county and study, to one of four groups (Standard Provider Training Only, Standard Provider Training + Leader Training, Enhanced Provider Training, Enhanced Provider Training + Leader Training) to test the effectiveness of combining standard, EBI-specific training with the two TEAMS modules individually and together on multiple implementation outcomes. Implementation outcomes including provider training completion, fidelity (coded by observers blind to group assignment) and child behavior change will be examined for 295 mental health providers, 295 teachers, and 590 children. This implementation intervention has the potential to increase quality of care for ASD in publicly funded settings by improving effectiveness of intervention implementation. The process and modules will be generalizable to multiple service systems, providers, and interventions, providing broad impact in community services. This study is registered with Clinicaltrials.gov ( NCT03380078 ). Registered 20 December 2017, retrospectively registered.

AtlasCBS: a web server to map and explore chemico-biological space

NASA Astrophysics Data System (ADS)

Cortés-Cabrera, Álvaro; Morreale, Antonio; Gago, Federico; Abad-Zapatero, Celerino

2012-09-01

New approaches are needed that can help decrease the unsustainable failure in small-molecule drug discovery. Ligand Efficiency Indices (LEI) are making a great impact on early-stage compound selection and prioritization. Given a target-ligand database with chemical structures and associated biological affinities/activities for a target, the AtlasCBS server generates two-dimensional, dynamical representations of its contents in terms of LEI. These variables allow an effective decoupling of the chemical (angular) and biological (radial) components. BindingDB, PDBBind and ChEMBL databases are currently implemented. Proprietary datasets can also be uploaded and compared. The utility of this atlas-like representation in the future of drug design is highlighted with some examples. The web server can be accessed at http://ub.cbm.uam.es/atlascbs and https://www.ebi.ac.uk/chembl/atlascbs.

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

AtlasCBS: a web server to map and explore chemico-biological space.

PubMed

Cortés-Cabrera, Alvaro; Morreale, Antonio; Gago, Federico; Abad-Zapatero, Celerino

2012-09-01

New approaches are needed that can help decrease the unsustainable failure in small-molecule drug discovery. Ligand Efficiency Indices (LEI) are making a great impact on early-stage compound selection and prioritization. Given a target-ligand database with chemical structures and associated biological affinities/activities for a target, the AtlasCBS server generates two-dimensional, dynamical representations of its contents in terms of LEI. These variables allow an effective decoupling of the chemical (angular) and biological (radial) components. BindingDB, PDBBind and ChEMBL databases are currently implemented. Proprietary datasets can also be uploaded and compared. The utility of this atlas-like representation in the future of drug design is highlighted with some examples. The web server can be accessed at http://ub.cbm.uam.es/atlascbs and https://www.ebi.ac.uk/chembl/atlascbs.

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

PubMed

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

2017-04-01

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

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...

Dietary intake, eating behaviors, and quality of life in women with polycystic ovary syndrome who are trying to conceive.

PubMed

Turner-McGrievy, Gabrielle; Davidson, Charis R; Billings, Deborah L

2015-03-01

The Healthy Eating for Reproductive Health study was conducted among 18 (45% non-white) mostly obese (BMI 39.9 ± 6.1) women with polycystic ovary syndrome (PCOS) who were experiencing infertility and interested in losing weight. A variety of markers were measured at baseline: body mass index (BMI), diet, physical activity, eating behaviors (using an Eating Behavior Inventory, a questionnaire which assesses both positive and negative eating behaviors associated with weight status, with a higher score indicating adoption of eating behaviors which have been shown in prior weight-loss research to promote a healthy weight (EBI) and the Three-Factor Eating Questionnaire, which assesses cognitive and behavioral components of eating among overweight adults), and a quality of life (PCOS Health-Related Quality of Life (PCOSQ)) index, which assesses satisfaction around five 'domains': emotional health, presence of body hair, infertility, weight, and menstrual problems). A comparison group of overweight women without PCOS (n = 28) was used to examine differences in measured outcomes between women with and without PCOS. Participants' habitual diets were high in fat and saturated fat and low in fiber, folate, and iron and contained significantly lower amounts of carbohydrate, iron, and whole grains compared with women without PCOS who had enrolled in a behavioral weight loss programme. Participants had a low EBI (indicating that most were not adopting eating behaviors associated with achieving a healthy weight), disinhibition (indicating participants had a tendency to overeat in the presence of highly palatable foods or were susceptible to emotional cues for eating, such as stress), and hunger scores (indicating participants did not report being susceptible to hunger, prompting overeating) and moderate dietary restraint (indicating they were not consistently attempting to restrict food intake consciously). PCOSQ scores were lowest for infertility and weight domains (indicating low satisfaction with current infertility and weight status); however all domains received low scores (emotional health, body hair, and menstrual problems). Higher energy intakes (kcal/day) were associated with a lower EBI score (r = - 0.60, P = 0.02), lower dietary restraint (r =- 0.50, P = 0.04), and higher disinhibition (r = 0.63, P = 0.01). Greater energy expenditure (kcal/day) was associated with lower PCOSQ scores for body weight (r =-0.54, P = 002) and infertility (r =- 0.51, P = 0.003) domains. Results suggest that overweight women with PCOS-related infertility have poor dietary intake, particularly in terms of whole grains, fiber, and iron, and eating behaviors inconsistent with achieving a healthy body weight, as well as low scores for PCOS-related quality of life.

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.…

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.

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.

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.

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

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

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

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

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

PubMed

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

2013-01-01

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

The Androgen Receptor Gene Mutations Database.

PubMed

Gottlieb, B; Lehvaslaiho, H; Beitel, L K; Lumbroso, R; Pinsky, L; Trifiro, M

1998-01-01

The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 272 to 309 in the past year. We have expanded the database: (i) by giving each entry an accession number; (ii) by adding information on the length of polymorphic polyglutamine (polyGln) and polyglycine (polyGly) tracts in exon 1; (iii) by adding information on large gene deletions; (iv) by providing a direct link with a completely searchable database (courtesy EMBL-European Bioinformatics Institute). The addition of the exon 1 polymorphisms is discussed in light of their possible relevance as markers for predisposition to prostate or breast cancer. The database is also available on the internet (http://www.mcgill. ca/androgendb/ ), from EMBL-European Bioinformatics Institute (ftp. ebi.ac.uk/pub/databases/androgen ), or as a Macintosh FilemakerPro or Word file (MC33@musica.mcgill.ca).

The Androgen Receptor Gene Mutations Database.

PubMed Central

Gottlieb, B; Lehvaslaiho, H; Beitel, L K; Lumbroso, R; Pinsky, L; Trifiro, M

1998-01-01

The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 272 to 309 in the past year. We have expanded the database: (i) by giving each entry an accession number; (ii) by adding information on the length of polymorphic polyglutamine (polyGln) and polyglycine (polyGly) tracts in exon 1; (iii) by adding information on large gene deletions; (iv) by providing a direct link with a completely searchable database (courtesy EMBL-European Bioinformatics Institute). The addition of the exon 1 polymorphisms is discussed in light of their possible relevance as markers for predisposition to prostate or breast cancer. The database is also available on the internet (http://www.mcgill. ca/androgendb/ ), from EMBL-European Bioinformatics Institute (ftp. ebi.ac.uk/pub/databases/androgen ), or as a Macintosh FilemakerPro or Word file (MC33@musica.mcgill.ca). PMID:9399843

Multipotent human stromal cells isolated from cord blood, term placenta and adult bone marrow show distinct differences in gene expression pattern

PubMed Central

Matigian, Nicholas; Brooke, Gary; Zaibak, Faten; Rossetti, Tony; Kollar, Katarina; Pelekanos, Rebecca; Heazlewood, Celena; Mackay-Sim, Alan; Wells, Christine A.; Atkinson, Kerry

2014-01-01

Multipotent mesenchymal stromal cells derived from human placenta (pMSCs), and unrestricted somatic stem cells (USSCs) derived from cord blood share many properties with human bone marrow-derived mesenchymal stromal cells (bmMSCs) and are currently in clinical trials for a wide range of clinical settings. Here we present gene expression profiles of human cord blood-derived unrestricted somatic stem cells (USSCs), human placental-derived mesenchymal stem cells (hpMSCs), and human bone marrow-derived mesenchymal stromal cells (bmMSCs), all derived from four different donors. The microarray data are available on the ArrayExpress database (www.ebi.ac.uk/arrayexpress) under accession number E-TABM-880. Additionally, the data has been integrated into a public portal, www.stemformatics.org. Our data provide a resource for understanding the differences in MSCs derived from different tissues. PMID:26484151

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

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

PubMed

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

2018-06-09

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

Interleukin-27 is a novel candidate diagnostic biomarker for bacterial infection in critically ill children.

PubMed

Wong, Hector R; Cvijanovich, Natalie Z; Hall, Mark; Allen, Geoffrey L; Thomas, Neal J; Freishtat, Robert J; Anas, Nick; Meyer, Keith; Checchia, Paul A; Lin, Richard; Bigham, Michael T; Sen, Anita; Nowak, Jeffrey; Quasney, Michael; Henricksen, Jared W; Chopra, Arun; Banschbach, Sharon; Beckman, Eileen; Harmon, Kelli; Lahni, Patrick; Shanley, Thomas P

2012-10-29

Differentiating between sterile inflammation and bacterial infection in critically ill patients with fever and other signs of the systemic inflammatory response syndrome (SIRS) remains a clinical challenge. The objective of our study was to mine an existing genome-wide expression database for the discovery of candidate diagnostic biomarkers to predict the presence of bacterial infection in critically ill children. Genome-wide expression data were compared between patients with SIRS having negative bacterial cultures (n = 21) and patients with sepsis having positive bacterial cultures (n = 60). Differentially expressed genes were subjected to a leave-one-out cross-validation (LOOCV) procedure to predict SIRS or sepsis classes. Serum concentrations of interleukin-27 (IL-27) and procalcitonin (PCT) were compared between 101 patients with SIRS and 130 patients with sepsis. All data represent the first 24 hours of meeting criteria for either SIRS or sepsis. Two hundred twenty one gene probes were differentially regulated between patients with SIRS and patients with sepsis. The LOOCV procedure correctly predicted 86% of the SIRS and sepsis classes, and Epstein-Barr virus-induced gene 3 (EBI3) had the highest predictive strength. Computer-assisted image analyses of gene-expression mosaics were able to predict infection with a specificity of 90% and a positive predictive value of 94%. Because EBI3 is a subunit of the heterodimeric cytokine, IL-27, we tested the ability of serum IL-27 protein concentrations to predict infection. At a cut-point value of ≥5 ng/ml, serum IL-27 protein concentrations predicted infection with a specificity and a positive predictive value of >90%, and the overall performance of IL-27 was generally better than that of PCT. A decision tree combining IL-27 and PCT improved overall predictive capacity compared with that of either biomarker alone. Genome-wide expression analysis has provided the foundation for the identification of IL-27 as a novel candidate diagnostic biomarker for predicting bacterial infection in critically ill children. Additional studies will be required to test further the diagnostic performance of IL-27. The microarray data reported in this article have been deposited in the Gene Expression Omnibus under accession number GSE4607.

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

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…

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

ERIC Educational Resources Information Center

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

2016-01-01

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

Research Output from CPTC highlighted in recent articles | Office of Cancer Clinical Proteomics Research

Cancer.gov

In the special December issue of Proteomics Clinical Applications , two articles focus directly on scientific outputs from CPTC. A Viewpoint article, authored by Participants of a Wellcome Trust/EBI meeting and retreat (Patterson et al.), advocate the leveraging of the mock 510 (k) documents developed by CPTC for further development in order to better understand regulatory need.

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

ERIC Educational Resources Information Center

Robinson, Lee; Bond, Caroline; Oldfield, Jeremy

2018-01-01

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

Inference to the Best Explanation (IBE) versus Explaining for the Best Inference (EBI)

ERIC Educational Resources Information Center

Wilkenfeld, Daniel A.; Lombrozo, Tania

2015-01-01

In pedagogical contexts and in everyday life, we often come to believe something because it would best explain the data. What is it about the explanatory endeavor that makes it essential to everyday learning and to scientific progress? There are at least two plausible answers. On one view, there is something special about having true…

Verbal Behavior in Young Children with Autism Spectrum Disorders at the Onset of an Early Behavioral Intervention Program

ERIC Educational Resources Information Center

Rivard, Melina; Forget, Jacques

2012-01-01

The scope of this study was direct observation of verbal behaviors of 14 children with autism spectrum disorders at the onset of an early behavioral intervention (EBI) program delivered in a public services agency. Objectives were to (1) describe frequencies of vocal, verbal, and listener behaviors; (2) evaluate the relationship between the…

The functional therapeutic chemical classification system.

PubMed

Croset, Samuel; Overington, John P; Rebholz-Schuhmann, Dietrich

2014-03-15

Drug repositioning is the discovery of new indications for compounds that have already been approved and used in a clinical setting. Recently, some computational approaches have been suggested to unveil new opportunities in a systematic fashion, by taking into consideration gene expression signatures or chemical features for instance. We present here a novel method based on knowledge integration using semantic technologies, to capture the functional role of approved chemical compounds. In order to computationally generate repositioning hypotheses, we used the Web Ontology Language to formally define the semantics of over 20 000 terms with axioms to correctly denote various modes of action (MoA). Based on an integration of public data, we have automatically assigned over a thousand of approved drugs into these MoA categories. The resulting new resource is called the Functional Therapeutic Chemical Classification System and was further evaluated against the content of the traditional Anatomical Therapeutic Chemical Classification System. We illustrate how the new classification can be used to generate drug repurposing hypotheses, using Alzheimers disease as a use-case. https://www.ebi.ac.uk/chembl/ftc; https://github.com/loopasam/ftc. croset@ebi.ac.uk Supplementary data are available at Bioinformatics online.

PRIDE: new developments and new datasets.

PubMed

Jones, Philip; Côté, Richard G; Cho, Sang Yun; Klie, Sebastian; Martens, Lennart; Quinn, Antony F; Thorneycroft, David; Hermjakob, Henning

2008-01-01

The PRIDE (http://www.ebi.ac.uk/pride) database of protein and peptide identifications was previously described in the NAR Database Special Edition in 2006. Since this publication, the volume of public data in the PRIDE relational database has increased by more than an order of magnitude. Several significant public datasets have been added, including identifications and processed mass spectra generated by the HUPO Brain Proteome Project and the HUPO Liver Proteome Project. The PRIDE software development team has made several significant changes and additions to the user interface and tool set associated with PRIDE. The focus of these changes has been to facilitate the submission process and to improve the mechanisms by which PRIDE can be queried. The PRIDE team has developed a Microsoft Excel workbook that allows the required data to be collated in a series of relatively simple spreadsheets, with automatic generation of PRIDE XML at the end of the process. The ability to query PRIDE has been augmented by the addition of a BioMart interface allowing complex queries to be constructed. Collaboration with groups outside the EBI has been fruitful in extending PRIDE, including an approach to encode iTRAQ quantitative data in PRIDE XML.

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

NASA Astrophysics Data System (ADS)

Modafe, Alireza

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

Papers and Proceedings of the Annual Meeting of the Midwest History of Education Society (19th, Chicago, Illinois, October 28-29, 1983).

ERIC Educational Resources Information Center

Rutkowski, Edward, Ed.

1984-01-01

The papers of this proceedings are grouped in five parts. The three papers in part 1 discuss the exposure of Italian scholars to Dewey's philosophies and include the titles (1) "John Dewey in the Evolution of Italian Education" (C. R. Wolf); (2) "Frederick Eby and the Dewey Lectures: An Essentialist Present at Educational…

PDBsum new things.

PubMed

Laskowski, Roman A

2009-01-01

PDBsum (http://www.ebi.ac.uk/pdbsum) provides summary information about each experimentally determined structural model in the Protein Data Bank (PDB). Here we describe some of its most recent features, including figures from the structure's key reference, citation data, Pfam domain diagrams, topology diagrams and protein-protein interactions. Furthermore, it now accepts users' own PDB format files and generates a private set of analyses for each uploaded structure.

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

ERIC Educational Resources Information Center

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

2016-01-01

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

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.

Adaptation of an evidence-based intervention to promote colorectal cancer screening: a quasi-experimental study

PubMed Central

2014-01-01

Background To accelerate the translation of research findings into practice for underserved populations, we investigated the adaptation of an evidence-based intervention (EBI), designed to increase colorectal cancer (CRC) screening in one limited English-proficient (LEP) population (Chinese), for another LEP group (Vietnamese) with overlapping cultural and health beliefs. Methods Guided by Diffusion of Innovations Theory, we adapted the EBI to achieve greater reach. Core elements of the adapted intervention included: small media (a DVD and pamphlet) translated into Vietnamese from Chinese; medical assistants distributing the small media instead of a health educator; and presentations on CRC screening to the medical assistants. A quasi-experimental study examined CRC screening adherence among eligible Vietnamese patients at the intervention and control clinics, before and after the 24-month intervention. The proportion of the adherence was assessed using generalized linear mixed models that account for clustering under primary care providers and also within-patient correlation between baseline and follow up. Results Our study included two cross-sectional samples: 1,016 at baseline (604 in the intervention clinic and 412 in the control clinic) and 1,260 post-intervention (746 in the intervention and 514 in the control clinic), including appreciable overlaps between the two time points. Pre-post change in CRC screening over time, expressed as an odds ratio (OR) of CRC screening adherence by time, showed a marginally-significant greater increase in CRC screening adherence at the intervention clinic compared to the control clinic (the ratio of the two ORs = 1.42; 95% CI 0.95, 2.15). In the sample of patients who were non-adherent to CRC screening at baseline, compared to the control clinic, the intervention clinic had marginally-significant greater increase in FOBT (adjusted OR = 1.77; 95% CI 0.98, 3.18) and a statistically-significantly greater increase in CRC screening adherence (adjusted OR = 1.70; 95% CI 1.05, 2.75). Conclusions Theoretically guided adaptations of EBIs may accelerate the translation of research into practice. Adaptation has the potential to mitigate health disparities for hard-to-reach populations in a timely manner. PMID:24989083

Wrapping SRS with CORBA: from textual data to distributed objects.

PubMed

Coupaye, T

1999-04-01

Biological data come in very different shapes. Databanks are maintained and used by distinct organizations. Text is the de facto Standard exchange format. The SRS system can integrate heterogeneous textual databanks but it was lacking a way to structure the extracted data. This paper presents a CORBA interface to the SRS system which manages databanks in a flat file format. SRS Object Servers are CORBA wrappers for SRS. They allow client applications (visualisation tools, data mining tools, etc.) to access and query SRS servers remotely through an Object Request Broker (ORB). They provide loader objects that contain the information extracted from the databanks by SRS. Loader objects are not hard-coded but generated in a flexible way by using loader specifications which allow SRS administrators to package data coming from distinct databanks. The prototype may be available for beta-testing. Please contact the SRS group (http://srs.ebi.ac.uk).

Update of the androgen receptor gene mutations database.

PubMed

Gottlieb, B; Beitel, L K; Lumbroso, R; Pinsky, L; Trifiro, M

1999-01-01

The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 309 to 374 during the past year. We have expanded the database by adding information on AR-interacting proteins; and we have improved the database by identifying those mutation entries that have been updated. Mutations of unknown significance have now been reported in both the 5' and 3' untranslated regions of the AR gene, and in individuals who are somatic mosaics constitutionally. In addition, single nucleotide polymorphisms, including silent mutations, have been discovered in normal individuals and in individuals with male infertility. A mutation hotspot associated with prostatic cancer has been identified in exon 5. The database is available on the internet (http://www.mcgill.ca/androgendb/), from EMBL-European Bioinformatics Institute (ftp.ebi.ac.uk/pub/databases/androgen), or as a Macintosh FilemakerPro or Word file (MC33@musica.mcgill.ca). Copyright 1999 Wiley-Liss, Inc.

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

BioModels: expanding horizons to include more modelling approaches and formats

PubMed Central

Nguyen, Tung V N; Graesslin, Martin; Hälke, Robert; Ali, Raza; Schramm, Jochen; Wimalaratne, Sarala M; Kothamachu, Varun B; Rodriguez, Nicolas; Swat, Maciej J; Eils, Jurgen; Eils, Roland; Laibe, Camille; Chelliah, Vijayalakshmi

2018-01-01

Abstract BioModels serves as a central repository of mathematical models representing biological processes. It offers a platform to make mathematical models easily shareable across the systems modelling community, thereby supporting model reuse. To facilitate hosting a broader range of model formats derived from diverse modelling approaches and tools, a new infrastructure for BioModels has been developed that is available at http://www.ebi.ac.uk/biomodels. This new system allows submitting and sharing of a wide range of models with improved support for formats other than SBML. It also offers a version-control backed environment in which authors and curators can work collaboratively to curate models. This article summarises the features available in the current system and discusses the potential benefit they offer to the users over the previous system. In summary, the new portal broadens the scope of models accepted in BioModels and supports collaborative model curation which is crucial for model reproducibility and sharing. PMID:29106614

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

PubMed

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

2018-04-11

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

Interleukin-27 is a novel candidate diagnostic biomarker for bacterial infection in critically ill children

PubMed Central

2012-01-01

Introduction Differentiating between sterile inflammation and bacterial infection in critically ill patients with fever and other signs of the systemic inflammatory response syndrome (SIRS) remains a clinical challenge. The objective of our study was to mine an existing genome-wide expression database for the discovery of candidate diagnostic biomarkers to predict the presence of bacterial infection in critically ill children. Methods Genome-wide expression data were compared between patients with SIRS having negative bacterial cultures (n = 21) and patients with sepsis having positive bacterial cultures (n = 60). Differentially expressed genes were subjected to a leave-one-out cross-validation (LOOCV) procedure to predict SIRS or sepsis classes. Serum concentrations of interleukin-27 (IL-27) and procalcitonin (PCT) were compared between 101 patients with SIRS and 130 patients with sepsis. All data represent the first 24 hours of meeting criteria for either SIRS or sepsis. Results Two hundred twenty one gene probes were differentially regulated between patients with SIRS and patients with sepsis. The LOOCV procedure correctly predicted 86% of the SIRS and sepsis classes, and Epstein-Barr virus-induced gene 3 (EBI3) had the highest predictive strength. Computer-assisted image analyses of gene-expression mosaics were able to predict infection with a specificity of 90% and a positive predictive value of 94%. Because EBI3 is a subunit of the heterodimeric cytokine, IL-27, we tested the ability of serum IL-27 protein concentrations to predict infection. At a cut-point value of ≥5 ng/ml, serum IL-27 protein concentrations predicted infection with a specificity and a positive predictive value of >90%, and the overall performance of IL-27 was generally better than that of PCT. A decision tree combining IL-27 and PCT improved overall predictive capacity compared with that of either biomarker alone. Conclusions Genome-wide expression analysis has provided the foundation for the identification of IL-27 as a novel candidate diagnostic biomarker for predicting bacterial infection in critically ill children. Additional studies will be required to test further the diagnostic performance of IL-27. The microarray data reported in this article have been deposited in the Gene Expression Omnibus under accession number GSE4607. PMID:23107287

The Process of Adaptation of a Community-Level, Evidence-Based Intervention for HIV-Positive African American Men Who Have Sex with Men in Two Cities

ERIC Educational Resources Information Center

Robinson, Beatrice E.; Galbraith, Jennifer S.; Lund, Sharon M.; Hamilton, Autumn R.; Shankle, Michael D.

2012-01-01

We describe the process of adapting a community-level, evidence-based behavioral intervention (EBI), Community PROMISE, for HIV-positive African American men who have sex with men (AAMSM). The Centers for Disease Control and Prevention (CDC) Map of the Adaptation Process (MAP) guided the adaptation process for this new target population by two…

Complete Genome Sequence of Bordetella pertussis Strain VA-190 Isolated from a Vaccinated 10-Year-Old Patient with Whooping Cough.

