Creating an Online Library To Support a Virtual Learning Community.

ERIC Educational Resources Information Center

Sandelands, Eric

1998-01-01

International Management Centres (IMC), an independent business school, and Anbar Electronic Intelligence (AEI), a database publisher, have created a virtual library for IMC's virtual business school. Topics discussed include action learning; IMC's partnership with AEI; the virtual university model; designing virtual library resources; and…

Alignment of systematic reviews published in the Cochrane Database of Systematic Reviews and the Database of Abstracts and Reviews of Effectiveness with global burden-of-disease data: a bibliographic analysis.

PubMed

Yoong, Sze Lin; Hall, Alix; Williams, Christopher M; Skelton, Eliza; Oldmeadow, Christopher; Wiggers, John; Karimkhani, Chante; Boyers, Lindsay N; Dellavalle, Robert P; Hilton, John; Wolfenden, Luke

2015-07-01

Systematic reviews of high-quality evidence are used to inform policy and practice. To improve community health, the production of such reviews should align with burden of disease. This study aims to assess if the volume of research output from systematic reviews proportionally aligns with burden of disease assessed using percentages of mortality and disability-adjusted life years (DALYs). A cross-sectional audit of reviews published between January 2012 and August 2013 in the Cochrane Database of Systematic Reviews (CDSR) and Database of Abstracts of Reviews of Effects (DARE) was undertaken. Percentages of mortality and DALYs were obtained from the 2010 Global Burden of Disease study. Standardised residual differences (SRD) based on percentages of mortality and DALYs were calculated, where conditions with SRD of more than or less than three were considered overstudied or understudied, respectively. 1029 reviews from CDSR and 1928 reviews from DARE were examined. There was a significant correlation between percentage DALYs and systematic reviews published in CDSR and DARE databases (CDSR: r=0.68, p=0.001; DARE: r=0.60, p<0.001). There was no significant correlation between percentage mortality and number of systematic reviews published in either database (CDSR: r=0.34, p=0.14; DARE: r=0.22, p=0.34). Relative to percentage of mortality, mental and behavioural disorders, musculoskeletal conditions and other non-communicable diseases were overstudied. Maternal disorders were overstudied relative to percentages of mortality and DALYs in CDSR. The focus of systematic reviews is moderately correlated with DALYs. A number of conditions may be overstudied relative to percentage of mortality particularly in the context of health and medical reviews. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes.

PubMed

Forster, Samuel C; Browne, Hilary P; Kumar, Nitin; Hunt, Martin; Denise, Hubert; Mitchell, Alex; Finn, Robert D; Lawley, Trevor D

2016-01-04

The Human Pan-Microbe Communities (HPMC) database (http://www.hpmcd.org/) provides a manually curated, searchable, metagenomic resource to facilitate investigation of human gastrointestinal microbiota. Over the past decade, the application of metagenome sequencing to elucidate the microbial composition and functional capacity present in the human microbiome has revolutionized many concepts in our basic biology. When sufficient high quality reference genomes are available, whole genome metagenomic sequencing can provide direct biological insights and high-resolution classification. The HPMC database provides species level, standardized phylogenetic classification of over 1800 human gastrointestinal metagenomic samples. This is achieved by combining a manually curated list of bacterial genomes from human faecal samples with over 21000 additional reference genomes representing bacteria, viruses, archaea and fungi with manually curated species classification and enhanced sample metadata annotation. A user-friendly, web-based interface provides the ability to search for (i) microbial groups associated with health or disease state, (ii) health or disease states and community structure associated with a microbial group, (iii) the enrichment of a microbial gene or sequence and (iv) enrichment of a functional annotation. The HPMC database enables detailed analysis of human microbial communities and supports research from basic microbiology and immunology to therapeutic development in human health and disease. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

A possible extension to the RInChI as a means of providing machine readable process data.

PubMed

Jacob, Philipp-Maximilian; Lan, Tian; Goodman, Jonathan M; Lapkin, Alexei A

2017-04-11

The algorithmic, large-scale use and analysis of reaction databases such as Reaxys is currently hindered by the absence of widely adopted standards for publishing reaction data in machine readable formats. Crucial data such as yields of all products or stoichiometry are frequently not explicitly stated in the published papers and, hence, not reported in the database entry for those reactions, limiting their usefulness for algorithmic analysis. This paper presents a possible extension to the IUPAC RInChI standard via an auxiliary layer, termed ProcAuxInfo, which is a standardised, extensible form in which to report certain key reaction parameters such as declaration of all products and reactants as well as auxiliaries known in the reaction, reaction stoichiometry, amounts of substances used, conversion, yield and operating conditions. The standard is demonstrated via creation of the RInChI including the ProcAuxInfo layer based on three published reactions and demonstrates accurate data recoverability via reverse translation of the created strings. Implementation of this or another method of reporting process data by the publishing community would ensure that databases, such as Reaxys, would be able to abstract crucial data for big data analysis of their contents.

Statistical Learning in Specific Language Impairment: A Meta-Analysis

ERIC Educational Resources Information Center

Lammertink, Imme; Boersma, Paul; Wijnen, Frank; Rispens, Judith

2017-01-01

Purpose: The current meta-analysis provides a quantitative overview of published and unpublished studies on statistical learning in the auditory verbal domain in people with and without specific language impairment (SLI). The database used for the meta-analysis is accessible online and open to updates (Community-Augmented Meta-Analysis), which…

Evolution of primary care databases in UK: a scientometric analysis of research output.

PubMed

Vezyridis, Paraskevas; Timmons, Stephen

2016-10-11

To identify publication and citation trends, most productive institutions and countries, top journals, most cited articles and authorship networks from articles that used and analysed data from primary care databases (CPRD, THIN, QResearch) of pseudonymised electronic health records (EHRs) in UK. Descriptive statistics and scientometric tools were used to analyse a SCOPUS data set of 1891 articles. Open access software was used to extract networks from the data set (Table2Net), visualise and analyse coauthorship networks of scholars and countries (Gephi) and density maps (VOSviewer) of research topics co-occurrence and journal cocitation. Research output increased overall at a yearly rate of 18.65%. While medicine is the main field of research, studies in more specialised areas include biochemistry and pharmacology. Researchers from UK, USA and Spanish institutions have published the most papers. Most of the journals that publish this type of research and most cited papers come from UK and USA. Authorship varied between 3 and 6 authors. Keyword analyses show that smoking, diabetes, cardiovascular diseases and mental illnesses, as well as medication that can treat such medical conditions, such as non-steroid anti-inflammatory agents, insulin and antidepressants constitute the main topics of research. Coauthorship network analyses show that lead scientists, directors or founders of these databases are, to various degrees, at the centre of clusters in this scientific community. There is a considerable increase of publications in primary care research from EHRs. The UK has been well placed at the centre of an expanding global scientific community, facilitating international collaborations and bringing together international expertise in medicine, biochemical and pharmaceutical research. 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/.

Making open data work for plant scientists.

PubMed

Leonelli, Sabina; Smirnoff, Nicholas; Moore, Jonathan; Cook, Charis; Bastow, Ruth

2013-11-01

Despite the clear demand for open data sharing, its implementation within plant science is still limited. This is, at least in part, because open data-sharing raises several unanswered questions and challenges to current research practices. In this commentary, some of the challenges encountered by plant researchers at the bench when generating, interpreting, and attempting to disseminate their data have been highlighted. The difficulties involved in sharing sequencing, transcriptomics, proteomics, and metabolomics data are reviewed. The benefits and drawbacks of three data-sharing venues currently available to plant scientists are identified and assessed: (i) journal publication; (ii) university repositories; and (iii) community and project-specific databases. It is concluded that community and project-specific databases are the most useful to researchers interested in effective data sharing, since these databases are explicitly created to meet the researchers' needs, support extensive curation, and embody a heightened awareness of what it takes to make data reuseable by others. Such bottom-up and community-driven approaches need to be valued by the research community, supported by publishers, and provided with long-term sustainable support by funding bodies and government. At the same time, these databases need to be linked to generic databases where possible, in order to be discoverable to the majority of researchers and thus promote effective and efficient data sharing. As we look forward to a future that embraces open access to data and publications, it is essential that data policies, data curation, data integration, data infrastructure, and data funding are linked together so as to foster data access and research productivity.

Birds of Upland Oak Forests in the Arkansas Ozarks: Present Community Structure and Potential Impacts of Burning, Borers, and Forestry Practices

Treesearch

Kimberly Smith; Michael Mlodinow; Janet S. Self; Thomas M. Haggerty; Tamara R. Hocut

2004-01-01

Based on published works, our own research, and the U.S. Forest Service’s R8 Bird database, we characterize breeding bird communities in mesic and xeric upland hardwood forests of the Arkansas Ozarks. Although 59 species have been recorded as breeding, typical breeding assemblages in mesic forests are 20-25 species, with only 5 species commonly found in xeric forests....

Community pharmacy based research activity in India: A bibliometric study of the past ten years

PubMed Central

Basak, Subal Chandra; Sathyanarayana, Dondeti

2010-01-01

Objectives: The objective of this study was to analyze and record the published evidence regarding community pharmacy practice in India during the past decade (1998-2008). Methods: A bibliometric review analysis of the original papers was undertaken to assess the different aspects of community pharmacy practice in India. The MEDLINE, Index Copernicus, IndMed, DOAJ databases and the journals such as Indian Journal of Pharmaceutical Sciences and Indian Journal of Hospital Pharmacy were used as data sources. Type of papers, type of journals, category of papers, production indicators and impact factor of the journals were analyzed. Results: Thirty papers were included in the study. The papers were published in 13 different journals, 33.3% of them being in the Indian Journal of Hospital Pharmacy. The average number of authors per paper was 2.73 (SD=1.41). Impact factor was available for only three journals. Conclusions: There are limited studies being published in India which cover the community pharmacy related activities in India. The key indicators which emerge from the literature review present some fundamental challenges to the development of the role of the community pharmacist in India. PMID:23093877

FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis.

PubMed

Parente, Eugenio; Cocolin, Luca; De Filippis, Francesca; Zotta, Teresa; Ferrocino, Ilario; O'Sullivan, Orla; Neviani, Erasmo; De Angelis, Maria; Cotter, Paul D; Ercolini, Danilo

2016-02-16

Amplicon targeted high-throughput sequencing has become a popular tool for the culture-independent analysis of microbial communities. Although the data obtained with this approach are portable and the number of sequences available in public databases is increasing, no tool has been developed yet for the analysis and presentation of data obtained in different studies. This work describes an approach for the development of a database for the rapid exploration and analysis of data on food microbial communities. Data from seventeen studies investigating the structure of bacterial communities in dairy, meat, sourdough and fermented vegetable products, obtained by 16S rRNA gene targeted high-throughput sequencing, were collated and analysed using Gephi, a network analysis software. The resulting database, which we named FoodMicrobionet, was used to analyse nodes and network properties and to build an interactive web-based visualisation. The latter allows the visual exploration of the relationships between Operational Taxonomic Units (OTUs) and samples and the identification of core- and sample-specific bacterial communities. It also provides additional search tools and hyperlinks for the rapid selection of food groups and OTUs and for rapid access to external resources (NCBI taxonomy, digital versions of the original articles). Microbial interaction network analysis was carried out using CoNet on datasets extracted from FoodMicrobionet: the complexity of interaction networks was much lower than that found for other bacterial communities (human microbiome, soil and other environments). This may reflect both a bias in the dataset (which was dominated by fermented foods and starter cultures) and the lower complexity of food bacterial communities. Although some technical challenges exist, and are discussed here, the net result is a valuable tool for the exploration of food bacterial communities by the scientific community and food industry. Copyright © 2015. Published by Elsevier B.V.

Digital plagiarism - The web giveth and the web shall taketh

PubMed Central

Presti, David E

2000-01-01

Publishing students' and researchers' papers on the World Wide Web (WWW) facilitates the sharing of information within and between academic communities. However, the ease of copying and transporting digital information leaves these authors' ideas open to plagiarism. Using tools such as the Plagiarism.org database, which compares submissions to reports and papers available on the Internet, could discover instances of plagiarism, revolutionize the peer review process, and raise the quality of published research everywhere. PMID:11720925

Digital plagiarism--the Web giveth and the Web shall taketh.

PubMed

Barrie, J M; Presti, D E

2000-01-01

Publishing students' and researchers' papers on the World Wide Web (WWW) facilitates the sharing of information within and between academic communities. However, the ease of copying and transporting digital information leaves these authors' ideas open to plagiarism. Using tools such as the Plagiarism.org database, which compares submissions to reports and papers available on the Internet, could discover instances of plagiarism, revolutionize the peer review process, and raise the quality of published research everywhere.

Vertical distribution of chlorophyll a concentration and phytoplankton community composition from in situ fluorescence profiles: a first database for the global ocean

NASA Astrophysics Data System (ADS)

Sauzède, R.; Lavigne, H.; Claustre, H.; Uitz, J.; Schmechtig, C.; D'Ortenzio, F.; Guinet, C.; Pesant, S.

2015-10-01

In vivo chlorophyll a fluorescence is a proxy of chlorophyll a concentration, and is one of the most frequently measured biogeochemical properties in the ocean. Thousands of profiles are available from historical databases and the integration of fluorescence sensors to autonomous platforms has led to a significant increase of chlorophyll fluorescence profile acquisition. To our knowledge, this important source of environmental data has not yet been included in global analyses. A total of 268 127 chlorophyll fluorescence profiles from several databases as well as published and unpublished individual sources were compiled. Following a robust quality control procedure detailed in the present paper, about 49 000 chlorophyll fluorescence profiles were converted into phytoplankton biomass (i.e., chlorophyll a concentration) and size-based community composition (i.e., microphytoplankton, nanophytoplankton and picophytoplankton), using a method specifically developed to harmonize fluorescence profiles from diverse sources. The data span over 5 decades from 1958 to 2015, including observations from all major oceanic basins and all seasons, and depths ranging from the surface to a median maximum sampling depth of around 700 m. Global maps of chlorophyll a concentration and phytoplankton community composition are presented here for the first time. Monthly climatologies were computed for three of Longhurst's ecological provinces in order to exemplify the potential use of the data product. Original data sets (raw fluorescence profiles) as well as calibrated profiles of phytoplankton biomass and community composition are available on open access at PANGAEA, Data Publisher for Earth and Environmental Science. Raw fluorescence profiles: http://doi.pangaea.de/10.1594/PANGAEA.844212 and Phytoplankton biomass and community composition: http://doi.pangaea.de/10.1594/PANGAEA.844485

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.

PubMed

Xu, Huilei; Baroukh, Caroline; Dannenfelser, Ruth; Chen, Edward Y; Tan, Christopher M; Kou, Yan; Kim, Yujin E; Lemischka, Ihor R; Ma'ayan, Avi

2013-01-01

High content studies that profile mouse and human embryonic stem cells (m/hESCs) using various genome-wide technologies such as transcriptomics and proteomics are constantly being published. However, efforts to integrate such data to obtain a global view of the molecular circuitry in m/hESCs are lagging behind. Here, we present an m/hESC-centered database called Embryonic Stem Cell Atlas from Pluripotency Evidence integrating data from many recent diverse high-throughput studies including chromatin immunoprecipitation followed by deep sequencing, genome-wide inhibitory RNA screens, gene expression microarrays or RNA-seq after knockdown (KD) or overexpression of critical factors, immunoprecipitation followed by mass spectrometry proteomics and phosphoproteomics. The database provides web-based interactive search and visualization tools that can be used to build subnetworks and to identify known and novel regulatory interactions across various regulatory layers. The web-interface also includes tools to predict the effects of combinatorial KDs by additive effects controlled by sliders, or through simulation software implemented in MATLAB. Overall, the Embryonic Stem Cell Atlas from Pluripotency Evidence database is a comprehensive resource for the stem cell systems biology community. Database URL: http://www.maayanlab.net/ESCAPE

The Cambridge Structural Database

PubMed Central

Groom, Colin R.; Bruno, Ian J.; Lightfoot, Matthew P.; Ward, Suzanna C.

2016-01-01

The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface. PMID:27048719

The Cambridge Structural Database.

PubMed

Groom, Colin R; Bruno, Ian J; Lightfoot, Matthew P; Ward, Suzanna C

2016-04-01

The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal-organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.

Online World Conference and Expo: A Zillion Things at Once.

ERIC Educational Resources Information Center

Chuck, Lysbeth B.

1997-01-01

Presents the keynote speakers of the Online World 1997 conference, as well as HotBot and other search engines, the CyberClinic tracks (Practical Searching, Resource Management, Trends and Technology, Corporate Electronic Publishing, Content Reviews, and Roundtable Discussions), Web-based communities, and an exhibited database of over 12,000…

Directly e-mailing authors of newly published papers encourages community curation

PubMed Central

Bunt, Stephanie M.; Grumbling, Gary B.; Field, Helen I.; Marygold, Steven J.; Brown, Nicholas H.; Millburn, Gillian H.

2012-01-01

Much of the data within Model Organism Databases (MODs) comes from manual curation of the primary research literature. Given limited funding and an increasing density of published material, a significant challenge facing all MODs is how to efficiently and effectively prioritize the most relevant research papers for detailed curation. Here, we report recent improvements to the triaging process used by FlyBase. We describe an automated method to directly e-mail corresponding authors of new papers, requesting that they list the genes studied and indicate (‘flag’) the types of data described in the paper using an online tool. Based on the author-assigned flags, papers are then prioritized for detailed curation and channelled to appropriate curator teams for full data extraction. The overall response rate has been 44% and the flagging of data types by authors is sufficiently accurate for effective prioritization of papers. In summary, we have established a sustainable community curation program, with the result that FlyBase curators now spend less time triaging and can devote more effort to the specialized task of detailed data extraction. Database URL: http://flybase.org/ PMID:22554788

Interventions to enhance effective communication during over-the-counter consultations in the community pharmacy setting: A systematic review.

PubMed

Seubert, Liza J; Whitelaw, Kerry; Hattingh, Laetitia; Watson, Margaret C; Clifford, Rhonda M

2017-12-13

Easy access to effective over-the-counter (OTC) treatments allows self-management of some conditions, however inappropriate or incorrect supply or use of OTC medicines can cause harm. Pharmacy personnel should support consumers in their health-seeking behaviour by utilising effective communication skills underpinned by clinical knowledge. To identify interventions targeted towards improving communication between consumers and pharmacy personnel during OTC consultations in the community pharmacy setting. Systematic review and narrative analysis. Databases searched were MEDLINE, EMBASE, Psycinfo, Cochrane Central Register and Cochrane Database of Systematic Reviews for literature published between 2000 and 30 October 2014, as well as reference lists of included articles. The search was re-run on 18 January 2016 and 25 September 2017 to maximise the currency. Two reviewers independently screened retrieved articles for inclusion, assessed study quality and extracted data. Full publications of intervention studies were included. Participants were community pharmacy personnel and/or consumers involved in OTC consultations. Interventions which aimed to improve communication during OTC consultations in the community pharmacy setting were included if they involved a direct measurable communication outcome. Studies reporting attitudes and measures not quantifiable were excluded. The protocol was published on Prospero Database of Systematic Reviews. Of 4978 records identified, 11 studies met inclusion criteria. Interventions evaluated were: face-to-face training sessions (n = 10); role-plays (n = 9); a software decision making program (n = 1); and simulated patient (SP) visits followed by immediate feedback (n = 1). Outcomes were measured using: SP methodology (n = 10) and a survey (n = 1), with most (n = 10) reporting a level of improvement in some communication behaviours. Empirical evaluation of interventions using active learning techniques such as face-to-face training with role-play can improve some communication skills. However interventions that are not fully described limit the ability for replication and/or generalisability. This review identified interventions targeting pharmacy personnel. Future interventions to improve communication should consider the consumer's role in OTC consultations. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Astronomical Publishing: Yesterday, Today and Tomorrow

NASA Astrophysics Data System (ADS)

Huchra, John

Just in the last few years scientific publishing has moved rapidly away from the modes that served it well for over two centuries. As "digital natives" take over the field and rapid and open access comes to dominate the way we communicate, both scholarly journals and libraries need to adopt new business models to serve their communities. This is best done by identifying new "added value" such as databases, full text searching, full cross indexing while at the same time retaining the high quality of peer reviewed publication.

Sharing mutants and experimental information prepublication using FgMutantDb (https://scabusa.org/FgMutantDb).

PubMed

Baldwin, Thomas T; Basenko, Evelina; Harb, Omar; Brown, Neil A; Urban, Martin; Hammond-Kosack, Kim E; Bregitzer, Phil P

2018-06-01

There is no comprehensive storage for generated mutants of Fusarium graminearum or data associated with these mutants. Instead, researchers relied on several independent and non-integrated databases. FgMutantDb was designed as a simple spreadsheet that is accessible globally on the web that will function as a centralized source of information on F. graminearum mutants. FgMutantDb aids in the maintenance and sharing of mutants within a research community. It will serve also as a platform for disseminating prepublication results as well as negative results that often go unreported. Additionally, the highly curated information on mutants in FgMutantDb will be shared with other databases (FungiDB, Ensembl, PhytoPath, and PHI-base) through updating reports. Here we describe the creation and potential usefulness of FgMutantDb to the F. graminearum research community, and provide a tutorial on its use. This type of database could be easily emulated for other fungal species. Published by Elsevier Inc.

STRBase: a short tandem repeat DNA database for the human identity testing community

PubMed Central

Ruitberg, Christian M.; Reeder, Dennis J.; Butler, John M.

2001-01-01

The National Institute of Standards and Technology (NIST) has compiled and maintained a Short Tandem Repeat DNA Internet Database (http://www.cstl.nist.gov/biotech/strbase/) since 1997 commonly referred to as STRBase. This database is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. STRBase consolidates and organizes the abundant literature on this subject to facilitate on-going efforts in DNA typing. Observed alleles and annotated sequence for each STR locus are described along with a review of STR analysis technologies. Additionally, commercially available STR multiplex kits are described, published polymerase chain reaction (PCR) primer sequences are reported, and validation studies conducted by a number of forensic laboratories are listed. To supplement the technical information, addresses for scientists and hyperlinks to organizations working in this area are available, along with the comprehensive reference list of over 1300 publications on STRs used for DNA typing purposes. PMID:11125125

EVpedia: a community web portal for extracellular vesicles research.