PubMed

Eby, Joshua C; Turner, Lauren; Nguyen, Bryan; Kang, June; Neville, Carly; Temple, Louise

2016-09-15

The number of cases of pertussis has increased in the United States despite vaccination. We present the genome of an isolate of Bordetella pertussis from a vaccinated patient from Virginia. The genome was sequenced by long-read methodology and compared to that of a clinical isolate used for laboratory studies, D420. Copyright © 2016 Eby et al.

A Qualitative and Quantitative Assessment of Readiness for Organizational Change Literature

DTIC Science & Technology

2008-06-01

The behavioral sciences and management: An evaluation of relevant journals. Journal of Management, 16(3), 539. Fishbein , M ., & Ajzen , I . (1975...discovery to change beliefs, attitudes, intentions, and behavior ( Fishbein & Ajzen , 1975). In the context of strategic change, participation produces high...Science Quarterly, 21, 700-714. 44 *Eby, L. T., Adams, D. M ., Russell, J. E. A., & Gaby, S. H. ( 2000 ). Perceptions of organizational readiness

Building a Joint-Service Classification Research Roadmap: Individual Differences Measurement

DTIC Science & Technology

1994-04-01

designed to tap personality constructs), while some others have categorized it as a biodata instrument (e.g., Steinhaus & Waters, 1991). Mael (1991), in...have been empirically-keyed against early attrition from the 90 military and factor analyzed using their keyed values ( Steinhaus , 1988). Six factors...scale across all subgroups. Research with the EBIS ( Steinhaus , 1988) evidenced similar findings: minority subgroups tended to score higher on the

MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status

PubMed Central

Attimonelli, M.; Altamura, N.; Benne, R.; Brennicke, A.; Cooper, J. M.; D’Elia, D.; Montalvo, A. de; Pinto, B. de; De Robertis, M.; Golik, P.; Knoop, V.; Lanave, C.; Lazowska, J.; Licciulli, F.; Malladi, B. S.; Memeo, F.; Monnerot, M.; Pasimeni, R.; Pilbout, S.; Schapira, A. H. V.; Sloof, P.; Saccone, C.

2000-01-01

MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects, under a single interface, databases for Plant, Vertebrate, Invertebrate, Human, Protist and Fungal mtDNA and a Pilot database on nuclear genes involved in mitochondrial biogenesis in Saccharomyces cerevisiae. MitBASE reports all available information from different organisms and from intraspecies variants and mutants. Data have been drawn from the primary databases and from the literature; value adding information has been structured, e.g., editing information on protist mtDNA genomes, pathological information for human mtDNA variants, etc. The different databases, some of which are structured using commercial packages (Microsoft Access, File Maker Pro) while others use a flat-file format, have been integrated under ORACLE. Ad hoc retrieval systems have been devised for some of the above listed databases keeping into account their peculiarities. The database is resident at the EBI and is available at the following site: http://www3.ebi.ac.uk/Research/Mitbase/mitbase.pl . The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecies diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme. PMID:10592207

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/.

Local Coulomb explosion of boron nitride nanotubes under electron beam irradiation.

PubMed

Wei, Xianlong; Tang, Dai-Ming; Chen, Qing; Bando, Yoshio; Golberg, Dmitri

2013-04-23

In many previous reports, the engineering of nanostructures using electron beam irradiation (EBI) in a high vacuum has primarily been based on the knock-on atom displacement. Herein, we report a new phenomenon under EBI that can also be effectively used to engineer a nanostructure: local Coulomb explosion (LCE) of cantilevered multiwalled boron nitride nanotubes (BNNTs) resulted from their profound positive charging. The nanotubes are gradually shortened, while the tubular shells at free ends are torn into graphene-like pieces and then removed during LCE. The phenomenon is dependent not only on the characteristics of an incident electron beam, as in the case of a common knock-on process, but also on the cantilevered tube length. Only after the electron beam density and tube length exceed the threshold values can LCE take place, and the threshold value for one of the parameters decreases with increasing the value of the other one. A model based on the diffusion of electron-irradiation-induced holes along a BNNT is proposed to describe the positive charge accumulation and can well explain the observed LCE. LCE opens up an efficient and versatile way to engineer BNNTs and other dielectric nanostructures with a shorter time and a lower beam density than those required for the knock-on effect-based engineering.

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

Development and Evaluation of a Manual for Extended Brief Intervention for Alcohol Misuse for Adults with Mild to Moderate Intellectual Disabilities Living in the Community: The EBI-LD Study Manual

ERIC Educational Resources Information Center

Kouimtsidis, Christos; Scior, Katrina; Baio, Gianluca; Hunter, Rachael; Pezzoni, Vittoria; Hassiotis, Angela

2017-01-01

Background: Extended brief interventions for alcohol misuse are effective in the general population. The process of manualising the first ever such intervention for people with mild to moderate intellectual disabilities in the UK is the focus of this study. Methods: The manual was an adaptation of existing manuals based on Motivational Enhancement…

Processing, Properties and Morphology of Optical Limiting Silk Membranes

DTIC Science & Technology

2006-02-28

Christopher Brewer, Donald Ott, Polymer, 45 8451 (2004). 2. Electrospun Bombyx mori Gland Silk, S. Putthanarat, R.K. Eby, W. Kataphinan, S. Jones, R...Science, The University of Akron, Akron, OH. 3. American Physical Society (APS) meeting, March 2005, "Electrospun liquid silk from the gland of Bombyx Mori ...provide a good compatible matrix. They have previously demonstrated that GFP molecules can be incorporated into cast membranes of silk from B. mori

Industry Study, Environment Industry, Spring 2009

DTIC Science & Technology

2009-01-01

Amazonia (LBA), Tapajós National Forest, Brazil Oficinas Caboclas Project, Santarém, Brazil Maguari, Jamaraquá, Nuquini, and Suruacá communities...from clear cut, however. Research at the Large-Scale Biosphere-Atmosphere Experiment in Amazonia suggests that the Amazon basin may not be, as...Times Magazine , April 15, 2007, http://www.nytimes.com/2007/04/15/ magazine /15green.t.html. 26 EBI, 100 27 OECD, 23. 28 Ban Ki-moon, “Acting on Climate

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data

PubMed Central

Kibbe, Warren A.; Arze, Cesar; Felix, Victor; Mitraka, Elvira; Bolton, Evan; Fu, Gang; Mungall, Christopher J.; Binder, Janos X.; Malone, James; Vasant, Drashtti; Parkinson, Helen; Schriml, Lynn M.

2015-01-01

The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands the utility of the ontology for the examination and comparison of genetic variation, phenotype, protein, drug and epitope data through the lens of human disease. DO is a biomedical resource of standardized common and rare disease concepts with stable identifiers organized by disease etiology. The content of DO has had 192 revisions since 2012, including the addition of 760 terms. Thirty-two percent of all terms now include definitions. DO has expanded the number and diversity of research communities and community members by 50+ during the past two years. These community members actively submit term requests, coordinate biomedical resource disease representation and provide expert curation guidance. Since the DO 2012 NAR paper, there have been hundreds of term requests and a steady increase in the number of DO listserv members, twitter followers and DO website usage. DO is moving to a multi-editor model utilizing Protégé to curate DO in web ontology language. This will enable closer collaboration with the Human Phenotype Ontology, EBI's Ontology Working Group, Mouse Genome Informatics and the Monarch Initiative among others, and enhance DO's current asserted view and multiple inferred views through reasoning. PMID:25348409

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.

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

PubMed

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

2015-08-01

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

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 human-induced pluripotent stem cell initiative—data resources for cellular genetics

PubMed Central

Streeter, Ian; Harrison, Peter W.; Faulconbridge, Adam; Flicek, Paul; Parkinson, Helen; Clarke, Laura

2017-01-01

The Human Induced Pluripotent Stem Cell Initiative (HipSci) isf establishing a large catalogue of human iPSC lines, arguably the most well characterized collection to date. The HipSci portal enables researchers to choose the right cell line for their experiment, and makes HipSci's rich catalogue of assay data easy to discover and reuse. Each cell line has genomic, transcriptomic, proteomic and cellular phenotyping data. Data are deposited in the appropriate EMBL-EBI archives, including the European Nucleotide Archive (ENA), European Genome-phenome Archive (EGA), ArrayExpress and PRoteomics IDEntifications (PRIDE) databases. The project will make 500 cell lines from healthy individuals, and from 150 patients with rare genetic diseases; these will be available through the European Collection of Authenticated Cell Cultures (ECACC). As of August 2016, 238 cell lines are available for purchase. Project data is presented through the HipSci data portal (http://www.hipsci.org/lines) and is downloadable from the associated FTP site (ftp://ftp.hipsci.ebi.ac.uk/vol1/ftp). The data portal presents a summary matrix of the HipSci cell lines, showing available data types. Each line has its own page containing descriptive metadata, quality information, and links to archived assay data. Analysis results are also available in a Track Hub, allowing visualization in the context of public genomic annotations (http://www.hipsci.org/data/trackhubs). PMID:27733501

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.

Population information resources.

PubMed

Pasquariella, S K

1984-12-01

This article describes print and computerized services that are dedicated to bibliographic coverage of 1 or more areas of population studies. Major printed bibliographic information resources for population material include: ADOPT, DOCPAL Resumenes sobre Poblacion en America Latina, PIDSA Abstracts, Population Index and Review of Population Reviews. ADOPT is an annotated computer-aided current-awareness bibliographic journal which has been published monthly since January 1975 by the Regional Population Information Center of the Economic and Social Commission for Asia and the Pacific (ESCAP). DOCPAL Resumenes is a computer-produced biannual collection of abstracts containing indexes and between 600 and 700 summaries of both published and unpublished population documents. PIDSA is intended to make available documentary information about population matters in sub-Saharan Africa. Population Index, 1 of the oldest and most definitive bibliographies in the demography field, is international in scope and is arranged as a classified and annotated bibliography of monographs, journal articles and 2ndary source material relevant to all aspects of demography. Review of Population Reviews, published 4 times a year, are annotated bibliographies containing summaries of articles that have been published in 83 periodicals in 37 countries. Cited articles are assigned subject-heading descriptors from the Population Multilingual Thesaurus. Major computerized information resources are: DOCPAL, DOCPOP, EBIS/POPFILE, MANPINS, POPLINE and POPULATION BIBLIOGRAPHY. DOCPAL was established to assist Latin Ameran countries in the collection, storage, processing and retrieval of population documents about Latin America. DOCPAL contains over 19,000 bibliographic citations. DOCPOP was established as the 1st Latin American national computerized population documentation system for Brazilian material. POPLINE is a computerized retrieval service cooperatively produced in the US which covers the worldwide literature on population and family planning. POPULATION BIBLIOGRAPHY consists of bibliographic records of the Carolina Population Center Library at the University of North Carolina. EBIS/PROFILE provides computerized literature search services using improved information processing techniques. The system enables interactive information retrieval using a combination of subject descriptors, free text, author names and words in other fields and can be utilized to generate various lists. MANPINS is a cooperative network of 28 population and other libraries in Peninsular Malaysia. Its data bank includes contributions from member libraries in the form of bibliographic information on monographs and journal articles.

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

PubMed Central

Passman, Dina B.

2013-01-01

Objective The objective of this demonstration is to show conference attendees how they can integrate, analyze, and visualize diverse data type data from across a variety of systems by leveraging an off-the-shelf enterprise business intelligence (EBI) solution to support decision-making in disasters. Introduction Fusion Analytics is the data integration system developed by the Fusion Cell at the U.S. Department of Health and Human Services (HHS), Office of the Assistant Secretary for Preparedness and Response (ASPR). Fusion Analytics meaningfully augments traditional public and population health surveillance reporting by providing web-based data analysis and visualization tools. Methods Fusion Analytics serves as a one-stop-shop for the web-based data visualizations of multiple real-time data sources within ASPR. The 24-7 web availability makes it an ideal analytic tool for situational awareness and response allowing stakeholders to access the portal from any internet-enabled device without installing any software. The Fusion Analytics data integration system was built using off-the-shelf EBI software. Fusion Analytics leverages the full power of statistical analysis software and delivers reports to users in a secure web-based environment. Fusion Analytics provides an example of how public health staff can develop and deploy a robust public health informatics solution using an off-the shelf product and with limited development funding. It also provides the unique example of a public health information system that combines patient data for traditional disease surveillance with manpower and resource data to provide overall decision support for federal public health and medical disaster response operations. Conclusions We are currently in a unique position within public health. One the one hand, we have been gaining greater and greater access to electronic data of all kinds over the last few years. On the other, we are working in a time of reduced government spending to support leveraging this data for decision support with robust analytics and visualizations. Fusion Analytics provides an opportunity for attendees to see how various types of data are integrated into a single application for population health decision support. It also can provide them with ideas of how they can use their own staff to create analyses and reports that support their public health activities.

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.

The human-induced pluripotent stem cell initiative-data resources for cellular genetics.

PubMed

Streeter, Ian; Harrison, Peter W; Faulconbridge, Adam; Flicek, Paul; Parkinson, Helen; Clarke, Laura

2017-01-04

The Human Induced Pluripotent Stem Cell Initiative (HipSci) isf establishing a large catalogue of human iPSC lines, arguably the most well characterized collection to date. The HipSci portal enables researchers to choose the right cell line for their experiment, and makes HipSci's rich catalogue of assay data easy to discover and reuse. Each cell line has genomic, transcriptomic, proteomic and cellular phenotyping data. Data are deposited in the appropriate EMBL-EBI archives, including the European Nucleotide Archive (ENA), European Genome-phenome Archive (EGA), ArrayExpress and PRoteomics IDEntifications (PRIDE) databases. The project will make 500 cell lines from healthy individuals, and from 150 patients with rare genetic diseases; these will be available through the European Collection of Authenticated Cell Cultures (ECACC). As of August 2016, 238 cell lines are available for purchase. Project data is presented through the HipSci data portal (http://www.hipsci.org/lines) and is downloadable from the associated FTP site (ftp://ftp.hipsci.ebi.ac.uk/vol1/ftp). The data portal presents a summary matrix of the HipSci cell lines, showing available data types. Each line has its own page containing descriptive metadata, quality information, and links to archived assay data. Analysis results are also available in a Track Hub, allowing visualization in the context of public genomic annotations (http://www.hipsci.org/data/trackhubs). © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.

PubMed

Kibbe, Warren A; Arze, Cesar; Felix, Victor; Mitraka, Elvira; Bolton, Evan; Fu, Gang; Mungall, Christopher J; Binder, Janos X; Malone, James; Vasant, Drashtti; Parkinson, Helen; Schriml, Lynn M

2015-01-01

The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands the utility of the ontology for the examination and comparison of genetic variation, phenotype, protein, drug and epitope data through the lens of human disease. DO is a biomedical resource of standardized common and rare disease concepts with stable identifiers organized by disease etiology. The content of DO has had 192 revisions since 2012, including the addition of 760 terms. Thirty-two percent of all terms now include definitions. DO has expanded the number and diversity of research communities and community members by 50+ during the past two years. These community members actively submit term requests, coordinate biomedical resource disease representation and provide expert curation guidance. Since the DO 2012 NAR paper, there have been hundreds of term requests and a steady increase in the number of DO listserv members, twitter followers and DO website usage. DO is moving to a multi-editor model utilizing Protégé to curate DO in web ontology language. This will enable closer collaboration with the Human Phenotype Ontology, EBI's Ontology Working Group, Mouse Genome Informatics and the Monarch Initiative among others, and enhance DO's current asserted view and multiple inferred views through reasoning. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Disease Ontology 2015 update: An expanded and updated database of human diseases for linking biomedical knowledge through disease data

DOE PAGES

Kibbe, Warren A.; Arze, Cesar; Felix, Victor; ...

2014-10-27

The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands the utility of the ontology for the examination and comparison of genetic variation, phenotype, protein, drug and epitope data through the lens of human disease. DO is a biomedical resource of standardized common and rare disease concepts with stable identifiers organized by disease etiology. The content of DO has had 192 revisions since 2012, including the addition of 760 terms. Thirty-two percent of all terms now include definitions. DO has expanded the number and diversity of research communities and community members by 50+ during the past two years.more » These community members actively submit term requests, coordinate biomedical resource disease representation and provide expert curation guidance. Since the DO 2012 NAR paper, there have been hundreds of term requests and a steady increase in the number of DO listserv members, twitter followers and DO website usage. DO is moving to a multi-editor model utilizing Protégé to curate DO in web ontology language. In conclusion, this will enable closer collaboration with the Human Phenotype Ontology, EBI's Ontology Working Group, Mouse Genome Informatics and the Monarch Initiative among others, and enhance DO's current asserted view and multiple inferred views through reasoning.« less

Disease Ontology 2015 update: An expanded and updated database of human diseases for linking biomedical knowledge through disease data

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

Kibbe, Warren A.; Arze, Cesar; Felix, Victor

The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands the utility of the ontology for the examination and comparison of genetic variation, phenotype, protein, drug and epitope data through the lens of human disease. DO is a biomedical resource of standardized common and rare disease concepts with stable identifiers organized by disease etiology. The content of DO has had 192 revisions since 2012, including the addition of 760 terms. Thirty-two percent of all terms now include definitions. DO has expanded the number and diversity of research communities and community members by 50+ during the past two years.more » These community members actively submit term requests, coordinate biomedical resource disease representation and provide expert curation guidance. Since the DO 2012 NAR paper, there have been hundreds of term requests and a steady increase in the number of DO listserv members, twitter followers and DO website usage. DO is moving to a multi-editor model utilizing Protégé to curate DO in web ontology language. In conclusion, this will enable closer collaboration with the Human Phenotype Ontology, EBI's Ontology Working Group, Mouse Genome Informatics and the Monarch Initiative among others, and enhance DO's current asserted view and multiple inferred views through reasoning.« less

Uterine disease and its effect on subsequent reproductive performance of dairy cattle: a comparison of two cow-side diagnostic methods.

PubMed

Šavc, Miha; Duane, Mary; O'Grady, Luke E; Somers, Joris R; Beltman, Marijke E

2016-11-01

The aim of this study was to compare vaginal mucus scoring and ultrasonographic assessment of uterine content as predictors of future reproductive performance of dairy cows. Holstein-Friesian cows (n = 493) from seven commercial dairy farms were enrolled in this study. All cows received one prebreeding examination (PBE) between 21 and 38 days after parturition. During the PBE, vaginal mucus was scored (MS) and the transrectal ultrasonographic examination of the uterus to assess content (UTS) took place. The MS was scored on a scale of 0 to 3 using a Metricheck device and appearance of the uterus on transrectal ultrasound was scored on a scale of 0 to 4 based on the presence and consistency of intraluminal fluid. Other data collected from each cow included the farm ID (F_ID), conception rate to first service, length of breeding window, lactation number, calving month, body condition score (BCS) at calving, BCS loss after calving, BCS at PBE, days in milk at PBE, 305 day milk yield, economic breeding index (EBI), EBI fertility subindex and EBI health subindex. For each cow these parameters were analyzed using univariate Cox proportional hazard model to evaluate the effect of variables on the reproductive performance, measured as positive pregnancy status (PS) at the end of the breeding season. Receiver-operating characteristic analysis of the diagnostic tests compared with each other took place as well. Cows with positive UTS were 7.75 times more likely to have a positive MS as well (P < 0.01). The PS hazard ratios for cows with UTS0, 1, 2, 3, and 4 were 1; 0.84; 0.53; 0.78; 0.28, respectively (P < 0.001). For the cows with MS0, 1, 2, and 3, the PR hazard ratios were 1; 1.02; 0.51; 0.75; respectively (P = 0.01). Conception rate to first service, breeding window, and PS were significantly better for the cows with UTS0, 1 and 2 compared with the cows with UTS3-4 and MS2+3 (68%; 18%, [P = 0.020]; 29; 75 days, [P = 0.001]; 95%; 55%; [P = 0.010], respectively). There was a significant effect of days in milk at PBE in relation to the subsequent PS (P = 0.04). Cows in lactation number 5 or more were less likely (r = 0.69) to get in calf before the end of the breeding season than cows in their first lactation. Cows that calved later in the season were less likely to become pregnant before the end of the breeding season (P < 0.03). Younger cows (lactation <5) and cows with MS and UTS scores of 0 and -1 had significantly better reproductive performance (P < 0.04). Receiver-operating characteristic analysis showed that MS did not always reflect UTS, but cows with positive UTS were 7.75 times more likely to have a positive MS (P < 0.01) and a high UTS had a larger negative effect on time to PS than a high MS (P < 0.05). In conclusion, both prebreeding vaginal mucus evaluation with the Metricheck device and an ultrasound scan of the uterus serve as a good predictor of the subsequent PS. There is overlap between the two systems, but the best predictor for future reproductive outcome of the cow is a combination of both. Copyright © 2016 Elsevier Inc. All rights reserved.

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

PubMed

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

2010-09-01

The objective of the study was to quantify the effect of genetic improvement using the Irish total merit index, the Economic Breeding Index (EBI), on overall performance and lactation profiles for milk, milk solids, body weight (BW), and body condition score (BCS) within 2 pasture-based systems of milk production likely to be used in the future, following abolition of the European Union's milk quota system. Three genotypes of Holstein-Friesian dairy cattle were established from within the Moorepark dairy research herd: LowNA, indicative of animals with North American origin and average or lower genetic merit at the time of the study; HighNA, North American Holstein-Friesians of high genetic merit; and HighNZ, New Zealand Holstein-Friesians of high genetic merit. Animals from within each genotype were randomly allocated to 1 of 2 possible pasture-based feeding systems (FS): 1) The Moorepark pasture (MP) system (2.64 cows/ha and 344 kg of concentrate supplement per cow per lactation) and 2) a high output per hectare (HC) system (2.85 cows/ha and 1,056 kg of concentrate supplement per cow per lactation). Pasture was allocated to achieve similar postgrazing residual sward heights for both treatments. A total of 126, 128, and 140 spring-calving dairy cows were used during the years 2006, 2007, and 2008, respectively. Each group had an individual farmlet of 17 paddocks and all groups were managed similarly throughout the study. The effects of genotype, FS, and the interaction between genotype and FS on milk production, BW, and BCS across lactation were studied using mixed models with factorial arrangements of genotype and FS accounting for the repeated cow records across years. No significant genotype by FS interaction was observed for any of the variables measured. Results show that milk solids production of the national average dairy cow can be increased across lactation through increased EBI. High EBI genotypes (HighNA and HighNZ) produced more milk solids per cow and per hectare than the LowNA genotype (2.7 and 4.1%, respectively). The results also suggest that when concentrate supplementation is used to facilitate increased stocking rates, increased herbage utilization and decreased substitution of concentrate for herbage can be achieved. When implemented, the HC FS could increase the overall productivity of pasture-fed dairy farming systems where land availability is the primary limiting factor of production. Copyright (c) 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

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.

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

PubMed

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

2005-09-01

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

A Comparison of Pathophysiology in Humans and Rodent Models of Subarachnoid Hemorrhage

PubMed Central

Leclerc, Jenna L.; Garcia, Joshua M.; Diller, Matthew A.; Carpenter, Anne-Marie; Kamat, Pradip K.; Hoh, Brian L.; Doré, Sylvain

2018-01-01

Non-traumatic subarachnoid hemorrhage (SAH) affects an estimated 30,000 people each year in the United States, with an overall mortality of ~30%. Most cases of SAH result from a ruptured intracranial aneurysm, require long hospital stays, and result in significant disability and high fatality. Early brain injury (EBI) and delayed cerebral vasospasm (CV) have been implicated as leading causes of morbidity and mortality in these patients, necessitating intense focus on developing preclinical animal models that replicate clinical SAH complete with delayed CV. Despite the variety of animal models currently available, translation of findings from rodent models to clinical trials has proven especially difficult. While the explanation for this lack of translation is unclear, possibilities include the lack of standardized practices and poor replication of human pathophysiology, such as delayed cerebral vasospasm and ischemia, in rodent models of SAH. In this review, we summarize the different approaches to simulating SAH in rodents, in particular elucidating the key pathophysiology of the various methods and models. Ultimately, we suggest the development of standardized model of rodent SAH that better replicates human pathophysiology for moving forward with translational research. PMID:29623028

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

PubMed

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

2017-01-04

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

Mean Expected Error in Prediction of Total Body Water: A True Accuracy Comparison between Bioimpedance Spectroscopy and Single Frequency Regression Equations

PubMed Central

Abtahi, Shirin; Abtahi, Farhad; Ellegård, Lars; Johannsson, Gudmundur; Bosaeus, Ingvar

2015-01-01

For several decades electrical bioimpedance (EBI) has been used to assess body fluid distribution and body composition. Despite the development of several different approaches for assessing total body water (TBW), it remains uncertain whether bioimpedance spectroscopic (BIS) approaches are more accurate than single frequency regression equations. The main objective of this study was to answer this question by calculating the expected accuracy of a single measurement for different EBI methods. The results of this study showed that all methods produced similarly high correlation and concordance coefficients, indicating good accuracy as a method. Even the limits of agreement produced from the Bland-Altman analysis indicated that the performance of single frequency, Sun's prediction equations, at population level was close to the performance of both BIS methods; however, when comparing the Mean Absolute Percentage Error value between the single frequency prediction equations and the BIS methods, a significant difference was obtained, indicating slightly better accuracy for the BIS methods. Despite the higher accuracy of BIS methods over 50 kHz prediction equations at both population and individual level, the magnitude of the improvement was small. Such slight improvement in accuracy of BIS methods is suggested insufficient to warrant their clinical use where the most accurate predictions of TBW are required, for example, when assessing over-fluidic status on dialysis. To reach expected errors below 4-5%, novel and individualized approaches must be developed to improve the accuracy of bioimpedance-based methods for the advent of innovative personalized health monitoring applications. PMID:26137489

The Porphyromonas gingivalis/Host Interactome Shows Enrichment in GWASdb Genes Related to Alzheimer's Disease, Diabetes and Cardiovascular Diseases

PubMed Central

Carter, Chris J.; France, James; Crean, StJohn; Singhrao, Sim K.

2017-01-01

Periodontal disease is of established etiology in which polymicrobial synergistic ecology has become dysbiotic under the influence of Porphyromonas gingivalis. Following breakdown of the host's protective oral tissue barriers, P. gingivalis migrates to developing inflammatory pathologies that associate with Alzheimer's disease (AD). Periodontal disease is a risk factor for cardiovascular disorders (CVD), type II diabetes mellitus (T2DM), AD and other chronic diseases, whilst T2DM exacerbates periodontitis. This study analyzed the relationship between the P. gingivalis/host interactome and the genes identified in genome-wide association studies (GWAS) for the aforementioned conditions using data from GWASdb (P < 1E-03) and, in some cases, from the NCBI/EBI GWAS database (P < 1E-05). Gene expression data from periodontitis or P. gingivalis microarray was compared to microarray datasets from the AD hippocampus and/or from carotid artery plaques. The results demonstrated that the host genes of the P. gingivalis interactome were significantly enriched in genes deposited in GWASdb genes related to cognitive disorders, AD and dementia, and its co-morbid conditions T2DM, obesity, and CVD. The P. gingivalis/host interactome was also enriched in GWAS genes from the more stringent NCBI-EBI database for AD, atherosclerosis and T2DM. The misregulated genes in periodontitis tissue or P. gingivalis infected macrophages also matched those in the AD hippocampus or atherosclerotic plaques. Together, these data suggest important gene/environment interactions between P. gingivalis and susceptibility genes or gene expression changes in conditions where periodontal disease is a contributory factor. PMID:29311898

The Porphyromonas gingivalis/Host Interactome Shows Enrichment in GWASdb Genes Related to Alzheimer's Disease, Diabetes and Cardiovascular Diseases.

PubMed

Carter, Chris J; France, James; Crean, StJohn; Singhrao, Sim K

2017-01-01

Periodontal disease is of established etiology in which polymicrobial synergistic ecology has become dysbiotic under the influence of Porphyromonas gingivalis . Following breakdown of the host's protective oral tissue barriers, P. gingivalis migrates to developing inflammatory pathologies that associate with Alzheimer's disease (AD). Periodontal disease is a risk factor for cardiovascular disorders (CVD), type II diabetes mellitus (T2DM), AD and other chronic diseases, whilst T2DM exacerbates periodontitis. This study analyzed the relationship between the P. gingivalis /host interactome and the genes identified in genome-wide association studies (GWAS) for the aforementioned conditions using data from GWASdb ( P < 1E-03) and, in some cases, from the NCBI/EBI GWAS database ( P < 1E-05). Gene expression data from periodontitis or P. gingivalis microarray was compared to microarray datasets from the AD hippocampus and/or from carotid artery plaques. The results demonstrated that the host genes of the P. gingivalis interactome were significantly enriched in genes deposited in GWASdb genes related to cognitive disorders, AD and dementia, and its co-morbid conditions T2DM, obesity, and CVD. The P. gingivalis /host interactome was also enriched in GWAS genes from the more stringent NCBI-EBI database for AD, atherosclerosis and T2DM. The misregulated genes in periodontitis tissue or P. gingivalis infected macrophages also matched those in the AD hippocampus or atherosclerotic plaques. Together, these data suggest important gene/environment interactions between P. gingivalis and susceptibility genes or gene expression changes in conditions where periodontal disease is a contributory factor.

Bioinformatics meets user-centred design: a perspective.

PubMed

Pavelin, Katrina; Cham, Jennifer A; de Matos, Paula; Brooksbank, Cath; Cameron, Graham; Steinbeck, Christoph

2012-01-01

Designers have a saying that "the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years." It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI), and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD) strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics.

ProCarDB: a database of bacterial carotenoids.

PubMed

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

2016-05-26

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

PDBsum: Structural summaries of PDB entries.

PubMed

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

2018-01-01

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

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.

Panel--lawyers' perspectives on strategic litigation.

PubMed

Eby, David; Olson, Derek; Shime, Jonathan; Sigurdson, Elin

2011-10-01

This article contains summaries of the four presentations made during this panel. David Eby provides a framework for questions every organization should consider before deciding to proceed with litigation. Derek Olson discusses the criminal law of aggravated sexual assault as related to the strategic litigation in R v. Mabior. Jonathan Shime stresses the need for players in the legal sector to educate themselves better on the science surrounding HIV. Finally, Elin Sigurdson outlines the legal arguments advanced in SWUAV, British Columbia's parallel litigation to Ontario's Bedford case, challenging the constitutional validity of provisions of the Criminal Code that endanger the lives of sex workers.

Interleukin 35 Expression Correlates With Microvessel Density in Pancreatic Ductal Adenocarcinoma, Recruits Monocytes, and Promotes Growth and Angiogenesis of Xenograft Tumors in Mice.

PubMed

Huang, Chongbiao; Li, Zengxun; Li, Na; Li, Yang; Chang, Antao; Zhao, Tiansuo; Wang, Xiuchao; Wang, Hongwei; Gao, Song; Yang, Shengyu; Hao, Jihui; Ren, He

2018-02-01

Cells of the monocyte lineage contribute to tumor angiogenesis. Interleukin 35 (IL35) is a member of the IL12 family produced by regulatory, but not effector, T cells. IL35 is a dimer comprising the IL12 alpha and IL27 beta chains, encoded by IL12A and EBI3, respectively. Expression of IL35 is increased in pancreatic ductal adenocarcinomas (PDACs) compared with normal pancreatic tissues, and promotes metastasis. We investigated the role of IL35 in monocyte-induced angiogenesis of PDAC in mice. We measured levels of IL35 protein, microvessel density, and numbers of monocytes in 123 sequential PDAC tissues from patients who underwent surgery in China in 2010. We performed studies with the human PDAC cell lines CFPAC-1, BxPC-3, Panc-1, MIA-PaCa-2, and mouse PDAC cell line Pan02. Monocyte subsets were isolated by flow cytometry from human peripheral blood mononuclear cells. Fused human or mouse IL12A and EBI3 genes were overexpressed in PDAC cells or knocked down using small hairpin RNAs. Cells were grown as xenograft tumors in SCID mice; some mice were given injections of an IL35-neutralizing antibody and tumor growth was monitored. We performed chemotaxis assays to measure the ability of IL35 to recruit monocytes. We analyzed mRNA sequences of 179 PDACs in the Cancer Genome Atlas to identify correlations between expression of IL12A and EBI3 and monocyte markers. Monocytes incubated with IL35 or PDAC cell supernatants were analyzed in tube formation and endothelial migration assays. In PDAC samples from patients, levels of IL35 mRNA and protein correlated with microvessel density and infiltration of monocyte lineage cells. In cells and mice with xenograft tumors, IL35 increased recruitment of monocytes into PDAC tumors, which required CCL5. Upon exposure to IL35, monocytes increased expression of genes whose products promote angiogenesis (CXCL1 and CXCL8). IL35 activated transcription of CCL5, CXCL1, and CXCL8 by inducing GP130 signaling, via IL12RB2 and phosphorylation of STAT1 and STAT4. A combination of a neutralizing antibody against IL35 and gemcitabine significantly decreased monocyte infiltration, microvessel density, and volume of xenograft tumors grown from PDAC cells in mice. PDAC cells produce IL35 to recruit monocytes via CCL5 and induce macrophage to promote angiogenesis via expression of CXCL1 and CXCL8. IL35 signaling promotes angiogenesis and growth of xenograft tumors from PDAC cells in mice. IL35 might serve as a therapeutic target for patients with pancreatic cancer. Copyright © 2018. Published by Elsevier Inc.

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

Loss of GCN5 leads to increased neuronal apoptosis by upregulating E2F1- and Egr-1-dependent BH3-only protein Bim.

PubMed

Wu, Yanna; Ma, Shanshan; Xia, Yong; Lu, Yangpeng; Xiao, Shiyin; Cao, Yali; Zhuang, Sidian; Tan, Xiangpeng; Fu, Qiang; Xie, Longchang; Li, Zhiming; Yuan, Zhongmin

2017-01-26

Cellular acetylation homeostasis is a kinetic balance precisely controlled by histone acetyl-transferase (HAT) and histone deacetylase (HDAC) activities. The loss of the counterbalancing function of basal HAT activity alters the precious HAT:HDAC balance towards enhanced histone deacetylation, resulting in a loss of acetylation homeostasis, which is closely associated with neuronal apoptosis. However, the critical HAT member whose activity loss contributes to neuronal apoptosis remains to be identified. In this study, we found that inactivation of GCN5 by either pharmacological inhibitors, such as CPTH2 and MB-3, or by inactivation with siRNAs leads to a typical apoptosis in cultured cerebellar granule neurons. Mechanistically, the BH3-only protein Bim is transcriptionally upregulated by activated Egr-1 and E2F1 and mediates apoptosis following GCN5 inhibition. Furthermore, in the activity withdrawal- or glutamate-evoked neuronal apoptosis models, GCN5 loses its activity, in contrast to Bim induction. Adenovirus-mediated overexpression of GCN5 suppresses Bim induction and apoptosis. Interestingly, the loss of GCN5 activity and the induction of Egr-1, E2F1 and Bim are involved in the early brain injury (EBI) following subarachnoid haemorrhage (SAH) in rats. HDAC inhibition not only significantly rescues Bim expression and apoptosis induced by either potassium deprivation or GCN5 inactivation but also ameliorates these events and EBI in SAH rats. Taken together, our results highlight a new mechanism by which the loss of GCN5 activity promotes neuronal apoptosis through the transcriptional upregulation of Bim, which is probably a critical event in triggering neuronal death when cellular acetylation homeostasis is impaired.

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

Reducing eating disorder risk factors: A pilot effectiveness trial of a train-the-trainer approach to dissemination and implementation.

PubMed

Greif, Rebecca; Becker, Carolyn Black; Hildebrandt, Tom

2015-12-01

Impediments limit dissemination and implementation of evidence-based interventions (EBIs), including lack of sufficient training. One strategy to increase implementation of EBIs is the train-the-trainer (TTT) model. The Body Project is a peer-led body image program that reduces eating disorder (ED) risk factors. This study examined the effectiveness of a TTT model at reducing risk factors in Body Project participants. Specifically, this study examined whether a master trainer could train a novice trainer to train undergraduate peer leaders to administer the Body Project such that individuals who received the Body Project (i.e., participants) would evidence comparable outcomes to previous trials. We hypothesized that participants would evidence reductions in ED risk factors, with effect sizes similar to previous trials. Utilizing a TTT model, a master trainer trained a novice trainer to train undergraduate peer leaders to administer the Body Project to undergraduate women. Undergraduate women aged 18 years or older who received the Body Project intervention participated in the trial and completed measures at baseline, post-treatment, and five-month follow-up. Primary outcomes included body dissatisfaction, thin ideal internalization, negative affect, and ED pathology. Participants demonstrated significant reductions in thin ideal internalization, ED pathology and body dissatisfaction at post-treatment and 5-month follow-up. At 5 months, using three different strategies for managing missing data, effect sizes were larger or comparable to earlier trials for 3 out of 4 variables. Results support a TTT model for Body Project implementation and the importance of utilizing sensitivity analyses for longitudinal datasets with missing data. © 2015 Wiley Periodicals, Inc.

Interleukin-35 Inhibits Endothelial Cell Activation by Suppressing MAPK-AP-1 Pathway.

PubMed

Sha, Xiaojin; Meng, Shu; Li, Xinyuan; Xi, Hang; Maddaloni, Massimo; Pascual, David W; Shan, Huimin; Jiang, Xiaohua; Wang, Hong; Yang, Xiao-feng

2015-07-31

Vascular response is an essential pathological mechanism underlying various inflammatory diseases. This study determines whether IL-35, a novel responsive anti-inflammatory cytokine, inhibits vascular response in acute inflammation. Using a mouse model of LPS-induced acute inflammation and plasma samples from sepsis patients, we found that IL-35 was induced in the plasma of mice after LPS injection as well as in the plasma of sepsis patients. In addition, IL-35 decreased LPS-induced proinflammatory cytokines and chemokines in the plasma of mice. Furthermore, IL-35 inhibited leukocyte adhesion to the endothelium in the vessels of lung and cremaster muscle and decreased the numbers of inflammatory cells in bronchoalveolar lavage fluid. Mechanistically, IL-35 inhibited the LPS-induced up-regulation of endothelial cell (EC) adhesion molecule VCAM-1 through IL-35 receptors gp130 and IL-12Rβ2 via inhibition of the MAPK-activator protein-1 (AP-1) signaling pathway. We also found that IL-27, which shares the EBI3 subunit with IL-35, promoted LPS-induced VCAM-1 in human aortic ECs and that EBI3-deficient mice had similar vascular response to LPS when compared with that of WT mice. These results demonstrated for the first time that inflammation-induced IL-35 inhibits LPS-induced EC activation by suppressing MAPK-AP1-mediated VCAM-1 expression and attenuates LPS-induced secretion of proinflammatory cytokines/chemokines. Our results provide insight into the control of vascular inflammation by IL-35 and suggest that IL-35 is an attractive novel therapeutic reagent for sepsis and cardiovascular diseases. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

A Randomized Trial of Brief Versus Extended Seizure Prophylaxis After Aneurysmal Subarachnoid Hemorrhage.

PubMed

Human, Theresa; Diringer, Michael N; Allen, Michelle; Zipfel, Gregory J; Chicoine, Michael; Dacey, Ralph; Dhar, Rajat

2018-04-01

Seizures occur in 10-20% of patients with subarachnoid hemorrhage (SAH), predominantly in the acute phase. However, anticonvulsant prophylaxis remains controversial, with studies suggesting a brief course may be adequate and longer exposure may be associated with worse outcomes. Nonetheless, in the absence of controlled trials to inform practice, patients continue to receive variable chemoprophylaxis. The objective of this study was to compare brief versus extended seizure prophylaxis after aneurysmal SAH. We performed a prospective, single-center, randomized, open-label trial of a brief (3-day) course of levetiracetam (LEV) versus extended treatment (until hospital discharge). The primary outcome was in-hospital seizure. Secondary outcomes included drug discontinuation and functional outcome. Eighty-four SAH patients had been randomized when the trial was terminated due to slow enrollment. In-hospital seizures occurred in three (9%) of 35 in the brief LEV group versus one (2%) of 49 in the extended group (p = 0.2). Ten (20%) of the extended group discontinued LEV prematurely, primarily due to sedation. Four of five seizures (including one pre-randomization) occurred in patients with early brain injury (EBI) on computed tomography (CT) scans (adjusted OR 12.5, 95% CI 1.2-122, p = 0.03). Good functional outcome (mRS 0-2) was more likely in the brief LEV group (83 vs. 61%, p = 0.04). This study was underpowered to demonstrate superiority of extended LEV for seizure prophylaxis, although a trend to benefit was seen. Seizures primarily occurred in those with radiographic EBI, suggesting targeted prophylaxis may be preferable. Larger trials are required to evaluate optimal chemoprophylaxis in SAH, especially in light of worse outcomes in those receiving extended treatment.

Enhanced LPS-induced activation of IL-27 signalling in sarcoidosis.

PubMed

Ringkowski, Sabine; Loke, Joshua; Huang, Shuying; Ahmadzai, Hasib; Herth, Felix J F; Thomas, Paul S; Herbert, Cristan

2016-08-01

Granulomas in sarcoidosis have recently been described as containing Interleukin (IL)-27, one of the members of the IL-12 family of cytokines, which also includes IL-35. Levels of these cytokines and the IL-27 receptor subunits were hypothesised to differ between patients with sarcoidosis compared to healthy controls in peripheral blood. Using a cross-sectional study design, plasma and peripheral blood mononuclear cells (PBMC) were collected from patients and control subjects. Protein and mRNA (in PBMC) levels for IL-27 and IL-35 (IL27, EBI3, IL12A subunits) as well as IL-27 receptor (IL6ST and IL27RA subunits) were assessed spontaneously and following direct (LPS) and indirect (anti-CD3/28 activation beads) macrophage stimulation using RT- PCR, ELISA and flow cytometry. Following stimulation with LPS, PBMC of patients with sarcoidosis displayed significantly enhanced expression of IL27 and EBI3 mRNA (p = 0.020 and p = 0.037 respectively) compared to PBMCs from healthy controls. There was also significantly enhanced production of IL-27 by PBMC from patients with sarcoidosis compared to healthy controls in response to LPS stimulation (p = 0.027). IL6ST mRNA and IL6ST protein were significantly lower in patients with sarcoidosis (mRNA p = 0.0002; MFI p = 0.0015) whilst IL27RA protein levels were significantly higher in patients with sarcoidosis compared to healthy controls (MFI p < 0.0001). Plasma IL-35 protein levels did not differ between control and sarcoidosis subjects (p = 0.23). These results suggest there may be exaggerated activation of IL-27 signalling in response to LPS in sarcoidosis. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Evaluating and optimizing horticultural regimes in space plant growth facilities

NASA Astrophysics Data System (ADS)

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

In designing innovative Space Plant Growth Facilities (SPGF) for long duration space f ightl various limitations must be addressed including onboard resources: volume, energy consumption, heat transfer and crew labor expenditure. The required accuracy in evaluating onboard resources by using the equivalent mass methodology and applying it to the design of such facilities is not precise. This is due to the uncertainty of the structure and not completely understanding of the properties of all associated hardware, including the technology in these systems. We present a simple criteria of optimization for horticultural regimes in SPGF: Qmax = max [M · (EBI) 2 / (V · E · T) ], where M is the crop harvest in terms of total dry biomass in the plant growth system; EBI is the edible biomass index (harvest index), V is a volume occupied by the crop; E is the crop light energy supply during growth; T is the crop growth duration. The criterion reflects directly on the consumption of onboard resources for crop production. We analyzed the efficiency of plant crops and the environmental parameters by examining the criteria for 15 salad and 12 wheat crops from the data in the ALS database at Kennedy Space Center. Some following conclusion have been established: 1. The technology involved in growing salad crops on a cylindrical type surface provides a more meaningful Q-criterion; 2. Wheat crops were less efficient than leafy greens (salad crops) when examining resource utilization; 3. By increasing light intensity of the crop the efficiency of the resource utilization could decrease. Using the existing databases and Q-criteria we have found that the criteria can be used in optimizing design and horticultural regimes in the SPGF.

Characterization of domestic and foreign image intensifier tubes

NASA Astrophysics Data System (ADS)

Bender, Edward J.; Wood, Michael V.; Hosek, Daniel J.; Hart, Steve D.

2013-06-01

The market for military-use Generation 2 and Generation 3 image intensifier (I2) tubes has become truly global, with major manufacturers and customers spanning five continents. This worldwide market is becoming increasingly important to U.S. manufacturers, with the majority of U.S. Army intensifier fielding having been completed in 2012. Given this keen global competition, it is not surprising that the advertised tube performance of a given source is often discounted by competitors, and the customers have no objective "honest broker" to determine the relative accuracy of these claims. To help fill this void, the U.S. Army RDECOM CERDEC NVESD recently measured a number of domestic and foreign image intensifier tubes, using consistent test equipment/procedures with which the U.S. industry must correlate for Army tube deliveries. Data and analysis will be presented for the major tube parameters of luminance gain, equivalent background input (EBI), signal-to-noise ratio (SNR), limiting resolution, halo, and modulation transfer function (MTF). The bright-light resolution provided by various auto-gated and non-gated tubes will also be addressed, since this area has been an important factor in the international market. RDECOM CERDEC NVESD measurement data will be compared to the corresponding manufacturer specifications whenever possible.

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

PubMed Central

2011-01-01

Background Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups. Results OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application. Conclusions OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases. Availability http://www.ontocat.org PMID:21619703

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

PubMed

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

2011-05-29

Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups. OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application. OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases. http://www.ontocat.org.

The CoFactor database: organic cofactors in enzyme catalysis.

PubMed

Fischer, Julia D; Holliday, Gemma L; Thornton, Janet M

2010-10-01

Organic enzyme cofactors are involved in many enzyme reactions. Therefore, the analysis of cofactors is crucial to gain a better understanding of enzyme catalysis. To aid this, we have created the CoFactor database. CoFactor provides a web interface to access hand-curated data extracted from the literature on organic enzyme cofactors in biocatalysis, as well as automatically collected information. CoFactor includes information on the conformational and solvent accessibility variation of the enzyme-bound cofactors, as well as mechanistic and structural information about the hosting enzymes. The database is publicly available and can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/CoFactor.

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

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

Beer, Tjaart A. P. de; Laskowski, Roman A.; Duban, Mark-Eugene

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

Embedding gender equality into institutional strategy.

PubMed

Ahmed, S

2017-01-01

The SiS (Sex in Science) Programme on the WGC (Wellcome Genome Campus) was established in 2011. Key participants include the Wellcome Trust Sanger Institute, EMB-EBI (EMBL-European Bioinformatics Institute), Open Targets and Elixir. The key objectives are to catalyse cultural change, develop partnerships, communicate activities and champion our women in science work at a national and international level (http://www.sanger.ac.uk/about/sex-science). In this paper, we highlight some of the many initiatives that have taken place since 2013, to address gender inequality at the highest levels; the challenges we have faced and how we have overcome these, and the future direction of travel.

Remediation of the protein data bank archive.

PubMed

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

2008-01-01

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

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

PubMed

Hermjakob, Henning; Montecchi-Palazzi, Luisa; Bader, Gary; Wojcik, Jérôme; Salwinski, Lukasz; Ceol, Arnaud; Moore, Susan; Orchard, Sandra; Sarkans, Ugis; von Mering, Christian; Roechert, Bernd; Poux, Sylvain; Jung, Eva; Mersch, Henning; Kersey, Paul; Lappe, Michael; Li, Yixue; Zeng, Rong; Rana, Debashis; Nikolski, Macha; Husi, Holger; Brun, Christine; Shanker, K; Grant, Seth G N; Sander, Chris; Bork, Peer; Zhu, Weimin; Pandey, Akhilesh; Brazma, Alvis; Jacq, Bernard; Vidal, Marc; Sherman, David; Legrain, Pierre; Cesareni, Gianni; Xenarios, Ioannis; Eisenberg, David; Steipe, Boris; Hogue, Chris; Apweiler, Rolf

2004-02-01

A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).