PubMed

Kim, Dae-Kyum; Lee, Jaewook; Kim, Sae Rom; Choi, Dong-Sic; Yoon, Yae Jin; Kim, Ji Hyun; Go, Gyeongyun; Nhung, Dinh; Hong, Kahye; Jang, Su Chul; Kim, Si-Hyun; Park, Kyong-Su; Kim, Oh Youn; Park, Hyun Taek; Seo, Ji Hye; Aikawa, Elena; Baj-Krzyworzeka, Monika; van Balkom, Bas W M; Belting, Mattias; Blanc, Lionel; Bond, Vincent; Bongiovanni, Antonella; Borràs, Francesc E; Buée, Luc; Buzás, Edit I; Cheng, Lesley; Clayton, Aled; Cocucci, Emanuele; Dela Cruz, Charles S; Desiderio, Dominic M; Di Vizio, Dolores; Ekström, Karin; Falcon-Perez, Juan M; Gardiner, Chris; Giebel, Bernd; Greening, David W; Gross, Julia Christina; Gupta, Dwijendra; Hendrix, An; Hill, Andrew F; Hill, Michelle M; Nolte-'t Hoen, Esther; Hwang, Do Won; Inal, Jameel; Jagannadham, Medicharla V; Jayachandran, Muthuvel; Jee, Young-Koo; Jørgensen, Malene; Kim, Kwang Pyo; Kim, Yoon-Keun; Kislinger, Thomas; Lässer, Cecilia; Lee, Dong Soo; Lee, Hakmo; van Leeuwen, Johannes; Lener, Thomas; Liu, Ming-Lin; Lötvall, Jan; Marcilla, Antonio; Mathivanan, Suresh; Möller, Andreas; Morhayim, Jess; Mullier, François; Nazarenko, Irina; Nieuwland, Rienk; Nunes, Diana N; Pang, Ken; Park, Jaesung; Patel, Tushar; Pocsfalvi, Gabriella; Del Portillo, Hernando; Putz, Ulrich; Ramirez, Marcel I; Rodrigues, Marcio L; Roh, Tae-Young; Royo, Felix; Sahoo, Susmita; Schiffelers, Raymond; Sharma, Shivani; Siljander, Pia; Simpson, Richard J; Soekmadji, Carolina; Stahl, Philip; Stensballe, Allan; Stępień, Ewa; Tahara, Hidetoshi; Trummer, Arne; Valadi, Hadi; Vella, Laura J; Wai, Sun Nyunt; Witwer, Kenneth; Yáñez-Mó, María; Youn, Hyewon; Zeidler, Reinhard; Gho, Yong Song

2015-03-15

Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular components are currently challenging. We present an improved version of EVpedia, a public database for EVs research. This community web portal contains a database of publications and vesicular components, identification of orthologous vesicular components, bioinformatic tools and a personalized function. EVpedia includes 6879 publications, 172 080 vesicular components from 263 high-throughput datasets, and has been accessed more than 65 000 times from more than 750 cities. In addition, about 350 members from 73 international research groups have participated in developing EVpedia. This free web-based database might serve as a useful resource to stimulate the emerging field of EV research. The web site was implemented in PHP, Java, MySQL and Apache, and is freely available at http://evpedia.info. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Lost in translation: the impact of publication language on citation frequency in the scientific dental literature.

PubMed

Poomkottayil, Deepak; Bornstein, Michael M; Sendi, Pedram

2011-01-28

Citation metrics are commonly used as a proxy for scientific merit and relevance. Papers published in English, however, may exhibit a higher citation frequency than research articles published in other languages, though this issue has not yet been investigated from a Swiss perspective where English is not the native language. To assess the impact of publication language on citation frequency we focused on oral surgery papers indexed in PubMed MEDLINE that were published by Swiss Dental Schools between 2002 and 2007. Citation frequency of research papers was extracted from the Institute for Scientific Information (ISI) and Google Scholar database. A univariate and multivariate logistic regression model was used to assess the impact of publication language (English versus German/French) on citation frequency, adjusted for journal impact factor, number of authors and research topic. Papers published in English showed a 6 (ISI database) and 7 (Google Scholar) times higher odds for being cited than research articles published in German or French. Our results suggest that publication language substantially influences the citation frequency of a research paper. Researchers should publish their work in English to render them accessible to the international scientific community.

The Molecule Pages database

PubMed Central

Saunders, Brian; Lyon, Stephen; Day, Matthew; Riley, Brenda; Chenette, Emily; Subramaniam, Shankar

2008-01-01

The UCSD-Nature Signaling Gateway Molecule Pages (http://www.signaling-gateway.org/molecule) provides essential information on more than 3800 mammalian proteins involved in cellular signaling. The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and sequence analysis. The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function. The expert-authored pages are anonymously peer reviewed by the Nature Publishing Group. The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer. The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture. The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community. PMID:17965093

The Molecule Pages database.

PubMed

Saunders, Brian; Lyon, Stephen; Day, Matthew; Riley, Brenda; Chenette, Emily; Subramaniam, Shankar; Vadivelu, Ilango

2008-01-01

The UCSD-Nature Signaling Gateway Molecule Pages (http://www.signaling-gateway.org/molecule) provides essential information on more than 3800 mammalian proteins involved in cellular signaling. The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and sequence analysis. The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function. The expert-authored pages are anonymously peer reviewed by the Nature Publishing Group. The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer. The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture. The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community.

Seeing the community's perspective through multiple emic and etic vistas.

PubMed

Gaber, John

2017-12-01

Health impact assessment (HIA) researchers regularly use community input in their investigations to help them better understand local health issues. Community data is commonly associated with the lived experiences of local impacted residents known as 'emic' data. It is becoming more common practice for HIA researchers to access outside experts and stakeholders ('etic' data) during the community input phase of their investigations. Utilizing published international HIA data, I look at who HIA researchers invite when they seek to get 'community input' in their HIA investigations. The HIA database was generated from an internet investigation of published HIAs (in English) from 1999 to 2011 and focused particularly on single authored assessments that were conducted by governments, non-governmental organizations (NGOs) or universities. HIA researchers access a wide range of emic and etic community perspectives in their search for the 'community's view'. Government, NGO and university investigators access community perspectives differently, with university HIA researchers inviting more emic-oriented community vistas than both government and NGO researchers. University and government HIA investigators are more likely to invite multiple emic and etic community perspectives during their community participation projects than NGO researchers. NGO HIA investigators tend to either invite emic perspectives or etic perspectives for their community input with less mixing of the two views in a single project. The paper concludes with a discussion on how HIA researchers can frame the 'community's perspective' in their HIA investigations through a combination of both 'insider' and 'outsider' community input sampling strategies. Published by Oxford University Press 2016. This work is written by a US Government employee and is in the public domain in the US.

Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.

PubMed

Winsor, Geoffrey L; Griffiths, Emma J; Lo, Raymond; Dhillon, Bhavjinder K; Shay, Julie A; Brinkman, Fiona S L

2016-01-04

The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Data Publication and Interoperability for Long Tail Researchers via the Open Data Repository's (ODR) Data Publisher.

NASA Astrophysics Data System (ADS)

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

2016-12-01

Working primarily with astrobiology researchers at NASA Ames, the Open Data Repository (ODR) has been conducting a software pilot to meet the varying needs of this multidisciplinary community. Astrobiology researchers often have small communities or operate individually with unique data sets that don't easily fit into existing database structures. The ODR constructed its Data Publisher software to allow researchers to create databases with common metadata structures and subsequently extend them to meet their individual needs and data requirements. The software accomplishes these tasks through a web-based interface that allows collaborative creation and revision of common metadata templates and individual extensions to these templates for custom data sets. This allows researchers to search disparate datasets based on common metadata established through the metadata tools, but still facilitates distinct analyses and data that may be stored alongside the required common metadata. The software produces web pages that can be made publicly available at the researcher's discretion so that users may search and browse the data in an effort to make interoperability and data discovery a human-friendly task while also providing semantic data for machine-based discovery. Once relevant data has been identified, researchers can utilize the built-in application programming interface (API) that exposes the data for machine-based consumption and integration with existing data analysis tools (e.g. R, MATLAB, Project Jupyter - http://jupyter.org). The current evolution of the project has created the Astrobiology Habitable Environments Database (AHED)[1] which provides an interface to databases connected through a common metadata core. In the next project phase, the goal is for small research teams and groups to be self-sufficient in publishing their research data to meet funding mandates and academic requirements as well as fostering increased data discovery and interoperability through human-readable and machine-readable interfaces. This project is supported by the Science-Enabling Research Activity (SERA) and NASA NNX11AP82A, MSL. [1] B. Lafuente et al. (2016) AGU, submitted.

Enhancing stewardship of community-engaged research through governance.

PubMed

Oetzel, John G; Villegas, Malia; Zenone, Heather; White Hat, Emily R; Wallerstein, Nina; Duran, Bonnie

2015-06-01

We explored the relationship of community-engaged research final approval type (tribal government, health board, or public health office (TG/HB); agency staff or advisory board; or individual or no community approval) with governance processes, productivity, and perceived outcomes. We identified 294 federally funded community-engaged research projects in 2009 from the National Institutes of Health's Research Portfolio Online Reporting Tools, Centers for Disease Control and Prevention's Prevention Research Centers, and Native American Research Centers for Health databases. Two hundred (68.0%) investigators completed a survey about governance processes and productivity measures; 312 partners (77.2% of 404 invited) and 138 investigators (69.0% of 200 invited) completed a survey about perceived outcomes. Projects with TG/HB approval had increased likelihood of community control of resources (odds ratios [ORs] ≥ 4.80). Projects with other approvals had decreased likelihood of development or revision of institutional review board policies (ORs ≤ 0.37), having written agreements (ORs ≤ 0.17), and agreements about publishing (ORs ≤ 0.28), data use (ORs ≤ 0.17), and publishing approval (ORs ≤ 0.14). Community-engaged research projects with TG/HB approval had strong stewardship of project resources and agreements. Governance as stewardship protects community interests; thus, is an ethical imperative for communities, especially native communities, to adopt.

EarthRef.org: Exploring aspects of a Cyber Infrastructure in Earth Science and Education

NASA Astrophysics Data System (ADS)

Staudigel, H.; Koppers, A.; Tauxe, L.; Constable, C.; Helly, J.

2004-12-01

EarthRef.org is the common host and (co-) developer of a range of earth science databases and IT resources providing a test bed for a Cyberinfrastructure in Earth Science and Education (CIESE). EarthRef.org data base efforts include in particular the Geochemical Earth Reference Model (GERM), the Magnetics Information Consortium (MagIC), the Educational Resources for Earth Science Education (ERESE) project, the Seamount Catalog, the Mid-Ocean Ridge Catalog, the Radio-Isotope Geochronology (RiG) initiative for CHRONOS, and the Microbial Observatory for Fe oxidizing microbes on Loihi Seamount (FeMO; the most recent development). These diverse databases are developed under a single database umbrella and webserver at the San Diego Supercomputing Center. All the data bases have similar structures, with consistent metadata concepts, a common database layout, and automated upload wizards. Shared resources include supporting databases like an address book, a reference/publication catalog, and a common digital archive making database development and maintenance cost-effective, while guaranteeing interoperability. The EarthRef.org CIESE provides a common umbrella for synthesis information as well as sample-based data, and it bridges the gap between science and science education in middle and high schools, validating the potential for a system wide data infrastructure in a CIESE. EarthRef.org experiences have shown that effective communication with the respective communities is a key part of a successful CIESE facilitating both utility and community buy-in. GERM has been particularly successful at developing a metadata scheme for geochemistry and in the development of a new electronic journal (G-cubed) that has made much progress in data publication and linkages between journals and community data bases. GERM also has worked, through editors and publishers, towards interfacing databases with the publication process, to accomplish a more scholarly and database friendly data publication environment, and to interface with the respective science communities. MagIC has held several workshops that have resulted in an integrated data archival environment using metadata that are interchangeable with the geochemical metadata. MagIC archives a wide array of paleo and rock magnetic directional, intensity and magnetic property data as well as integrating computational tools. ERESE brought together librarians, teachers, and scientists to create an educational environment that supports inquiry driven education and the use of science data. Experiences in EarthRef.org demonstrates the feasibility of an effective, community wide CIESE for data publication, archival and modeling, as well as the outreach to the educational community.

Is Biblioleaks inevitable?

PubMed

Dunn, Adam G; Coiera, Enrico; Mandl, Kenneth D

2014-04-22

In 2014, the vast majority of published biomedical research is still hidden behind paywalls rather than open access. For more than a decade, similar restrictions over other digitally available content have engendered illegal activity. Music file sharing became rampant in the late 1990s as communities formed around new ways to share. The frequency and scale of cyber-attacks against commercial and government interests has increased dramatically. Massive troves of classified government documents have become public through the actions of a few. Yet we have not seen significant growth in the illegal sharing of peer-reviewed academic articles. Should we truly expect that biomedical publishing is somehow at less risk than other content-generating industries? What of the larger threat--a "Biblioleaks" event--a database breach and public leak of the substantial archives of biomedical literature? As the expectation that all research should be available to everyone becomes the norm for a younger generation of researchers and the broader community, the motivations for such a leak are likely to grow. We explore the feasibility and consequences of a Biblioleaks event for researchers, journals, publishers, and the broader communities of doctors and the patients they serve.

The gene expression database for mouse development (GXD): putting developmental expression information at your fingertips.

PubMed

Smith, Constance M; Finger, Jacqueline H; Kadin, James A; Richardson, Joel E; Ringwald, Martin

2014-10-01

Because molecular mechanisms of development are extraordinarily complex, the understanding of these processes requires the integration of pertinent research data. Using the Gene Expression Database for Mouse Development (GXD) as an example, we illustrate the progress made toward this goal, and discuss relevant issues that apply to developmental databases and developmental research in general. Since its first release in 1998, GXD has served the scientific community by integrating multiple types of expression data from publications and electronic submissions and by making these data freely and widely available. Focusing on endogenous gene expression in wild-type and mutant mice and covering data from RNA in situ hybridization, in situ reporter (knock-in), immunohistochemistry, reverse transcriptase-polymerase chain reaction, Northern blot, and Western blot experiments, the database has grown tremendously over the years in terms of data content and search utilities. Currently, GXD includes over 1.4 million annotated expression results and over 260,000 images. All these data and images are readily accessible to many types of database searches. Here we describe the data and search tools of GXD; explain how to use the database most effectively; discuss how we acquire, curate, and integrate developmental expression information; and describe how the research community can help in this process. Copyright © 2014 The Authors Developmental Dynamics published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists.

Community pharmacy-based research in Spain (1995-2005): A bibliometric study

PubMed Central

Andrés Iglesias, José Carlos; Andrés Rodríguez, N. Floro; Fornos Pérez, José Antonio

Only one study evaluated the scientific activity in community pharmacies in Spain, and it was restricted to articles published in just two journals. Objective To assess the scientific activity in community pharmacies in Spain through a bibliometric analysis of the original papers published during the years 1995-2005. Methods IPA, MEDLINE, CSIC database and the journals Seguimiento Farmacoterapéutico y Pharmaceutical Care España were used as data sources. Production indicators, consumption indicators and the impact factor (IF) as a repercussion index were analyzed. Results 122 articles were included in the review. The articles were published in 12 journals, 78.7% of them in Pharmaceutical Care España and Seguimiento Farmacoterapéutico. The mean number of authors per article was 4.2 (SD=2.1). The transitivity index was 71.3%. The total number of references cited in the articles was 2110. The mean number of references per article was 17.3 SD=9.3. The value of the insularity index was 57.6%. Self citation was 6.8% and the Price index was 66.5%. No impact factor was available for 6 journals. Conclusions Publication of articles on community pharmacy-based research in Spain has undergone an important increase in the last 5 years. The existence of authors who publish very few studies, the high insularity index and the lack of randomized, controlled trials may be considered as negative indicators in community pharmacy-based research in Spain. PMID:25214914

Antarctic Meteorite Classification and Petrographic Database

NASA Technical Reports Server (NTRS)

Todd, Nancy S.; Satterwhite, C. E.; Righter, Kevin

2011-01-01

The Antarctic Meteorite collection, which is comprised of over 18,700 meteorites, is one of the largest collections of meteorites in the world. These meteorites have been collected since the late 1970's as part of a three-agency agreement between NASA, the National Science Foundation, and the Smithsonian Institution [1]. Samples collected each season are analyzed at NASA s Meteorite Lab and the Smithsonian Institution and results are published twice a year in the Antarctic Meteorite Newsletter, which has been in publication since 1978. Each newsletter lists the samples collected and processed and provides more in-depth details on selected samples of importance to the scientific community. Data about these meteorites is also published on the NASA Curation website [2] and made available through the Meteorite Classification Database allowing scientists to search by a variety of parameters

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions.

PubMed

Hume, Maxwell A; Barrera, Luis A; Gisselbrecht, Stephen S; Bulyk, Martha L

2015-01-01

The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides in vitro data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length k ('k-mers'). The database displays important information about the proteins and displays their DNA-binding specificity data in terms of k-mers, position weight matrices and graphical sequence logos. This update to the database documents the growth of UniPROBE since the last update 4 years ago, and introduces a variety of new features and tools, including a new streamlined pipeline that facilitates data deposition by universal PBM data generators in the research community, a tool that generates putative nonbinding (i.e. negative control) DNA sequences for one or more proteins and novel motifs obtained by analyzing the PBM data using the BEEML-PBM algorithm for motif inference. The UniPROBE database is available at http://uniprobe.org. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Kalium: a database of potassium channel toxins from scorpion venom.

PubMed

Kuzmenkov, Alexey I; Krylov, Nikolay A; Chugunov, Anton O; Grishin, Eugene V; Vassilevski, Alexander A

2016-01-01

Kalium (http://kaliumdb.org/) is a manually curated database that accumulates data on potassium channel toxins purified from scorpion venom (KTx). This database is an open-access resource, and provides easy access to pages of other databases of interest, such as UniProt, PDB, NCBI Taxonomy Browser, and PubMed. General achievements of Kalium are a strict and easy regulation of KTx classification based on the unified nomenclature supported by researchers in the field, removal of peptides with partial sequence and entries supported by transcriptomic information only, classification of β-family toxins, and addition of a novel λ-family. Molecules presented in the database can be processed by the Clustal Omega server using a one-click option. Molecular masses of mature peptides are calculated and available activity data are compiled for all KTx. We believe that Kalium is not only of high interest to professional toxinologists, but also of general utility to the scientific community.Database URL:http://kaliumdb.org/. © The Author(s) 2016. Published by Oxford University Press.

EarthChem: International Collaboration for Solid Earth Geochemistry in Geoinformatics

NASA Astrophysics Data System (ADS)

Walker, J. D.; Lehnert, K. A.; Hofmann, A. W.; Sarbas, B.; Carlson, R. W.

2005-12-01

The current on-line information systems for igneous rock geochemistry - PetDB, GEOROC, and NAVDAT - convincingly demonstrate the value of rigorous scientific data management of geochemical data for research and education. The next generation of hypothesis formulation and testing can be vastly facilitated by enhancing these electronic resources through integration of available datasets, expansion of data coverage in location, time, and tectonic setting, timely updates with new data, and through intuitive and efficient access and data analysis tools for the broader geosciences community. PetDB, GEOROC, and NAVDAT have therefore formed the EarthChem consortium (www.earthchem.org) as a international collaborative effort to address these needs and serve the larger earth science community by facilitating the compilation, communication, serving, and visualization of geochemical data, and their integration with other geological, geochronological, geophysical, and geodetic information to maximize their scientific application. We report on the status of and future plans for EarthChem activities. EarthChem's development plan includes: (1) expanding the functionality of the web portal to become a `one-stop shop for geochemical data' with search capability across databases, standardized and integrated data output, generally applicable tools for data quality assessment, and data analysis/visualization including plotting methods and an information-rich map interface; and (2) expanding data holdings by generating new datasets as identified and prioritized through community outreach, and facilitating data contributions from the community by offering web-based data submission capability and technical assistance for design, implementation, and population of new databases and their integration with all EarthChem data holdings. Such federated databases and datasets will retain their identity within the EarthChem system. We also plan on working with publishers to ease the assimilation of geochemical data into the EarthChem database. As a community resource, EarthChem will address user concerns and respond to broad scientific and educational needs. EarthChem will hold yearly workshops, town hall meetings, and/or exhibits at major meetings. The group has established a two-tier committee structure to help ease the communication and coordination of database and IT issues between existing data management projects, and to receive feedback and support from individuals and groups from the larger geosciences community.

ORCID Uptake in the Astronomical Community

NASA Astrophysics Data System (ADS)

Holmquist, Jane

2015-08-01

The IAU General Assembly provides librarians with a unique opportunity to interact with astronomers from all over the world. From the perspective of an ORCID Ambassador, the Focus Group Meeting on "Scholarly Publication in Astronomy" also provides an opportunity to demonstrate the cooperation and collaboration needed by individual astronomers, societies, librarians, publishers and bibliographic database providers to achieve universal adoption of ORCID, a standard unique identifier for authors, just as the DOI (digital object identifier) has been adopted for each journal article published.I propose to 1) present at the Focus Group Meeting an update on the uptake of ORCID by members of the astronomical community and 2) set up a small station (TBA) near the IAU registration area where librarians can show researchers how to register for an ORCID in 30 seconds.

NUBASE2012 Evaluation of Nuclear Properties

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

Wang, M., E-mail: wangm@impcas.ac.cn; CSNSM-Orsay, MPI-K, D-69117 Heidelberg; Audi, G.

NUBASE is a database containing the recommended values for the main properties of all known nuclides in their ground and excited isomeric states. Since the publication of the first version in 1997, NUBASE has been widely used in the nuclear science community. The latest version (NUBASE2012) was published in December 2012. Two specific examples are given to illustrate the evaluation policy of NUBASE2012.

A systematic review of studies evaluating Australian indigenous community development projects: the extent of community participation, their methodological quality and their outcomes.

PubMed

Snijder, Mieke; Shakeshaft, Anthony; Wagemakers, Annemarie; Stephens, Anne; Calabria, Bianca

2015-11-21

Community development is a health promotion approach identified as having great potential to improve Indigenous health, because of its potential for extensive community participation. There has been no systematic examination of the extent of community participation in community development projects and little analysis of their effectiveness. This systematic review aims to identify the extent of community participation in community development projects implemented in Australian Indigenous communities, critically appraise the qualitative and quantitative methods used in their evaluation, and summarise their outcomes. Ten electronic peer-reviewed databases and two electronic grey literature databases were searched for relevant studies published between 1990 and 2015. The level of community participation and the methodological quality of the qualitative and quantitative components of the studies were assessed against standardised criteria. Thirty one evaluation studies of community development projects were identified. Community participation varied between different phases of project development, generally high during project implementation, but low during the evaluation phase. For the majority of studies, methodological quality was low and the methods were poorly described. Although positive qualitative or quantitative outcomes were reported in all studies, only two studies reported statistically significant outcomes. Partnerships between researchers, community members and service providers have great potential to improve methodological quality and community participation when research skills and community knowledge are integrated to design, implement and evaluate community development projects. The methodological quality of studies evaluating Australian Indigenous community development projects is currently too weak to confidently determine the cost-effectiveness of community development projects in improving the health and wellbeing of Indigenous Australians. Higher quality studies evaluating community development projects would strengthen the evidence base.

The future application of GML database in GIS

NASA Astrophysics Data System (ADS)

Deng, Yuejin; Cheng, Yushu; Jing, Lianwen

2006-10-01

In 2004, the Geography Markup Language (GML) Implementation Specification (version 3.1.1) was published by Open Geospatial Consortium, Inc. Now more and more applications in geospatial data sharing and interoperability depend on GML. The primary purpose of designing GML is for exchange and transportation of geo-information by standard modeling and encoding of geography phenomena. However, the problems of how to organize and access lots of GML data effectively arise in applications. The research on GML database focuses on these problems. The effective storage of GML data is a hot topic in GIS communities today. GML Database Management System (GDBMS) mainly deals with the problem of storage and management of GML data. Now two types of XML database, namely Native XML Database, and XML-Enabled Database are classified. Since GML is an application of the XML standard to geographic data, the XML database system can also be used for the management of GML. In this paper, we review the status of the art of XML database, including storage, index and query languages, management systems and so on, then move on to the GML database. At the end, the future prospect of GML database in GIS application is presented.

Community collaboration as a disaster mental health competency: a systematic literature review.

PubMed

Lebowitz, Adam Jon

2015-02-01

Disasters impact the mental health of entire communities through destruction and physical displacement. There is growing recognition of the need for disaster mental health competencies. Professional organizations such as the AAFP and the ASPH recommend engaging with communities in equal partnership for their recovery. This systematic study was undertaken for the purpose of reviewing published disaster medicine competencies to determine if core competencies included community cooperation and collaboration. A search of Internet databases was conducted using major keywords "disaster" and "competencies". Articles eligible contained laundry lists of basic core competency curriculum beyond emergency response. Data were qualitatively analyzed to identify types of competencies, and the degree of community cooperation. A total of 12 studies were reviewed. Only one study listed competencies specifying community cooperation, although others refer indirectly to it. Findings suggest competency-based education programs could do more to educate future disaster health professionals about the importance of community collaboration.

The Global Genome Biodiversity Network (GGBN) Data Standard specification.

PubMed

Droege, G; Barker, K; Seberg, O; Coddington, J; Benson, E; Berendsohn, W G; Bunk, B; Butler, C; Cawsey, E M; Deck, J; Döring, M; Flemons, P; Gemeinholzer, B; Güntsch, A; Hollowell, T; Kelbert, P; Kostadinov, I; Kottmann, R; Lawlor, R T; Lyal, C; Mackenzie-Dodds, J; Meyer, C; Mulcahy, D; Nussbeck, S Y; O'Tuama, É; Orrell, T; Petersen, G; Robertson, T; Söhngen, C; Whitacre, J; Wieczorek, J; Yilmaz, P; Zetzsche, H; Zhang, Y; Zhou, X

2016-01-01

Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today's ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard.Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard. © The Author(s) 2016. Published by Oxford University Press.

A systematic review of chronic disease management interventions in primary care.

PubMed

Reynolds, Rebecca; Dennis, Sarah; Hasan, Iqbal; Slewa, Jan; Chen, Winnie; Tian, David; Bobba, Sangeetha; Zwar, Nicholas

2018-01-09

Primary and community care are key settings for the effective management of long term conditions. We aimed to evaluate the pattern of health outcomes in chronic disease management interventions for adults with physical health problems implemented in primary or community care settings. The methods were based on our previous review published in 2006. We performed database searches for articles published from 2006 to 2014 and conducted a systematic review with narrative synthesis using the Cochrane Effective Practice and Organisation of Care taxonomy to classify interventions and outcomes. The interventions were mapped to Chronic Care Model elements. The pattern of outcomes related to interventions was summarized by frequency of statistically significant improvements in health care provision and patient outcomes. A total of 9589 journal articles were retrieved from database searches and snowballing. After screening and verification, 165 articles that detailed 157 studies were included. There were few studies with Health Care Organization (1.9% of studies) or Community Resources (0.6% of studies) as the primary intervention element. Self-Management Support interventions (45.8% of studies) most frequently resulted in improvements in patient-level outcomes. Delivery System Design interventions (22.6% of studies) showed benefits in both professional and patient-level outcomes for a narrow range of conditions. Decision Support interventions (21.3% of studies) had impact limited to professional-level outcomes, in particular use of medications. The small number of studies of Clinical Information System interventions (8.9%) showed benefits for both professional- and patient-level outcomes. The published literature has expanded substantially since 2006. This review confirms that Self-Management Support is the most frequent Chronic Care Model intervention that is associated with statistically significant improvements, predominately for diabetes and hypertension.

Bridging knowledge translation gap in health in developing countries: visibility, impact and publishing standards in journals from the Eastern Mediterranean

PubMed Central

2012-01-01

Background Local and regional scientific journals are important factors in bridging gaps in health knowledge translation in low-and middle-income countries. We assessed indexing, citations and publishing standards of journals from the Eastern Mediterranean region. Methods For journals from 22 countries in the collection of the Index Medicus for the Eastern Mediterranean Region (IMEMR), we analyzed indexing in bibliographical databases and citations during 2006–2009 to published items in 2006 in Web of Science (WoS) and SCOPUS. Adherence to editorial and publishing standards was assessed using a special checklist. Results Out of 419 journals in IMEMR, 19 were indexed in MEDLINE, 23 in WoS and 46 in SCOPUS. Their impact factors ranged from 0.016 to 1.417. For a subset of 175 journals with available tables of contents from 2006, articles published in 2006 from 93 journals received 2068 citations in SCOPUS (23.5% self-citations) and articles in 86 journals received 1579 citations in WoS (24.3% self-citations) during 2006–2009. Citations to articles came mostly from outside of the Eastern Mediterranean region (76.8% in WoS and 75.4% in SCOPUS). Articles receiving highest number of citations presented topics specific for the region. Many journals did not follow editorial and publishing standards, such addressing requirements about the patient’s privacy rights (68.0% out of 244 analyzed), policy on managing conflicts of interest (66.4%), and ethical conduct in clinical and animal research (66.4%). Conclusion Journals from the Eastern Mediterranean are visible in and have impact on global scientific community. Coordinated effort of all stakeholders in journal publishing, including researchers, journal editors and owners, policy makers and citation databases, is needed to further promote local journals as windows to the research in the developing world and the doors for valuable regional research to the global scientific community. PMID:22577965

Bridging knowledge translation gap in health in developing countries: visibility, impact and publishing standards in journals from the Eastern Mediterranean.

PubMed

Utrobičić, Ana; Chaudhry, Nauman; Ghaffar, Abdul; Marušić, Ana

2012-05-11

Local and regional scientific journals are important factors in bridging gaps in health knowledge translation in low-and middle-income countries. We assessed indexing, citations and publishing standards of journals from the Eastern Mediterranean region. For journals from 22 countries in the collection of the Index Medicus for the Eastern Mediterranean Region (IMEMR), we analyzed indexing in bibliographical databases and citations during 2006-2009 to published items in 2006 in Web of Science (WoS) and SCOPUS. Adherence to editorial and publishing standards was assessed using a special checklist. Out of 419 journals in IMEMR, 19 were indexed in MEDLINE, 23 in WoS and 46 in SCOPUS. Their impact factors ranged from 0.016 to 1.417. For a subset of 175 journals with available tables of contents from 2006, articles published in 2006 from 93 journals received 2068 citations in SCOPUS (23.5% self-citations) and articles in 86 journals received 1579 citations in WoS (24.3% self-citations) during 2006-2009. Citations to articles came mostly from outside of the Eastern Mediterranean region (76.8% in WoS and 75.4% in SCOPUS). Articles receiving highest number of citations presented topics specific for the region. Many journals did not follow editorial and publishing standards, such addressing requirements about the patient's privacy rights (68.0% out of 244 analyzed), policy on managing conflicts of interest (66.4%), and ethical conduct in clinical and animal research (66.4%). Journals from the Eastern Mediterranean are visible in and have impact on global scientific community. Coordinated effort of all stakeholders in journal publishing, including researchers, journal editors and owners, policy makers and citation databases, is needed to further promote local journals as windows to the research in the developing world and the doors for valuable regional research to the global scientific community.

Enhancing Stewardship of Community-Engaged Research Through Governance

PubMed Central

Villegas, Malia; Zenone, Heather; White Hat, Emily R.; Wallerstein, Nina; Duran, Bonnie

2015-01-01

Objectives. We explored the relationship of community-engaged research final approval type (tribal government, health board, or public health office (TG/HB); agency staff or advisory board; or individual or no community approval) with governance processes, productivity, and perceived outcomes. Methods. We identified 294 federally funded community-engaged research projects in 2009 from the National Institutes of Health’s Research Portfolio Online Reporting Tools, Centers for Disease Control and Prevention’s Prevention Research Centers, and Native American Research Centers for Health databases. Two hundred (68.0%) investigators completed a survey about governance processes and productivity measures; 312 partners (77.2% of 404 invited) and 138 investigators (69.0% of 200 invited) completed a survey about perceived outcomes. Results. Projects with TG/HB approval had increased likelihood of community control of resources (odds ratios [ORs] ≥ 4.80). Projects with other approvals had decreased likelihood of development or revision of institutional review board policies (ORs ≤ 0.37), having written agreements (ORs ≤ 0.17), and agreements about publishing (ORs ≤ 0.28), data use (ORs ≤ 0.17), and publishing approval (ORs ≤ 0.14). Conclusions. Community-engaged research projects with TG/HB approval had strong stewardship of project resources and agreements. Governance as stewardship protects community interests; thus, is an ethical imperative for communities, especially native communities, to adopt. PMID:25880952

NCBI-compliant genome submissions: tips and tricks to save time and money.

PubMed

Pirovano, Walter; Boetzer, Marten; Derks, Martijn F L; Smit, Sandra

2017-03-01

Genome sequences nowadays play a central role in molecular biology and bioinformatics. These sequences are shared with the scientific community through sequence databases. The sequence repositories of the International Nucleotide Sequence Database Collaboration (INSDC, comprising GenBank, ENA and DDBJ) are the largest in the world. Preparing an annotated sequence in such a way that it will be accepted by the database is challenging because many validation criteria apply. In our opinion, it is an undesirable situation that researchers who want to submit their sequence need either a lot of experience or help from partners to get the job done. To save valuable time and money, we list a number of recommendations for people who want to submit an annotated genome to a sequence database, as well as for tool developers, who could help to ease the process. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease.

PubMed

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. http://rged.wall-eva.net. © The Author(s) 2014. Published by Oxford University Press.

Respiratory cancer database: An open access database of respiratory cancer gene and miRNA.

PubMed

Choubey, Jyotsna; Choudhari, Jyoti Kant; Patel, Ashish; Verma, Mukesh Kumar

2017-01-01

Respiratory cancer database (RespCanDB) is a genomic and proteomic database of cancer of respiratory organ. It also includes the information of medicinal plants used for the treatment of various respiratory cancers with structure of its active constituents as well as pharmacological and chemical information of drug associated with various respiratory cancers. Data in RespCanDB has been manually collected from published research article and from other databases. Data has been integrated using MySQL an object-relational database management system. MySQL manages all data in the back-end and provides commands to retrieve and store the data into the database. The web interface of database has been built in ASP. RespCanDB is expected to contribute to the understanding of scientific community regarding respiratory cancer biology as well as developments of new way of diagnosing and treating respiratory cancer. Currently, the database consist the oncogenomic information of lung cancer, laryngeal cancer, and nasopharyngeal cancer. Data for other cancers, such as oral and tracheal cancers, will be added in the near future. The URL of RespCanDB is http://ridb.subdic-bioinformatics-nitrr.in/.

Distribution to the Astronomy Community of the Compressed Digitized Sky Survey

NASA Astrophysics Data System (ADS)

Postman, Marc

1996-03-01

The Space Telescope Science Institute has compressed an all-sky collection of ground-based images and has printed the data on a two volume, 102 CD-ROM disc set. The first part of the survey (containing images of the southern sky) was published in May 1994. The second volume (containing images of the northern sky) was published in January 1995. Software which manages the image retrieval is included with each volume. The Astronomical Society of the Pacific (ASP) is handling the distribution of the lOx compressed data and has sold 310 sets as of October 1996. ASP is also handling the distribution of the recently published 100x version of the northern sky survey which is publicly available at a low cost. The target markets for the 100x compressed data set are the amateur astronomy community, educational institutions, and the general public. During the next year, we plan to publish the first version of a photometric calibration database which will allow users of the compressed sky survey to determine the brightness of stars in the images.

Distribution to the Astronomy Community of the Compressed Digitized Sky Survey

NASA Technical Reports Server (NTRS)

Postman, Marc

1996-01-01

The Space Telescope Science Institute has compressed an all-sky collection of ground-based images and has printed the data on a two volume, 102 CD-ROM disc set. The first part of the survey (containing images of the southern sky) was published in May 1994. The second volume (containing images of the northern sky) was published in January 1995. Software which manages the image retrieval is included with each volume. The Astronomical Society of the Pacific (ASP) is handling the distribution of the lOx compressed data and has sold 310 sets as of October 1996. ASP is also handling the distribution of the recently published 100x version of the northern sky survey which is publicly available at a low cost. The target markets for the 100x compressed data set are the amateur astronomy community, educational institutions, and the general public. During the next year, we plan to publish the first version of a photometric calibration database which will allow users of the compressed sky survey to determine the brightness of stars in the images.

Astronomy Education Research Observations from the iSTAR international Study of Astronomical Reasoning Database

NASA Astrophysics Data System (ADS)

Tatge, C. B.; Slater, S. J.; Slater, T. F.; Schleigh, S.; McKinnon, D.

2016-12-01

Historically, an important part of the scientific research cycle is to situate any research project within the landscape of the existing scientific literature. In the field of discipline-based astronomy education research, grappling with the existing literature base has proven difficult because of the difficulty in obtaining research reports from around the world, particularly early ones. In order to better survey and efficiently utilize the wide and fractured range and domain of astronomy education research methods and results, the iSTAR international Study of Astronomical Reasoning database project was initiated. The project aims to host a living, online repository of dissertations, theses, journal articles, and grey literature resources to serve the world's discipline-based astronomy education research community. The first domain of research artifacts ingested into the iSTAR database were doctoral dissertations. To the authors' great surprise, nearly 300 astronomy education research dissertations were found from the last 100-years. Few, if any, of the literature reviews from recent astronomy education dissertations surveyed even come close to summarizing this many dissertations, most of which have not been published in traditional journals, as re-publishing one's dissertation research as a journal article was not a widespread custom in the education research community until recently. A survey of the iSTAR database dissertations reveals that the vast majority of work has been largely quantitative in nature until the last decade. We also observe that modern-era astronomy education research writings reaches as far back as 1923 and that the majority of dissertations come from the same eight institutions. Moreover, most of the astronomy education research work has been done covering learners' grasp of broad knowledge of astronomy rather than delving into specific learning targets, which has been more in vogue during the last two decades. The surprisingly wide breadth of largely unknown research revealed in the iSTAR database motivates us to begin to synthesize the research and look for broader themes using widely accepted meta analysis techniques.

A Change to the Platinum Publications | Poster

Cancer.gov

Please be advised that the Poster will no longer publish the “Platinum Publications” series listing recent NCI at Frederick publications. All published research represents a valuable addition to the fight against cancer, AIDS, and infectious diseases—thus, the “Platinum Publications” did not adequately commend all of the important work done by NCI at Frederick researchers. Going forward, we will highlight a broad cross section of research with more tightly focused stories that should interest the entire NCI at Frederick community. In addition, we encourage readers to visit the Scientific Library's NCI at Frederick Scientific Publications database to see recently published research as well as a list of past NCI at Frederick publications. Thank you.

miRwayDB: a database for experimentally validated microRNA-pathway associations in pathophysiological conditions

PubMed Central

Das, Sankha Subhra; Saha, Pritam

2018-01-01

Abstract MicroRNAs (miRNAs) are well-known as key regulators of diverse biological pathways. A series of experimental evidences have shown that abnormal miRNA expression profiles are responsible for various pathophysiological conditions by modulating genes in disease associated pathways. In spite of the rapid increase in research data confirming such associations, scientists still do not have access to a consolidated database offering these miRNA-pathway association details for critical diseases. We have developed miRwayDB, a database providing comprehensive information of experimentally validated miRNA-pathway associations in various pathophysiological conditions utilizing data collected from published literature. To the best of our knowledge, it is the first database that provides information about experimentally validated miRNA mediated pathway dysregulation as seen specifically in critical human diseases and hence indicative of a cause-and-effect relationship in most cases. The current version of miRwayDB collects an exhaustive list of miRNA-pathway association entries for 76 critical disease conditions by reviewing 663 published articles. Each database entry contains complete information on the name of the pathophysiological condition, associated miRNA(s), experimental sample type(s), regulation pattern (up/down) of miRNA, pathway association(s), targeted member of dysregulated pathway(s) and a brief description. In addition, miRwayDB provides miRNA, gene and pathway score to evaluate the role of a miRNA regulated pathways in various pathophysiological conditions. The database can also be used for other biomedical approaches such as validation of computational analysis, integrated analysis and prediction of computational model. It also offers a submission page to submit novel data from recently published studies. We believe that miRwayDB will be a useful tool for miRNA research community. Database URL: http://www.mirway.iitkgp.ac.in PMID:29688364

RaftProt: mammalian lipid raft proteome database.

PubMed

Shah, Anup; Chen, David; Boda, Akash R; Foster, Leonard J; Davis, Melissa J; Hill, Michelle M

2015-01-01

RaftProt (http://lipid-raft-database.di.uq.edu.au/) is a database of mammalian lipid raft-associated proteins as reported in high-throughput mass spectrometry studies. Lipid rafts are specialized membrane microdomains enriched in cholesterol and sphingolipids thought to act as dynamic signalling and sorting platforms. Given their fundamental roles in cellular regulation, there is a plethora of information on the size, composition and regulation of these membrane microdomains, including a large number of proteomics studies. To facilitate the mining and analysis of published lipid raft proteomics studies, we have developed a searchable database RaftProt. In addition to browsing the studies, performing basic queries by protein and gene names, searching experiments by cell, tissue and organisms; we have implemented several advanced features to facilitate data mining. To address the issue of potential bias due to biochemical preparation procedures used, we have captured the lipid raft preparation methods and implemented advanced search option for methodology and sample treatment conditions, such as cholesterol depletion. Furthermore, we have identified a list of high confidence proteins, and enabled searching only from this list of likely bona fide lipid raft proteins. Given the apparent biological importance of lipid raft and their associated proteins, this database would constitute a key resource for the scientific community. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Outreach and online training services at the Saccharomyces Genome Database.

PubMed

MacPherson, Kevin A; Starr, Barry; Wong, Edith D; Dalusag, Kyla S; Hellerstedt, Sage T; Lang, Olivia W; Nash, Robert S; Skrzypek, Marek S; Engel, Stacia R; Cherry, J Michael

2017-01-01

The Saccharomyces Genome Database (SGD; www.yeastgenome.org ), the primary genetics and genomics resource for the budding yeast S. cerevisiae , provides free public access to expertly curated information about the yeast genome and its gene products. As the central hub for the yeast research community, SGD engages in a variety of social outreach efforts to inform our users about new developments, promote collaboration, increase public awareness of the importance of yeast to biomedical research, and facilitate scientific discovery. Here we describe these various outreach methods, from networking at scientific conferences to the use of online media such as blog posts and webinars, and include our perspectives on the benefits provided by outreach activities for model organism databases. http://www.yeastgenome.org. © The Author(s) 2017. Published by Oxford University Press.

Factors influencing community nursing roles and health service provision in rural areas: a review of literature.

PubMed

Barrett, Annette; Terry, Daniel R; Lê, Quynh; Hoang, Ha

2016-02-01

This review sought to better understand the issues and challenges experienced by community nurses working in rural areas and how these factors shape their role. Databases were searched to identify relevant studies, published between 1990 and 2015, that focussed on issues and challenges experienced by rural community nurses. Generic and grey literature relating to the subject was also searched. The search was systematically conducted multiple times to assure accuracy. A total of 14 articles met the inclusion criteria. This critical review identified common issues impacting community nursing and included role definition, organisational change, human resource, workplace and geographic challenges. Community nurses are flexible, autonomous, able to adapt care to the service delivery setting, and have a diversity of knowledge and skills. Considerably more research is essential to identify factors that impact rural community nursing practice. In addition, greater advocacy is required to develop the role.

Nursing Child Assessment Satellite Training Parent-Child Interaction Scales: Comparing American and Canadian Normative and High-Risk Samples.

PubMed

Letourneau, Nicole L; Tryphonopoulos, Panagiota D; Novick, Jason; Hart, J Martha; Giesbrecht, Gerald; Oxford, Monica L

Many nurses rely on the American Nursing Child Assessment Satellite Training (NCAST) Parent-Child Interaction (PCI) Teaching and Feeding Scales to identify and target interventions for families affected by severe/chronic stressors (e.g. postpartum depression (PPD), intimate partner violence (IPV), low-income). However, the NCAST Database that provides normative data for comparisons may not apply to Canadian families. The purpose of this study was to compare NCAST PCI scores in Canadian and American samples and to assess the reliability of the NCAST PCI Scales in Canadian samples. This secondary analysis employed independent samples t-tests (p < 0.005) to compare PCI between the American NCAST Database and Canadian high-risk (families with PPD, exposure to IPV or low-income) and community samples. Cronbach's alphas were calculated for the Canadian and American samples. In both American and Canadian samples, belonging to a high-risk population reduced parents' abilities to engage in sensitive and responsive caregiving (i.e. healthy serve and return relationships) as measured by the PCI Scales. NCAST Database mothers were more effective at executing caregiving responsibilities during PCI compared to the Canadian community sample, while infants belonging to the Canadian community sample provided clearer cues to caregivers during PCI compared to those of the NCAST Database. Internal consistency coefficients for the Canadian samples were generally acceptable. The NCAST Database can be reliably used for assessing PCI in normative and high-risk Canadian families. Canadian nurses can be assured that the PCI Scales adequately identify risks and can help target interventions to promote optimal parent-child relationships and ultimately child development. Crown Copyright © 2018. Published by Elsevier Inc. All rights reserved.