A new reference implementation of the PSICQUIC web service.

PubMed

del-Toro, Noemi; Dumousseau, Marine; Orchard, Sandra; Jimenez, Rafael C; Galeota, Eugenia; Launay, Guillaume; Goll, Johannes; Breuer, Karin; Ono, Keiichiro; Salwinski, Lukasz; Hermjakob, Henning

2013-07-01

The Proteomics Standard Initiative Common QUery InterfaCe (PSICQUIC) specification was created by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to enable computational access to molecular-interaction data resources by means of a standard Web Service and query language. Currently providing >150 million binary interaction evidences from 28 servers globally, the PSICQUIC interface allows the concurrent search of multiple molecular-interaction information resources using a single query. Here, we present an extension of the PSICQUIC specification (version 1.3), which has been released to be compliant with the enhanced standards in molecular interactions. The new release also includes a new reference implementation of the PSICQUIC server available to the data providers. It offers augmented web service capabilities and improves the user experience. PSICQUIC has been running for almost 5 years, with a user base growing from only 4 data providers to 28 (April 2013) allowing access to 151 310 109 binary interactions. The power of this web service is shown in PSICQUIC View web application, an example of how to simultaneously query, browse and download results from the different PSICQUIC servers. This application is free and open to all users with no login requirement (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml).

Improvements in the Protein Identifier Cross-Reference service.

PubMed

Wein, Samuel P; Côté, Richard G; Dumousseau, Marine; Reisinger, Florian; Hermjakob, Henning; Vizcaíno, Juan A

2012-07-01

The Protein Identifier Cross-Reference (PICR) service is a tool that allows users to map protein identifiers, protein sequences and gene identifiers across over 100 different source databases. PICR takes input through an interactive website as well as Representational State Transfer (REST) and Simple Object Access Protocol (SOAP) services. It returns the results as HTML pages, XLS and CSV files. It has been in production since 2007 and has been recently enhanced to add new functionality and increase the number of databases it covers. Protein subsequences can be Basic Local Alignment Search Tool (BLAST) against the UniProt Knowledgebase (UniProtKB) to provide an entry point to the standard PICR mapping algorithm. In addition, gene identifiers from UniProtKB and Ensembl can now be submitted as input or mapped to as output from PICR. We have also implemented a 'best-guess' mapping algorithm for UniProt. In this article, we describe the usefulness of PICR, how these changes have been implemented, and the corresponding additions to the web services. Finally, we explain that the number of source databases covered by PICR has increased from the initial 73 to the current 102. New resources include several new species-specific Ensembl databases as well as the Ensembl Genome ones. PICR can be accessed at http://www.ebi.ac.uk/Tools/picr/.

IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex

PubMed Central

Maccari, Giuseppe; Robinson, James; Ballingall, Keith; Guethlein, Lisbeth A.; Grimholt, Unni; Kaufman, Jim; Ho, Chak-Sum; de Groot, Natasja G.; Flicek, Paul; Bontrop, Ronald E.; Hammond, John A.; Marsh, Steven G. E.

2017-01-01

The IPD-MHC Database project (http://www.ebi.ac.uk/ipd/mhc/) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and tools to enable accurate analysis. Since the first release of the database in 2003, IPD-MHC has grown and currently hosts a number of specific sections, with more than 7000 alleles from 70 species, including non-human primates, canines, felines, equids, ovids, suids, bovins, salmonids and murids. These sequences are expertly curated and made publicly available through an open access website. The IPD-MHC Database is a key resource in its field, and this has led to an average of 1500 unique visitors and more than 5000 viewed pages per month. As the database has grown in size and complexity, it has created a number of challenges in maintaining and organizing information, particularly the need to standardize nomenclature and taxonomic classification, while incorporating new allele submissions. Here, we describe the latest database release, the IPD-MHC 2.0 and discuss planned developments. This release incorporates sequence updates and new tools that enhance database queries and improve the submission procedure by utilizing common tools that are able to handle the varied requirements of each MHC-group. PMID:27899604

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).

The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics.

PubMed

de Matos, Paula; Cham, Jennifer A; Cao, Hong; Alcántara, Rafael; Rowland, Francis; Lopez, Rodrigo; Steinbeck, Christoph

2013-03-20

User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of the design process for a service or product; often for software applications and websites. Its goal is to facilitate the design of software that is both useful and easy to use. To achieve this, you must characterise users' requirements, design suitable interactions to meet their needs, and test your designs using prototypes and real life scenarios.For bioinformatics, there is little practical information available regarding how to carry out UCD in practice. To address this we describe a complete, multi-stage UCD process used for creating a new bioinformatics resource for integrating enzyme information, called the Enzyme Portal (http://www.ebi.ac.uk/enzymeportal). This freely-available service mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature.We employed several UCD techniques, including: persona development, interviews, 'canvas sort' card sorting, user workflows, usability testing and others. Our hope is that this case study will motivate the reader to apply similar UCD approaches to their own software design for bioinformatics. Indeed, we found the benefits included more effective decision-making for design ideas and technologies; enhanced team-working and communication; cost effectiveness; and ultimately a service that more closely meets the needs of our target audience.

EUCLID: automatic classification of proteins in functional classes by their database annotations.

PubMed

Tamames, J; Ouzounis, C; Casari, G; Sander, C; Valencia, A

1998-01-01

A tool is described for the automatic classification of sequences in functional classes using their database annotations. The Euclid system is based on a simple learning procedure from examples provided by human experts. Euclid is freely available for academics at http://www.gredos.cnb.uam.es/EUCLID, with the corresponding dictionaries for the generation of three, eight and 14 functional classes. E-mail: valencia@cnb.uam.es The results of the EUCLID classification of different genomes are available at http://www.sander.ebi.ac. uk/genequiz/. A detailed description of the different applications mentioned in the text is available at http://www.gredos.cnb.uam. es/EUCLID/Full_Paper

Remediation of the protein data bank archive

PubMed Central

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

2008-01-01

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

Development of Retardation and Automatic Flotation System (R.A.F.T.)

DTIC Science & Technology

1980-07-07

recovery search Category I Hazard -i ’tationE is necessary. Detailed assembly operations inhibited. Classification eck list must be implemented...VW.KIDD=E CYL.NDER.A AH2)SPRcDS 6IEE AH4 I -86 54 3 2 ECK SIR DESO!fr4VA mr= . . z -i * - = Ik r 075 i AITZ~~ R__ roARK:8 .L,,I CE AI FITTSKE Ew Eb~I A \\t...INER VOWE5 .-...... U-...... 13 1 N5ERT DOWEL F~~INE, FLUSH WITH To FITM1 SET3t INER DWE 6I LSHWT 5 REVISIONS Eck SYM DESCR-PtM DT AO A EAEL..Y RELE-A

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

PubMed

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

2016-02-01

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

Characterization of the covalent binding of N-phenyl-N'-(2-chloroethyl)ureas to {beta}-tubulin: importance of Glu198 in microtubule stability.

PubMed

Fortin, Sébastien; Bouchon, Bernadette; Chambon, Christophe; Lacroix, Jacques; Moreau, Emmanuel; Chezal, Jean-Michel; Degoul, Françoise; C-Gaudreault, René

2011-02-01

N-Phenyl-N'-(2-chloroethyl)ureas (CEUs) are antimicrotubule agents interacting covalently with β-tubulin near the colchicine-binding site (C-BS). Glutamyl 198 residue in β-tubulin (Glu198), which is adjacent to the C-BS behind the two potent nucleophilic residues, Cys239 and Cys354, has been shown to covalently react with 1-(2-chloroethyl)-3-(4-iodophenyl)urea (ICEU). By use of mass spectrometry, we have now identified residues in β-tubulin that have become modified irreversibly by 1-(2-chloroethyl)-3-[3-(5-hydroxypentyl)phenyl]urea (HPCEU), 1-[4-(3-hydroxy-4-methoxystyryl)phenyl]-3-(2-chloroethyl)urea (4ZCombCEU), and N,N'-ethylenebis(iodoacetamide) (EBI). The binding of HPCEU and 4ZCombCEU to β-tubulin resulted in the acylation of Glu198, a protein modification of uncommon occurrence in living cells. Prototypical CEUs then were used as molecular probes to assess, in mouse B16F0 and human MDA-MB-231 cells, the role of Glu198 in microtubule stability. For that purpose, we studied the effect of Glu198 modification by ICEU, HPCEU, and 4ZCombCEU on the acetylation of Lys40 on α-tubulin, a key indicator of microtubule stability. We show that modification of Glu198 by prototypical CEUs correlates with a decrease in Lys40 acetylation, as observed also with other microtubule depolymerizing agents. Therefore, CEU affects the stability and the dynamics of microtubule, likewise a E198G mutation, which is unusual for xenobiotics. We demonstrate for the first time that EBI forms an intramolecular cross-link between Cys239 and Cys354 of β-tubulin in living cells. This work establishes a novel basis for the development of future chemotherapeutic agents and provides a framework for the design of molecules useful for studying the role of Asp and Glu residues in the structure/function and the biological activity of several cellular proteins under physiological conditions.

Relationship between dairy cow genetic merit and profit on commercial spring calving dairy farms.

PubMed

Ramsbottom, G; Cromie, A R; Horan, B; Berry, D P

2012-07-01

Because not all animal factors influencing profitability can be included in total merit breeding indices for profitability, the association between animal total merit index and true profitability, taking cognisance of all factors associated with costs and revenues, is generally not known. One method to estimate such associations is at the herd level, associating herd average genetic merit with herd profitability. The objective of this study was to primarily relate herd average genetic merit for a range of traits, including the Irish total merit index, with indicators of performance, including profitability, using correlation and multiple regression analyses. Physical, genetic and financial performance data from 1131 Irish seasonal calving pasture-based dairy farms were available following edits; data on some herds were available for more than 1 year of the 3-year study period (2007 to 2009). Herd average economic breeding index (EBI) was associated with reduced herd average phenotypic milk yield but with greater milk composition, resulting in higher milk prices. Moderate positive correlations (0.26 to 0.61) existed between genetic merit for an individual trait and average herd performance for that trait (e.g. genetic merit for milk yield and average per cow milk yield). Following adjustment for year, stocking rate, herd size and quantity of purchased feed in the multiple regression analysis, average herd EBI was positively and linearly associated with net margin per cow and per litre as well as gross revenue output per cow and per litre. The change in net margin per cow per unit change in the total merit index was €1.94 (s.e. = 0.42), which was not different from the expectation of €2. This study, based on a large data set of commercial herds with accurate information on profitability and genetic merit, confirms that, after accounting for confounding factors, the change in herd profitability per unit change in herd genetic merit for the total merit index is within expectations.

Synoviocytes-derived Interleukin 35 Potentiates B Cell Response in Patients with Osteoarthritis and Rheumatoid Arthritis.

PubMed

Kam, Ngar-Woon; Liu, Dehua; Cai, Zhe; Mak, Wah-Yan; Wong, Chun-Kwok; Chiu, Kwok-Hing; Wong, Kam-Yiu; Tsang, Wai-Leuk; Tam, Lai-Shan

2018-04-01

Elevated expression of interleukin 35 (IL-35) is associated with autoimmune disease, including rheumatoid arthritis (RA). The present study was undertaken to determine the functional interaction among IL-35, B cells, and stromal cells residing in the synovium of patients with RA and osteoarthritis (OA). IL-35 (EBI-3/p35) expression was investigated in RA and OA synovium using quantitative real-time PCR (qRT-PCR) and immunohistochemistry. IL-35 receptor (IL-35R) expression on B cells dissociated from synovium and periphery of patients with RA, OA, and healthy donor controls (HC) was determined by flow cytometry. The degree of B cells activation after IL-4 and/or IL-35 stimulation was measured by flow cytometry and qRT-PCR. Synovial fibroblasts (SF) purified from RA and OA synovium were cocultured with peripheral HC B cells in the presence/absence of tumor necrosis factor-α (TNF-α) and with/without anti-IL-35-blocking antibodies. EBI-3/p35 transcripts were expressed in close proximity to B cells residing in RA and OA synovium. IL-35R subunits, gp130 and IL-27Rα, but not IL-12Rβ2, were expressed in B cells extracted from the synovium and periphery of patients with RA/OA. Notably, RA synovium expressed the highest level of IL-27Rα on their cell surface. IL-35 induced proliferation and IgG production in HC B cells. Cocultures of HC B cells with RASF, but not OASF, exhibited significantly elevated B cells activation. TNF-α-induced, RASF-dependent secretion of IgG in B cells is partly IL-35-dependent. To our knowledge, for the first time we demonstrated that synovial/peripheral B cells expressed IL-35R and were responsive to IL-35 stimulation. SF residing in RA synovium can be linked to B cell activation and maintenance in RA synovium through IL-35.

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

PubMed

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

2017-01-17

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

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

2016 update of the PRIDE database and its related tools

PubMed Central

Vizcaíno, Juan Antonio; Csordas, Attila; del-Toro, Noemi; Dianes, José A.; Griss, Johannes; Lavidas, Ilias; Mayer, Gerhard; Perez-Riverol, Yasset; Reisinger, Florian; Ternent, Tobias; Xu, Qing-Wei; Wang, Rui; Hermjakob, Henning

2016-01-01

The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system, replacing the original PRIDE database. Here we summarize the developments in PRIDE resources and related tools since the previous update manuscript in the Database Issue in 2013. PRIDE Archive constitutes a complete redevelopment of the original PRIDE, comprising a new storage backend, data submission system and web interface, among other components. PRIDE Archive supports the most-widely used PSI (Proteomics Standards Initiative) data standard formats (mzML and mzIdentML) and implements the data requirements and guidelines of the ProteomeXchange Consortium. The wide adoption of ProteomeXchange within the community has triggered an unprecedented increase in the number of submitted data sets (around 150 data sets per month). We outline some statistics on the current PRIDE Archive data contents. We also report on the status of the PRIDE related stand-alone tools: PRIDE Inspector, PRIDE Converter 2 and the ProteomeXchange submission tool. Finally, we will give a brief update on the resources under development ‘PRIDE Cluster’ and ‘PRIDE Proteomes’, which provide a complementary view and quality-scored information of the peptide and protein identification data available in PRIDE Archive. PMID:26527722

UniEuk: Time to Speak a Common Language in Protistology!

PubMed

Berney, Cédric; Ciuprina, Andreea; Bender, Sara; Brodie, Juliet; Edgcomb, Virginia; Kim, Eunsoo; Rajan, Jeena; Parfrey, Laura Wegener; Adl, Sina; Audic, Stéphane; Bass, David; Caron, David A; Cochrane, Guy; Czech, Lucas; Dunthorn, Micah; Geisen, Stefan; Glöckner, Frank Oliver; Mahé, Frédéric; Quast, Christian; Kaye, Jonathan Z; Simpson, Alastair G B; Stamatakis, Alexandros; Del Campo, Javier; Yilmaz, Pelin; de Vargas, Colomban

2017-05-01

Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho-taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental '-omics' surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta-omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist -omics age to the fragile, centuries-old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community-based and expert-driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL-EBI, ensuring its broad use and long-term preservation as a reference taxonomy for eukaryotes. © 2017 The Author(s) Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists.

IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex.

PubMed

Maccari, Giuseppe; Robinson, James; Ballingall, Keith; Guethlein, Lisbeth A; Grimholt, Unni; Kaufman, Jim; Ho, Chak-Sum; de Groot, Natasja G; Flicek, Paul; Bontrop, Ronald E; Hammond, John A; Marsh, Steven G E

2017-01-04

The IPD-MHC Database project (http://www.ebi.ac.uk/ipd/mhc/) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and tools to enable accurate analysis. Since the first release of the database in 2003, IPD-MHC has grown and currently hosts a number of specific sections, with more than 7000 alleles from 70 species, including non-human primates, canines, felines, equids, ovids, suids, bovins, salmonids and murids. These sequences are expertly curated and made publicly available through an open access website. The IPD-MHC Database is a key resource in its field, and this has led to an average of 1500 unique visitors and more than 5000 viewed pages per month. As the database has grown in size and complexity, it has created a number of challenges in maintaining and organizing information, particularly the need to standardize nomenclature and taxonomic classification, while incorporating new allele submissions. Here, we describe the latest database release, the IPD-MHC 2.0 and discuss planned developments. This release incorporates sequence updates and new tools that enhance database queries and improve the submission procedure by utilizing common tools that are able to handle the varied requirements of each MHC-group. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Regional Environmental Impacts of Biofuel Feedstock Production--Scaling Biogeochemical Cycles in Space and Time

NASA Astrophysics Data System (ADS)

Vanloocke, A.; Bernacchi, C.

2008-12-01

Recently there has been increasing socio-economic and scientific interest in the use of alternative sources of energy to offset the negative effects of current fossil fuel dependence and consequent greenhouse gas emissions. Currently, one of the most popular alternatives is to use ethanol produced from domestically grown crops for use as fuel in the transportation sector. In 2007, over 7.5 billion gallons of ethanol were produced in the U.S. from corn, a traditional food crop. Recent research indicates that it may be logistically impractical, ecologically counterproductive (i.e. a net carbon source), and economically devastating to produce ethanol from crops previously grown to produce food. The EBI (Energy Biosciences Institute, at University of California Berkley and University of Illinois Urbana-Champaign) is now conducting research to assess the ability of traditional crops as well as dedicated biofuel feedstocks (e.g. Panicum virgatum (switchgrass), Miscanthus x Giganteus (Miscanthus), and Saccharum spp (sugar cane)) to provide a productive and sustainable alternative to fossil fuel. This is an important step to take before implementing the large-scale growth necessary to meet U.S. energy needs .A process-based terrestrial ecosystem model, Agro-IBIS (Agricultural Integrated Biosphere Simulator) was adapted to simulate the growth of Miscanthus. The model was calibrated using data collected from sites at the University of Illinois south farms. Simulations indicated significant implications on the regional carbon and water budgets. Next this locally validated method will be extrapolated to simulate the regional scale growth of Miscanthus in the Midwestern U.S. and sugarcane in Brazil and a similar analysis will be conducted for switchgrass. The results should provide insight on optimal land-use decisions and legislation that regard meeting energy demands and mitigating climate change in the near future.

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

ProbOnto: ontology and knowledge base of probability distributions.

PubMed

Swat, Maciej J; Grenon, Pierre; Wimalaratne, Sarala

2016-09-01

Probability distributions play a central role in mathematical and statistical modelling. The encoding, annotation and exchange of such models could be greatly simplified by a resource providing a common reference for the definition of probability distributions. Although some resources exist, no suitably detailed and complex ontology exists nor any database allowing programmatic access. ProbOnto, is an ontology-based knowledge base of probability distributions, featuring more than 80 uni- and multivariate distributions with their defining functions, characteristics, relationships and re-parameterization formulas. It can be used for model annotation and facilitates the encoding of distribution-based models, related functions and quantities. http://probonto.org mjswat@ebi.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics

PubMed Central

2013-01-01

User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of the design process for a service or product; often for software applications and websites. Its goal is to facilitate the design of software that is both useful and easy to use. To achieve this, you must characterise users’ requirements, design suitable interactions to meet their needs, and test your designs using prototypes and real life scenarios. For bioinformatics, there is little practical information available regarding how to carry out UCD in practice. To address this we describe a complete, multi-stage UCD process used for creating a new bioinformatics resource for integrating enzyme information, called the Enzyme Portal (http://www.ebi.ac.uk/enzymeportal). This freely-available service mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature. We employed several UCD techniques, including: persona development, interviews, ‘canvas sort’ card sorting, user workflows, usability testing and others. Our hope is that this case study will motivate the reader to apply similar UCD approaches to their own software design for bioinformatics. Indeed, we found the benefits included more effective decision-making for design ideas and technologies; enhanced team-working and communication; cost effectiveness; and ultimately a service that more closely meets the needs of our target audience. PMID:23514033

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.

Bioinformatics Goes to School—New Avenues for Teaching Contemporary Biology

PubMed Central

Wood, Louisa; Gebhardt, Philipp

2013-01-01

Since 2010, the European Molecular Biology Laboratory's (EMBL) Heidelberg laboratory and the European Bioinformatics Institute (EMBL-EBI) have jointly run bioinformatics training courses developed specifically for secondary school science teachers within Europe and EMBL member states. These courses focus on introducing bioinformatics, databases, and data-intensive biology, allowing participants to explore resources and providing classroom-ready materials to support them in sharing this new knowledge with their students. In this article, we chart our progress made in creating and running three bioinformatics training courses, including how the course resources are received by participants and how these, and bioinformatics in general, are subsequently used in the classroom. We assess the strengths and challenges of our approach, and share what we have learned through our interactions with European science teachers. PMID:23785266

Reaction Decoder Tool (RDT): extracting features from chemical reactions.

PubMed

Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W; Holliday, Gemma L; Steinbeck, Christoph; Thornton, Janet M

2016-07-01

Extracting chemical features like Atom-Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder : asad@ebi.ac.uk or s9asad@gmail.com. © The Author 2016. Published by Oxford University Press.

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach

PubMed Central

Henriques, David; Rocha, Miguel; Saez-Rodriguez, Julio; Banga, Julio R.

2015-01-01

Motivation: Systems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no information about the kinetic parameters. Results: In this work, we combine a logic-based formalism, to describe all the possible regulatory structures for a given dynamic model of a pathway, with mixed-integer dynamic optimization (MIDO). This framework aims to simultaneously identify the regulatory structure (represented by binary parameters) and the real-valued parameters that are consistent with the available experimental data, resulting in a logic-based differential equation model. The alternative to this would be to perform real-valued parameter estimation for each possible model structure, which is not tractable for models of the size presented in this work. The performance of the method presented here is illustrated with several case studies: a synthetic pathway problem of signaling regulation, a two-component signal transduction pathway in bacterial homeostasis, and a signaling network in liver cancer cells. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: julio@iim.csic.es or saezrodriguez@ebi.ac.uk PMID:26002881

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.

PubMed

Henriques, David; Rocha, Miguel; Saez-Rodriguez, Julio; Banga, Julio R

2015-09-15

Systems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no information about the kinetic parameters. In this work, we combine a logic-based formalism, to describe all the possible regulatory structures for a given dynamic model of a pathway, with mixed-integer dynamic optimization (MIDO). This framework aims to simultaneously identify the regulatory structure (represented by binary parameters) and the real-valued parameters that are consistent with the available experimental data, resulting in a logic-based differential equation model. The alternative to this would be to perform real-valued parameter estimation for each possible model structure, which is not tractable for models of the size presented in this work. The performance of the method presented here is illustrated with several case studies: a synthetic pathway problem of signaling regulation, a two-component signal transduction pathway in bacterial homeostasis, and a signaling network in liver cancer cells. Supplementary data are available at Bioinformatics online. julio@iim.csic.es or saezrodriguez@ebi.ac.uk. © The Author 2015. Published by Oxford University Press.

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

PubMed

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

2009-11-15

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

Knowledge Representation and Management: a Linked Data Perspective.

PubMed

Barros, M; Couto, F M

2016-11-10

Biomedical research is increasingly becoming a data-intensive science in several areas, where prodigious amounts of data is being generated that has to be stored, integrated, shared and analyzed. In an effort to improve the accessibility of data and knowledge, the Linked Data initiative proposed a well-defined set of recommendations for exposing, sharing and integrating data, information and knowledge, using semantic web technologies. The main goal of this paper is to identify the current status and future trends of knowledge representation and management in Life and Health Sciences, mostly with regard to linked data technologies. We selected three prominent linked data studies, namely Bio2RDF, Open PHACTS and EBI RDF platform, and selected 14 studies published after 2014 (inclusive) that cited any of the three studies. We manually analyzed these 14 papers in relation to how they use linked data techniques. The analyses show a tendency to use linked data techniques in Life and Health Sciences, and even if some studies do not follow all of the recommendations, many of them already represent and manage their knowledge using RDF and biomedical ontologies. These insights from RDF and biomedical ontologies are having a strong impact on how knowledge is generated from biomedical data, by making data elements increasingly connected and by providing a better description of their semantics. As health institutes become more data centric, we believe that the adoption of linked data techniques will continue to grow and be an effective solution to knowledge representation and management.