The Crisis in Scholarly Communication, Open Access, and Open Data Policies: The Libraries' Perspective

NASA Astrophysics Data System (ADS)

Besara, Rachel

2015-03-01

For years the cost of STEM databases have exceeded the rate of inflation. Libraries have reallocated funds for years to continue to provide support to their scientific communities, but they are reaching a point at many institutions where they are no longer able to provide access to many databases considered standard to support research. A possible or partial alleviation to this problem is the federal open access mandate. However, this shift challenges the current model of publishing and data management in the sciences. This talk will discuss these topics from the perspective of research libraries supporting physics and the STEM disciplines.

Is Biblioleaks Inevitable?

PubMed Central

Coiera, Enrico; Mandl, Kenneth D

2014-01-01

In 2014, the vast majority of published biomedical research is still hidden behind paywalls rather than open access. For more than a decade, similar restrictions over other digitally available content have engendered illegal activity. Music file sharing became rampant in the late 1990s as communities formed around new ways to share. The frequency and scale of cyber-attacks against commercial and government interests has increased dramatically. Massive troves of classified government documents have become public through the actions of a few. Yet we have not seen significant growth in the illegal sharing of peer-reviewed academic articles. Should we truly expect that biomedical publishing is somehow at less risk than other content-generating industries? What of the larger threat—a “Biblioleaks” event—a database breach and public leak of the substantial archives of biomedical literature? As the expectation that all research should be available to everyone becomes the norm for a younger generation of researchers and the broader community, the motivations for such a leak are likely to grow. We explore the feasibility and consequences of a Biblioleaks event for researchers, journals, publishers, and the broader communities of doctors and the patients they serve. PMID:24755534

Walking the Path Together: Indigenous Health Data at ICES.

PubMed

Pyper, Evelyn; Henry, David; Yates, Erika A; Mecredy, Graham; Ratnasingham, Sujitha; Slegers, Brian; Walker, Jennifer D

2018-01-01

Indigenous data governance principles assert that Indigenous communities have a right to data that identifies their people or communities, and a right to determine the use of that data in ways that support Indigenous health and self-determination. Indigenous-driven use of the databases held at the Institute for Clinical Evaluative Sciences (ICES) has resulted in ongoing partnerships between ICES and diverse Indigenous organizations and communities. To respond to this emerging and complex landscape, ICES has established a team whose goal is to support the infrastructure for responding to community-initiated research priorities. ICES works closely with Indigenous partners to develop unique data governance agreements and supports processes, which ensure that ICES scientists must work with Indigenous organizations when conducting research that involves Indigenous peoples. © 2018 Longwoods Publishing.

A new online database of nuclear electromagnetic moments

NASA Astrophysics Data System (ADS)

Mertzimekis, Theo J.

2017-09-01

Nuclear electromagnetic (EM) moments, i.e., the magnetic dipole and the electric quadrupole moments, provide important information of nuclear structure. As in other types of experimental data available to the community, measurements of nuclear EM moments have been organized systematically in compilations since the dawn of nuclear science. However, the wealth of recent moments measurements with radioactive beams, as well as earlier existing measurements, lack an online, easy-to-access, systematically organized presence to disseminate information to researchers. In addition, available printed compilations suffer a rather long life cycle, being left behind experimental measurements published in journals or elsewhere. A new, online database (http://magneticmoments.info) focusing on nuclear EM moments has been recently developed to disseminate experimental data to the community. The database includes non-evaluated experimental data of nuclear EM moments, giving strong emphasis on frequent updates (life cycle is 3 months) and direct connection to the sources via DOI and NSR hyperlinks. It has been recently integrated in IAEA LiveChart [1], but can also be found as a standalone webapp [2]. A detailed review of the database features, as well as plans for further development and expansion in the near future is discussed.

Ethics and Community Involvement in Syntheses Concerning American Indian, Alaska Native, or Native Hawaiian Health: A Systematic Review

PubMed Central

Around Him, Deana M.

2014-01-01

Background The objective of the research was to review reporting of ethical concerns and community involvement in peer-reviewed systematic reviews or meta-analyses concerning American Indian, Alaska Native, or Native Hawaiian (AI/AN/NH) health. Methods Text words and indexed vocabulary terms were used to query PubMed, Embase, Cochrane Library, and the Native Health Database for systematic reviews or meta-analyses concerning AI/AN/NH health published in peer-reviewed journals, followed by a search through reference lists. Each article was abstracted by two independent reviewers; results were discussed until consensus was reached. Results We identified 107 papers published from 1986–2012 that were primarily about AI/AN/NH health or presented findings separately for AI/AN/NH communities. Two reported seeking indigenous reviewer feedback; none reported seeking input from tribes and communities. Approximately 7% reported on institutional review board (IRB) approval of included studies, 5% reported on tribal approval, and 4% referenced the sovereignty of AI/AN tribes. Approximately 63% used evidence from more than one AI/AN/NH population study, and 28% discussed potential benefits to communities from the synthesis research. Conclusions Reporting of ethics and community involvement are not prominent. Systematic reviews and meta-analyses making community-level inferences may pose risks to communities. Future systematic reviews and meta-analyses should consider ethical and participatory dimensions of research. PMID:25089283

[Predatory journals: how their publishers operate and how to avoid them].

PubMed

Kratochvíl, Jiří; Plch, Lukáš

Authors who publish in scientific or scholarly journals today face the risk of publishing in so-called predatory journals. These journals exploit the noble idea of the Open Access movement, whose goal is to make the latest scientific findings available for free. Predatory journals, unlike the reputable ones working on an Open Access basis, neglect the review process and publish low-quality submissions. The basic attributes of predatory journals are a very quick review process or even none at all, failure to be transparent about author fees for publishing an article, misleading potential authors by imitating the names of well-established journals, and false information on indexing in renowned databases or assigned impact factor. Some preventive measures against publishing in predatory journals or drawing information from them are: a thorough credibility check of the journals webpages, verification of the journals indexing on Bealls List and in the following databases: Web of Science Core Collection, Scopus, ERIH PLUS and DOAJ. Asking other scientists or scholars about their experience with a given journal can also be helpful. Without these necessary steps authors face an increased risk of publishing in a journal of poor quality, which will prevent them from obtaining Research and Development Council points (awarded based on the Information Register of Research & Development results); even more importantly, it may damage their reputation as well as the good name of their home institution in the professional community.Key words: academic writing - medical journals - Open Access - predatory journals - predatory publishers - scientific publications.

Examining the social determinants of children's developmental health: protocol for building a pan-Canadian population-based monitoring system for early childhood development.

PubMed

Guhn, Martin; Janus, Magdalena; Enns, Jennifer; Brownell, Marni; Forer, Barry; Duku, Eric; Muhajarine, Nazeem; Raos, Rob

2016-04-29

Early childhood is a key period to establish policies and practices that optimise children's health and development, but Canada lacks nationally representative data on social indicators of children's well-being. To address this gap, the Early Development Instrument (EDI), a teacher-administered questionnaire completed for kindergarten-age children, has been implemented across most Canadian provinces over the past 10 years. The purpose of this protocol is to describe the Canadian Neighbourhoods and Early Child Development (CanNECD) Study, the aims of which are to create a pan-Canadian EDI database to monitor trends over time in children's developmental health and to advance research examining the social determinants of health. Canada-wide EDI records from 2004 to 2014 (representing over 700,000 children) will be linked to Canada Census and Income Taxfiler data. Variables of socioeconomic status derived from these databases will be used to predict neighbourhood-level EDI vulnerability rates by conducting a series of regression analyses and latent variable models at provincial/territorial and national levels. Where data are available, we will measure the neighbourhood-level change in developmental vulnerability rates over time and model the socioeconomic factors associated with those trends. Ethics approval for this study was granted by the Behavioural Research Ethics Board at the University of British Columbia. Study findings will be disseminated to key partners, including provincial and federal ministries, schools and school districts, collaborative community groups and the early childhood development research community. The database created as part of this longitudinal population-level monitoring system will allow researchers to associate practices, programmes and policies at school and community levels with trends in developmental health outcomes. The CanNECD Study will guide future early childhood development action and policies, using the database as a tool for formative programme and policy evaluation. 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/

PAGES-Powell North America 2k database

NASA Astrophysics Data System (ADS)

McKay, N.

2014-12-01

Syntheses of paleoclimate data in North America are essential for understanding long-term spatiotemporal variability in climate and for properly assessing risk on decadal and longer timescales. Existing reconstructions of the past 2,000 years rely almost exclusively on tree-ring records, which can underestimate low-frequency variability and rarely extend beyond the last millennium. Meanwhile, many records from the full spectrum of paleoclimate archives are available and hold the potential of enhancing our understanding of past climate across North America over the past 2000 years. The second phase of the Past Global Changes (PAGES) North America 2k project began in 2014, with a primary goal of assembling these disparate paleoclimate records into a unified database. This effort is currently supported by the USGS Powell Center together with PAGES. Its success requires grassroots support from the community of researchers developing and interpreting paleoclimatic evidence relevant to the past 2000 years. Most likely, fewer than half of the published records appropriate for this database are publicly archived, and far fewer include the data needed to quantify geochronologic uncertainty, or to concisely describe how best to interpret the data in context of a large-scale paleoclimatic synthesis. The current version of the database includes records that (1) have been published in a peer-reviewed journal (including evidence of the record's relationship to climate), (2) cover a substantial portion of the past 2000 yr (>300 yr for annual records, >500 yr for lower frequency records) at relatively high resolution (<50 yr/observation), and (3) have reasonably small and quantifiable age uncertainty. Presently, the database includes records from boreholes, ice cores, lake and marine sediments, speleothems, and tree rings. This poster presentation will display the site locations and basic metadata of the records currently in the database. We invite anyone with interest in participating in the project to visit the poster or contact the author to help identify and assimilate relevant records that have not yet been included. The goal is to develop a comprehensive and open-access resource that will serve the diverse community interested in the climate of the Common Era in North America.

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

PubMed

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

2018-06-01

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

The BRENDA enzyme information system-From a database to an expert system.

PubMed

Schomburg, I; Jeske, L; Ulbrich, M; Placzek, S; Chang, A; Schomburg, D

2017-11-10

Enzymes, representing the largest and by far most complex group of proteins, play an essential role in all processes of life, including metabolism, gene expression, cell division, the immune system, and others. Their function, also connected to most diseases or stress control makes them interesting targets for research and applications in biotechnology, medical treatments, or diagnosis. Their functional parameters and other properties are collected, integrated, and made available to the scientific community in the BRaunschweig ENzyme DAtabase (BRENDA). In the last 30 years BRENDA has developed into one of the most highly used biological databases worldwide. The data contents, the process of data acquisition, data integration and control, the ways to access the data, and visualizations provided by the website are described and discussed. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Community-based interventions to prevent fatal overdose from illegal drugs: a systematic review protocol.

PubMed

Okolie, Chukwudi; Evans, Bridie Angela; John, Ann; Moore, Chris; Russell, Daphne; Snooks, Helen

2015-11-03

Drug overdose is the most frequent cause of death among people who misuse illegal drugs. People who inject these drugs are 14-17 times more likely to die than their non-drug using peers. Various strategies to reduce drug-related deaths have failed to meet target reductions. Research into community-based interventions for preventing drug overdose deaths is promising. This review seeks to identify published studies describing community-based interventions and to evaluate their effectiveness at reducing drug overdose deaths. We will systematically search key electronic databases using a search strategy which groups terms into four facets: (1) Overdose event, (2) Drug classification, (3) Intervention and (4) Setting. Searches will be limited where possible to international literature published in English between 1998 and 2014. Data will be extracted by two independent reviewers using a predefined table adapted from the Cochrane Collaboration handbook. The quality of included studies will be evaluated using the Cochrane Collaboration's tool for assessing risk of bias. We will conduct a meta-analysis for variables which can be compared across studies, using statistical methods to control for heterogeneity where appropriate. Where clinical or statistical heterogeneity prevents a valid numerical synthesis, we will employ a narrative synthesis to describe community-based interventions, their delivery and use and how effectively they prevent fatal overdoses. We will publish findings from this systematic review in a peer-reviewed scientific journal and present results at national and international conferences. It will be disseminated electronically and in print. PROSPERO CRD42015017833. 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/

The seed bank longevity index revisited: limited reliability evident from a burial experiment and database analyses.

PubMed

Saatkamp, Arne; Affre, Laurence; Dutoit, Thierry; Poschlod, Peter

2009-09-01

Seed survival in the soil contributes to population persistence and community diversity, creating a need for reliable measures of soil seed bank persistence. Several methods estimate soil seed bank persistence, most of which count seedlings emerging from soil samples. Seasonality, depth distribution and presence (or absence) in vegetation are then used to classify a species' soil seed bank into persistent or transient, often synthesized into a longevity index. This study aims to determine if counts of seedlings from soil samples yield reliable seed bank persistence estimates and if this is correlated to seed production. Seeds of 38 annual weeds taken from arable fields were buried in the field and their viability tested by germination and tetrazolium tests at 6 month intervals for 2.5 years. This direct measure of soil seed survival was compared with indirect estimates from the literature, which use seedling emergence from soil samples to determine seed bank persistence. Published databases were used to explore the generality of the influence of reproductive capacity on seed bank persistence estimates from seedling emergence data. There was no relationship between a species' soil seed survival in the burial experiment and its seed bank persistence estimate from published data using seedling emergence from soil samples. The analysis of complementary data from published databases revealed that while seed bank persistence estimates based on seedling emergence from soil samples are generally correlated with seed production, estimates of seed banks from burial experiments are not. The results can be explained in terms of the seed size-seed number trade-off, which suggests that the higher number of smaller seeds is compensated after germination. Soil seed bank persistence estimates correlated to seed production are therefore not useful for studies on population persistence or community diversity. Confusion of soil seed survival and seed production can be avoided by separate use of soil seed abundance and experimental soil seed survival.

Marketing activity in the community pharmacy sector - A scoping review.

PubMed

Mirzaei, Ardalan; Carter, Stephen R; Schneider, Carl R

2018-02-01

Community pharmacy ownership requires engaging with marketing strategies to influence consumer behaviour. There is a plethora of information from trade journals, expert opinion, and published discussion surrounding this issue. Despite this, evidence relating to the efficacy of marketing activity within the pharmacy sector is scant. To review how marketing activity has been conceptualised in the community pharmacy sector and to determine the evidence for the effect of marketing activity. Seven databases were systematically searched using a scoping review framework with the reporting protocol of PRISMA-P. The search yielded 33 studies that were analysed for year of publication, journal, country of focus, and framework of marketing. The majority of marketing research papers focused on the United States and were published in healthcare journals. These were various marketing strategy elements, including; segmentation, targeting, differentiation, and positioning. Also evident was research regarding marketing mix, which predominately involved the "4Ps" model. Actual marketing activity comprised little of the research. Research into marketing activity in community pharmacy is limited, and little evidence is available to show the effects of such activities. Future research needs to demonstrate the causality for the effect of marketing activities on consumer behaviour and economic outcomes. Copyright © 2017 Elsevier Inc. All rights reserved.

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.

PubMed

Salek, Reza M; Neumann, Steffen; Schober, Daniel; Hummel, Jan; Billiau, Kenny; Kopka, Joachim; Correa, Elon; Reijmers, Theo; Rosato, Antonio; Tenori, Leonardo; Turano, Paola; Marin, Silvia; Deborde, Catherine; Jacob, Daniel; Rolin, Dominique; Dartigues, Benjamin; Conesa, Pablo; Haug, Kenneth; Rocca-Serra, Philippe; O'Hagan, Steve; Hao, Jie; van Vliet, Michael; Sysi-Aho, Marko; Ludwig, Christian; Bouwman, Jildau; Cascante, Marta; Ebbels, Timothy; Griffin, Julian L; Moing, Annick; Nikolski, Macha; Oresic, Matej; Sansone, Susanna-Assunta; Viant, Mark R; Goodacre, Royston; Günther, Ulrich L; Hankemeier, Thomas; Luchinat, Claudio; Walther, Dirk; Steinbeck, Christoph

Metabolomics has become a crucial phenotyping technique in a range of research fields including medicine, the life sciences, biotechnology and the environmental sciences. This necessitates the transfer of experimental information between research groups, as well as potentially to publishers and funders. After the initial efforts of the metabolomics standards initiative, minimum reporting standards were proposed which included the concepts for metabolomics databases. Built by the community, standards and infrastructure for metabolomics are still needed to allow storage, exchange, comparison and re-utilization of metabolomics data. The Framework Programme 7 EU Initiative 'coordination of standards in metabolomics' (COSMOS) is developing a robust data infrastructure and exchange standards for metabolomics data and metadata. This is to support workflows for a broad range of metabolomics applications within the European metabolomics community and the wider metabolomics and biomedical communities' participation. Here we announce our concepts and efforts asking for re-engagement of the metabolomics community, academics and industry, journal publishers, software and hardware vendors, as well as those interested in standardisation worldwide (addressing missing metabolomics ontologies, complex-metadata capturing and XML based open source data exchange format), to join and work towards updating and implementing metabolomics standards.

A Systematic Review of Community-Based Participatory Research to Enhance Clinical Trials in Racial and Ethnic Minority Groups

PubMed Central

De Las Nueces, Denise; Hacker, Karen; DiGirolamo, Ann; Hicks, LeRoi S

2012-01-01

Objective To examine the effectiveness of current community-based participatory research (CBPR) clinical trials involving racial and ethnic minorities. Data Source All published peer-reviewed CBPR intervention articles in PubMed and CINAHL databases from January 2003 to May 2010. Study Design We performed a systematic literature review. Data Collection/Extraction Methods Data were extracted on each study's characteristics, community involvement in research, subject recruitment and retention, and intervention effects. Principle Findings We found 19 articles meeting inclusion criteria. Of these, 14 were published from 2007 to 2010. Articles described some measures of community participation in research with great variability. Although CBPR trials examined a wide range of behavioral and clinical outcomes, such trials had very high success rates in recruiting and retaining minority participants and achieving significant intervention effects. Conclusions Significant publication gaps remain between CBPR and other interventional research methods. CBPR may be effective in increasing participation of racial and ethnic minority subjects in research and may be a powerful tool in testing the generalizability of effective interventions among these populations. CBPR holds promise as an approach that may contribute greatly to the study of health care delivery to disadvantaged populations. PMID:22353031

Catalogs of Space Shuttle earth observations photography

NASA Technical Reports Server (NTRS)

Lulla, Kamlesh; Helfert, Michael

1990-01-01

A review is presented of postflight cataloging and indexing activities of mission data obtained from Space Shuttle earth observations photography. Each Space Shuttle mission acquires 1300-4400 photographs of the earth that are reviewed and interpreted by a team of photointerpreters and cataloging specialists. Every photograph's manual and electronic set of plots is compared for accuracy of its locational coordinates. This cataloging activity is a critical and principal part of postflight activity and ensures that the database is accurate, updated and consequently made meaningful for further utilization in the applications and research communities. A final product in the form of a Catalog of Space Shuttle Earth Observations Handheld Photography is published for users of this database.

On the evolving portfolio of community-standards and data sharing policies: turning challenges into new opportunities.

PubMed

Sansone, Susanna-Assunta; Rocca-Serra, Philippe

2012-07-12

There are thousands of biology databases with hundreds of terminologies, reporting guidelines, representations models, and exchange formats to help annotate, report, and share bioscience investigations. It is evident, however, that researchers and bioinformaticians struggle to navigate the various standards and to find the appropriate database to collect, manage, and share data. Further, policy makers, funders, and publishers lack sufficient information to formulate their guidelines. In this paper, we highlight a number of key issues that can be used to turn these challenges into new opportunities. It is time for all stakeholders to work together to reconcile cause and effect and make the data-sharing culture functional and efficient.

BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types

PubMed Central

Howe, E.A.; de Souza, A.; Lahr, D.L.; Chatwin, S.; Montgomery, P.; Alexander, B.R.; Nguyen, D.-T.; Cruz, Y.; Stonich, D.A.; Walzer, G.; Rose, J.T.; Picard, S.C.; Liu, Z.; Rose, J.N.; Xiang, X.; Asiedu, J.; Durkin, D.; Levine, J.; Yang, J.J.; Schürer, S.C.; Braisted, J.C.; Southall, N.; Southern, M.R.; Chung, T.D.Y.; Brudz, S.; Tanega, C.; Schreiber, S.L.; Bittker, J.A.; Guha, R.; Clemons, P.A.

2015-01-01

BARD, the BioAssay Research Database (https://bard.nih.gov/) is a public database and suite of tools developed to provide access to bioassay data produced by the NIH Molecular Libraries Program (MLP). Data from 631 MLP projects were migrated to a new structured vocabulary designed to capture bioassay data in a formalized manner, with particular emphasis placed on the description of assay protocols. New data can be submitted to BARD with a user-friendly set of tools that assist in the creation of appropriately formatted datasets and assay definitions. Data published through the BARD application program interface (API) can be accessed by researchers using web-based query tools or a desktop client. Third-party developers wishing to create new tools can use the API to produce stand-alone tools or new plug-ins that can be integrated into BARD. The entire BARD suite of tools therefore supports three classes of researcher: those who wish to publish data, those who wish to mine data for testable hypotheses, and those in the developer community who wish to build tools that leverage this carefully curated chemical biology resource. PMID:25477388

A food environments feedback system (FoodBack) for empowering citizens and change agents to create healthier community food places.

PubMed

Vandevijvere, Stefanie; Williams, Rachel; Tawfiq, Essa; Swinburn, Boyd

2017-11-14

This study developed a systems-based approach (called FoodBack) to empower citizens and change agents to create healthier community food places. Formative evaluations were held with citizens and change agents in six diverse New Zealand communities, supplemented by semi-structured interviews with 85 change agents in Auckland and Hamilton in 2015-2016. The emerging system was additionally reviewed by public health experts from diverse organizations. A food environments feedback system was constructed to crowdsource key indicators of the healthiness of diverse community food places (i.e. schools, hospitals, supermarkets, fast food outlets, sport centers) and outdoor spaces (i.e. around schools), comments/pictures about barriers and facilitators to healthy eating and exemplar stories on improving the healthiness of food environments. All the information collected is centrally processed and translated into 'short' (immediate) and 'long' (after analyses) feedback loops to stimulate actions to create healthier food places. FoodBack, as a comprehensive food environment feedback system (with evidence databases and feedback and recognition processes), has the potential to increase food sovereignty, and generate a sustainable, fine-grained database of food environments for real-time food policy research. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The use of fatty acid methyl esters as biomarkers to determine aerobic, facultatively aerobic and anaerobic communities in wastewater treatment systems.

PubMed

Quezada, Maribel; Buitrón, Germán; Moreno-Andrade, Iván; Moreno, Gloria; López-Marín, Luz M

2007-01-01

The use of fatty acid methyl esters (FAME) as biomarkers to identify groups of microorganisms was studied. A database was constructed using previously published results that identify FAME biomarkers for aerobic, anaerobic and facultatively aerobic bacteria. FAME profiles obtained from pure cultures were utilized to confirm the predicted presence of biomarkers. Principal component analysis demonstrated that the FAME profiles can be used to determine the incidence of these bacterial groups. The presence of aerobic, anaerobic and facultatively aerobic bacteria in the communities, in four bioreactors being used to treat different wastewaters, was investigated by applying FAME biomarkers.

On the level of coverage and citation of publications by mechanicians of the national academy of sciences of Ukraine in the Scopus database

NASA Astrophysics Data System (ADS)

Guz, A. N.; Rushchitsky, J. J.

2009-11-01

The paper analyzes the level of coverage and citation of publications by mechanicians of the National Academy of Sciences of Ukraine (NASU) in the Scopus database. Two groups of mechanicians are considered. One group includes 66 doctors of sciences of the S. P. Timoshenko Institute of Mechanics as representatives of the oldest institute of the NASU. The other group includes 34 members (academicians and corresponding members) of the Division of Mechanics of the NASU as representatives of the authoritative community of mechanicians in Ukraine. The results are presented for each scientist in the form of two indices—the total number of publications accessible in the database as the level of coverage of the scientist's publications in this database and the h-index as the citation level of these publications. This paper may be considered to continue the papers [6-12] published in Prikladnaya Mekhanika (International Applied Mechanics) in 2005-2009

Improved group-specific primers based on the full SILVA 16S rRNA gene reference database.

PubMed

Pfeiffer, Stefan; Pastar, Milica; Mitter, Birgit; Lippert, Kathrin; Hackl, Evelyn; Lojan, Paul; Oswald, Andreas; Sessitsch, Angela

2014-08-01

Quantitative PCR (qPCR) and community fingerprinting methods, such as the Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis,are well-suited techniques for the examination of microbial community structures. The use of phylum and class-specific primers can provide enhanced sensitivity and phylogenetic resolution as compared with domain-specific primers. To date, several phylum- and class-specific primers targeting the 16S ribosomal RNA gene have been published. However, many of these primers exhibit low discriminatory power against non-target bacteria in PCR. In this study, we evaluated the precision of certain published primers in silico and via specific PCR. We designed new qPCR and T-RFLP primer pairs (for the classes Alphaproteobacteria and Betaproteobacteria, and the phyla Bacteroidetes, Firmicutes and Actinobacteria) by combining the sequence information from a public dataset (SILVA SSU Ref 102 NR) with manual primer design. We evaluated the primer pairs via PCR using isolates of the above-mentioned groups and via screening of clone libraries from environmental soil samples and human faecal samples. As observed through theoretical and practical evaluation, the primers developed in this study showed a higher level of precision than previously published primers, thus allowing a deeper insight into microbial community dynamics.

The Danish Inguinal Hernia database.

PubMed

Friis-Andersen, Hans; Bisgaard, Thue

2016-01-01

To monitor and improve nation-wide surgical outcome after groin hernia repair based on scientific evidence-based surgical strategies for the national and international surgical community. Patients ≥18 years operated for groin hernia. Type and size of hernia, primary or recurrent, type of surgical repair procedure, mesh and mesh fixation methods. According to the Danish National Health Act, surgeons are obliged to register all hernia repairs immediately after surgery (3 minute registration time). All institutions have continuous access to their own data stratified on individual surgeons. Registrations are based on a closed, protected Internet system requiring personal codes also identifying the operating institution. A national steering committee consisting of 13 voluntary and dedicated surgeons, 11 of whom are unpaid, handles the medical management of the database. The Danish Inguinal Hernia Database comprises intraoperative data from >130,000 repairs (May 2015). A total of 49 peer-reviewed national and international publications have been published from the database (June 2015). The Danish Inguinal Hernia Database is fully active monitoring surgical quality and contributes to the national and international surgical society to improve outcome after groin hernia repair.

The Coral Trait Database, a curated database of trait information for coral species from the global oceans

NASA Astrophysics Data System (ADS)

Madin, Joshua S.; Anderson, Kristen D.; Andreasen, Magnus Heide; Bridge, Tom C. L.; Cairns, Stephen D.; Connolly, Sean R.; Darling, Emily S.; Diaz, Marcela; Falster, Daniel S.; Franklin, Erik C.; Gates, Ruth D.; Hoogenboom, Mia O.; Huang, Danwei; Keith, Sally A.; Kosnik, Matthew A.; Kuo, Chao-Yang; Lough, Janice M.; Lovelock, Catherine E.; Luiz, Osmar; Martinelli, Julieta; Mizerek, Toni; Pandolfi, John M.; Pochon, Xavier; Pratchett, Morgan S.; Putnam, Hollie M.; Roberts, T. Edward; Stat, Michael; Wallace, Carden C.; Widman, Elizabeth; Baird, Andrew H.

2016-03-01

Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism’s function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research.

The Coral Trait Database, a curated database of trait information for coral species from the global oceans

PubMed Central

Madin, Joshua S.; Anderson, Kristen D.; Andreasen, Magnus Heide; Bridge, Tom C.L.; Cairns, Stephen D.; Connolly, Sean R.; Darling, Emily S.; Diaz, Marcela; Falster, Daniel S.; Franklin, Erik C.; Gates, Ruth D.; Hoogenboom, Mia O.; Huang, Danwei; Keith, Sally A.; Kosnik, Matthew A.; Kuo, Chao-Yang; Lough, Janice M.; Lovelock, Catherine E.; Luiz, Osmar; Martinelli, Julieta; Mizerek, Toni; Pandolfi, John M.; Pochon, Xavier; Pratchett, Morgan S.; Putnam, Hollie M.; Roberts, T. Edward; Stat, Michael; Wallace, Carden C.; Widman, Elizabeth; Baird, Andrew H.

2016-01-01

Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism’s function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research. PMID:27023900

The Coral Trait Database, a curated database of trait information for coral species from the global oceans.

PubMed

Madin, Joshua S; Anderson, Kristen D; Andreasen, Magnus Heide; Bridge, Tom C L; Cairns, Stephen D; Connolly, Sean R; Darling, Emily S; Diaz, Marcela; Falster, Daniel S; Franklin, Erik C; Gates, Ruth D; Harmer, Aaron; Hoogenboom, Mia O; Huang, Danwei; Keith, Sally A; Kosnik, Matthew A; Kuo, Chao-Yang; Lough, Janice M; Lovelock, Catherine E; Luiz, Osmar; Martinelli, Julieta; Mizerek, Toni; Pandolfi, John M; Pochon, Xavier; Pratchett, Morgan S; Putnam, Hollie M; Roberts, T Edward; Stat, Michael; Wallace, Carden C; Widman, Elizabeth; Baird, Andrew H

2016-03-29

Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism's function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research.

Systematic analysis of snake neurotoxins' functional classification using a data warehousing approach.

PubMed

Siew, Joyce Phui Yee; Khan, Asif M; Tan, Paul T J; Koh, Judice L Y; Seah, Seng Hong; Koo, Chuay Yeng; Chai, Siaw Ching; Armugam, Arunmozhiarasi; Brusic, Vladimir; Jeyaseelan, Kandiah

2004-12-12

Sequence annotations, functional and structural data on snake venom neurotoxins (svNTXs) are scattered across multiple databases and literature sources. Sequence annotations and structural data are available in the public molecular databases, while functional data are almost exclusively available in the published articles. There is a need for a specialized svNTXs database that contains NTX entries, which are organized, well annotated and classified in a systematic manner. We have systematically analyzed svNTXs and classified them using structure-function groups based on their structural, functional and phylogenetic properties. Using conserved motifs in each phylogenetic group, we built an intelligent module for the prediction of structural and functional properties of unknown NTXs. We also developed an annotation tool to aid the functional prediction of newly identified NTXs as an additional resource for the venom research community. We created a searchable online database of NTX proteins sequences (http://research.i2r.a-star.edu.sg/Templar/DB/snake_neurotoxin). This database can also be found under Swiss-Prot Toxin Annotation Project website (http://www.expasy.org/sprot/).

TMDB: a literature-curated database for small molecular compounds found from tea.

PubMed

Yue, Yi; Chu, Gang-Xiu; Liu, Xue-Shi; Tang, Xing; Wang, Wei; Liu, Guang-Jin; Yang, Tao; Ling, Tie-Jun; Wang, Xiao-Gang; Zhang, Zheng-Zhu; Xia, Tao; Wan, Xiao-Chun; Bao, Guan-Hu

2014-09-16

Tea is one of the most consumed beverages worldwide. The healthy effects of tea are attributed to a wealthy of different chemical components from tea. Thousands of studies on the chemical constituents of tea had been reported. However, data from these individual reports have not been collected into a single database. The lack of a curated database of related information limits research in this field, and thus a cohesive database system should necessarily be constructed for data deposit and further application. The Tea Metabolome database (TMDB), a manually curated and web-accessible database, was developed to provide detailed, searchable descriptions of small molecular compounds found in Camellia spp. esp. in the plant Camellia sinensis and compounds in its manufactured products (different kinds of tea infusion). TMDB is currently the most complete and comprehensive curated collection of tea compounds data in the world. It contains records for more than 1393 constituents found in tea with information gathered from 364 published books, journal articles, and electronic databases. It also contains experimental 1H NMR and 13C NMR data collected from the purified reference compounds or collected from other database resources such as HMDB. TMDB interface allows users to retrieve tea compounds entries by keyword search using compound name, formula, occurrence, and CAS register number. Each entry in the TMDB contains an average of 24 separate data fields including its original plant species, compound structure, formula, molecular weight, name, CAS registry number, compound types, compound uses including healthy benefits, reference literatures, NMR, MS data, and the corresponding ID from databases such as HMDB and Pubmed. Users can also contribute novel regulatory entries by using a web-based submission page. The TMDB database is freely accessible from the URL of http://pcsb.ahau.edu.cn:8080/TCDB/index.jsp. The TMDB is designed to address the broad needs of tea biochemists, natural products chemists, nutritionists, and members of tea related research community. The TMDB database provides a solid platform for collection, standardization, and searching of compounds information found in tea. As such this database will be a comprehensive repository for tea biochemistry and tea health research community.

The database on transgenic luminescent microorganisms as an instrument of studying a microbial component of closed ecosystems

NASA Astrophysics Data System (ADS)

Boyandin, A. N.; Lankin, Y. P.; Kargatova, T. V.; Popova, L. Y.; Pechurkin, N. S.

Luminescent transgenic microorganisms are widely used for study of microbial communities' functioning including closed ones. Bioluminescence is of high sensitive to effects of different environmental factors. Integration of lux-genes into different metabolic ways allows studying many aspects of microorganisms' life permitting to carry out measurements in situ. There is much information about applications of bioluminescent bacteria in different researches. But for effective using these data their summarizing and accumulation in common source is required. Therefore an information system on characteristics of transgenic microorganisms with cloned lux-genes was created. The database and client software related were developed. A database structure includes information on common characteristics of cloned lux-genes, their sources and properties, on regulation of gene expression in bacterial cells, on dependence of bioluminescence manifestation on biotic, abiotic and anthropogenic environmental factors. The database also can store description of changes in bacterial populations depending on environmental changes. The database created allows storing and using bibliographic information and also links to web sites of world collections of microorganisms. Internet publishing software permitting to open access to the database through the Internet is developed.

A decade of Web Server updates at the Bioinformatics Links Directory: 2003-2012.

PubMed

Brazas, Michelle D; Yim, David; Yeung, Winston; Ouellette, B F Francis

2012-07-01

The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field.

Sharing and community curation of mass spectrometry data with GNPS

PubMed Central

Nguyen, Don Duy; Watrous, Jeramie; Kapono, Clifford A; Luzzatto-Knaan, Tal; Porto, Carla; Bouslimani, Amina; Melnik, Alexey V; Meehan, Michael J; Liu, Wei-Ting; Crüsemann, Max; Boudreau, Paul D; Esquenazi, Eduardo; Sandoval-Calderón, Mario; Kersten, Roland D; Pace, Laura A; Quinn, Robert A; Duncan, Katherine R; Hsu, Cheng-Chih; Floros, Dimitrios J; Gavilan, Ronnie G; Kleigrewe, Karin; Northen, Trent; Dutton, Rachel J; Parrot, Delphine; Carlson, Erin E; Aigle, Bertrand; Michelsen, Charlotte F; Jelsbak, Lars; Sohlenkamp, Christian; Pevzner, Pavel; Edlund, Anna; McLean, Jeffrey; Piel, Jörn; Murphy, Brian T; Gerwick, Lena; Liaw, Chih-Chuang; Yang, Yu-Liang; Humpf, Hans-Ulrich; Maansson, Maria; Keyzers, Robert A; Sims, Amy C; Johnson, Andrew R.; Sidebottom, Ashley M; Sedio, Brian E; Klitgaard, Andreas; Larson, Charles B; P., Cristopher A Boya; Torres-Mendoza, Daniel; Gonzalez, David J; Silva, Denise B; Marques, Lucas M; Demarque, Daniel P; Pociute, Egle; O'Neill, Ellis C; Briand, Enora; Helfrich, Eric J. N.; Granatosky, Eve A; Glukhov, Evgenia; Ryffel, Florian; Houson, Hailey; Mohimani, Hosein; Kharbush, Jenan J; Zeng, Yi; Vorholt, Julia A; Kurita, Kenji L; Charusanti, Pep; McPhail, Kerry L; Nielsen, Kristian Fog; Vuong, Lisa; Elfeki, Maryam; Traxler, Matthew F; Engene, Niclas; Koyama, Nobuhiro; Vining, Oliver B; Baric, Ralph; Silva, Ricardo R; Mascuch, Samantha J; Tomasi, Sophie; Jenkins, Stefan; Macherla, Venkat; Hoffman, Thomas; Agarwal, Vinayak; Williams, Philip G; Dai, Jingqui; Neupane, Ram; Gurr, Joshua; Rodríguez, Andrés M. C.; Lamsa, Anne; Zhang, Chen; Dorrestein, Kathleen; Duggan, Brendan M; Almaliti, Jehad; Allard, Pierre-Marie; Phapale, Prasad; Nothias, Louis-Felix; Alexandrov, Theodore; Litaudon, Marc; Wolfender, Jean-Luc; Kyle, Jennifer E; Metz, Thomas O; Peryea, Tyler; Nguyen, Dac-Trung; VanLeer, Danielle; Shinn, Paul; Jadhav, Ajit; Müller, Rolf; Waters, Katrina M; Shi, Wenyuan; Liu, Xueting; Zhang, Lixin; Knight, Rob; Jensen, Paul R; Palsson, Bernhard O; Pogliano, Kit; Linington, Roger G; Gutiérrez, Marcelino; Lopes, Norberto P; Gerwick, William H; Moore, Bradley S; Dorrestein, Pieter C; Bandeira, Nuno

2017-01-01

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry techniques are well-suited to high-throughput characterization of natural products, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social molecular networking (GNPS, http://gnps.ucsd.edu), an open-access knowledge base for community wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of ‘living data’ through continuous reanalysis of deposited data. PMID:27504778

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

PubMed

Wang, Mingxun; Carver, Jeremy J; Phelan, Vanessa V; Sanchez, Laura M; Garg, Neha; Peng, Yao; Nguyen, Don Duy; Watrous, Jeramie; Kapono, Clifford A; Luzzatto-Knaan, Tal; Porto, Carla; Bouslimani, Amina; Melnik, Alexey V; Meehan, Michael J; Liu, Wei-Ting; Crüsemann, Max; Boudreau, Paul D; Esquenazi, Eduardo; Sandoval-Calderón, Mario; Kersten, Roland D; Pace, Laura A; Quinn, Robert A; Duncan, Katherine R; Hsu, Cheng-Chih; Floros, Dimitrios J; Gavilan, Ronnie G; Kleigrewe, Karin; Northen, Trent; Dutton, Rachel J; Parrot, Delphine; Carlson, Erin E; Aigle, Bertrand; Michelsen, Charlotte F; Jelsbak, Lars; Sohlenkamp, Christian; Pevzner, Pavel; Edlund, Anna; McLean, Jeffrey; Piel, Jörn; Murphy, Brian T; Gerwick, Lena; Liaw, Chih-Chuang; Yang, Yu-Liang; Humpf, Hans-Ulrich; Maansson, Maria; Keyzers, Robert A; Sims, Amy C; Johnson, Andrew R; Sidebottom, Ashley M; Sedio, Brian E; Klitgaard, Andreas; Larson, Charles B; P, Cristopher A Boya; Torres-Mendoza, Daniel; Gonzalez, David J; Silva, Denise B; Marques, Lucas M; Demarque, Daniel P; Pociute, Egle; O'Neill, Ellis C; Briand, Enora; Helfrich, Eric J N; Granatosky, Eve A; Glukhov, Evgenia; Ryffel, Florian; Houson, Hailey; Mohimani, Hosein; Kharbush, Jenan J; Zeng, Yi; Vorholt, Julia A; Kurita, Kenji L; Charusanti, Pep; McPhail, Kerry L; Nielsen, Kristian Fog; Vuong, Lisa; Elfeki, Maryam; Traxler, Matthew F; Engene, Niclas; Koyama, Nobuhiro; Vining, Oliver B; Baric, Ralph; Silva, Ricardo R; Mascuch, Samantha J; Tomasi, Sophie; Jenkins, Stefan; Macherla, Venkat; Hoffman, Thomas; Agarwal, Vinayak; Williams, Philip G; Dai, Jingqui; Neupane, Ram; Gurr, Joshua; Rodríguez, Andrés M C; Lamsa, Anne; Zhang, Chen; Dorrestein, Kathleen; Duggan, Brendan M; Almaliti, Jehad; Allard, Pierre-Marie; Phapale, Prasad; Nothias, Louis-Felix; Alexandrov, Theodore; Litaudon, Marc; Wolfender, Jean-Luc; Kyle, Jennifer E; Metz, Thomas O; Peryea, Tyler; Nguyen, Dac-Trung; VanLeer, Danielle; Shinn, Paul; Jadhav, Ajit; Müller, Rolf; Waters, Katrina M; Shi, Wenyuan; Liu, Xueting; Zhang, Lixin; Knight, Rob; Jensen, Paul R; Palsson, Bernhard O; Pogliano, Kit; Linington, Roger G; Gutiérrez, Marcelino; Lopes, Norberto P; Gerwick, William H; Moore, Bradley S; Dorrestein, Pieter C; Bandeira, Nuno

2016-08-09

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Challenges and perspectives of metaproteomic data analysis.

PubMed

Heyer, Robert; Schallert, Kay; Zoun, Roman; Becher, Beatrice; Saake, Gunter; Benndorf, Dirk

2017-11-10

In nature microorganisms live in complex microbial communities. Comprehensive taxonomic and functional knowledge about microbial communities supports medical and technical application such as fecal diagnostics as well as operation of biogas plants or waste water treatment plants. Furthermore, microbial communities are crucial for the global carbon and nitrogen cycle in soil and in the ocean. Among the methods available for investigation of microbial communities, metaproteomics can approximate the activity of microorganisms by investigating the protein content of a sample. Although metaproteomics is a very powerful method, issues within the bioinformatic evaluation impede its success. In particular, construction of databases for protein identification, grouping of redundant proteins as well as taxonomic and functional annotation pose big challenges. Furthermore, growing amounts of data within a metaproteomics study require dedicated algorithms and software. This review summarizes recent metaproteomics software and addresses the introduced issues in detail. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Community Education for Family Planning in the U.S.: A Systematic Review.

PubMed

Carter, Marion W; Tregear, Michelle L; Moskosky, Susan B

2015-08-01

Community education may involve activities that seek to raise awareness and promote behavior change, using mass media, social media, and other media or interpersonal methods in community settings. This systematic review evaluated the evidence of the effects of community education on select short- and medium-term family planning outcomes. Using an analytic approach drawn from the U.S. Preventive Services Task Force, multiple databases were searched for articles published from January 1985 through February 2011 describing studies of community education related to family planning in the U.S. Included articles were reviewed and assessed for potential bias using a standardized process in 2011. An updated, targeted review for the 2011-2014 period was conducted in early 2015. Seventeen papers were identified. Most (nine) related to mass media interventions; three involved targeted print media, two involved text messaging or e-mail, two described outcome workers conducting community education, and one involved community theater. Study designs, strength of evidence, and levels of possible bias varied widely. Twelve of 15 studies that addressed outcomes such as increased awareness found positive associations with those outcomes, with six also reporting null findings. Seven of eight studies that addressed use of services reported positive associations, with two also reporting null findings. The targeted, additional review identified two other studies. Evidence related to community education for family planning purposes is limited and highly variable. As goals of community education are usually limited to shorter-term outcomes, the evidence suggests that a range of approaches may be effective. Published by Elsevier Inc.

DataBase on Demand

NASA Astrophysics Data System (ADS)

Gaspar Aparicio, R.; Gomez, D.; Coterillo Coz, I.; Wojcik, D.

2012-12-01

At CERN a number of key database applications are running on user-managed MySQL database services. The database on demand project was born out of an idea to provide the CERN user community with an environment to develop and run database services outside of the actual centralised Oracle based database services. The Database on Demand (DBoD) empowers the user to perform certain actions that had been traditionally done by database administrators, DBA's, providing an enterprise platform for database applications. It also allows the CERN user community to run different database engines, e.g. presently open community version of MySQL and single instance Oracle database server. This article describes a technology approach to face this challenge, a service level agreement, the SLA that the project provides, and an evolution of possible scenarios.

A systematic review of economic evaluations of CHW interventions aimed at improving child health outcomes.