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

PubMed Central

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

2017-01-01

Abstract Summary Submission to the MetaboLights repository for metabolomics data currently places the burden of reporting instrument and acquisition parameters in ISA-Tab format on users, who have to do it manually, a process that is time consuming and prone to user input error. Since the large majority of these parameters are embedded in instrument raw data files, an opportunity exists to capture this metadata more accurately. Here we report a set of Python packages that can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files. The parsing packages are separated into mzML2ISA (encompassing mzML and imzML formats) and nmrML2ISA (nmrML format only). Overall, the use of mzML2ISA & nmrML2ISA reduces the time needed to capture metadata substantially (capturing 90% of metadata on assay and sample levels), is much less prone to user input errors, improves compliance with minimum information reporting guidelines and facilitates more finely grained data exploration and querying of datasets. Availability and Implementation mzML2ISA & nmrML2ISA are available under version 3 of the GNU General Public Licence at https://github.com/ISA-tools. Documentation is available from http://2isa.readthedocs.io/en/latest/. Contact reza.salek@ebi.ac.uk or isatools@googlegroups.com Supplementary information Supplementary data are available at Bioinformatics online. PMID:28402395

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

PubMed

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

2017-08-15

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

LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.

PubMed

Foster, Joseph M; Moreno, Pablo; Fabregat, Antonio; Hermjakob, Henning; Steinbeck, Christoph; Apweiler, Rolf; Wakelam, Michael J O; Vizcaíno, Juan Antonio

2013-01-01

Protein sequence databases are the pillar upon which modern proteomics is supported, representing a stable reference space of predicted and validated proteins. One example of such resources is UniProt, enriched with both expertly curated and automatic annotations. Taken largely for granted, similar mature resources such as UniProt are not available yet in some other "omics" fields, lipidomics being one of them. While having a seasoned community of wet lab scientists, lipidomics lies significantly behind proteomics in the adoption of data standards and other core bioinformatics concepts. This work aims to reduce the gap by developing an equivalent resource to UniProt called 'LipidHome', providing theoretically generated lipid molecules and useful metadata. Using the 'FASTLipid' Java library, a database was populated with theoretical lipids, generated from a set of community agreed upon chemical bounds. In parallel, a web application was developed to present the information and provide computational access via a web service. Designed specifically to accommodate high throughput mass spectrometry based approaches, lipids are organised into a hierarchy that reflects the variety in the structural resolution of lipid identifications. Additionally, cross-references to other lipid related resources and papers that cite specific lipids were used to annotate lipid records. The web application encompasses a browser for viewing lipid records and a 'tools' section where an MS1 search engine is currently implemented. LipidHome can be accessed at http://www.ebi.ac.uk/apweiler-srv/lipidhome.

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

PubMed

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

2012-06-30

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

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

NASA Astrophysics Data System (ADS)

Donaldson, Jason L.

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

Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data.

PubMed

Marco-Ramell, Anna; Palau-Rodriguez, Magali; Alay, Ania; Tulipani, Sara; Urpi-Sarda, Mireia; Sanchez-Pla, Alex; Andres-Lacueva, Cristina

2018-01-02

Bioinformatic tools for the enrichment of 'omics' datasets facilitate interpretation and understanding of data. To date few are suitable for metabolomics datasets. The main objective of this work is to give a critical overview, for the first time, of the performance of these tools. To that aim, datasets from metabolomic repositories were selected and enriched data were created. Both types of data were analysed with these tools and outputs were thoroughly examined. An exploratory multivariate analysis of the most used tools for the enrichment of metabolite sets, based on a non-metric multidimensional scaling (NMDS) of Jaccard's distances, was performed and mirrored their diversity. Codes (identifiers) of the metabolites of the datasets were searched in different metabolite databases (HMDB, KEGG, PubChem, ChEBI, BioCyc/HumanCyc, LipidMAPS, ChemSpider, METLIN and Recon2). The databases that presented more identifiers of the metabolites of the dataset were PubChem, followed by METLIN and ChEBI. However, these databases had duplicated entries and might present false positives. The performance of over-representation analysis (ORA) tools, including BioCyc/HumanCyc, ConsensusPathDB, IMPaLA, MBRole, MetaboAnalyst, Metabox, MetExplore, MPEA, PathVisio and Reactome and the mapping tool KEGGREST, was examined. Results were mostly consistent among tools and between real and enriched data despite the variability of the tools. Nevertheless, a few controversial results such as differences in the total number of metabolites were also found. Disease-based enrichment analyses were also assessed, but they were not found to be accurate probably due to the fact that metabolite disease sets are not up-to-date and the difficulty of predicting diseases from a list of metabolites. We have extensively reviewed the state-of-the-art of the available range of tools for metabolomic datasets, the completeness of metabolite databases, the performance of ORA methods and disease-based analyses. Despite the variability of the tools, they provided consistent results independent of their analytic approach. However, more work on the completeness of metabolite and pathway databases is required, which strongly affects the accuracy of enrichment analyses. Improvements will be translated into more accurate and global insights of the metabolome.

Gene expression of subunits of the IL-12 family cytokines in moDCs derived in vitro from the cord blood of children of healthy and allergic mothers.

PubMed

Hrdý, J; Novotná, O; Kocourková, I; Prokešová, L

2014-01-01

The incidence of allergic diseases is steadily increasing an urgent need to clarify the immunologic processes which occur early in life and signal an increased risk of possible future allergy development. The ratio and maturation state of DCs together with the cytokine environment are important in directing and modulating immune responses. The maturation state (presence of CD83) of cord blood monocyte-derived dendritic cells (moDCs) of 52 children of healthy mothers and 58 children of allergic mothers was estimated by flow cytometry. The capacity of moDCs to express genes for subunits of IL-12 family cytokines was monitored using real-time PCR and protein secretion in cell culture supernatants by ELISA. The percentage of CD83+ moDCs was significantly higher in the allergic group after LPS stimulation (43.11 ± 4.41) in comparison to the healthy group (24.85 ± 3.37). Significantly higher gene expression of subunits of IL-12 family members was observed in moDCs of children of allergic mothers, in comparison with children of healthy mothers. The differences were evident mainly after LPS stimulation of moDCs (healthy group: p19: 3.05 ± 1.24; p28: 14.8 ± 6.8; p35: 1.8 ± 0.6; p40: 8.0 ± 3.5; EBI3: 3.0 ± 1.2; allergic group: p19: 6.1 ± 2.7; p28: 61.4 ± 22.2; p35: 14.9 ± 6.5; p40: 36.4 ± 18.8; EBI3: 11.3 ± 3.2), with the exception of p28, whose expression was significantly higher in the allergic group even without stimulation (healthy group: 0.28 ± 0.12, allergic group: 0.87 ± 0.62). No significant difference between the healthy and allergic groups was found at the protein level. The observation of both increased presence of cell surface activation marker on moDCs and higher IL-12 family gene expression in LPS-stimulated moDCs of children of allergic mothers indicates a higher reactivity of these cells.

Structure-based classification and ontology in chemistry

PubMed Central

2012-01-01

Background Recent years have seen an explosion in the availability of data in the chemistry domain. With this information explosion, however, retrieving relevant results from the available information, and organising those results, become even harder problems. Computational processing is essential to filter and organise the available resources so as to better facilitate the work of scientists. Ontologies encode expert domain knowledge in a hierarchically organised machine-processable format. One such ontology for the chemical domain is ChEBI. ChEBI provides a classification of chemicals based on their structural features and a role or activity-based classification. An example of a structure-based class is 'pentacyclic compound' (compounds containing five-ring structures), while an example of a role-based class is 'analgesic', since many different chemicals can act as analgesics without sharing structural features. Structure-based classification in chemistry exploits elegant regularities and symmetries in the underlying chemical domain. As yet, there has been neither a systematic analysis of the types of structural classification in use in chemistry nor a comparison to the capabilities of available technologies. Results We analyze the different categories of structural classes in chemistry, presenting a list of patterns for features found in class definitions. We compare these patterns of class definition to tools which allow for automation of hierarchy construction within cheminformatics and within logic-based ontology technology, going into detail in the latter case with respect to the expressive capabilities of the Web Ontology Language and recent extensions for modelling structured objects. Finally we discuss the relationships and interactions between cheminformatics approaches and logic-based approaches. Conclusion Systems that perform intelligent reasoning tasks on chemistry data require a diverse set of underlying computational utilities including algorithmic, statistical and logic-based tools. For the task of automatic structure-based classification of chemical entities, essential to managing the vast swathes of chemical data being brought online, systems which are capable of hybrid reasoning combining several different approaches are crucial. We provide a thorough review of the available tools and methodologies, and identify areas of open research. PMID:22480202

The Encyclopedia of Systems Biology and OMICS (first presentation) and The ISA Infrastructure for Multi-omics Data (second presentation) (GSC8 Meeting)

ScienceCinema

Kolker, Eugene; Sansone, Susanna

2018-01-15

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Eugene Kolker from Seattle Children's Hospital briefly discusses "The Encyclopedia of Systems Biology and OMICS," followed by Susanna Sansone from the EBI on "The ISA Infrastructure for multi-omics data" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA. on Sept. 11, 2009.

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

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

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

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.

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.

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

PubMed

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

2013-09-01

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

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

PubMed Central

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

2013-01-01

The widespread adoption of high-throughput next-generation sequencing (NGS) technology among the Australian life science research community is highlighting an urgent need to up-skill biologists in tools required for handling and analysing their NGS data. There is currently a shortage of cutting-edge bioinformatics training courses in Australia as a consequence of a scarcity of skilled trainers with time and funding to develop and deliver training courses. To address this, a consortium of Australian research organizations, including Bioplatforms Australia, the Commonwealth Scientific and Industrial Research Organisation and the Australian Bioinformatics Network, have been collaborating with EMBL-EBI training team. A group of Australian bioinformaticians attended the train-the-trainer workshop to improve training skills in developing and delivering bioinformatics workshop curriculum. A 2-day NGS workshop was jointly developed to provide hands-on knowledge and understanding of typical NGS data analysis workflows. The road show–style workshop was successfully delivered at five geographically distant venues in Australia using the newly established Australian NeCTAR Research Cloud. We highlight the challenges we had to overcome at different stages from design to delivery, including the establishment of an Australian bioinformatics training network and the computing infrastructure and resource development. A virtual machine image, workshop materials and scripts for configuring a machine with workshop contents have all been made available under a Creative Commons Attribution 3.0 Unported License. This means participants continue to have convenient access to an environment they had become familiar and bioinformatics trainers are able to access and reuse these resources. PMID:23543352

Knowledge Representation and Management: A Linked Data Perspective

PubMed Central

Barros, M.

2016-01-01

Summary Introduction Biomedical research is increasingly becoming a data-intensive science in several areas, where prodigious amounts of data is being generated that has to be stored, integrated, shared and analyzed. In an effort to improve the accessibility of data and knowledge, the Linked Data initiative proposed a well-defined set of recommendations for exposing, sharing and integrating data, information and knowledge, using semantic web technologies. Objective The main goal of this paper is to identify the current status and future trends of knowledge representation and management in Life and Health Sciences, mostly with regard to linked data technologies. Methods We selected three prominent linked data studies, namely Bio2RDF, Open PHACTS and EBI RDF platform, and selected 14 studies published after 2014 (inclusive) that cited any of the three studies. We manually analyzed these 14 papers in relation to how they use linked data techniques. Results The analyses show a tendency to use linked data techniques in Life and Health Sciences, and even if some studies do not follow all of the recommendations, many of them already represent and manage their knowledge using RDF and biomedical ontologies. Conclusion These insights from RDF and biomedical ontologies are having a strong impact on how knowledge is generated from biomedical data, by making data elements increasingly connected and by providing a better description of their semantics. As health institutes become more data centric, we believe that the adoption of linked data techniques will continue to grow and be an effective solution to knowledge representation and management. PMID:27830248

Intensive virtual reality-based training for upper limb motor function in chronic stroke: a feasibility study using a single case experimental design and fMRI.

PubMed

Schuster-Amft, Corina; Henneke, Andrea; Hartog-Keisker, Birgit; Holper, Lisa; Siekierka, Ewa; Chevrier, Edith; Pyk, Pawel; Kollias, Spyros; Kiper, Daniel; Eng, Kynan

2015-01-01

To evaluate feasibility and neurophysiological changes after virtual reality (VR)-based training of upper limb (UL) movements. Single-case A-B-A-design with two male stroke patients (P1:67 y and 50 y, 3.5 and 3 y after onset) with UL motor impairments, 45-min therapy sessions 5×/week over 4 weeks. Patients facing screen, used bimanual data gloves to control virtual arms. Three applications trained bimanual reaching, grasping, hand opening. Assessments during 2-week baseline, weekly during intervention, at 3-month follow-up (FU): Goal Attainment Scale (GAS), Chedoke Arm and Hand Activity Inventory (CAHAI), Chedoke-McMaster Stroke Assessment (CMSA), Extended Barthel Index (EBI), Motor Activity Log (MAL). Functional magnetic resonance imaging scans (FMRI) before, immediately after treatment and at FU. P1 executed 5478 grasps (paretic arm). Improvements in CAHAI (+4) were maintained at FU. GAS changed to +1 post-test and +2 at FU. P2 executed 9835 grasps (paretic arm). CAHAI improvements (+13) were maintained at FU. GAS scores changed to -1 post-test and +1 at FU. MAL scores changed from 3.7 at pre-test to 5.5 post-test and 3.3 at FU. The VR-based intervention was feasible, safe, and intense. Adjustable application settings maintained training challenge and patient motivation. ADL-relevant UL functional improvements persisted at FU and were related to changed cortical activation patterns. Implications for Rehabilitation YouGrabber trains uni- and bimanual upper motor function. Its application is feasible, safe, and intense. The control of the virtual arms can be done in three main ways: (a) normal (b) virtual mirror therapy, or (c) virtual following. The mirroring feature provides an illusion of affected limb movements during the period when the affected upper limb (UL) is resting. The YouGrabber training led to ADL-relevant UL functional improvements that were still assessable 12 weeks after intervention finalization and were related to changed cortical activation patterns.

Submitting MIGS, MIMS, MIENS Information to EMBL and Standards and the Sequencing Pipelines of the Gordon and Betty Moore Foundation (GSC8 Meeting)

ScienceCinema

Vaughan, Bob; Kaye, Jon

2018-01-24

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Bob Vaughan of EMBL on submitting MIGS/MIMS/MIENS information to EMBL-EBI's system, followed by a brief talk from Jon Kaye of the Gordon and Betty Moore Foundation on standards and the foundation's sequencing pipelines at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

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

Purified terephthalic acid wastewater biodegradation and toxicity.

PubMed

Zhang, Xu-xiang; Wan, Yu-qiu; Cheng, Shu-pei; Sun, Shi-lei; Zhu, Cheng-jun; Li, Wei-xin; Zhang, Xiao-chun; Wang, Gui-lin; Lu, Jian-hua; Luo, Xiang; Gu, Ji-dong

2005-01-01

The biodegradation and toxicity of the purified terephthalic acid (PTA) processing wastewater was researched at NJYZ pilot with the fusant strain Fhhh in the carrier activated sludge process (CASP). Sludge loading rate (SLR) for Fhhh to COD of the wastewater was 1.09 d(-1) and to PTA in the wastewater was 0.29 d(-1). The results of bioassay at the pilot and calculation with software Ebis3 showed that the 48h-LC50 (median lethal concentration) to Daphnia magna for the PTA concentration in the wastewater was only 1/10 of that for the chemical PTA. There were 5 kinds of benzoate pollutants and their toxicities existing in the wastewater at least. The toxicity parameter value of the pure chemical PTA cannot be used to predicate the PTA wastewater toxicity. The toxicity of the NJYZ PTA wastewater will be discussed in detail in this paper.

Intent to sustain use of a mental health innovation by school providers: What matters most?

PubMed Central

Livet, Melanie; Yannayon, Mary; Kocher, Kelly; McMillen, Janey

2017-01-01

Despite innovations being routinely introduced in schools to support the mental health of students, few are successfully maintained over time. This study explores the role of innovation characteristics, individual attitudes and skills, and organizational factors in school providers’ decisions to continue use of Centervention, a technology-based tool that supports implementation of evidence-based mental health interventions (EBIs). Data were collected from 44 providers through online surveys following use of Centervention over a one-year period. When considered with individual and organizational factors, experience with Centervention (usability, usefulness, and satisfaction) was found to be the most influential predictor of intent to sustain use. Results reinforce the importance of (1) differentiating between factors that predict initial adoption vs. those that enable sustainability and (2) tailoring sustainability decision models to the nature of the innovation. They also support the need to incorporate strategies to enhance provider experience during implementation of an innovation. PMID:29403540

Submitting MIGS, MIMS, MIENS Information to EMBL and Standards and the Sequencing Pipelines of the Gordon and Betty Moore Foundation (GSC8 Meeting)

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

Vaughan, Bob; Kaye, Jon

2009-09-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Bob Vaughan of EMBL on submitting MIGS/MIMS/MIENS information to EMBL-EBI's system, followed by a brief talk from Jon Kaye of the Gordon and Bettymore » Moore Foundation on standards and the foundation's sequencing pipelines at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.« less

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

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

PubMed

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

2016-06-01

Phosphorylation is one of the main post-translational modification (PTM) involved in signaling network in the ascomycete Botrytis cinerea , one of the most relevant phytopathogenic fungus. The data presented in this article provided a differential mass spectrometry-based analysis of the phosphoproteome of B. cinerea under two different phenotypical conditions induced by the use of two different elicitors: glucose and deproteinized Tomate Cell Walls (TCW). A total 1138 and 733 phosphoproteins were identified for glucose and TCW culture conditions respectively. Raw data are deposited at the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier (PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD003099). Further interpretation and discussion of these data are provided in our research article entitled "Phosphoproteome analysis of B.cinerea in response to different plant-based elicitors" (Liñeiro et al., 2016) [1].

The Encyclopedia of Systems Biology and OMICS (first presentation) and The ISA Infrastructure for Multi-omics Data (second presentation) (GSC8 Meeting)

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

Kolker, Eugene; Sansone, Susanna

2011-09-11

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Eugene Kolker from Seattle Children's Hospital briefly discusses "The Encyclopedia of Systems Biology and OMICS," followed by Susanna Sansone from the EBI on "Themore » ISA Infrastructure for multi-omics data" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA. on Sept. 11, 2009.« less

DNA Data Bank of Japan

PubMed Central

Mashima, Jun; Kodama, Yuichi; Fujisawa, Takatomo; Katayama, Toshiaki; Okuda, Yoshihiro; Kaminuma, Eli; Ogasawara, Osamu; Okubo, Kousaku; Nakamura, Yasukazu; Takagi, Toshihisa

2017-01-01

The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration with the US National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI). The DDBJ Center also services Japanese Genotype-phenotype Archive (JGA), with the National Bioscience Database Center to collect human-subjected data from Japanese researchers. Here, we report our database activities for INSDC and JGA over the past year, and introduce retrieval and analytical services running on our supercomputer system and their recent modifications. Furthermore, with the Database Center for Life Science, the DDBJ Center improves semantic web technologies to integrate and to share biological data, for providing the RDF version of the sequence data. PMID:27924010

SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.

PubMed

Schweiger, Dominik; Trajanoski, Zlatko; Pabinger, Stephan

2014-08-15

Semantic Web has established itself as a framework for using and sharing data across applications and database boundaries. Here, we present a web-based platform for querying biological Semantic Web databases in a graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into a query and executes it on a public endpoint. The tool integrates several publicly available Semantic Web databases, including the databases of the just recently released EBI RDF platform. Furthermore, it provides several predefined template queries for answering biological questions. Users can easily create and save new query graphs, which can also be shared with other researchers. This new graphical way of creating queries for biological Semantic Web databases considerably facilitates usability as it removes the requirement of knowing specific query languages and database structures. The system is freely available at http://sparqlgraph.i-med.ac.at.

Interacting spin-2 fields in the Stückelberg picture

NASA Astrophysics Data System (ADS)

Noller, Johannes; Scargill, James H. C.; Ferreira, Pedro G.

2014-02-01

We revisit and extend the `Effective field theory for massive gravitons' constructed by Arkani-Hamed, Georgi and Schwartz in the light of recent progress in constructing ghost-free theories with multiple interacting spin-2 fields. We show that there exist several dual ways of restoring gauge invariance in such multi-gravity theories, find a generalised Fierz-Pauli tuning condition relevant in this context and highlight subtleties in demixing tensor and scalar modes. The generic multi-gravity feature of scalar mixing and its consequences for higher order interactions are discussed. In particular we show how the decoupling limit is qualitatively changed in theories of interacting spin-2 fields. We relate this to dRGT (de Rham, Gabadadze, Tolley) massive gravity, Hassan-Rosen bigravity and the multi-gravity constructions by Hinterbichler and Rosen. As an additional application we show that EBI (Eddington-Born-Infeld) bigravity and higher order generalisations thereof possess ghost-like instabilities.

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

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

PubMed

Tian, Xiaoqing; Xu, Jianbin; Wang, Xiaomu

2010-09-09

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

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.

Renewable Energy at NASA's Johnson Space Center

NASA Technical Reports Server (NTRS)

McDowall, Lindsay

2014-01-01

NASA's Johnson Space Center has implemented a great number of renewable energy systems. Renewable energy systems are necessary to research and implement if we humans are expected to continue to grow and thrive on this planet. These systems generate energy using renewable sources - water, wind, sun - things that we will not run out of. Johnson Space Center is helping to pave the way by installing and studying various renewable energy systems. The objective of this report will be to examine the completed renewable energy projects at NASA's Johnson Space Center for a time span of ten years, beginning in 2003 and ending in early 2014. This report will analyze the success of each project based on actual vs. projected savings and actual vs. projected efficiency. Additionally, both positive and negative experiences are documented so that lessons may be learned from past experiences. NASA is incorporating renewable energy wherever it can, including into buildings. According to the 2012 JSC Annual Sustainability Report, there are 321,660 square feet of green building space on JSC's campus. The two projects discussed here are major contributors to that statistic. These buildings were designed to meet various Leadership in Energy and Environmental Design (LEED) Certification criteria. LEED Certified buildings use 30 to 50 percent less energy and water compared to non-LEED buildings. The objectives of this project were to examine data from the renewable energy systems in two of the green buildings onsite - Building 12 and Building 20. In Building 12, data was examined from the solar photovoltaic arrays. In Building 20, data was examined from the solar water heater system. By examining the data from the two buildings, it could be determined if the renewable energy systems are operating efficiently. Objectives In Building 12, the data from the solar photovoltaic arrays shows that the system is continuously collecting energy from the sun, as shown by the graph below. Building 12 has two solar inverters, located on the second floor, that collected the data from the solar photovoltaic arrays. The data displayed here is the total energy produced by the system. These are cumulative amounts, so the last point on the graph shows all of the energy collected from the system since the start of its operation. The data shown here was manually collected from the solar inverters. However, the data is also automatically recorded through EBI. Through analysis of both sets of data it was determined that the EBI data was faulty. For example, from the manually collected data it can be determined that a total of 73 kWh of energy was collected between the dates of 1/16/2014 – 1/22/2014. The EBI data reports that approximately 17800 kWh of energy was collected during the same time frame. Not only does this exceed the time frame examined, but it also exceeds the total energy collected from the start of collection as recorded from the inverters. This leads to the belief that there is a malfunction with the automatic recording of the energy. In Building 20, data was examined from the solar water heater dating back many months and found that the pump for the solar water heater system was not operating properly, as exhibited in the graph shown below. The pump operates on a solar energy system, meaning that it collects energy throughout the day from the sun. Because of this, the system would stop operating shortly after the sun set because of a lack of sunlight. At that point, the graph should show a zero flow rate, but as exhibited in the graph below, that is not the case. It is clearly shown that the pump is continuously operating, even during the night. It was also observed that the majority of the time the pump would not turn on at all, despite good weather conditions. This led to the conclusion that the pump is malfunctioning, and needs to be examined and fixed.

Accessing and distributing EMBL data using CORBA (common object request broker architecture).

PubMed

Wang, L; Rodriguez-Tomé, P; Redaschi, N; McNeil, P; Robinson, A; Lijnzaad, P

2000-01-01

The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems.

Accessing and distributing EMBL data using CORBA (common object request broker architecture)

PubMed Central

Wang, Lichun; Rodriguez-Tomé, Patricia; Redaschi, Nicole; McNeil, Phil; Robinson, Alan; Lijnzaad, Philip

2000-01-01

Background: The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. Results: A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. Conclusions: The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems. PMID:11178259

A gene expression inflammatory signature specifically predicts multiple myeloma evolution and patients survival.

PubMed

Botta, C; Di Martino, M T; Ciliberto, D; Cucè, M; Correale, P; Rossi, M; Tagliaferri, P; Tassone, P

2016-12-16

Multiple myeloma (MM) is closely dependent on cross-talk between malignant plasma cells and cellular components of the inflammatory/immunosuppressive bone marrow milieu, which promotes disease progression, drug resistance, neo-angiogenesis, bone destruction and immune-impairment. We investigated the relevance of inflammatory genes in predicting disease evolution and patient survival. A bioinformatics study by Ingenuity Pathway Analysis on gene expression profiling dataset of monoclonal gammopathy of undetermined significance, smoldering and symptomatic-MM, identified inflammatory and cytokine/chemokine pathways as the most progressively affected during disease evolution. We then selected 20 candidate genes involved in B-cell inflammation and we investigated their role in predicting clinical outcome, through univariate and multivariate analyses (log-rank test, logistic regression and Cox-regression model). We defined an 8-genes signature (IL8, IL10, IL17A, CCL3, CCL5, VEGFA, EBI3 and NOS2) identifying each condition (MGUS/smoldering/symptomatic-MM) with 84% accuracy. Moreover, six genes (IFNG, IL2, LTA, CCL2, VEGFA, CCL3) were found independently correlated with patients' survival. Patients whose MM cells expressed high levels of Th1 cytokines (IFNG/LTA/IL2/CCL2) and low levels of CCL3 and VEGFA, experienced the longest survival. On these six genes, we built a prognostic risk score that was validated in three additional independent datasets. In this study, we provide proof-of-concept that inflammation has a critical role in MM patient progression and survival. The inflammatory-gene prognostic signature validated in different datasets clearly indicates novel opportunities for personalized anti-MM treatment.

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

PubMed

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

2017-02-15

Acute cerebral hypoperfusion following subarachnoid hemorrhage (SAH) is highly related to the pathogenesis of delayed cerebral ischemia (DCI), but the therapeutic option is poorly available. This study aimed to clarify the effect of milrinone (MIL) on cerebral blood flow (CBF) and related outcomes after experimental SAH. Twenty-seven male C57BL/6 mice were assigned to either sham surgery (SAH-sham; n=6), SAH induced by endovascular perforation (control; n=10), or SAH followed by cardiac support with intravenous MIL (n=11) performed 1.5-h after SAH induction. CBF, neurobehavioral function, occurrence of DCI were assessed by MR-continuous arterial spin labeling, daily neurological score testing, and diffusion- and T2-weighted MR images on days 1 and 3, respectively. Initial global CBF depression was notable in mice of control and MIL groups as compared to the SAH-sham group (P<0.05). MIL raised CBF in a dose-dependent manner (P<0.001), resulted in lower incidence of DCI (P=0.008) and better recovery from neurobehavioral decline than control (P<0.001). The CBF values on day 1 predicted DCI with a cut-off of 42.5ml/100g/min (82% specificity and 83% sensitivity), which was greater in mice treated with MIL than those of control (51.7 versus 37.6ml/100g/min; P<0.001). MIL improves post-SAH acute hypoperfusion that can lead to the prevention of DCI and functional worsening, acting as a neurocardiac protective agent against EBI. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

The BioStudies database-one stop shop for all data supporting a life sciences study.

PubMed

Sarkans, Ugis; Gostev, Mikhail; Athar, Awais; Behrangi, Ehsan; Melnichuk, Olga; Ali, Ahmed; Minguet, Jasmine; Rada, Juan Camillo; Snow, Catherine; Tikhonov, Andrew; Brazma, Alvis; McEntyre, Johanna

2018-01-04

BioStudies (www.ebi.ac.uk/biostudies) is a new public database that organizes data from biological studies. Typically, but not exclusively, a study is associated with a publication. BioStudies offers a simple way to describe the study structure, and provides flexible data deposition tools and data access interfaces. The actual data can be stored either in BioStudies or remotely, or both. BioStudies imports supplementary data from Europe PMC, and is a resource for authors and publishers for packaging data during the manuscript preparation process. It also can support data management needs of collaborative projects. The growth in multiomics experiments and other multi-faceted approaches to life sciences research mean that studies result in a diversity of data outputs in multiple locations. BioStudies presents a solution to ensuring that all these data and the associated publication(s) can be found coherently in the longer term. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets

PubMed Central

Griss, Johannes; Perez-Riverol, Yasset; Lewis, Steve; Tabb, David L.; Dianes, José A.; del-Toro, Noemi; Rurik, Marc; Walzer, Mathias W.; Kohlbacher, Oliver; Hermjakob, Henning; Wang, Rui; Vizcaíno, Juan Antonio

2016-01-01

Mass spectrometry (MS) is the main technology used in proteomics approaches. However, on average 75% of spectra analysed in an MS experiment remain unidentified. We propose to use spectrum clustering at a large-scale to shed a light on these unidentified spectra. PRoteomics IDEntifications database (PRIDE) Archive is one of the largest MS proteomics public data repositories worldwide. By clustering all tandem MS spectra publicly available in PRIDE Archive, coming from hundreds of datasets, we were able to consistently characterize three distinct groups of spectra: 1) incorrectly identified spectra, 2) spectra correctly identified but below the set scoring threshold, and 3) truly unidentified spectra. Using a multitude of complementary analysis approaches, we were able to identify less than 20% of the consistently unidentified spectra. The complete spectrum clustering results are available through the new version of the PRIDE Cluster resource (http://www.ebi.ac.uk/pride/cluster). This resource is intended, among other aims, to encourage and simplify further investigation into these unidentified spectra. PMID:27493588

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.

PubMed

Griss, Johannes; Perez-Riverol, Yasset; Lewis, Steve; Tabb, David L; Dianes, José A; Del-Toro, Noemi; Rurik, Marc; Walzer, Mathias W; Kohlbacher, Oliver; Hermjakob, Henning; Wang, Rui; Vizcaíno, Juan Antonio

2016-08-01

Mass spectrometry (MS) is the main technology used in proteomics approaches. However, on average 75% of spectra analysed in an MS experiment remain unidentified. We propose to use spectrum clustering at a large-scale to shed a light on these unidentified spectra. PRoteomics IDEntifications database (PRIDE) Archive is one of the largest MS proteomics public data repositories worldwide. By clustering all tandem MS spectra publicly available in PRIDE Archive, coming from hundreds of datasets, we were able to consistently characterize three distinct groups of spectra: 1) incorrectly identified spectra, 2) spectra correctly identified but below the set scoring threshold, and 3) truly unidentified spectra. Using a multitude of complementary analysis approaches, we were able to identify less than 20% of the consistently unidentified spectra. The complete spectrum clustering results are available through the new version of the PRIDE Cluster resource (http://www.ebi.ac.uk/pride/cluster). This resource is intended, among other aims, to encourage and simplify further investigation into these unidentified spectra.

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

PubMed

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

2014-12-01

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

Interacting spin-2 fields in the Stückelberg picture

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

Noller, Johannes; Ferreira, Pedro G.; Scargill, James H.C., E-mail: noller@physics.ox.ac.uk, E-mail: james.scargill@physics.ox.ac.uk, E-mail: p.ferreira1@physics.ox.ac.uk

2014-02-01

We revisit and extend the 'Effective field theory for massive gravitons' constructed by Arkani-Hamed, Georgi and Schwartz in the light of recent progress in constructing ghost-free theories with multiple interacting spin-2 fields. We show that there exist several dual ways of restoring gauge invariance in such multi-gravity theories, find a generalised Fierz-Pauli tuning condition relevant in this context and highlight subtleties in demixing tensor and scalar modes. The generic multi-gravity feature of scalar mixing and its consequences for higher order interactions are discussed. In particular we show how the decoupling limit is qualitatively changed in theories of interacting spin-2 fields.more » We relate this to dRGT (de Rham, Gabadadze, Tolley) massive gravity, Hassan-Rosen bigravity and the multi-gravity constructions by Hinterbichler and Rosen. As an additional application we show that EBI (Eddington-Born-Infeld) bigravity and higher order generalisations thereof possess ghost-like instabilities.« less

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

PubMed

Hamdallah, Myriam; Vargo, Sue; Herrera, Jennifer

2006-08-01

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

Comprehensive evaluation of disease- and trait-specific enrichment for eight functional elements among GWAS-identified variants.

PubMed

Markunas, Christina A; Johnson, Eric O; Hancock, Dana B

2017-07-01

Genome-wide association study (GWAS)-identified variants are enriched for functional elements. However, we have limited knowledge of how functional enrichment may differ by disease/trait and tissue type. We tested a broad set of eight functional elements for enrichment among GWAS-identified SNPs (p < 5×10 -8 ) from the NHGRI-EBI Catalog across seven disease/trait categories: cancer, cardiovascular disease, diabetes, autoimmune disease, psychiatric disease, neurological disease, and anthropometric traits. SNPs were annotated using HaploReg for the eight functional elements across any tissue: DNase sites, expression quantitative trait loci (eQTL), sequence conservation, enhancers, promoters, missense variants, sequence motifs, and protein binding sites. In addition, tissue-specific annotations were considered for brain vs. blood. Disease/trait SNPs were compared to a control set of 4809 SNPs matched to the GWAS SNPs (N = 1639) on allele frequency, gene density, distance to nearest gene, and linkage disequilibrium at ~3:1 ratio. Enrichment analyses were conducted using logistic regression, with Bonferroni correction. Overall, a significant enrichment was observed for all functional elements, except sequence motifs. Missense SNPs showed the strongest magnitude of enrichment. eQTLs were the only functional element significantly enriched across all diseases/traits. Magnitudes of enrichment were generally similar across diseases/traits, where enrichment was statistically significant. Blood vs. brain tissue effects on enrichment were dependent on disease/trait and functional element (e.g., cardiovascular disease: eQTLs P TissueDifference  = 1.28 × 10 -6 vs. enhancers P TissueDifference  = 0.94). Identifying disease/trait-relevant functional elements and tissue types could provide new insight into the underlying biology, by guiding a priori GWAS analyses (e.g., brain enhancer elements for psychiatric disease) or facilitating post hoc interpretation.

ForCent Model Development and Testing using the Enriched Background Isotope Study (EBIS) Experiment

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

Parton, William; Hanson, Paul J; Swanston, Chris

The ForCent forest ecosystem model was developed by making major revisions to the DayCent model including: (1) adding a humus organic pool, (2) incorporating a detailed root growth model, and (3) including plant phenological growth patterns. Observed plant production and soil respiration data from 1993 to 2000 were used to demonstrate that the ForCent model could accurately simulate ecosystem carbon dynamics for the Oak Ridge National Laboratory deciduous forest. A comparison of ForCent versus observed soil pool 14C signature (? 14C) data from the Enriched Background Isotope Study 14C experiment (1999-2006) shows that the model correctly simulates the temporal dynamicsmore » of the 14C label as it moved from the surface litter and roots into the mineral soil organic matter pools. ForCent model validation was performed by comparing the observed Enriched Background Isotope Study experimental data with simulated live and dead root biomass ? 14C data, and with soil respiration ? 14C (mineral soil, humus layer, leaf litter layer, and total soil respiration) data. Results show that the model correctly simulates the impact of the Enriched Background Isotope Study 14C experimental treatments on soil respiration ? 14C values for the different soil organic matter pools. Model results suggest that a two-pool root growth model correctly represents root carbon dynamics and inputs to the soil. The model fitting process and sensitivity analysis exposed uncertainty in our estimates of the fraction of mineral soil in the slow and passive pools, dissolved organic carbon flux out of the litter layer into the mineral soil, and mixing of the humus layer into the mineral soil layer.« 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

[Genome-wide screening of predicted sugar transporters in Neurospora crassa and the application in hexose fermentation by Saccharomyces cerevisiae].

PubMed

Gao, Jingfang; Wang, Bang; Han, Xiaoyun; Tian, Chaoguang

2017-01-25

The lignocellulolytic filamentous fungus Neurospora crassa is able to assimilate various mono- and oligo-saccharides. However, more than half of predicted sugar transporters in the genome are still waiting for functional elucidation. In this study, system analysis of substrate spectra of predicted sugar transporters in N. crassa was performed at genome-wide level. NCU01868 and NCU08152 have the capability of uptaking various hexose, which are named as NcHXT-1 and NcHXT-2 respectively. Their transport activities for glucose were further confirmed by fluorescence resonance energy transfer analysis. Over-expression of either NcHXT-1 or NcHXT-2 in the null-hexose-transporter yeast EBY.VW4000 restored the growth and ethanol fermentation under submerged fermentation with glucose, galactose, or mannose as the sole carbon source. NcHXT-1/-2 homologues were found in a variety of cellulolytic fungi. Functional identification of two filamentous fungal-conserved hexose transporters NcHXT-1/-2 via genome scanning would represent novel targets for ongoing efforts in engineering cellulolytic fungi and hexose fermentation in yeast.

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

PubMed Central

Berman, Helen; Henrick, Kim; Nakamura, Haruki; Markley, John L.

2007-01-01

The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the coordinates and related information for more than 38 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The founding members of the wwPDB are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan) [H.M. Berman, K. Henrick and H. Nakamura (2003) Nature Struct. Biol., 10, 980]. The BMRB group (USA) joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community. Additionally, the wwPDB provides a variety of services to a broad community of users. The wwPDB website at provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB. PMID:17142228

Tumour-derived Interleukin 35 promotes pancreatic ductal adenocarcinoma cell extravasation and metastasis by inducing ICAM1 expression

PubMed Central

Huang, Chongbiao; Li, Na; Li, Zengxun; Chang, Antao; Chen, Yanan; Zhao, Tiansuo; Li, Yang; Wang, Xiuchao; Zhang, Wei; Wang, Zhimin; Luo, Lin; Shi, Jingjing; Yang, Shengyu; Ren, He; Hao, Jihui

2017-01-01

Interleukin 35 (IL-35) is a novel member of the IL-12 family, consisting of an EBV-induced gene 3 (EBI3) subunit and a P35 subunit. IL-35 is an immune-suppressive cytokine mainly produced by regulatory T cells. However, the role of IL-35 in cancer metastasis and progression is not well understood. Here we demonstrate that IL-35 is overexpressed in human pancreatic ductal adenocarcinoma (PDAC) tissues, and that IL-35 overexpression is associated with poor prognosis in PDAC patients. IL-35 has critical roles in PDAC cell extravasation and metastasis by facilitating the adhesion to endothelial cells and transendothelial extravasation. Mechanistically, IL-35 promotes ICAM1 overexpression through a GP130-STAT1 signalling pathway, which facilitates endothelial adhesion and transendothelial migration via an ICAM1–fibrinogen–ICAM1 bridge. In an orthotopic xenograft model, IL-35 promotes spontaneous pancreatic cancer metastasis in an ICAM1-dependent manner. Together, our results indicate additional functions of IL-35 in promoting PDAC metastasis through mediating ICAM1 expression. PMID:28102193

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

PubMed

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

2016-04-01

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

Social reintegration of traumatic brain-injured: the French experience.

PubMed

Truelle, J-L; Wild, K Von; Onillon, M; Montreuil, M

2010-01-01

Traumatic Brain Injury (TBI) may lead to specific handicap, often hidden, mainly due to cognitive and behavioural sequelae. Social re-entry is a long-term, fluctuant and precarious process. The French experience will be illustrated by 6 initiatives answering to 6 challenges to do with TBI specificities:1. bridging the gap, between initial rehabilitation and community re-entry, via transitional units dealing with assessment, retraining, social/vocational orientation and follow-up. Today, there are 30 such units based on multidisciplinary teams.2. assessing recovery by TBI-specific and validated evaluation tools: EBIS holistic document, BNI Screening of higher cerebral functions, Glasgow outcome extended, and QOLIBRI, a TBI-specific quality of life tool.3. promoting specific re-entry programmes founded on limited medication, ecological neuro-psychological rehabilitation, exchange groups and workshops, violence prevention, continuity of care, environmental structuration, and "resocialisation".4. taking into account the "head injured family"5. facilitating recovery after sports-related concussion6. facing medico-legal consequences and compensation: In that perspective, we developed guidelines for TBI-specific expert appraisal, including mandatory neuro-psychological assessment, family interview and an annual forum gathering lawyers and health professionals.

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.

PubMed

Caldas, José; Gehlenborg, Nils; Kettunen, Eeva; Faisal, Ali; Rönty, Mikko; Nicholson, Andrew G; Knuutila, Sakari; Brazma, Alvis; Kaski, Samuel

2012-01-15

Genome-wide measurement of transcript levels is an ubiquitous tool in biomedical research. As experimental data continues to be deposited in public databases, it is becoming important to develop search engines that enable the retrieval of relevant studies given a query study. While retrieval systems based on meta-data already exist, data-driven approaches that retrieve studies based on similarities in the expression data itself have a greater potential of uncovering novel biological insights. We propose an information retrieval method based on differential expression. Our method deals with arbitrary experimental designs and performs competitively with alternative approaches, while making the search results interpretable in terms of differential expression patterns. We show that our model yields meaningful connections between biological conditions from different studies. Finally, we validate a previously unknown connection between malignant pleural mesothelioma and SIM2s suggested by our method, via real-time polymerase chain reaction in an independent set of mesothelioma samples. Supplementary data and source code are available from http://www.ebi.ac.uk/fg/research/rex.

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

PubMed Central

Alberti, Adriana; Poulain, Julie; Engelen, Stefan; Labadie, Karine; Romac, Sarah; Ferrera, Isabel; Albini, Guillaume; Aury, Jean-Marc; Belser, Caroline; Bertrand, Alexis; Cruaud, Corinne; Da Silva, Corinne; Dossat, Carole; Gavory, Frédérick; Gas, Shahinaz; Guy, Julie; Haquelle, Maud; Jacoby, E'krame; Jaillon, Olivier; Lemainque, Arnaud; Pelletier, Eric; Samson, Gaëlle; Wessner, Mark; Bazire, Pascal; Beluche, Odette; Bertrand, Laurie; Besnard-Gonnet, Marielle; Bordelais, Isabelle; Boutard, Magali; Dubois, Maria; Dumont, Corinne; Ettedgui, Evelyne; Fernandez, Patricia; Garcia, Espérance; Aiach, Nathalie Giordanenco; Guerin, Thomas; Hamon, Chadia; Brun, Elodie; Lebled, Sandrine; Lenoble, Patricia; Louesse, Claudine; Mahieu, Eric; Mairey, Barbara; Martins, Nathalie; Megret, Catherine; Milani, Claire; Muanga, Jacqueline; Orvain, Céline; Payen, Emilie; Perroud, Peggy; Petit, Emmanuelle; Robert, Dominique; Ronsin, Murielle; Vacherie, Benoit; Acinas, Silvia G.; Royo-Llonch, Marta; Cornejo-Castillo, Francisco M.; Logares, Ramiro; Fernández-Gómez, Beatriz; Bowler, Chris; Cochrane, Guy; Amid, Clara; Hoopen, Petra Ten; De Vargas, Colomban; Grimsley, Nigel; Desgranges, Elodie; Kandels-Lewis, Stefanie; Ogata, Hiroyuki; Poulton, Nicole; Sieracki, Michael E.; Stepanauskas, Ramunas; Sullivan, Matthew B.; Brum, Jennifer R.; Duhaime, Melissa B.; Poulos, Bonnie T.; Hurwitz, Bonnie L.; Acinas, Silvia G.; Bork, Peer; Boss, Emmanuel; Bowler, Chris; De Vargas, Colomban; Follows, Michael; Gorsky, Gabriel; Grimsley, Nigel; Hingamp, Pascal; Iudicone, Daniele; Jaillon, Olivier; Kandels-Lewis, Stefanie; Karp-Boss, Lee; Karsenti, Eric; Not, Fabrice; Ogata, Hiroyuki; Pesant, Stéphane; Raes, Jeroen; Sardet, Christian; Sieracki, Michael E.; Speich, Sabrina; Stemmann, Lars; Sullivan, Matthew B.; Sunagawa, Shinichi; Wincker, Patrick; Pesant, Stéphane; Karsenti, Eric; Wincker, Patrick

2017-01-01

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world’s planktonic ecosystems. PMID:28763055

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.

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

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

Brady, Brendan W.

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

Emerging role of IL-35 in inflammatory autoimmune diseases.

PubMed

Su, Lin-Chong; Liu, Xiao-Yan; Huang, An-Fang; Xu, Wang-Dong

2018-05-03

Interleukin 35 (IL-35) is the recently identified member of the IL-12 family of cytokines and provides the possibility to be a target for new therapies for autoimmune, inflammatory diseases. It is composed of an α chain (p35) and a β chain (EBI3). IL-35 mediates signaling by binding to its receptors, activates subsequent signaling pathways, and therefore, regulates the differentiation, function of T, B cells, macrophages, dendritic cells. Recent findings have shown abnormal expression of IL-35 in inflammatory autoimmune diseases, such as systemic lupus erythematosus, rheumatoid arthritis, inflammatory bowel disease, multiple sclerosis, type 1 diabetes, psoriasis, multiple sclerosis, autoimmune hepatitis, experimental autoimmune uveitis. In addition, functional analysis suggested that IL-35 is critical in the onset and development of these diseases. Therefore, the present study will systematically review what had been occurred regarding IL-35 in inflammatory autoimmune disease. The information collected will help to understand the biologic role of IL-35 in immune cells, and give information about the therapeutic potential of IL-35 in these diseases. Copyright © 2018. Published by Elsevier B.V.

Time-course proteomics dataset to monitor protein-bound methionine oxidation in Bacillus cereus ATCC 14579.

PubMed

Madeira, Jean-Paul; Alpha-Bazin, Béatrice; Armengaud, Jean; Duport, Catherine

2018-06-01

Aerobic respiratory growth generates endogenous reactive oxygen species (ROS). ROS oxidize protein-bound methionine residues into methionine sulfoxide. Methionine sulfoxide reductases catalyze the reduction of methionine sulfoxide to methionine in proteins. Here, we use high-throughput nanoLC-MS/MS methodology to establish detailed maps of oxidized proteins from Bacillus cereus ATCC 14579 ΔpBClin15 and its mutant for which the methionine sulfoxide reductase AB gene ( msrAB ) has been inactivated (Madeira et al., 2017) [1]. Lists of oxidized peptides and proteins identified at early exponential, late exponential and stationary growth phases are supplied in this article as data files. Raw data are deposited at the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers, PXD006169 and PDX006205 (http://www.ebi.ac/uk). Given the importance of methionine oxidation in several key cellular processes and its impact in the field of medical and food microbiology, this paper should be useful for further insightful redox studies in B. cereus and its numerous relatives.

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

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.