PubMed

Nkonki, L; Tugendhaft, A; Hofman, K

2017-02-28

Evidence of the cost-effectiveness of community health worker interventions is pertinent for decision-makers and programme planners who are turning to community services in order to strengthen health systems in the context of the momentum generated by strategies to support universal health care, the post-2015 Sustainable Development Goal agenda.We conducted a systematic review of published economic evaluation studies of community health worker interventions aimed at improving child health outcomes. Four public health and economic evaluation databases were searched for studies that met the inclusion criteria: National Health Service Economic Evaluation Database (NHS EED), Cochrane, Paediatric Economic Evaluation Database (PEED), and PubMed. The search strategy was tailored to each database.The 19 studies that met the inclusion criteria were conducted in either high income countries (HIC), low- income countries (LIC) and/or middle-income countries (MIC). The economic evaluations covered a wide range of interventions. Studies were grouped together by intended outcome or objective of each study. The data varied in quality. We found evidence of cost-effectiveness of community health worker (CHW) interventions in reducing malaria and asthma, decreasing mortality of neonates and children, improving maternal health, increasing exclusive breastfeeding and improving malnutrition, and positively impacting physical health and psychomotor development amongst children.Studies measured varied outcomes, due to the heterogeneous nature of studies included; a meta-analysis was not conducted. Outcomes included disease- or condition -specific outcomes, morbidity, mortality, and generic measures (e.g. disability-adjusted life years (DALYs)). Nonetheless, all 19 interventions were found to be either cost-effective or highly cost-effective at a threshold specific to their respective countries.There is a growing body of economic evaluation literature on cost-effectiveness of CHW interventions. However, this is largely for small scale and vertical programmes. There is a need for economic evaluations of larger and integrated CHW programmes in order to achieve the post-2015 Sustainable Development Goal agenda so that appropriate resources can be allocated to this subset of human resources for health. This is the first systematic review to assess the cost-effectiveness of community health workers in delivering child health interventions.

Rationale and methods of a multicentre randomised controlled trial of the effectiveness of a Community Health Assessment Programme with Emergency Medical Services (CHAP-EMS) implemented on residents aged 55 years and older in subsidised seniors' housing buildings in Ontario, Canada.

PubMed

Agarwal, Gina; McDonough, Beatrice; Angeles, Ricardo; Pirrie, Melissa; Marzanek, Francine; McLeod, Brent; Dolovich, Lisa

2015-06-11

Chronic diseases and falls substantially contribute to morbidity/mortality among seniors, causing this population to frequently seek emergency medical care. Research suggests the paramedic role can be successfully expanded to include community-based health promotion and prevention. This study implements a community paramedicine programme targeting seniors in subsidised housing, a high-risk population and frequent users of emergency medical services (EMS). The aims are to reduce EMS calls, improve health outcomes and healthcare utilisation. This is a pragmatic clustered randomised control trial in four communities across Ontario, Canada. Within each, four to eight seniors' apartment buildings will be paired and within each pair one building will be randomly assigned to receive the Community Health Assessment Programme through EMS (CHAP-EMS) intervention, while the other building receives no intervention. During the 1-year intervention, paramedics will run weekly sessions in a common area of the building, assessing risk factors for cardiovascular disease, diabetes and falls; providing health education and referrals to community programmes; and communicating results to the participant's primary physician. The primary outcomes are rate of emergency calls per 100 residents, change in blood pressure and change in Canadian Diabetes Risk (CANRISK) score, as collected by the local EMS and study databases. The secondary outcomes are change in health behaviours, measured using a preintervention and postintervention survey and healthcare utilisation, available through administrative databases. Analysis will mainly consist of descriptive statistics and generalised estimating equations, including subgroup cluster analysis. This study is approved by the Hamilton Integrated Research Ethics Board and will follow the Tri-Council Policy Statement. Findings will be disseminated through reports to local stakeholders, publication in peer-reviewed journals and conference presentations. NCT02152891. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Publishing Linked Open Data for Physical Samples - Lessons Learned

NASA Astrophysics Data System (ADS)

Ji, P.; Arko, R. A.; Lehnert, K.; Bristol, S.

2016-12-01

Most data and information about physical samples and associated sampling features currently reside in relational databases. Integrating common concepts from various databases has motivated us to publish Linked Open Data for collections of physical samples, using Semantic Web technologies including the Resource Description Framework (RDF), RDF Query Language (SPARQL), and Web Ontology Language (OWL). The goal of our work is threefold: To evaluate and select ontologies in different granularities for common concepts; to establish best practices and develop a generic methodology for publishing physical sample data stored in relational database as Linked Open Data; and to reuse standard community vocabularies from the International Commission on Stratigraphy (ICS), Global Volcanism Program (GVP), General Bathymetric Chart of the Oceans (GEBCO), and others. Our work leverages developments in the EarthCube GeoLink project and the Interdisciplinary Earth Data Alliance (IEDA) facility for modeling and extracting physical sample data stored in relational databases. Reusing ontologies developed by GeoLink and IEDA has facilitated discovery and integration of data and information across multiple collections including the USGS National Geochemical Database (NGDB), System for Earth Sample Registration (SESAR), and Index to Marine & Lacustrine Geological Samples (IMLGS). We have evaluated, tested, and deployed Linked Open Data tools including Morph, Virtuoso Server, LodView, LodLive, and YASGUI for converting, storing, representing, and querying data in a knowledge base (RDF triplestore). Using persistent identifiers such as Open Researcher & Contributor IDs (ORCIDs) and International Geo Sample Numbers (IGSNs) at the record level makes it possible for other repositories to link related resources such as persons, datasets, documents, expeditions, awards, etc. to samples, features, and collections. This work is supported by the EarthCube "GeoLink" project (NSF# ICER14-40221 and others) and the "USGS-IEDA Partnership to Support a Data Lifecycle Framework and Tools" project (USGS# G13AC00381).

National Geochronological Database

USGS Publications Warehouse

Revised by Sloan, Jan; Henry, Christopher D.; Hopkins, Melanie; Ludington, Steve; Original database by Zartman, Robert E.; Bush, Charles A.; Abston, Carl

2003-01-01

The National Geochronological Data Base (NGDB) was established by the United States Geological Survey (USGS) to collect and organize published isotopic (also known as radiometric) ages of rocks in the United States. The NGDB (originally known as the Radioactive Age Data Base, RADB) was started in 1974. A committee appointed by the Director of the USGS was given the mission to investigate the feasibility of compiling the published radiometric ages for the United States into a computerized data bank for ready access by the user community. A successful pilot program, which was conducted in 1975 and 1976 for the State of Wyoming, led to a decision to proceed with the compilation of the entire United States. For each dated rock sample reported in published literature, a record containing information on sample location, rock description, analytical data, age, interpretation, and literature citation was constructed and included in the NGDB. The NGDB was originally constructed and maintained on a mainframe computer, and later converted to a Helix Express relational database maintained on an Apple Macintosh desktop computer. The NGDB and a program to search the data files were published and distributed on Compact Disc-Read Only Memory (CD-ROM) in standard ISO 9660 format as USGS Digital Data Series DDS-14 (Zartman and others, 1995). As of May 1994, the NGDB consisted of more than 18,000 records containing over 30,000 individual ages, which is believed to represent approximately one-half the number of ages published for the United States through 1991. Because the organizational unit responsible for maintaining the database was abolished in 1996, and because we wanted to provide the data in more usable formats, we have reformatted the data, checked and edited the information in some records, and provided this online version of the NGDB. This report describes the changes made to the data and formats, and provides instructions for the use of the database in geographic information system (GIS) applications. The data are provided in .mdb (Microsoft Access), .xls (Microsoft Excel), and .txt (tab-separated value) formats. We also provide a single non-relational file that contains a subset of the data for ease of use.

Nurse practitioner caseload in primary health care: Scoping review.

PubMed

Martin-Misener, Ruth; Kilpatrick, Kelley; Donald, Faith; Bryant-Lukosius, Denise; Rayner, Jennifer; Valaitis, Ruta; Carter, Nancy; Miller, Patricia A; Landry, Véronique; Harbman, Patricia; Charbonneau-Smith, Renee; McKinlay, R James; Ziegler, Erin; Boesveld, Sarah; Lamb, Alyson

2016-10-01

To identify recommendations for determining patient panel/caseload size for nurse practitioners in community-based primary health care settings. Scoping review of the international published and grey literature. The search included electronic databases, international professional and governmental websites, contact with experts, and hand searches of reference lists. Eligible papers had to (a) address caseload or patient panels for nurse practitioners in community-based primary health care settings serving an all-ages population; and (b) be published in English or French between January 2000 and July 2014. Level one testing included title and abstract screening by two team members. Relevant papers were retained for full text review in level two testing, and reviewed by two team members. A third reviewer acted as a tiebreaker. Data were extracted using a structured extraction form by one team member and verified by a second member. Descriptive statistics were estimated. Content analysis was used for qualitative data. We identified 111 peer-reviewed articles and grey literature documents. Most of the papers were published in Canada and the United States after 2010. Current methods to determine panel/caseload size use large administrative databases, provider work hours and the average number of patient visits. Most of the papers addressing the topic of patient panel/caseload size in community-based primary health care were descriptive. The average number of patients seen by nurse practitioners per day varied considerably within and between countries; an average of 9-15 patients per day was common. Patient characteristics (e.g., age, gender) and health conditions (e.g., multiple chronic conditions) appear to influence patient panel/caseload size. Very few studies used validated tools to classify patient acuity levels or disease burden scores. The measurement of productivity and the determination of panel/caseload size is complex. Current metrics may not capture activities relevant to community-based primary health care nurse practitioners. Tools to measure all the components of these role are needed when determining panel/caseload size. Outcomes research is absent in the determination of panel/caseload size. There are few systems in place to track and measure community-based primary health care nurse practitioner activities. The development of such mechanisms is an important next step to assess community-based primary health care nurse practitioner productivity and determine patient panel/caseload size. Decisions about panel/caseload size must take into account the effects of nurse practitioner activities on outcomes of care. Copyright © 2016 Elsevier Ltd. All rights reserved.

Geographic distance and ecosystem size determine the distribution of smallest protists in lacustrine ecosystems.

PubMed

Lepère, Cécile; Domaizon, Isabelle; Taïb, Najwa; Mangot, Jean-François; Bronner, Gisèle; Boucher, Delphine; Debroas, Didier

2013-07-01

Understanding the spatial distribution of aquatic microbial diversity and the underlying mechanisms causing differences in community composition is a challenging and central goal for ecologists. Recent insights into protistan diversity and ecology are increasing the debate over their spatial distribution. In this study, we investigate the importance of spatial and environmental factors in shaping the small protists community structure in lakes. We analyzed small protists community composition (beta-diversity) and richness (alpha-diversity) at regional scale by different molecular methods targeting the gene coding for 18S rRNA gene (T-RFLP and 454 pyrosequencing). Our results show a distance-decay pattern for rare and dominant taxa and the spatial distribution of the latter followed the prediction of the island biogeography theory. Furthermore, geographic distances between lakes seem to be the main force shaping the protists community composition in the lakes studied here. Finally, the spatial distribution of protists was discussed at the global scale (11 worldwide distributed lakes) by comparing these results with those present in the public database. UniFrac analysis showed 18S rRNA gene OTUs compositions significantly different among most of lakes, and this difference does not seem to be related to the trophic status. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Forensic Tools to Track and Connect Physical Samples to Related Data

NASA Astrophysics Data System (ADS)

Molineux, A.; Thompson, A. C.; Baumgardner, R. W.

2016-12-01

Identifiers, such as local sample numbers, are critical to successfully connecting physical samples and related data. However, identifiers must be globally unique. The International Geo Sample Number (IGSN) generated when registering the sample in the System for Earth Sample Registration (SESAR) provides a globally unique alphanumeric code associated with basic metadata, related samples and their current physical storage location. When registered samples are published, users can link the figured samples to the basic metadata held at SESAR. The use cases we discuss include plant specimens from a Permian core, Holocene corals and derived powders, and thin sections with SEM stubs. Much of this material is now published. The plant taxonomic study from the core is a digital pdf and samples can be directly linked from the captions to the SESAR record. The study of stable isotopes from the corals is not yet digitally available, but individual samples are accessible. Full data and media records for both studies are located in our database where higher quality images, field notes, and section diagrams may exist. Georeferences permit mapping in current and deep time plate configurations. Several aspects emerged during this study. The first, ensure adequate and consistent details are registered with SESAR. Second, educate and encourage the researcher to obtain IGSNs. Third, publish the archive numbers, assigned prior to publication, alongside the IGSN. This provides access to further data through an Integrated Publishing Toolkit (IPT)/aggregators/or online repository databases, thus placing the initial sample in a much richer context for future studies. Fourth, encourage software developers to customize community software to extract data from a database and use it to register samples in bulk. This would improve workflow and provide a path for registration of large legacy collections.

Harnessing the wealth of Chinese scientific literature: schistosomiasis research and control in China

PubMed Central

Liu, Qin; Tian, Li-Guang; Xiao, Shu-Hua; Qi, Zhen; Steinmann, Peter; Mak, Tippi K; Utzinger, Jürg; Zhou, Xiao-Nong

2008-01-01

The economy of China continues to boom and so have its biomedical research and related publishing activities. Several so-called neglected tropical diseases that are most common in the developing world are still rampant or even emerging in some parts of China. The purpose of this article is to document the significant research potential from the Chinese biomedical bibliographic databases. The research contributions from China in the epidemiology and control of schistosomiasis provide an excellent illustration. We searched two widely used databases, namely China National Knowledge Infrastructure (CNKI) and VIP Information (VIP). Employing the keyword "Schistosoma" () and covering the period 1990–2006, we obtained 10,244 hits in the CNKI database and 5,975 in VIP. We examined 10 Chinese biomedical journals that published the highest number of original research articles on schistosomiasis for issues including languages and open access. Although most of the journals are published in Chinese, English abstracts are usually available. Open access to full articles was available in China Tropical Medicine in 2005/2006 and is granted by the Chinese Journal of Parasitology and Parasitic Diseases since 2003; none of the other journals examined offered open access. We reviewed (i) the discovery and development of antischistosomal drugs, (ii) the progress made with molluscicides and (iii) environmental management for schistosomiasis control in China over the past 20 years. In conclusion, significant research is published in the Chinese literature, which is relevant for local control measures and global scientific knowledge. Open access should be encouraged and language barriers removed so the wealth of Chinese research can be more fully appreciated by the scientific community. PMID:18826598

GeneSigDB—a curated database of gene expression signatures

PubMed Central

Culhane, Aedín C.; Schwarzl, Thomas; Sultana, Razvan; Picard, Kermshlise C.; Picard, Shaita C.; Lu, Tim H.; Franklin, Katherine R.; French, Simon J.; Papenhausen, Gerald; Correll, Mick; Quackenbush, John

2010-01-01

The primary objective of most gene expression studies is the identification of one or more gene signatures; lists of genes whose transcriptional levels are uniquely associated with a specific biological phenotype. Whilst thousands of experimentally derived gene signatures are published, their potential value to the community is limited by their computational inaccessibility. Gene signatures are embedded in published article figures, tables or in supplementary materials, and are frequently presented using non-standard gene or probeset nomenclature. We present GeneSigDB (http://compbio.dfci.harvard.edu/genesigdb) a manually curated database of gene expression signatures. GeneSigDB release 1.0 focuses on cancer and stem cells gene signatures and was constructed from more than 850 publications from which we manually transcribed 575 gene signatures. Most gene signatures (n = 560) were successfully mapped to the genome to extract standardized lists of EnsEMBL gene identifiers. GeneSigDB provides the original gene signature, the standardized gene list and a fully traceable gene mapping history for each gene from the original transcribed data table through to the standardized list of genes. The GeneSigDB web portal is easy to search, allows users to compare their own gene list to those in the database, and download gene signatures in most common gene identifier formats. PMID:19934259

Fine-grained Database Field Search Using Attribute-Based Encryption for E-Healthcare Clouds.

PubMed

Guo, Cheng; Zhuang, Ruhan; Jie, Yingmo; Ren, Yizhi; Wu, Ting; Choo, Kim-Kwang Raymond

2016-11-01

An effectively designed e-healthcare system can significantly enhance the quality of access and experience of healthcare users, including facilitating medical and healthcare providers in ensuring a smooth delivery of services. Ensuring the security of patients' electronic health records (EHRs) in the e-healthcare system is an active research area. EHRs may be outsourced to a third-party, such as a community healthcare cloud service provider for storage due to cost-saving measures. Generally, encrypting the EHRs when they are stored in the system (i.e. data-at-rest) or prior to outsourcing the data is used to ensure data confidentiality. Searchable encryption (SE) scheme is a promising technique that can ensure the protection of private information without compromising on performance. In this paper, we propose a novel framework for controlling access to EHRs stored in semi-trusted cloud servers (e.g. a private cloud or a community cloud). To achieve fine-grained access control for EHRs, we leverage the ciphertext-policy attribute-based encryption (CP-ABE) technique to encrypt tables published by hospitals, including patients' EHRs, and the table is stored in the database with the primary key being the patient's unique identity. Our framework can enable different users with different privileges to search on different database fields. Differ from previous attempts to secure outsourcing of data, we emphasize the control of the searches of the fields within the database. We demonstrate the utility of the scheme by evaluating the scheme using datasets from the University of California, Irvine.

Cadmium exposure: Toxicity in humans. (Latest citations from the Life Sciences collection database). Published Search

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

Not Available

1994-12-01

The bibliography contains citations concerning the effects of cadmium on humans. Biological monitoring of workers exposed to cadmium is discussed in depth. The effects of cadmium on visual-motor performance, community health, and child and infant development are presented. The citations discuss cadmium as a contributing factor in infertility and renal, kidney, and liver diseases. The effects of smoking on cadmium retention are mentioned. (Contains 250 citations and includes a subject term index and title list.)

Composition of Micro-eukaryotes on the Skin of the Cascades Frog (Rana cascadae) and Patterns of Correlation between Skin Microbes and Batrachochytrium dendrobatidis.

PubMed

Kueneman, Jordan G; Weiss, Sophie; McKenzie, Valerie J

2017-01-01

Global amphibian decline linked to fungal pathogens has galvanized research on applied amphibian conservation. Skin-associated bacterial communities of amphibians have been shown to mediate fungal skin infections and the development of probiotic treatments with antifungal bacteria has become an emergent area of research. While exploring the role of protective bacteria has been a primary focus for amphibian conservation, we aim to expand and study the other microbes present in amphibian skin communities including fungi and other micro-eukaryotes. Here, we characterize skin-associated bacteria and micro-eukaryotic diversity found across life stages of Cascades frog ( Rana cascadae ) and their associated aquatic environments using culture independent 16S and 18S rRNA marker-gene sequencing. Individuals of various life stages of Cascades frogs were sampled from a population located in the Trinity Alps in Northern California during an epidemic of the chytrid fungus, Batrachochytrium dendrobatidis . We filtered the bacterial sequences against a published database of bacteria known to inhibit B. dendrobatidis in co-culture to estimate the proportion of the skin bacterial community that is likely to provide defense against B. dendrobatidis . Tadpoles had a significantly higher proportion of B. dendrobatidis -inhibitory bacterial sequence matches relative to subadult and adult Cascades frogs. We applied a network analysis to examine patterns of correlation between bacterial taxa and B. dendrobatidis , as well as micro-eukaryotic taxa and B. dendrobatidis . Combined with the published database of bacteria known to inhibit B. dendrobatidis , we used the network analysis to identify bacteria that negatively correlated with B. dendrobatidis and thus could be good probiotic candidates in the Cascades frog system.

Spatial cyberinfrastructures, ontologies, and the humanities.

PubMed

Sieber, Renee E; Wellen, Christopher C; Jin, Yuan

2011-04-05

We report on research into building a cyberinfrastructure for Chinese biographical and geographic data. Our cyberinfrastructure contains (i) the McGill-Harvard-Yenching Library Ming Qing Women's Writings database (MQWW), the only online database on historical Chinese women's writings, (ii) the China Biographical Database, the authority for Chinese historical people, and (iii) the China Historical Geographical Information System, one of the first historical geographic information systems. Key to this integration is that linked databases retain separate identities as bases of knowledge, while they possess sufficient semantic interoperability to allow for multidatabase concepts and to support cross-database queries on an ad hoc basis. Computational ontologies create underlying semantics for database access. This paper focuses on the spatial component in a humanities cyberinfrastructure, which includes issues of conflicting data, heterogeneous data models, disambiguation, and geographic scale. First, we describe the methodology for integrating the databases. Then we detail the system architecture, which includes a tier of ontologies and schema. We describe the user interface and applications that allow for cross-database queries. For instance, users should be able to analyze the data, examine hypotheses on spatial and temporal relationships, and generate historical maps with datasets from MQWW for research, teaching, and publication on Chinese women writers, their familial relations, publishing venues, and the literary and social communities. Last, we discuss the social side of cyberinfrastructure development, as people are considered to be as critical as the technical components for its success.

Oral cancer databases: A comprehensive review.

PubMed

Sarode, Gargi S; Sarode, Sachin C; Maniyar, Nikunj; Anand, Rahul; Patil, Shankargouda

2017-11-29

Cancer database is a systematic collection and analysis of information on various human cancers at genomic and molecular level that can be utilized to understand various steps in carcinogenesis and for therapeutic advancement in cancer field. Oral cancer is one of the leading causes of morbidity and mortality all over the world. The current research efforts in this field are aimed at cancer etiology and therapy. Advanced genomic technologies including microarrays, proteomics, transcrpitomics, and gene sequencing development have culminated in generation of extensive data and subjection of several genes and microRNAs that are distinctively expressed and this information is stored in the form of various databases. Extensive data from various resources have brought the need for collaboration and data sharing to make effective use of this new knowledge. The current review provides comprehensive information of various publicly accessible databases that contain information pertinent to oral squamous cell carcinoma (OSCC) and databases designed exclusively for OSCC. The databases discussed in this paper are Protein-Coding Gene Databases and microRNA Databases. This paper also describes gene overlap in various databases, which will help researchers to reduce redundancy and focus on only those genes, which are common to more than one databases. We hope such introduction will promote awareness and facilitate the usage of these resources in the cancer research community, and researchers can explore the molecular mechanisms involved in the development of cancer, which can help in subsequent crafting of therapeutic strategies. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Adult community health-promoting interventions in primary health care: A systematic review.

PubMed

March, Sebastià; Torres, Elena; Ramos, María; Ripoll, Joana; García, Atanasio; Bulilete, Oana; Medina, David; Vidal, Clara; Cabeza, Elena; Llull, Micaela; Zabaleta-del-Olmo, Edurne; Aranda, José Manuel; Sastre, Silvia; Llobera, Joan

2015-07-01

To examine evidence on the effectiveness of health-promoting community interventions carried out in primary health care. Systematic review of originals and systematic reviews of health-promoting community interventions with the participation of primary health care. A working definition of community activities was used in the inclusion criteria. Databases searched up to 2013: PUBMED, EMBASE, CINHAL, Web of SCIENCE, IBECS, IME, and PSICODOC. No restrictions on year of publication or design. Articles were reviewed by separate researchers to identify risks of bias. Fifty-one articles published between 1966 and 2013 were included: 11 systematic reviews and 40 originals that described 39 community interventions. There is evidence on the effectiveness of community interventions in reducing cardiovascular risk factors, encouraging physical exercise, preventing falls and improving self-care among chronic patients compared with usual individual care. The effectiveness of some interventions increases when the community is involved in their development. Most assessments show positive results despite design limitations. The community approach may be more effective than the individual in usual preventive interventions in primary care. There is a lack of evidence on many community interventions in primary care and further research is needed. Copyright © 2015 Elsevier Inc. All rights reserved.

MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups.

PubMed

McIlroy, Simon Jon; Kirkegaard, Rasmus Hansen; McIlroy, Bianca; Nierychlo, Marta; Kristensen, Jannie Munk; Karst, Søren Michael; Albertsen, Mads; Nielsen, Per Halkjær

2017-01-01

Wastewater is increasingly viewed as a resource, with anaerobic digester technology being routinely implemented for biogas production. Characterising the microbial communities involved in wastewater treatment facilities and their anaerobic digesters is considered key to their optimal design and operation. Amplicon sequencing of the 16S rRNA gene allows high-throughput monitoring of these systems. The MiDAS field guide is a public resource providing amplicon sequencing protocols and an ecosystem-specific taxonomic database optimized for use with wastewater treatment facility samples. The curated taxonomy endeavours to provide a genus-level-classification for abundant phylotypes and the online field guide links this identity to published information regarding their ecology, function and distribution. This article describes the expansion of the database resources to cover the organisms of the anaerobic digester systems fed primary sludge and surplus activated sludge. The updated database includes descriptions of the abundant genus-level-taxa in influent wastewater, activated sludge and anaerobic digesters. Abundance information is also included to allow assessment of the role of emigration in the ecology of each phylotype. MiDAS is intended as a collaborative resource for the progression of research into the ecology of wastewater treatment, by providing a public repository for knowledge that is accessible to all interested in these biotechnologically important systems. http://www.midasfieldguide.org. © The Author(s) 2017. Published by Oxford University Press.

Community Engagement to Drive Best Practices and Scientific Advancement

NASA Astrophysics Data System (ADS)

Goring, S. J.; Williams, J. W.; Uhen, M. D.; McClennen, M.; Jenkins, J.; Peters, S. E.; Grimm, E. C.; Anderson, M.; Fils, D.; Lehnert, K.; Carter, M.

2016-12-01

The development of databases, data models, and tools around Earth Science data requires constant feedback from user communities. Users must be engaged in all aspects of data upload and access, curation and governance, and, particularly, in highlighting future opportunities for scientific discovery using the data resources. A challenge for data repositories, many of which have evolved organically and independently, is moving from Systems of Record - data silos with only limited input and output options - to Systems of Engagement, that respond to users and interact with other user communities and data repositories across the geosciences and beyond. The Cyber4Paleo Community Development Workshop (http://cyber4paleo.github.io), held June 20 & 21st in Boulder, CO, was organized by the EarthCube Research Coordination Network C4P (Cyber4Paleo) to bring together disciplinary researchers and Principles within data collectives in an effort to drive scientific applications of the collective data resources. C4P focuses on coordinating data and user groups within the allied paleogeoscientific disciplines. Over the course of two days researchers developed research projects that examined standards of 210Pb dating in the published literature, a framework for implementing a common geological time scale across resources, the continued development of underlying data resources, tools to integrate climate and occupation data from paleoecological resources, and the implementation of harmonizing standards across databases. Scientific outcomes of the workshop serve to underpin our understanding of the interrelations between paleoecological data and geophysical components of the Earth System at short and long time scales. These tools enhance our ability to understand connections between and among proxies, across space and time, the serve as outreach tools for training and education, and, importantly, they help to define and improve best practices within the databases, by engaging directly with user communities to fill unanticipated needs.

Biomedical journals and databases in Russia and Russian language in the former Soviet Union and beyond

PubMed Central

Vlassov, Vasiliy V; Danishevskiy, Kirill D

2008-01-01

In the 20th century, Russian biomedical science experienced a decline from the blossom of the early years to a drastic state. Through the first decades of the USSR, it was transformed to suit the ideological requirements of a totalitarian state and biased directives of communist leaders. Later, depressing economic conditions and isolation from the international research community further impeded its development. Contemporary Russia has inherited a system of medical education quite different from the west as well as counterproductive regulations for the allocation of research funding. The methodology of medical and epidemiological research in Russia is largely outdated. Epidemiology continues to focus on infectious disease and results of the best studies tend to be published in international periodicals. MEDLINE continues to be the best database to search for Russian biomedical publications, despite only a small proportion being indexed. The database of the Moscow Central Medical Library is the largest national database of medical periodicals, but does not provide abstracts and full subject heading codes, and it does not cover even the entire collection of the Library. New databases and catalogs (e.g. Panteleimon) that have appeared recently are incomplete and do not enable effective searching. PMID:18826569

Biomedical journals and databases in Russia and Russian language in the former Soviet Union and beyond.

PubMed

Vlassov, Vasiliy V; Danishevskiy, Kirill D

2008-09-30

In the 20th century, Russian biomedical science experienced a decline from the blossom of the early years to a drastic state. Through the first decades of the USSR, it was transformed to suit the ideological requirements of a totalitarian state and biased directives of communist leaders. Later, depressing economic conditions and isolation from the international research community further impeded its development. Contemporary Russia has inherited a system of medical education quite different from the west as well as counterproductive regulations for the allocation of research funding. The methodology of medical and epidemiological research in Russia is largely outdated. Epidemiology continues to focus on infectious disease and results of the best studies tend to be published in international periodicals. MEDLINE continues to be the best database to search for Russian biomedical publications, despite only a small proportion being indexed. The database of the Moscow Central Medical Library is the largest national database of medical periodicals, but does not provide abstracts and full subject heading codes, and it does not cover even the entire collection of the Library. New databases and catalogs (e.g. Panteleimon) that have appeared recently are incomplete and do not enable effective searching.

Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model.

PubMed

Reiser, Leonore; Berardini, Tanya Z; Li, Donghui; Muller, Robert; Strait, Emily M; Li, Qian; Mezheritsky, Yarik; Vetushko, Andrey; Huala, Eva

2016-01-01

Databases and data repositories provide essential functions for the research community by integrating, curating, archiving and otherwise packaging data to facilitate discovery and reuse. Despite their importance, funding for maintenance of these resources is increasingly hard to obtain. Fueled by a desire to find long term, sustainable solutions to database funding, staff from the Arabidopsis Information Resource (TAIR), founded the nonprofit organization, Phoenix Bioinformatics, using TAIR as a test case for user-based funding. Subscription-based funding has been proposed as an alternative to grant funding but its application has been very limited within the nonprofit sector. Our testing of this model indicates that it is a viable option, at least for some databases, and that it is possible to strike a balance that maximizes access while still incentivizing subscriptions. One year after transitioning to subscription support, TAIR is self-sustaining and Phoenix is poised to expand and support additional resources that wish to incorporate user-based funding strategies. Database URL: www.arabidopsis.org. © The Author(s) 2016. Published by Oxford University Press.

The Fossil Calibration Database-A New Resource for Divergence Dating.

PubMed

Ksepka, Daniel T; Parham, James F; Allman, James F; Benton, Michael J; Carrano, Matthew T; Cranston, Karen A; Donoghue, Philip C J; Head, Jason J; Hermsen, Elizabeth J; Irmis, Randall B; Joyce, Walter G; Kohli, Manpreet; Lamm, Kristin D; Leehr, Dan; Patané, Josés L; Polly, P David; Phillips, Matthew J; Smith, N Adam; Smith, Nathan D; Van Tuinen, Marcel; Ware, Jessica L; Warnock, Rachel C M

2015-09-01

Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important-often least appreciated-step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for nonspecialists to formulate. The dynamic nature of the fossil record (e.g., new discoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open-access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this database are based on individual fossil specimens and follow best practices for phylogenetic justification and geochronological constraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, will serve as a key pipeline for peer-reviewed calibrations to enter the database. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Review of the nutritional implications of farmers' markets and community gardens: a call for evaluation and research efforts.

PubMed

McCormack, Lacey Arneson; Laska, Melissa Nelson; Larson, Nicole I; Story, Mary

2010-03-01

The development and promotion of farmers' markets and community gardens is growing in popularity as a strategy to increase community-wide fruit and vegetable consumption. Despite large numbers of farmers' markets and community gardens in the United States, as well as widespread enthusiasm for their use as a health promotion tool, little is known about their influence on dietary intake. This review examines the current scientific literature on the implications of farmers' market programs and community gardens on nutrition-related outcomes in adults. Studies published between January 1980 and January 2009 were identified via PubMed and Agricola database searches and by examining reference lists from relevant studies. Studies were included in this review if they took place in the United States and qualitatively or quantitatively examined nutrition-related outcomes, including dietary intake; attitudes and beliefs regarding buying, preparing, or eating fruits and vegetables; and behaviors and perceptions related to obtaining produce from a farmers' market or community garden. Studies focusing on garden-based youth programs were excluded. In total, 16 studies were identified for inclusion in this review. Seven studies focused on the impact of farmers' market nutrition programs for Special Supplemental Nutrition Program for Women, Infants, and Children participants, five focused on the influence of farmers' market programs for seniors, and four focused on community gardens. Findings from this review reveal that few well-designed research studies (eg, those incorporating control groups) utilizing valid and reliable dietary assessment methods to evaluate the influence of farmers' markets and community gardens on nutrition-related outcomes have been completed. Recommendations for future research on the dietary influences of farmers' markets and community gardens are provided. Copyright 2010 American Dietetic Association. Published by Elsevier Inc. All rights reserved.

Consistency of the Health of the Nation Outcome Scales (HoNOS) at inpatient-to-community transition.

PubMed

Luo, Wei; Harvey, Richard; Tran, Truyen; Phung, Dinh; Venkatesh, Svetha; Connor, Jason P

2016-04-27

The Health of the Nation Outcome Scales (HoNOS) are mandated outcome-measures in many mental-health jurisdictions. When HoNOS are used in different care settings, it is important to assess if setting specific bias exists. This article examines the consistency of HoNOS in a sample of psychiatric patients transitioned from acute inpatient care and community centres. A regional mental health service with both acute and community facilities. 111 psychiatric patients were transferred from inpatient care to community care from 2012 to 2014. Their HoNOS scores were extracted from a clinical database; Each inpatient-discharge assessment was followed by a community-intake assessment, with the median period between assessments being 4 days (range 0-14). Assessor experience and professional background were recorded. The difference of HoNOS at inpatient-discharge and community-intake were assessed with Pearson correlation, Cohen's κ and effect size. Inpatient-discharge HoNOS was on average lower than community-intake HoNOS. The average HoNOS was 8.05 at discharge (median 7, range 1-22), and 12.16 at intake (median 12, range 1-25), an average increase of 4.11 (SD 6.97). Pearson correlation between two total scores was 0.073 (95% CI -0.095 to 0.238) and Cohen's κ was 0.02 (95% CI -0.02 to 0.06). Differences did not appear to depend on assessor experience or professional background. Systematic change in the HoNOS occurs at inpatient-to-community transition. Some caution should be exercised in making direct comparisons between inpatient HoNOS and community HoNOS scores. 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/

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

PubMed Central

Hinchliff, Cody E.; Smith, Stephen A.; Allman, James F.; Burleigh, J. Gordon; Chaudhary, Ruchi; Coghill, Lyndon M.; Crandall, Keith A.; Deng, Jiabin; Drew, Bryan T.; Gazis, Romina; Gude, Karl; Hibbett, David S.; Katz, Laura A.; Laughinghouse, H. Dail; McTavish, Emily Jane; Midford, Peter E.; Owen, Christopher L.; Ree, Richard H.; Rees, Jonathan A.; Soltis, Douglas E.; Williams, Tiffani; Cranston, Karen A.

2015-01-01

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics. PMID:26385966

Synthesis of phylogeny and taxonomy into a comprehensive tree of life.

PubMed

Hinchliff, Cody E; Smith, Stephen A; Allman, James F; Burleigh, J Gordon; Chaudhary, Ruchi; Coghill, Lyndon M; Crandall, Keith A; Deng, Jiabin; Drew, Bryan T; Gazis, Romina; Gude, Karl; Hibbett, David S; Katz, Laura A; Laughinghouse, H Dail; McTavish, Emily Jane; Midford, Peter E; Owen, Christopher L; Ree, Richard H; Rees, Jonathan A; Soltis, Douglas E; Williams, Tiffani; Cranston, Karen A

2015-10-13

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips-the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.

Demonstrating the Open Data Repository's Data Publisher: The CheMin Database

NASA Astrophysics Data System (ADS)

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

2018-04-01

The Open Data Repository's Data Publisher aims to provide an easy-to-use software tool that will allow researchers to create and publish database templates and related data. The CheMin Database developed using this framework is shown as an example.

WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata

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

Putman, Tim E.; Lelong, Sebastien; Burgstaller-Muehlbacher, Sebastian

With the advancement of genome-sequencing technologies, new genomes are being sequenced daily. Although these sequences are deposited in publicly available data warehouses, their functional and genomic annotations (beyond genes which are predicted automatically) mostly reside in the text of primary publications. Professional curators are hard at work extracting those annotations from the literature for the most studied organisms and depositing them in structured databases. However, the resources don’t exist to fund the comprehensive curation of the thousands of newly sequenced organisms in this manner. Here, we describe WikiGenomes (wikigenomes.org), a web application that facilitates the consumption and curation of genomicmore » data by the entire scientific community. WikiGenomes is based on Wikidata, an openly editable knowledge graph with the goal of aggregating published knowledge into a free and open database. WikiGenomes empowers the individual genomic researcher to contribute their expertise to the curation effort and integrates the knowledge into Wikidata, enabling it to be accessed by anyone without restriction.« less

WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata

DOE PAGES

Putman, Tim E.; Lelong, Sebastien; Burgstaller-Muehlbacher, Sebastian; ...

2017-03-06

With the advancement of genome-sequencing technologies, new genomes are being sequenced daily. Although these sequences are deposited in publicly available data warehouses, their functional and genomic annotations (beyond genes which are predicted automatically) mostly reside in the text of primary publications. Professional curators are hard at work extracting those annotations from the literature for the most studied organisms and depositing them in structured databases. However, the resources don’t exist to fund the comprehensive curation of the thousands of newly sequenced organisms in this manner. Here, we describe WikiGenomes (wikigenomes.org), a web application that facilitates the consumption and curation of genomicmore » data by the entire scientific community. WikiGenomes is based on Wikidata, an openly editable knowledge graph with the goal of aggregating published knowledge into a free and open database. WikiGenomes empowers the individual genomic researcher to contribute their expertise to the curation effort and integrates the knowledge into Wikidata, enabling it to be accessed by anyone without restriction.« less

A maize database resource that captures tissue-specific and subcellular-localized gene expression, via fluorescent tags and confocal imaging (Maize Cell Genomics Database).

PubMed

Krishnakumar, Vivek; Choi, Yongwook; Beck, Erin; Wu, Qingyu; Luo, Anding; Sylvester, Anne; Jackson, David; Chan, Agnes P

2015-01-01

Maize is a global crop and a powerful system among grain crops for genetic and genomic studies. However, the development of novel biological tools and resources to aid in the functional identification of gene sequences is greatly needed. Towards this goal, we have developed a collection of maize marker lines for studying native gene expression in specific cell types and subcellular compartments using fluorescent proteins (FPs). To catalog FP expression, we have developed a public repository, the Maize Cell Genomics (MCG) Database, (http://maize.jcvi.org/cellgenomics), to organize a large data set of confocal images generated from the maize marker lines. To date, the collection represents major subcellular structures and also developmentally important progenitor cell populations. The resource is available to the research community, for example to study protein localization or interactions under various experimental conditions or mutant backgrounds. A subset of the marker lines can also be used to induce misexpression of target genes through a transactivation system. For future directions, the image repository can be expanded to accept new image submissions from the research community, and to perform customized large-scale computational image analysis. This community resource will provide a suite of new tools for gaining biological insights by following the dynamics of protein expression at the subcellular, cellular and tissue levels. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Community Organizing for Database Trial Buy-In by Patrons

ERIC Educational Resources Information Center

Pionke, J. J.

2015-01-01

Database trials do not often garner a lot of feedback. Using community-organizing techniques can not only potentially increase the amount of feedback received but also deepen the relationship between the librarian and his or her constituent group. This is a case study of the use of community-organizing techniques in a series of database trials for…

Outside Mainstream Electronic Databases: Review of Studies Conducted in the USSR and Post-Soviet Countries on Electric Current-Assisted Consolidation of Powder Materials

PubMed Central

Olevsky, Eugene A.; Aleksandrova, Elena V.; Ilyina, Alexandra M.; Dudina, Dina V.; Novoselov, Alexander N.; Pelve, Kirill Y.; Grigoryev, Eugene G.

2013-01-01

This paper reviews research articles published in the former USSR and post-soviet countries on the consolidation of powder materials using electric current that passes through the powder sample and/or a conductive die-punch set-up. Having been published in Russian, many of the reviewed papers are not included in the mainstream electronic databases of the scientific articles and thus are not known to the scientific community. The present review is aimed at filling this information gap. In the paper, the electric current-assisted sintering techniques based on high- and low-voltage approaches are presented. The main results of the theoretical modeling of the processes of electromagnetic field-assisted consolidation of powder materials are discussed. Sintering experiments and related equipment are described and the major experimental results are analyzed. Sintering conditions required to achieve the desired properties of the sintered materials are provided for selected material systems. Tooling materials used in the electric current-assisted consolidation set-ups are also described. PMID:28788337

A crystallographic perspective on sharing data and knowledge

NASA Astrophysics Data System (ADS)

Bruno, Ian J.; Groom, Colin R.

2014-10-01

The crystallographic community is in many ways an exemplar of the benefits and practices of sharing data. Since the inception of the technique, virtually every published crystal structure has been made available to others. This has been achieved through the establishment of several specialist data centres, including the Cambridge Crystallographic Data Centre, which produces the Cambridge Structural Database. Containing curated structures of small organic molecules, some containing a metal, the database has been produced for almost 50 years. This has required the development of complex informatics tools and an environment allowing expert human curation. As importantly, a financial model has evolved which has, to date, ensured the sustainability of the resource. However, the opportunities afforded by technological changes and changing attitudes to sharing data make it an opportune moment to review current practices.

The MIMIC Code Repository: enabling reproducibility in critical care research.

PubMed

Johnson, Alistair Ew; Stone, David J; Celi, Leo A; Pollard, Tom J

2018-01-01

Lack of reproducibility in medical studies is a barrier to the generation of a robust knowledge base to support clinical decision-making. In this paper we outline the Medical Information Mart for Intensive Care (MIMIC) Code Repository, a centralized code base for generating reproducible studies on an openly available critical care dataset. Code is provided to load the data into a relational structure, create extractions of the data, and reproduce entire analysis plans including research studies. Concepts extracted include severity of illness scores, comorbid status, administrative definitions of sepsis, physiologic criteria for sepsis, organ failure scores, treatment administration, and more. Executable documents are used for tutorials and reproduce published studies end-to-end, providing a template for future researchers to replicate. The repository's issue tracker enables community discussion about the data and concepts, allowing users to collaboratively improve the resource. The centralized repository provides a platform for users of the data to interact directly with the data generators, facilitating greater understanding of the data. It also provides a location for the community to collaborate on necessary concepts for research progress and share them with a larger audience. Consistent application of the same code for underlying concepts is a key step in ensuring that research studies on the MIMIC database are comparable and reproducible. By providing open source code alongside the freely accessible MIMIC-III database, we enable end-to-end reproducible analysis of electronic health records. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association.

A survey of the current status of web-based databases indexing Iranian journals.

PubMed

Merat, Shahin; Khatibzadeh, Shahab; Mesgarpour, Bita; Malekzadeh, Reza

2009-05-01

The scientific output of Iran is increasing rapidly during the recent years. Unfortunately, most papers are published in journals which are not indexed by popular indexing systems and many of them are in Persian without English translation. This makes the results of Iranian scientific research unavailable to other researchers, including Iranians. The aim of this study was to evaluate the quality of current web-based databases indexing scientific articles published in Iran. We identified web-based databases which indexed scientific journals published in Iran using popular search engines. The sites were then subjected to a series of tests to evaluate their coverage, search capabilities, stability, accuracy of information, consistency, accessibility, ease of use, and other features. Results were compared with each other to identify strengths and shortcomings of each site. Five web sites were indentified. None had a complete coverage on scientific Iranian journals. The search capabilities were less than optimal in most sites. English translations of research titles, author names, keywords, and abstracts of Persian-language articles did not follow standards. Some sites did not cover abstracts. Numerous typing errors make searches ineffective and citation indexing unreliable. None of the currently available indexing sites are capable of presenting Iranian research to the international scientific community. The government should intervene by enforcing policies designed to facilitate indexing through a systematic approach. The policies should address Iranian journals, authors, and indexing sites. Iranian journals should be required to provide their indexing data, including references, electronically; authors should provide correct indexing information to journals; and indexing sites should improve their software to meet standards set by the government.

The Astrobiology Habitable Environments Database (AHED)

NASA Astrophysics Data System (ADS)

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

2015-12-01

The Astrobiology Habitable Environments Database (AHED) is a central, high quality, long-term searchable repository for archiving and collaborative sharing of astrobiologically relevant data, including, morphological, textural and contextural images, chemical, biochemical, isotopic, sequencing, and mineralogical information. The aim of AHED is to foster long-term innovative research by supporting integration and analysis of diverse datasets in order to: 1) help understand and interpret planetary geology; 2) identify and characterize habitable environments and pre-biotic/biotic processes; 3) interpret returned data from present and past missions; 4) provide a citable database of NASA-funded published and unpublished data (after an agreed-upon embargo period). AHED uses the online open-source software "The Open Data Repository's Data Publisher" (ODR - http://www.opendatarepository.org) [1], which provides a user-friendly interface that research teams or individual scientists can use to design, populate and manage their own database according to the characteristics of their data and the need to share data with collaborators or the broader scientific community. This platform can be also used as a laboratory notebook. The database will have the capability to import and export in a variety of standard formats. Advanced graphics will be implemented including 3D graphing, multi-axis graphs, error bars, and similar scientific data functions together with advanced online tools for data analysis (e. g. the statistical package, R). A permissions system will be put in place so that as data are being actively collected and interpreted, they will remain proprietary. A citation system will allow research data to be used and appropriately referenced by other researchers after the data are made public. This project is supported by the Science-Enabling Research Activity (SERA) and NASA NNX11AP82A, Mars Science Laboratory Investigations. [1] Nate et al. (2015) AGU, submitted.