PubMed

Alberti, Adriana; Poulain, Julie; Engelen, Stefan; Labadie, Karine; Romac, Sarah; Ferrera, Isabel; Albini, Guillaume; Aury, Jean-Marc; Belser, Caroline; Bertrand, Alexis; Cruaud, Corinne; Da Silva, Corinne; Dossat, Carole; Gavory, Frédérick; Gas, Shahinaz; Guy, Julie; Haquelle, Maud; Jacoby, E'krame; Jaillon, Olivier; Lemainque, Arnaud; Pelletier, Eric; Samson, Gaëlle; Wessner, Mark; Acinas, Silvia G; Royo-Llonch, Marta; Cornejo-Castillo, Francisco M; Logares, Ramiro; Fernández-Gómez, Beatriz; Bowler, Chris; Cochrane, Guy; Amid, Clara; Hoopen, Petra Ten; De Vargas, Colomban; Grimsley, Nigel; Desgranges, Elodie; Kandels-Lewis, Stefanie; Ogata, Hiroyuki; Poulton, Nicole; Sieracki, Michael E; Stepanauskas, Ramunas; Sullivan, Matthew B; Brum, Jennifer R; Duhaime, Melissa B; Poulos, Bonnie T; Hurwitz, Bonnie L; Pesant, Stéphane; Karsenti, Eric; Wincker, Patrick

2017-08-01

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.

MetaboLights: towards a new COSMOS of metabolomics data management.

PubMed

Steinbeck, Christoph; Conesa, Pablo; Haug, Kenneth; Mahendraker, Tejasvi; Williams, Mark; Maguire, Eamonn; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Salek, Reza M; Griffin, Julian L

2012-10-01

Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years, including but not limited to resources such as MassBank in Japan and the Human Metabolome Database in Canada. Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://www.ebi.ac.uk/metabolights). It is the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. In October, the European COSMOS consortium will start its work on Metabolomics data standardization, publication and dissemination workflows. The NIH in the US is establishing 6-8 metabolomics services cores as well as a national metabolomics repository. This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics.

Re-use of standard ontologies in a water quality vocabulary (Invited)

NASA Astrophysics Data System (ADS)

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

2013-12-01

Observations provide the key constraints on environmental and earth science investigations. Where an investigation uses data sourced from multiple providers, data fusion depends on the observation classifications being comparable. Standard models for observation metadata are available (ISO 19156) which provide slots for key classifiers, in particular, the observed property and observation procedure. While universal use of common vocabularies might be desirable in achieving interoperability, this is unlikely in practice. However, semantic web vocabularies provide the means for asserting proximity and other relationships between items in different vocabularies, thus enabling mediation as an interoperability solution. Here we report on the development of a vocabulary for water quality observations in which recording relationships with existing vocabularies was a core strategy. The vocabulary is required to enable combination of a number of groundwater, surface water and marine water quality datasets on an ongoing basis. Our vocabulary model is based on the principle that observations generally report values of specific parameters which are defined by combining a number of facets. We start from Quantities, Units, Dimensions and Data Types (QUDT), which is an OWL ontology developed by NASA and TopQuadrant. We extend this with two additional classes, for Observed Property and Identified Object, and two linking properties, which enable us to create an observed property vocabulary for water quality applications. This ontology is comparable with models for observed properties developed as part of OGC's Observations and Measurements v1.0 standard, the INSPIRE Generic Conceptual Model, and may also be compared with the W3C SSN Ontology, which is based on the DOLCE Ultralite upper-ontology. Water quality observations commonly report concentrations of chemicals, both natural and contaminant, so we tie many of the Identified Objects to items from Chemical Entities of Biological Interest (ChEBI). ChEBI is an OWL-based dictionary of over 70 000 molecular entities, based on existing scientific work and linked through to International Union of Pure and Applied Chemistry (IUPAC) Nomenclature. Within the model the relevant classes, including those from QUDT, are declared to be subclasses of SKOS Concept, so the resulting vocabularies may be directly mapped to other SKOS-based vocabularies, such as from the NERC Vocabulary Service or the Marine Metadata Initiative, using SKOS predicates. Where the external vocabularies are not published with persistent URIs, such as CUAHSI, the mapping may be recorded more informally using annotations, or use proxy URIs for the external vocabulary. The resulting SKOS vocabularies demonstrate a separation of governance of key definitions such as units and quantities and chemical entities, ensuring reuse where possible and extending and adding detail where necessary.

Influence of Bi-related impurity states on the bandgap and spin-orbit splitting energy of dilute III-V-Bi alloys: InP1-xBix, InAs1-xBix, InSb1-xBix and GaSb1-xBix

NASA Astrophysics Data System (ADS)

Samajdar, D. P.; Dhar, S.

2016-01-01

Valence Band Anticrossing (VBAC) Model is used to calculate the changes in band structure of Bi containing alloys such as InP1-xBix, InAs1-xBix, InSb1-xBix and GaSb1-xBix due to the incorporation of dilute concentrations of bismuth. The coupling parameter CBi which gives the magnitude of interaction of Bi impurity states with the LH, HH and SO sub bands in VBAC depends on the increase in the HH/LH related energy level EHH/LH+, location of the Bi related impurity level EBi and valence band offset ΔEVBM between the endpoint compounds in the corresponding III-V-Bi. The reduction in band gap as well as the enhancement of the spin-orbit splitting energy is well explained using this model and the calculated results are compared with the results of Virtual Crystal Approximation (VCA) and Density Functional Theory (DFT) calculations, as well as with the available experimental data and are found to have good agreement. The incorporation of Bi mainly perturbs the valence band due to the interaction of the Bi impurity states with the HH, LH and SO bands. The lowering of the conduction band minimum (CBM) due to VCA is added with the upward movement of the HH/LH bands to get the total reduction in band gap for the bismides. The valence band shifts of 31.9, 32.5, 20.8 and 12.4 meV/at%Bi for InP1-xBix, InAs1-xBix, InSb1-xBix and GaSb1-xBix respectively constitute 65, 76, 59 and 31% of the total band gap reduction and the rest is the contribution of the conduction band shift. The spin-orbit splitting energy also shows significant increase with the maximum change in InPBi and the minimum in InSbBi. The same is true for Ga containing bismides if we make a comparison with the available values for GaAsBi and GaPBi with that of GaSbBi. It has also been observed that the increase in splitting energy is greater in case of the bismides such as InAsBi, InPBi and GaAsBi than the bismides such as InSbBi and GaSbBi with the parent substrates having higher values of splitting energy. This may be due to the proximity of the Bi related impurity level EBi with the SO bands of InAs, InP and GaAs.

The Ontology for Biomedical Investigations.

PubMed

Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H; Bug, Bill; Chibucos, Marcus C; Clancy, Kevin; Courtot, Mélanie; Derom, Dirk; Dumontier, Michel; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Gibson, Frank; Gonzalez-Beltran, Alejandra; Haendel, Melissa A; He, Yongqun; Heiskanen, Mervi; Hernandez-Boussard, Tina; Jensen, Mark; Lin, Yu; Lister, Allyson L; Lord, Phillip; Malone, James; Manduchi, Elisabetta; McGee, Monnie; Morrison, Norman; Overton, James A; Parkinson, Helen; Peters, Bjoern; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Scheuermann, Richard H; Schober, Daniel; Smith, Barry; Soldatova, Larisa N; Stoeckert, Christian J; Taylor, Chris F; Torniai, Carlo; Turner, Jessica A; Vita, Randi; Whetzel, Patricia L; Zheng, Jie

2016-01-01

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.

The Ontology for Biomedical Investigations

PubMed Central

Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H.; Chibucos, Marcus C.; Clancy, Kevin; Courtot, Mélanie; Derom, Dirk; Dumontier, Michel; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Gibson, Frank; Gonzalez-Beltran, Alejandra; Haendel, Melissa A.; He, Yongqun; Heiskanen, Mervi; Hernandez-Boussard, Tina; Jensen, Mark; Lin, Yu; Lister, Allyson L.; Lord, Phillip; Malone, James; Manduchi, Elisabetta; McGee, Monnie; Morrison, Norman; Overton, James A.; Parkinson, Helen; Peters, Bjoern; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Scheuermann, Richard H.; Schober, Daniel; Smith, Barry; Soldatova, Larisa N.; Stoeckert, Christian J.; Taylor, Chris F.; Torniai, Carlo; Turner, Jessica A.; Vita, Randi; Whetzel, Patricia L.; Zheng, Jie

2016-01-01

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl. PMID:27128319

GeneLab Analysis Working Group Kick-Off Meeting

NASA Technical Reports Server (NTRS)

Costes, Sylvain V.

2018-01-01

Goals to achieve for GeneLab AWG - GL vision - Review of GeneLab AWG charter Timeline and milestones for 2018 Logistics - Monthly Meeting - Workshop - Internship - ASGSR Introduction of team leads and goals of each group Introduction of all members Q/A Three-tier Client Strategy to Democratize Data Physiological changes, pathway enrichment, differential expression, normalization, processing metadata, reproducibility, Data federation/integration with heterogeneous bioinformatics external databases The GLDS currently serves over 100 omics investigations to the biomedical community via open access. In order to expand the scope of metadata record searches via the GLDS, we designed a metadata warehouse that collects and updates metadata records from external systems housing similar data. To demonstrate the capabilities of federated search and retrieval of these data, we imported metadata records from three open-access data systems into the GLDS metadata warehouse: NCBI's Gene Expression Omnibus (GEO), EBI's PRoteomics IDEntifications (PRIDE) repository, and the Metagenomics Analysis server (MG-RAST). Each of these systems defines metadata for omics data sets differently. One solution to bridge such differences is to employ a common object model (COM) to which each systems' representation of metadata can be mapped. Warehoused metadata records are then transformed at ETL to this single, common representation. Queries generated via the GLDS are then executed against the warehouse, and matching records are shown in the COM representation (Fig. 1). While this approach is relatively straightforward to implement, the volume of the data in the omics domain presents challenges in dealing with latency and currency of records. Furthermore, the lack of a coordinated has been federated data search for and retrieval of these kinds of data across other open-access systems, so that users are able to conduct biological meta-investigations using data from a variety of sources. Such meta-investigations are key to corroborating findings from many kinds of assays and translating them into systems biology knowledge and, eventually, therapeutics.

Land plants and DNA barcodes: short-term and long-term goals.

PubMed

Chase, Mark W; Salamin, Nicolas; Wilkinson, Mike; Dunwell, James M; Kesanakurthi, Rao Prasad; Haider, Nadia; Haidar, Nadia; Savolainen, Vincent

2005-10-29

Land plants have had the reputation of being problematic for DNA barcoding for two general reasons: (i) the standard DNA regions used in algae, animals and fungi have exceedingly low levels of variability and (ii) the typically used land plant plastid phylogenetic markers (e.g. rbcL, trnL-F, etc.) appear to have too little variation. However, no one has assessed how well current phylogenetic resources might work in the context of identification (versus phylogeny reconstruction). In this paper, we make such an assessment, particularly with two of the markers commonly sequenced in land plant phylogenetic studies, plastid rbcL and internal transcribed spacers of the large subunits of nuclear ribosomal DNA (ITS), and find that both of these DNA regions perform well even though the data currently available in GenBank/EBI were not produced to be used as barcodes and BLAST searches are not an ideal tool for this purpose. These results bode well for the use of even more variable regions of plastid DNA (such as, for example, psbA-trnH) as barcodes, once they have been widely sequenced. In the short term, efforts to bring land plant barcoding up to the standards being used now in other organisms should make swift progress. There are two categories of DNA barcode users, scientists in fields other than taxonomy and taxonomists. For the former, the use of mitochondrial and plastid DNA, the two most easily assessed genomes, is at least in the short term a useful tool that permits them to get on with their studies, which depend on knowing roughly which species or species groups they are dealing with, but these same DNA regions have important drawbacks for use in taxonomic studies (i.e. studies designed to elucidate species limits). For these purposes, DNA markers from uniparentally (usually maternally) inherited genomes can only provide half of the story required to improve taxonomic standards being used in DNA barcoding. In the long term, we will need to develop more sophisticated barcoding tools, which would be multiple, low-copy nuclear markers with sufficient genetic variability and PCR-reliability; these would permit the detection of hybrids and permit researchers to identify the 'genetic gaps' that are useful in assessing species limits.

Land plants and DNA barcodes: short-term and long-term goals

PubMed Central

Chase, Mark W; Salamin, Nicolas; Wilkinson, Mike; Dunwell, James M; Kesanakurthi, Rao Prasad; Haidar, Nadia; Savolainen, Vincent

2005-01-01

Land plants have had the reputation of being problematic for DNA barcoding for two general reasons: (i) the standard DNA regions used in algae, animals and fungi have exceedingly low levels of variability and (ii) the typically used land plant plastid phylogenetic markers (e.g. rbcL, trnL-F, etc.) appear to have too little variation. However, no one has assessed how well current phylogenetic resources might work in the context of identification (versus phylogeny reconstruction). In this paper, we make such an assessment, particularly with two of the markers commonly sequenced in land plant phylogenetic studies, plastid rbcL and internal transcribed spacers of the large subunits of nuclear ribosomal DNA (ITS), and find that both of these DNA regions perform well even though the data currently available in GenBank/EBI were not produced to be used as barcodes and BLAST searches are not an ideal tool for this purpose. These results bode well for the use of even more variable regions of plastid DNA (such as, for example, psbA-trnH) as barcodes, once they have been widely sequenced. In the short term, efforts to bring land plant barcoding up to the standards being used now in other organisms should make swift progress. There are two categories of DNA barcode users, scientists in fields other than taxonomy and taxonomists. For the former, the use of mitochondrial and plastid DNA, the two most easily assessed genomes, is at least in the short term a useful tool that permits them to get on with their studies, which depend on knowing roughly which species or species groups they are dealing with, but these same DNA regions have important drawbacks for use in taxonomic studies (i.e. studies designed to elucidate species limits). For these purposes, DNA markers from uniparentally (usually maternally) inherited genomes can only provide half of the story required to improve taxonomic standards being used in DNA barcoding. In the long term, we will need to develop more sophisticated barcoding tools, which would be multiple, low-copy nuclear markers with sufficient genetic variability and PCR-reliability; these would permit the detection of hybrids and permit researchers to identify the ‘genetic gaps’ that are useful in assessing species limits. PMID:16214746

Proteome data to explore the impact of pBClin15 on Bacillus cereus ATCC 14579.

PubMed

Madeira, Jean-Paul; Alpha-Bazin, Béatrice; Armengaud, Jean; Omer, Hélène; Duport, Catherine

2016-09-01

This data article reports changes in the cellular and exoproteome of B. cereus cured from pBClin15.Time-course changes of proteins were assessed by high-throughput nanoLC-MS/MS. We report all the peptides and proteins identified and quantified in B. cereus with and without pBClin15. Proteins were classified into functional groups using the information available in the KEGG classification and we reported their abundance in term of normalized spectral abundance factor. The repertoire of experimentally confirmed proteins of B. cereus presented here is the largest ever reported, and provides new insights into the interplay between pBClin15 and its host B. cereus ATCC 14579. The data reported here is related to a published shotgun proteomics analysis regarding the role of pBClin15, "Deciphering the interactions between the Bacillus cereus linear plasmid, pBClin15, and its host by high-throughput comparative proteomics" Madeira et al. [1]. All the associated mass spectrometry data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (http://www.ebi.ac.uk/pride/), with the dataset identifier PRIDE: PXD001568, PRIDE: PXD002788 and PRIDE: PXD002789.

Advances in genome studies in plants and animals.

PubMed

Appels, R; Nystrom-Persson, J; Keeble-Gagnere, G

2014-03-01

The area of plant and animal genomics covers the entire suite of issues in biology because it aims to determine the structure and function of genetic material. Although specific issues define research advances at an organism level, it is evident that many of the fundamental features of genome structure and the translation of encoded information to function share common ground. The Plant and Animal Genome (PAG) conference held in San Diego (California), in January each year provides an overview across all organisms at the genome level, and often it is evident that investments in the human area provide leadership, applications, and discoveries for researchers studying other organisms. This mini-review utilizes the plenary lectures as a basis for summarizing the trends in the genome-level studies of organisms, and the lectures include presentations by Ewan Birney (EBI, UK), Eric Green (NIH, USA), John Butler (NIST, USA), Elaine Mardis (Washington, USA), Caroline Dean (John Innes Centre, UK), Trudy Mackay (NC State University, USA), Sue Wessler (UC Riverside, USA), and Patrick Wincker (Genoscope, France). The work reviewed is based on published papers. Where unpublished information is cited, permission to include the information in this manuscript was obtained from the presenters.

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

NASA Astrophysics Data System (ADS)

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

2004-12-01

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

Advanced SPARQL querying in small molecule databases.

PubMed

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

2016-01-01

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

The HLA dictionary 2008: a summary of HLA-A, -B, -C, -DRB1/3/4/5, and -DQB1 alleles and their association with serologically defined HLA-A, -B, -C, -DR, and -DQ antigens.

PubMed

Holdsworth, R; Hurley, C K; Marsh, S G E; Lau, M; Noreen, H J; Kempenich, J H; Setterholm, M; Maiers, M

2009-02-01

The 2008 report of the human leukocyte antigen (HLA) data dictionary presents serologic equivalents of HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, and -DQB1 alleles. The dictionary is an update of the one published in 2004. The data summarize equivalents obtained by the World Health Organization Nomenclature Committee for Factors of the HLA System, the International Cell Exchange, UCLA, the National Marrow Donor Program, recent publications, and individual laboratories. The 2008 edition includes information on 832 new alleles (685 class I and 147 class II) and updated information on 766 previously listed alleles (577 class I and 189 class II). The tables list the alleles with remarks on the serologic patterns and the equivalents. The serological equivalents are listed as expert assigned types, and the data are useful for identifying potential stem cell donors who were typed by either serology or DNA-based methods. The tables with HLA equivalents are available as a searchable form on the IMGT/HLA database Web site (http://www.ebi.ac.uk/imgt/hla/dictionary.html).

Social Reintegration of Traumatic Brain-Injured: The French Experience

PubMed Central

Truelle, J.-L.; Wild, K. Von; Onillon, M.; Montreuil, M.

2010-01-01

Traumatic Brain Injury (TBI) may lead to specific handicap, often hidden, mainly due to cognitive and behavioural sequelae. Social re-entry is a long-term, fluctuant and precarious process. The French experience will be illustrated by 6 initiatives answering to 6 challenges to do with TBI specificities: 1. bridging the gap, between initial rehabilitation and community re-entry, via transitional units dealing with assessment, retraining, social/vocational orientation and follow-up. Today, there are 30 such units based on multidisciplinary teams. 2. assessing recovery by TBI-specific and validated evaluation tools: EBIS holistic document, BNI Screening of higher cerebral functions, Glasgow outcome extended, and QOLIBRI, a TBI-specific quality of life tool. 3. promoting specific re-entry programmes founded on limited medication, ecological neuro-psychological rehabilitation, exchange groups and workshops, violence prevention, continuity of care, environmental structuration, and “resocialisation”. 4. taking into account the “head injured family” 5. facilitating recovery after sports-related concussion 6. facing medico-legal consequences and compensation: In that perspective, we developed guidelines for TBI-specific expert appraisal, including mandatory neuro-psychological assessment, family interview and an annual forum gathering lawyers and health professionals. PMID:22028740

A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3

PubMed Central

Dietmann, Sabine; Park, Jong; Notredame, Cedric; Heger, Andreas; Lappe, Michael; Holm, Liisa

2001-01-01

The Dali Domain Dictionary (http://www.ebi.ac.uk/dali/domain) is a numerical taxonomy of all known structures in the Protein Data Bank (PDB). The taxonomy is derived fully automatically from measurements of structural, functional and sequence similarities. Here, we report the extension of the classification to match the traditional four hierarchical levels corresponding to: (i) supersecondary structural motifs (attractors in fold space), (ii) the topology of globular domains (fold types), (iii) remote homologues (functional families) and (iv) homologues with sequence identity above 25% (sequence families). The computational definitions of attractors and functional families are new. In September 2000, the Dali classification contained 10 531 PDB entries comprising 17 101 chains, which were partitioned into five attractor regions, 1375 fold types, 2582 functional families and 3724 domain sequence families. Sequence families were further associated with 99 582 unique homologous sequences in the HSSP database, which increases the number of effectively known structures several-fold. The resulting database contains the description of protein domain architecture, the definition of structural neighbours around each known structure, the definition of structurally conserved cores and a comprehensive library of explicit multiple alignments of distantly related protein families. PMID:11125048

Identification of copy number variation-driven genes for liver cancer via bioinformatics analysis.

PubMed

Lu, Xiaojie; Ye, Kun; Zou, Kailin; Chen, Jinlian

2014-11-01

To screen out copy number variation (CNV)-driven differentially expressed genes (DEGs) in liver cancer and advance our understanding of the pathogenesis, an integrated analysis of liver cancer-related CNV data from The Cancer Genome Atlas (TCGA) and gene expression data from EBI Array Express database were performed. The DEGs were identified by package limma based on the cut-off of |log2 (fold-change)|>0.585 and adjusted p-value<0.05. Using hg19 annotation information provided by UCSC, liver cancer-related CNVs were then screened out. TF-target gene interactions were also predicted with information from UCSC using DAVID online tools. As a result, 25 CNV-driven genes were obtained, including tripartite motif containing 28 (TRIM28) and RanBP-type and C3HC4-type zinc finger containing 1 (RBCK1). In the transcriptional regulatory network, 8 known cancer-related transcription factors (TFs) interacted with 21 CNV-driven genes, suggesting that the other 8 TFs may be involved in liver cancer. These genes may be potential biomarkers for early detection and prevention of liver cancer. These findings may improve our knowledge of the pathogenesis of liver cancer. Nevertheless, further experiments are still needed to confirm our findings.

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

PubMed

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

2014-11-15

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

Lower currents: a new choice for routine testing.

PubMed

Backes, John

2007-01-01

U.S. NFPA and AAMI standards both recommend a 10A ground bond test and, as has been described above, both 25A and 200mA are also recommended internationally as valid test currents for the in-service testing and inspection of medical electrical equipment. The reality is that both high and low test currents are of value to biomedical engineers and technicians in different circumstances. For benchtop testing in a workshop environment, where required test currents can be applied safely, then it seems likely that high current testing will remain the preferred option. However, for in-service test applications, where the portability and versatility of the tester is a key requirement, modern electronic technology now means that low current testing can now be applied effectively and safely. In summary, by using a low-energy, high current pulse prior to 200 mA test current, the lower test current is preferred for routine field maintenance as this can mean: Increased safety of the operator. Reduced risk of damage to the in-service medical equipment. Smaller test instruments to include valid ground bond measurements. Battery operated test equipment. Increased flexibility of the test engineer due to lightweight test equipment. Cost reduction due to reduced down time of medical equipment. More economical availability of test equipment.

Implementation of an efficacious intervention for high risk women in Mexico: protocol for a multi-site randomized trial with a parallel study of organizational factors.

PubMed

Patterson, Thomas L; Semple, Shirley J; Chavarin, Claudia V; Mendoza, Doroteo V; Santos, Lorena E; Chaffin, Mark; Palinkas, Lawrence A; Strathdee, Steffanie A; Aarons, Gregory A

2012-10-29

Studies of implementation of efficacious human immunodeficiency virus (HIV) prevention interventions are rare, especially in resource-poor settings, but important, because they have the potential to increase the impact of interventions by improving uptake and sustainability. Few studies have focused on provider and organizational factors that may influence uptake and fidelity to core intervention components. Using a hybrid design, we will study the implementation of an efficacious intervention to reduce sexually transmitted infections (STIs) among female sex workers (FSWs) in 12 cities across Mexico. Our protocol will test a 'train-the-trainer' implementation model for transporting the Mujer Segura (Healthy Woman) intervention into community-based organizations (CBOs). We have partnered with Mexican Foundation for Family Planning (Mexfam), a non-governmental organization that has CBOs throughout Mexico. At each CBO, trained ethnographers will survey CBO staff on characteristics of their organization and on their attitudes toward their CBO and toward the implementation of evidence-based interventions (EBIs). Then, after CBO staff recruit a sample of 80 eligible FSWs and deliver a standard-care, didactic intervention to 40 women randomly selected from that pool, a Mexfam staff person will be trained in the Mujer Segura intervention and will then train other counselors to deliver Mujer Segura to the 40 remaining participating FSWs. FSW participants will receive a baseline behavioral assessment and be tested for HIV and STIs (syphilis, gonorrhea, and chlamydia); they will be reassessed at six months post-intervention to measure for possible intervention effects. At the same time, both qualitative and quantitative data will be collected on the implementation process, including measures of counselors' fidelity to the intervention model. After data collection at each CBO is complete, the relative efficacy of the Mujer Segura intervention will be analyzed, and across CBOs, correlations will be examined between individual and organizational provider characteristics and intervention efficacy. This cooperative, bi-national research study will provide critical insights into barriers and facilitating factors associated with implementing interventions in CBOs using the 'train the trainer' model. Our work builds on similar scale-up strategies that have been effective in the United States. This study has the potential to increase our knowledge of the generalizability of such strategies across health issues, national contexts, and organizational contexts. NCT01465607.

Implementation of an efficacious intervention for high risk women in Mexico: protocol for a multi-site randomized trial with a parallel study of organizational factors

PubMed Central

2012-01-01

Background Studies of implementation of efficacious human immunodeficiency virus (HIV) prevention interventions are rare, especially in resource-poor settings, but important, because they have the potential to increase the impact of interventions by improving uptake and sustainability. Few studies have focused on provider and organizational factors that may influence uptake and fidelity to core intervention components. Using a hybrid design, we will study the implementation of an efficacious intervention to reduce sexually transmitted infections (STIs) among female sex workers (FSWs) in 12 cities across Mexico. Our protocol will test a ‘train-the-trainer’ implementation model for transporting the Mujer Segura (Healthy Woman) intervention into community-based organizations (CBOs). Methods We have partnered with Mexican Foundation for Family Planning (Mexfam), a non-governmental organization that has CBOs throughout Mexico. At each CBO, trained ethnographers will survey CBO staff on characteristics of their organization and on their attitudes toward their CBO and toward the implementation of evidence-based interventions (EBIs). Then, after CBO staff recruit a sample of 80 eligible FSWs and deliver a standard-care, didactic intervention to 40 women randomly selected from that pool, a Mexfam staff person will be trained in the Mujer Segura intervention and will then train other counselors to deliver Mujer Segura to the 40 remaining participating FSWs. FSW participants will receive a baseline behavioral assessment and be tested for HIV and STIs (syphilis, gonorrhea, and chlamydia); they will be reassessed at six months post-intervention to measure for possible intervention effects. At the same time, both qualitative and quantitative data will be collected on the implementation process, including measures of counselors’ fidelity to the intervention model. After data collection at each CBO is complete, the relative efficacy of the Mujer Segura intervention will be analyzed, and across CBOs, correlations will be examined between individual and organizational provider characteristics and intervention efficacy. Discussion This cooperative, bi-national research study will provide critical insights into barriers and facilitating factors associated with implementing interventions in CBOs using the ‘train the trainer’ model. Our work builds on similar scale-up strategies that have been effective in the United States. This study has the potential to increase our knowledge of the generalizability of such strategies across health issues, national contexts, and organizational contexts. Trial registration NCT01465607 PMID:23107285

Human growth is associated with distinct patterns of gene expression in evolutionarily conserved networks

PubMed Central

2013-01-01

Background A co-ordinated tissue-independent gene expression profile associated with growth is present in rodent models and this is hypothesised to extend to all mammals. Growth in humans has similarities to other mammals but the return to active long bone growth in the pubertal growth spurt is a distinctly human growth event. The aim of this study was to describe gene expression and biological pathways associated with stages of growth in children and to assess tissue-independent expression patterns in relation to human growth. Results We conducted gene expression analysis on a library of datasets from normal children with age annotation, collated from the NCBI Gene Expression Omnibus (GEO) and EBI Arrayexpress databases. A primary data set was generated using cells of lymphoid origin from normal children; the expression of 688 genes (ANOVA false discovery rate modified p-value, q < 0.1) was associated with age, and subsets of these genes formed clusters that correlated with the phases of growth – infancy, childhood, puberty and final height. Network analysis on these clusters identified evolutionarily conserved growth pathways (NOTCH, VEGF, TGFB, WNT and glucocorticoid receptor – Hyper-geometric test, q < 0.05). The greatest degree of network ‘connectivity’ and hence functional significance was present in infancy (Wilcoxon test, p < 0.05), which then decreased through to adulthood. These observations were confirmed in a separate validation data set from lymphoid tissue. Similar biological pathways were observed to be associated with development-related gene expression in other tissues (conjunctival epithelia, temporal lobe brain tissue and bone marrow) suggesting the existence of a tissue-independent genetic program for human growth and maturation. Conclusions Similar evolutionarily conserved pathways have been associated with gene expression and child growth in multiple tissues. These expression profiles associate with the developmental phases of growth including the return to active long bone growth in puberty, a distinctly human event. These observations also have direct medical relevance to pathological changes that induce disease in children. Taking into account development-dependent gene expression profiles for normal children will be key to the appropriate selection of genes and pathways as potential biomarkers of disease or as drug targets. PMID:23941278

Identification of a Novel L-rhamnose Uptake Transporter in the Filamentous Fungus Aspergillus niger.

PubMed

Sloothaak, Jasper; Odoni, Dorett I; Martins Dos Santos, Vitor A P; Schaap, Peter J; Tamayo-Ramos, Juan Antonio

2016-12-01

The study of plant biomass utilization by fungi is a research field of great interest due to its many implications in ecology, agriculture and biotechnology. Most of the efforts done to increase the understanding of the use of plant cell walls by fungi have been focused on the degradation of cellulose and hemicellulose, and transport and metabolism of their constituent monosaccharides. Pectin is another important constituent of plant cell walls, but has received less attention. In relation to the uptake of pectic building blocks, fungal transporters for the uptake of galacturonic acid recently have been reported in Aspergillus niger and Neurospora crassa. However, not a single L-rhamnose (6-deoxy-L-mannose) transporter has been identified yet in fungi or in other eukaryotic organisms. L-rhamnose is a deoxy-sugar present in plant cell wall pectic polysaccharides (mainly rhamnogalacturonan I and rhamnogalacturonan II), but is also found in diverse plant secondary metabolites (e.g. anthocyanins, flavonoids and triterpenoids), in the green seaweed sulfated polysaccharide ulvan, and in glycan structures from viruses and bacteria. Here, a comparative plasmalemma proteomic analysis was used to identify candidate L-rhamnose transporters in A. niger. Further analysis was focused on protein ID 1119135 (RhtA) (JGI A. niger ATCC 1015 genome database). RhtA was classified as a Family 7 Fucose: H+ Symporter (FHS) within the Major Facilitator Superfamily. Family 7 currently includes exclusively bacterial transporters able to use different sugars. Strong indications for its role in L-rhamnose transport were obtained by functional complementation of the Saccharomyces cerevisiae EBY.VW.4000 strain in growth studies with a range of potential substrates. Biochemical analysis using L-[3H(G)]-rhamnose confirmed that RhtA is a L-rhamnose transporter. The RhtA gene is located in tandem with a hypothetical alpha-L-rhamnosidase gene (rhaB). Transcriptional analysis of rhtA and rhaB confirmed that both genes have a coordinated expression, being strongly and specifically induced by L-rhamnose, and controlled by RhaR, a transcriptional regulator involved in the release and catabolism of the methyl-pentose. RhtA is the first eukaryotic L-rhamnose transporter identified and functionally validated to date.

Identification of a Novel L-rhamnose Uptake Transporter in the Filamentous Fungus Aspergillus niger

PubMed Central

Sloothaak, Jasper; Odoni, Dorett I.; Martins dos Santos, Vitor A. P.; Schaap, Peter J.

2016-01-01

The study of plant biomass utilization by fungi is a research field of great interest due to its many implications in ecology, agriculture and biotechnology. Most of the efforts done to increase the understanding of the use of plant cell walls by fungi have been focused on the degradation of cellulose and hemicellulose, and transport and metabolism of their constituent monosaccharides. Pectin is another important constituent of plant cell walls, but has received less attention. In relation to the uptake of pectic building blocks, fungal transporters for the uptake of galacturonic acid recently have been reported in Aspergillus niger and Neurospora crassa. However, not a single L-rhamnose (6-deoxy-L-mannose) transporter has been identified yet in fungi or in other eukaryotic organisms. L-rhamnose is a deoxy-sugar present in plant cell wall pectic polysaccharides (mainly rhamnogalacturonan I and rhamnogalacturonan II), but is also found in diverse plant secondary metabolites (e.g. anthocyanins, flavonoids and triterpenoids), in the green seaweed sulfated polysaccharide ulvan, and in glycan structures from viruses and bacteria. Here, a comparative plasmalemma proteomic analysis was used to identify candidate L-rhamnose transporters in A. niger. Further analysis was focused on protein ID 1119135 (RhtA) (JGI A. niger ATCC 1015 genome database). RhtA was classified as a Family 7 Fucose: H+ Symporter (FHS) within the Major Facilitator Superfamily. Family 7 currently includes exclusively bacterial transporters able to use different sugars. Strong indications for its role in L-rhamnose transport were obtained by functional complementation of the Saccharomyces cerevisiae EBY.VW.4000 strain in growth studies with a range of potential substrates. Biochemical analysis using L-[3H(G)]-rhamnose confirmed that RhtA is a L-rhamnose transporter. The RhtA gene is located in tandem with a hypothetical alpha-L-rhamnosidase gene (rhaB). Transcriptional analysis of rhtA and rhaB confirmed that both genes have a coordinated expression, being strongly and specifically induced by L-rhamnose, and controlled by RhaR, a transcriptional regulator involved in the release and catabolism of the methyl-pentose. RhtA is the first eukaryotic L-rhamnose transporter identified and functionally validated to date. PMID:27984587

The IMGT/HLA database

PubMed Central

Robinson, James; Waller, Matthew J.; Fail, Sylvie C.; McWilliam, Hamish; Lopez, Rodrigo; Parham, Peter; Marsh, Steven G. E.

2009-01-01

It is 10 years since the IMGT/HLA database was released, providing the HLA community with a searchable repository of highly curated HLA sequences. The HLA complex is located within the 6p21.3 region of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and are highly polymorphic. The naming of these HLA genes and alleles, and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to this data through the website http://www.ebi.ac.uk/imgt/hla/. The first release contained 964 sequences, the most recent release 3300 sequences, with around 450 new sequences been added each year. The tools provided on the website have been updated to allow more complex alignments, which include genomic sequence data, as well as the development of tools for probe and primer design and the inclusion of data from the HLA Dictionary. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the HLA community, and the wider research and clinical communities. PMID:18838392

PPDMs-a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains.

PubMed

Kruger, Felix A; Gaulton, Anna; Nowotka, Michal; Overington, John P

2015-03-01

PPDMs is a resource that maps small molecule bioactivities to protein domains from the Pfam-A collection of protein families. Small molecule bioactivities mapped to protein domains add important precision to approaches that use protein sequence searches alignments to assist applications in computational drug discovery and systems and chemical biology. We have previously proposed a mapping heuristic for a subset of bioactivities stored in ChEMBL with the Pfam-A domain most likely to mediate small molecule binding. We have since refined this mapping using a manual procedure. Here, we present a resource that provides up-to-date mappings and the possibility to review assigned mappings as well as to participate in their assignment and curation. We also describe how mappings provided through the PPDMs resource are made accessible through the main schema of the ChEMBL database. The PPDMs resource and curation interface is available at https://www.ebi.ac.uk/chembl/research/ppdms/pfam_maps. The source-code for PPDMs is available under the Apache license at https://github.com/chembl/pfam_maps. Source code is available at https://github.com/chembl/pfam_map_loader to demonstrate the integration process with the main schema of ChEMBL. © The Author 2014. Published by Oxford University Press.

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

PubMed

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

2017-06-15

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

Advances in Toxico-Cheminformatics: Supporting a New ...

EPA Pesticide Factsheets

EPA’s National Center for Computational Toxicology is building capabilities to support a new paradigm for toxicity screening and prediction through the harnessing of legacy toxicity data, creation of data linkages, and generation of new high-throughput screening (HTS) data. The DSSTox project is working to improve public access to quality structure-annotated chemical toxicity information in less summarized forms than traditionally employed in SAR modeling, and in ways that facilitate both data-mining and read-across. Both DSSTox Structure-Files and the dedicated on-line DSSTox Structure-Browser are enabling seamless structure-based searching and linkages to and from previously isolated, chemically indexed public toxicity data resources (e.g., NTP, EPA IRIS, CPDB). Most recently, structure-enabled search capabilities have been extended to chemical exposure-related microarray experiments in the public EBI Array Express database, additionally linking this resource to the NIEHS CEBS toxicogenomics database. The public DSSTox chemical and bioassay inventory has been recently integrated into PubChem, allowing a user to take full advantage of PubChem structure-activity and bioassay clustering features. The DSSTox project is providing cheminformatics support for EPA’s ToxCastTM project, as well as supporting collaborations with the National Toxicology Program (NTP) HTS and the NIH Chemical Genomics Center (NCGC). Phase I of the ToxCastTM project is generating HT

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

PubMed

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

2018-06-01

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

The Proteins API: accessing key integrated protein and genome information

PubMed Central

Antunes, Ricardo; Alpi, Emanuele; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd

2017-01-01

Abstract The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to ‘talk’ to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc). PMID:28383659

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

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

Friedberg, Iddo

2015-01-21

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

Statistical correction of the Winner’s Curse explains replication variability in quantitative trait genome-wide association studies

PubMed Central

Pe’er, Itsik

2017-01-01

Genome-wide association studies (GWAS) have identified hundreds of SNPs responsible for variation in human quantitative traits. However, genome-wide-significant associations often fail to replicate across independent cohorts, in apparent inconsistency with their apparent strong effects in discovery cohorts. This limited success of replication raises pervasive questions about the utility of the GWAS field. We identify all 332 studies of quantitative traits from the NHGRI-EBI GWAS Database with attempted replication. We find that the majority of studies provide insufficient data to evaluate replication rates. The remaining papers replicate significantly worse than expected (p < 10−14), even when adjusting for regression-to-the-mean of effect size between discovery- and replication-cohorts termed the Winner’s Curse (p < 10−16). We show this is due in part to misreporting replication cohort-size as a maximum number, rather than per-locus one. In 39 studies accurately reporting per-locus cohort-size for attempted replication of 707 loci in samples with similar ancestry, replication rate matched expectation (predicted 458, observed 457, p = 0.94). In contrast, ancestry differences between replication and discovery (13 studies, 385 loci) cause the most highly-powered decile of loci to replicate worse than expected, due to difference in linkage disequilibrium. PMID:28715421

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

PubMed

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

2017-11-15

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

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

PubMed

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

2017-07-01

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

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

PubMed

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

2016-01-01

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

Interleukin-35: Expanding Its Job Profile

PubMed Central

Sawant, Deepali V.; Hamilton, Kristia

2015-01-01

Counter-regulation afforded by specialized regulatory cell populations and immunosuppressive cytokines is critical for balancing immune outcome. The inhibitory potential of the established suppressive cytokines, IL-10 and TGFβ, has been well elucidated in diverse inflammatory scenarios in conjunction with their key roles in Treg development and function. Despite the early predictions for an immunomodulatory role for the Ebi3/p35 heterodimer in placental trophoblasts, IL-35 biology remained elusive until 2007 when it was established as a Treg-restricted inhibitory cytokine. Since then, Treg-derived IL-35 has been shown to exhibit its suppressive activities in a range of autoimmune diseases and cancer models. Recent studies are beginning to explore other cellular sources of IL-35, such as Bregs and CD8+ Tregs. Despite these new cellular sources and targets, the mode of IL-35 suppression remains restricted to inhibition of proliferation and induction of an IL-35-producing induced regulatory T cell population referred to as iTr35. In this review, we explore the early beginnings, status quo, and future prospects of IL-35 biology. The unparalleled opportunity of targeting multiple immunosuppressive populations (Tregs, Bregs, CD8+ Tregs) through IL-35 is highly exciting and offers tremendous promise from a translational standpoint, particularly for cancer immunotherapies. PMID:25919641

Expression Atlas: gene and protein expression across multiple studies and organisms

PubMed Central

Tang, Y Amy; Bazant, Wojciech; Burke, Melissa; Fuentes, Alfonso Muñoz-Pomer; George, Nancy; Koskinen, Satu; Mohammed, Suhaib; Geniza, Matthew; Preece, Justin; Jarnuczak, Andrew F; Huber, Wolfgang; Stegle, Oliver; Brazma, Alvis; Petryszak, Robert

2018-01-01

Abstract Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species and contexts, such as tissue, developmental stage, disease or cell type. The available public and controlled access data sets from different sources are curated and re-analysed using standardized, open source pipelines and made available for queries, download and visualization. As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants. Data from large-scale RNA sequencing studies including Blueprint, PCAWG, ENCODE, GTEx and HipSci can be visualized next to each other. In Expression Atlas, users can query genes or gene-sets of interest and explore their expression across or within species, tissues, developmental stages in a constitutive or differential context, representing the effects of diseases, conditions or experimental interventions. All processed data matrices are available for direct download in tab-delimited format or as R-data. In addition to the web interface, data sets can now be searched and downloaded through the Expression Atlas R package. Novel features and visualizations include the on-the-fly analysis of gene set overlaps and the option to view gene co-expression in experiments investigating constitutive gene expression across tissues or other conditions. PMID:29165655

Gramene 2016: comparative plant genomics and pathway resources

PubMed Central

Tello-Ruiz, Marcela K.; Stein, Joshua; Wei, Sharon; Preece, Justin; Olson, Andrew; Naithani, Sushma; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Jiao, Yinping; Mulvaney, Joseph; Kumari, Sunita; Chougule, Kapeel; Elser, Justin; Wang, Bo; Thomason, James; Bolser, Daniel M.; Kerhornou, Arnaud; Walts, Brandon; Fonseca, Nuno A.; Huerta, Laura; Keays, Maria; Tang, Y. Amy; Parkinson, Helen; Fabregat, Antonio; McKay, Sheldon; Weiser, Joel; D'Eustachio, Peter; Stein, Lincoln; Petryszak, Robert; Kersey, Paul J.; Jaiswal, Pankaj; Ware, Doreen

2016-01-01

Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials. PMID:26553803

Oxysterols and Their Cellular Effectors

PubMed Central

Olkkonen, Vesa M.; Béaslas, Olivier; Nissilä, Eija

2012-01-01

Oxysterols are oxidized 27-carbon cholesterol derivatives or by-products of cholesterol biosynthesis, with a spectrum of biologic activities. Several oxysterols have cytotoxic and pro-apoptotic activities, the ability to interfere with the lateral domain organization, and packing of membrane lipids. These properties may account for their suggested roles in the pathology of diseases such as atherosclerosis, age-onset macular degeneration and Alzheimer’s disease. Oxysterols also have the capacity to induce inflammatory responses and play roles in cell differentiation processes. The functions of oxysterols as intermediates in the synthesis of bile acids and steroid hormones, and as readily transportable forms of sterol, are well established. Furthermore, their actions as endogenous regulators of gene expression in lipid metabolism via liver X receptors and the Insig (insulin-induced gene) proteins have been investigated in detail. The cytoplasmic oxysterol-binding protein (OSBP) homologues form a group of oxysterol/cholesterol sensors that has recently attracted a lot of attention. However, their mode of action is, as yet, poorly understood. Retinoic acid receptor-related orphan receptors (ROR) α and γ, and Epstein-Barr virus induced gene 2 (EBI2) have been identified as novel oxysterol receptors, revealing new physiologic oxysterol effector mechanisms in development, metabolism, and immunity, and evoking enhanced interest in these compounds in the field of biomedicine. PMID:24970128

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

PubMed

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

2018-05-03

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

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

PubMed Central

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

2018-01-01

Abstract The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community. PMID:29126148

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

PubMed

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

2017-07-03

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

PDBe: Protein Data Bank in Europe

PubMed Central

Velankar, Sameer; Alhroub, Younes; Alili, Anaëlle; Best, Christoph; Boutselakis, Harry C.; Caboche, Ségolène; Conroy, Matthew J.; Dana, Jose M.; van Ginkel, Glen; Golovin, Adel; Gore, Swanand P.; Gutmanas, Aleksandras; Haslam, Pauline; Hirshberg, Miriam; John, Melford; Lagerstedt, Ingvar; Mir, Saqib; Newman, Laurence E.; Oldfield, Tom J.; Penkett, Chris J.; Pineda-Castillo, Jorge; Rinaldi, Luana; Sahni, Gaurav; Sawka, Grégoire; Sen, Sanchayita; Slowley, Robert; Sousa da Silva, Alan Wilter; Suarez-Uruena, Antonio; Swaminathan, G. Jawahar; Symmons, Martyn F.; Vranken, Wim F.; Wainwright, Michael; Kleywegt, Gerard J.

2011-01-01

The Protein Data Bank in Europe (PDBe; pdbe.org) is actively involved in managing the international archive of biomacromolecular structure data as one of the partners in the Worldwide Protein Data Bank (wwPDB; wwpdb.org). PDBe also develops new tools to make structural data more widely and more easily available to the biomedical community. PDBe has developed a browser to access and analyze the structural archive using classification systems that are familiar to chemists and biologists. The PDBe web pages that describe individual PDB entries have been enhanced through the introduction of plain-English summary pages and iconic representations of the contents of an entry (PDBprints). In addition, the information available for structures determined by means of NMR spectroscopy has been expanded. Finally, the entire web site has been redesigned to make it substantially easier to use for expert and novice users alike. PDBe works closely with other teams at the European Bioinformatics Institute (EBI) and in the international scientific community to develop new resources with value-added information. The SIFTS initiative is an example of such a collaboration—it provides extensive mapping data between proteins whose structures are available from the PDB and a host of other biomedical databases. SIFTS is widely used by major bioinformatics resources. PMID:21045060

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

PubMed

Gonçalves, Emanuel; Mirlach, Franz; Saez-Rodriguez, Julio

2013-01-01

There is an increasing number of software packages to analyse biological experimental data in the R environment. In particular, Bioconductor, a repository of curated R packages, is one of the most comprehensive resources for bioinformatics and biostatistics. The use of these packages is increasing, but it requires a basic understanding of the R language, as well as the syntax of the specific package used. The availability of user graphical interfaces for these packages would decrease the learning curve and broaden their application. Here, we present a Cytoscape app termed Cyrface that allows Cytoscape apps to connect to any function and package developed in R. Cyrface can be used to run R packages from within the Cytoscape environment making use of a graphical user interface. Moreover, it can link R packages with the capabilities of Cytoscape and its apps, in particular network visualization and analysis. Cyrface's utility has been demonstrated for two Bioconductor packages ( CellNOptR and DrugVsDisease), and here we further illustrate its usage by implementing a workflow of data analysis and visualization. Download links, installation instructions and user guides can be accessed from the Cyrface's homepage ( http://www.ebi.ac.uk/saezrodriguez/cyrface/) and from the Cytoscape app store ( http://apps.cytoscape.org/apps/cyrface).

Hot-spot heating susceptibility due to reverse bias operating conditions

NASA Technical Reports Server (NTRS)

Gonzalez, C. C.

1985-01-01

Because of field experience (indicating that cell and module degradation could occur as a result of hot spot heating), a laboratory test was developed at JPL to determine hot spot susceptibility of modules. The initial hot spot testing work at JPL formed a foundation for the test development. Test parameters are selected as follows. For high shunt resistance cells, the applied back bias test current is set equal to the test cell current at maximum power. For low shunt resistance cells, the test current is set equal to the cell short circuit current. The shadow level is selected to conform to that which would lead to maximum back bias voltage under the appropriate test current level. The test voltage is determined by the bypass diode frequency. The test conditions are meant to simulate the thermal boundary conditions for 100 mW/sq cm, 40C ambient environment. The test lasts 100 hours. A key assumption made during the development of the test is that no current imbalance results from the connecting of multiparallel cell strings. Therefore, the test as originally developed was applicable for single string case only.

20 CFR 216.15 - Special current connection test.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Special current connection test. 216.15... ELIGIBILITY FOR AN ANNUITY Current Connection With the Railroad Industry § 216.15 Special current connection test. (a) For survivor annuities. An employee who does not have a current connection under the regular...