Transformative Use of an Improved All-Payer Hospital Discharge Data Infrastructure for Community-Based Participatory Research: A Sustainability Pathway

PubMed Central

Salemi, Jason L; Salinas-Miranda, Abraham A; Wilson, Roneé E; Salihu, Hamisu M

2015-01-01

Objective To describe the use of a clinically enhanced maternal and child health (MCH) database to strengthen community-engaged research activities, and to support the sustainability of data infrastructure initiatives. Data Sources/Study Setting Population-based, longitudinal database covering over 2.3 million mother–infant dyads during a 12-year period (1998–2009) in Florida. Setting: A community-based participatory research (CBPR) project in a socioeconomically disadvantaged community in central Tampa, Florida. Study Design Case study of the use of an enhanced state database for supporting CBPR activities. Principal Findings A federal data infrastructure award resulted in the creation of an MCH database in which over 92 percent of all birth certificate records for infants born between 1998 and 2009 were linked to maternal and infant hospital encounter-level data. The population-based, longitudinal database was used to supplement data collected from focus groups and community surveys with epidemiological and health care cost data on important MCH disparity issues in the target community. Data were used to facilitate a community-driven, decision-making process in which the most important priorities for intervention were identified. Conclusions Integrating statewide all-payer, hospital-based databases into CBPR can empower underserved communities with a reliable source of health data, and it can promote the sustainability of newly developed data systems. PMID:25879276

Image Analysis in Plant Sciences: Publish Then Perish.

PubMed

Lobet, Guillaume

2017-07-01

Image analysis has become a powerful technique for most plant scientists. In recent years dozens of image analysis tools have been published in plant science journals. These tools cover the full spectrum of plant scales, from single cells to organs and canopies. However, the field of plant image analysis remains in its infancy. It still has to overcome important challenges, such as the lack of robust validation practices or the absence of long-term support. In this Opinion article, I: (i) present the current state of the field, based on data from the plant-image-analysis.org database; (ii) identify the challenges faced by its community; and (iii) propose workable ways of improvement. Copyright © 2017 Elsevier Ltd. All rights reserved.

A comprehensive company database analysis of biological assay variability.

PubMed

Kramer, Christian; Dahl, Göran; Tyrchan, Christian; Ulander, Johan

2016-08-01

Analysis of data from various compounds measured in diverse biological assays is a central part of drug discovery research projects. However, no systematic overview of the variability in biological assays has been published and judgments on assay quality and robustness of data are often based on personal belief and experience within the drug discovery community. To address this we performed a reproducibility analysis of all biological assays at AstraZeneca between 2005 and 2014. We found an average experimental uncertainty of less than a twofold difference and no technologies or assay types had higher variability than others. This work suggests that robust data can be obtained from the most commonly applied biological assays. Copyright © 2016. Published by Elsevier Ltd.

Mouse Genome Database: From sequence to phenotypes and disease models

PubMed Central

Richardson, Joel E.; Kadin, James A.; Smith, Cynthia L.; Blake, Judith A.; Bult, Carol J.

2015-01-01

Summary The Mouse Genome Database (MGD, www.informatics.jax.org) is the international scientific database for genetic, genomic, and biological data on the laboratory mouse to support the research requirements of the biomedical community. To accomplish this goal, MGD provides broad data coverage, serves as the authoritative standard for mouse nomenclature for genes, mutants, and strains, and curates and integrates many types of data from literature and electronic sources. Among the key data sets MGD supports are: the complete catalog of mouse genes and genome features, comparative homology data for mouse and vertebrate genes, the authoritative set of Gene Ontology (GO) annotations for mouse gene functions, a comprehensive catalog of mouse mutations and their phenotypes, and a curated compendium of mouse models of human diseases. Here, we describe the data acquisition process, specifics about MGD's key data areas, methods to access and query MGD data, and outreach and user help facilities. genesis 53:458–473, 2015. © 2015 The Authors. Genesis Published by Wiley Periodicals, Inc. PMID:26150326

Re-thinking organisms: The impact of databases on model organism biology.

PubMed

Leonelli, Sabina; Ankeny, Rachel A

2012-03-01

Community databases have become crucial to the collection, ordering and retrieval of data gathered on model organisms, as well as to the ways in which these data are interpreted and used across a range of research contexts. This paper analyses the impact of community databases on research practices in model organism biology by focusing on the history and current use of four community databases: FlyBase, Mouse Genome Informatics, WormBase and The Arabidopsis Information Resource. We discuss the standards used by the curators of these databases for what counts as reliable evidence, acceptable terminology, appropriate experimental set-ups and adequate materials (e.g., specimens). On the one hand, these choices are informed by the collaborative research ethos characterising most model organism communities. On the other hand, the deployment of these standards in databases reinforces this ethos and gives it concrete and precise instantiations by shaping the skills, practices, values and background knowledge required of the database users. We conclude that the increasing reliance on community databases as vehicles to circulate data is having a major impact on how researchers conduct and communicate their research, which affects how they understand the biology of model organisms and its relation to the biology of other species. Copyright © 2011 Elsevier Ltd. All rights reserved.

Focus Group in Community Mental Health Research: Need for Adaption.

PubMed

Zupančič, Vesna; Pahor, Majda; Kogovšek, Tina

2018-04-27

The article presents an analysis of the use of focus groups in researching community mental health users, starting with the reasons for using them, their implementation in mental health service users' research, and the adaptations of focus group use when researching the experiences of users. Based on personal research experience and a review of scientific publications in the Google Scholar, Web of Science, ProQuest, EBSCOhost, and Scopus databases, 20 articles published between 2010 and 2016 were selected for targeted content analysis. A checklist for reporting on the use of focus groups with community mental health service users, aiming to improve the comparability, verifiability and validity was developed. Adaptations of the implementation of focus groups in relation to participants' characteristics were suggested. Focus groups are not only useful as a scientific research technique, but also for ensuring service users' participation in decision-making in community mental health and evaluating the quality of the mental health system and services .

The relevance and role of homestays in medical education: a scoping study.

PubMed

Hughes, Bonnie Olivia; Moshabela, Mosa; Owen, Jenni; Gaede, Bernhard

2017-01-01

The community-based medical education curriculum is growing in popularity as a strategy to bring universal health coverage to underserved communities by providing medical students with hands-on training in primary health care. Accommodation and immersion of medical students within the community will become increasingly important to the success of community-based curricula. In the context of tourism, homestays, where local families host guests, have shown to provide an immersive accommodation experience. By exploring homestays in the educational context, this scoping study investigates their role in providing an immersive pedagogical experience for medical students. A scoping review was performed using the online databases ScienceDirect and the Duke University Library Database, which searches Academic Search Complete, JSTOR, LexisNexis Academic, Web of Science, Proquest, PubMed and WorldCat. Using the inclusion term 'homestays' and excluding the term 'tourism', 181 results were returned. AClose assessment using inclusion criteria narrowed this to 14 relevant articles. There is very little published research specific to the experience of medical students in community homestays, indicating a gap in the literature. However, the existing educational outcomes suggest homestays may have the potential to serve a significant role in medical education, especially as a component of decentralised or community-based programmes. The literature reveals that educational homestays influence language learning, cultural immersion, and the development of professional skills for health science careers. These outcomes relate to the level of engagement between students and hosts, including the catalytic role of community liaisons. Homestays offer a unique depth of experience that has the potential to enrich the education of participating students, and require further research, particularly in the context of distributed and decentralised training platforms for medical and health sciences students. Future studies should explore the potential for homestays as a pedagogical component of community-based medical curriculum. CBME: Community-based medical education.

The relevance and role of homestays in medical education: a scoping study

PubMed Central

Hughes, Bonnie Olivia; Moshabela, Mosa; Owen, Jenni; Gaede, Bernhard

2017-01-01

ABSTRACT Background: The community-based medical education curriculum is growing in popularity as a strategy to bring universal health coverage to underserved communities by providing medical students with hands-on training in primary health care. Accommodation and immersion of medical students within the community will become increasingly important to the success of community-based curricula. In the context of tourism, homestays, where local families host guests, have shown to provide an immersive accommodation experience. Objective: By exploring homestays in the educational context, this scoping study investigates their role in providing an immersive pedagogical experience for medical students. Design: A scoping review was performed using the online databases ScienceDirect and the Duke University Library Database, which searches Academic Search Complete, JSTOR, LexisNexis Academic, Web of Science, Proquest, PubMed and WorldCat. Using the inclusion term ‘homestays’ and excluding the term ‘tourism’, 181 results were returned. AClose assessment using inclusion criteria narrowed this to 14 relevant articles. Results: There is very little published research specific to the experience of medical students in community homestays, indicating a gap in the literature. However, the existing educational outcomes suggest homestays may have the potential to serve a significant role in medical education, especially as a component of decentralised or community-based programmes. The literature reveals that educational homestays influence language learning, cultural immersion, and the development of professional skills for health science careers. These outcomes relate to the level of engagement between students and hosts, including the catalytic role of community liaisons. Conclusions: Homestays offer a unique depth of experience that has the potential to enrich the education of participating students, and require further research, particularly in the context of distributed and decentralised training platforms for medical and health sciences students. Future studies should explore the potential for homestays as a pedagogical component of community-based medical curriculum. Abbreviations: CBME: Community-based medical education PMID:28460606

LEPER: Library of Experimental PhasE Relations

NASA Astrophysics Data System (ADS)

Davis, F.; Gordon, S.; Mukherjee, S.; Hirschmann, M.; Ghiorso, M.

2006-12-01

The Library of Experimental PhasE Relations (LEPER) seeks to compile published experimental determinations of magmatic phase equilibria and provide those data on the web with a searchable and downloadable interface. Compiled experimental data include the conditions and durations of experiments, the bulk compositions of experimental charges, and the identity, compositions and proportions of phases observed, and, where available, estimates of experimental and analytical uncertainties. Also included are metadata such as the type of experimental device, capsule material, and method(s) of quantitative analysis. The database may be of use to practicing experimentalists as well as the wider Earth science community. Experimentalists may find the data useful for planning new experiments and will easily be able to compare their results to the full body of previous experimentnal data. Geologists may use LEPER to compare rocks sampled in the field with experiments performed on similar bulk composition or with experiments that produced similar-composition product phases. Modelers may use LEPER to parameterize partial melting of various lithologies. One motivation for compiling LEPER is for calibration of updated and revised versions of MELTS, however, it is hoped that the availability of LEPER will facilitate formulation and calibration of additional thermodynamic or empirical models of magmatic phase relations and phase equilibria, geothermometers and more. Data entry for LEPER is occuring presently: As of August, 2006, >6200 experiments have been entered, chiefly from work published between 1997 and 2005. A prototype web interface has been written and beta release on the web is anticipated in Fall, 2006. Eventually, experimentalists will be able to submit their new experimental data to the database via the web. At present, the database contains only data pertaining to the phase equilibria of silicate melts, but extension to other experimental data involving other fluids or sub-solidus phase equilibria may be contemplated. Also, the data are at present limited to natural or near-natural systems, but in the future, extension to synthetic (i.e., CMAS, etc.) systems is also possible. Each would depend in part on whether there is community demand for such databases. A trace element adjunct to LEPER is presently in planning stages.

Assessment and application of national environmental databases and mapping tools at the local level to two community case studies.

PubMed

Hammond, Davyda; Conlon, Kathryn; Barzyk, Timothy; Chahine, Teresa; Zartarian, Valerie; Schultz, Brad

2011-03-01

Communities are concerned over pollution levels and seek methods to systematically identify and prioritize the environmental stressors in their communities. Geographic information system (GIS) maps of environmental information can be useful tools for communities in their assessment of environmental-pollution-related risks. Databases and mapping tools that supply community-level estimates of ambient concentrations of hazardous pollutants, risk, and potential health impacts can provide relevant information for communities to understand, identify, and prioritize potential exposures and risk from multiple sources. An assessment of existing databases and mapping tools was conducted as part of this study to explore the utility of publicly available databases, and three of these databases were selected for use in a community-level GIS mapping application. Queried data from the U.S. EPA's National-Scale Air Toxics Assessment, Air Quality System, and National Emissions Inventory were mapped at the appropriate spatial and temporal resolutions for identifying risks of exposure to air pollutants in two communities. The maps combine monitored and model-simulated pollutant and health risk estimates, along with local survey results, to assist communities with the identification of potential exposure sources and pollution hot spots. Findings from this case study analysis will provide information to advance the development of new tools to assist communities with environmental risk assessments and hazard prioritization. © 2010 Society for Risk Analysis.

To What Extent Do Neighborhood Differences Mediate Racial Disparities in Participation After Spinal Cord Injury?

PubMed

Botticello, Amanda L; Boninger, Mike; Charlifue, Susan; Chen, Yuying; Fyffe, Denise; Heinemann, Allen; Hoffman, Jeanne M; Jette, Alan; Kalpakjian, Claire; Rohrbach, Tanya

2016-10-01

To examine the role of residential neighborhood characteristics in accounting for race disparities in participation among a large sample of community-living adults with chronic spinal cord injury (SCI). Secondary analysis of cross-sectional survey data from the national Spinal Cord Injury Model Systems (SCIMS) database linked with national survey and spatial data. SCIMS database participants enrolled at 10 collaborating centers active in follow-up between 2000 and 2014. The sample consisted of persons with SCI (N=6892) in 5441 Census tracts from 50 states and the District of Columbia. Not applicable. The Craig Handicap Assessment and Reporting Technique was used to measure full participation across 4 domains: physical independence, mobility, occupation, and social integration. Racial minority groups had lower odds of reporting full participation relative to whites across all domains, suggesting that blacks and Hispanics are at risk for poorer community reintegration after SCI. Neighborhood characteristics, notably differences in socioeconomic advantage, reduced race group differences in the odds of full occupational and social integration, suggesting that the race disparities in community reintegration after SCI are partially attributable to variation in the economic characteristics of the places where people live. This investigation suggests that addressing disadvantage at the neighborhood level may modify gaps in community participation after medical rehabilitation and provides further support for the role of the environment in the experience of disability. Copyright © 2016 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Anthropogenic land use shapes the composition and phylogenetic structure of soil arbuscular mycorrhizal fungal communities.

PubMed

Moora, Mari; Davison, John; Öpik, Maarja; Metsis, Madis; Saks, Ülle; Jairus, Teele; Vasar, Martti; Zobel, Martin

2014-12-01

Arbuscular mycorrhizal (AM) fungi play an important role in ecosystems, but little is known about how soil AM fungal community composition varies in relation to habitat type and land-use intensity. We molecularly characterized AM fungal communities in soil samples (n = 88) from structurally open (permanent grassland, intensive and sustainable agriculture) and forested habitats (primeval forest and spruce plantation). The habitats harboured significantly different AM fungal communities, and there was a broad difference in fungal community composition between forested and open habitats, the latter being characterized by higher average AM fungal richness. Within both open and forest habitats, intensive land use significantly influenced community composition. There was a broad difference in the phylogenetic structure of AM fungal communities between mechanically disturbed and nondisturbed habitats. Taxa from Glomeraceae served as indicator species for the nondisturbed habitats, while taxa from Archaeosporaceae, Claroideoglomeraceae and Diversisporaceae were indicators for the disturbed habitats. The distribution of these indicator taxa among habitat types in the MaarjAM global database of AM fungal diversity was in accordance with their local indicator status. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Spatial cyberinfrastructures, ontologies, and the humanities

PubMed Central

Sieber, Renee E.; Wellen, Christopher C.; Jin, Yuan

2011-01-01

We report on research into building a cyberinfrastructure for Chinese biographical and geographic data. Our cyberinfrastructure contains (i) the McGill-Harvard-Yenching Library Ming Qing Women's Writings database (MQWW), the only online database on historical Chinese women's writings, (ii) the China Biographical Database, the authority for Chinese historical people, and (iii) the China Historical Geographical Information System, one of the first historical geographic information systems. Key to this integration is that linked databases retain separate identities as bases of knowledge, while they possess sufficient semantic interoperability to allow for multidatabase concepts and to support cross-database queries on an ad hoc basis. Computational ontologies create underlying semantics for database access. This paper focuses on the spatial component in a humanities cyberinfrastructure, which includes issues of conflicting data, heterogeneous data models, disambiguation, and geographic scale. First, we describe the methodology for integrating the databases. Then we detail the system architecture, which includes a tier of ontologies and schema. We describe the user interface and applications that allow for cross-database queries. For instance, users should be able to analyze the data, examine hypotheses on spatial and temporal relationships, and generate historical maps with datasets from MQWW for research, teaching, and publication on Chinese women writers, their familial relations, publishing venues, and the literary and social communities. Last, we discuss the social side of cyberinfrastructure development, as people are considered to be as critical as the technical components for its success. PMID:21444819

The Wannabee Culture: Why No-One Does What They Used To.

ERIC Educational Resources Information Center

Dixon, Anne

1998-01-01

Electronic publishing has been an agent for change in not just how one publishes but in what one publishes. Describes HyperCite, a joint project with the Institution of Electrical Engineers (IEE) to create INSPEC database. Highlights include the database; the research phase (cross database searching and new interface); and what and how much was…

A scoping review of 10 years of published literature on community-based rehabilitation.

PubMed

Cleaver, Shaun; Nixon, Stephanie

2014-01-01

To identify the characteristics of peer-reviewed literature on community-based rehabilitation (CBR) in low- and middle-income countries published in English from 2003 to 2012. This scoping review involved a systematic search of electronic databases using specific keyword/subject heading combinations. Journal articles were included if they were published in English, used "CBR" as related to rehabilitation with persons with disabilities and not limited to high-income countries (HICs). Data were charted according to both pre-determined and emergent categories. A subset of articles was charted by two reviewers to ensure reliability of variables. A total of 114 articles were included. Fifty-two articles presented empirical research and 49 were published in one of two journals. The articles represented CBR activity in 26 specific countries, although only two of these were in Europe and only one was in the Americas. Authors were predominantly affiliated at universities and in HICs. This scoping review identified and characterized a large pool of literature on CBR, facilitating its incorporation into research and practice. Future research should examine the engagement of persons with disabilities in creating CBR literature, and analysis of literature in languages other than English. Implications for Rehabilitation Community-based rehabilitation (CBR) has been promoted as a rehabilitation strategy of choice in low- and middle-income countries (LMICs), but it has been critiqued for lack of an evidence base. A large number (114) of peer-reviewed articles were published on CBR between 2003 and 2012. Just under half of these articles (45%) presented empirical research, indicating that the evidence base for CBR is growing but will benefit from continued, rigorous inquiry. Furthermore, researchers from LMICs appear to be largely under-represented in published CBR research, flagging the need to support LMIC partners to share their CBR research in peer-reviewed journals.

Cadmium exposure: Toxicity in humans. (Latest citations from the Life Sciences collection database). Published Search

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

NONE

1996-01-01

The bibliography contains citations concerning the effects of cadmium on humans. Biological monitoring of workers exposed to cadmium is discussed in depth. The effects of cadmium on visual-motor performance, community health, and child and infant development are presented. The citations discuss cadmium as a contributing factor in infertility and renal, kidney, and liver diseases. The effects of smoking on cadmium retention are mentioned. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

Cadmium exposure: Toxicity in humans. (Latest citations from the Life Sciences Collection database). Published Search

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

NONE

1997-05-01

The bibliography contains citations concerning the effects of cadmium on humans. Biological monitoring of workers exposed to cadmium is discussed in depth. The effects of cadmium on visual-motor performance, community health, and child and infant development are presented. The citations discuss cadmium as a contributing factor in infertility and renal, kidney, and liver diseases. The effects of smoking on cadmium retention are mentioned. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

ForC: a global database of forest carbon stocks and fluxes.

PubMed

Anderson-Teixeira, Kristina J; Wang, Maria M H; McGarvey, Jennifer C; Herrmann, Valentine; Tepley, Alan J; Bond-Lamberty, Ben; LeBauer, David S

2018-06-01

Forests play an influential role in the global carbon (C) cycle, storing roughly half of terrestrial C and annually exchanging with the atmosphere more than five times the carbon dioxide (CO 2 ) emitted by anthropogenic activities. Yet, scaling up from field-based measurements of forest C stocks and fluxes to understand global scale C cycling and its climate sensitivity remains an important challenge. Tens of thousands of forest C measurements have been made, but these data have yet to be integrated into a single database that makes them accessible for integrated analyses. Here we present an open-access global Forest Carbon database (ForC) containing previously published records of field-based measurements of ecosystem-level C stocks and annual fluxes, along with disturbance history and methodological information. ForC expands upon the previously published tropical portion of this database, TropForC (https://doi.org/10.5061/dryad.t516f), now including 17,367 records (previously 3,568) representing 2,731 plots (previously 845) in 826 geographically distinct areas. The database covers all forested biogeographic and climate zones, represents forest stands of all ages, and currently includes data collected between 1934 and 2015. We expect that ForC will prove useful for macroecological analyses of forest C cycling, for evaluation of model predictions or remote sensing products, for quantifying the contribution of forests to the global C cycle, and for supporting international efforts to inventory forest carbon and greenhouse gas exchange. A dynamic version of ForC is maintained at on GitHub (https://GitHub.com/forc-db), and we encourage the research community to collaborate in updating, correcting, expanding, and utilizing this database. ForC is an open access database, and we encourage use of the data for scientific research and education purposes. Data may not be used for commercial purposes without written permission of the database PI. Any publications using ForC data should cite this publication and Anderson-Teixeira et al. (2016a) (see Metadata S1). No other copyright or cost restrictions are associated with the use of this data set. © 2018 by the Ecological Society of America.

The VO-Dance web application at the IA2 data center

NASA Astrophysics Data System (ADS)

Molinaro, Marco; Knapic, Cristina; Smareglia, Riccardo

2012-09-01

Italian center for Astronomical Archives (IA2, http://ia2.oats.inaf.it) is a national infrastructure project of the Italian National Institute for Astrophysics (Istituto Nazionale di AstroFisica, INAF) that provides services for the astronomical community. Besides data hosting for the Large Binocular Telescope (LBT) Corporation, the Galileo National Telescope (Telescopio Nazionale Galileo, TNG) Consortium and other telescopes and instruments, IA2 offers proprietary and public data access through user portals (both developed and mirrored) and deploys resources complying the Virtual Observatory (VO) standards. Archiving systems and web interfaces are developed to be extremely flexible about adding new instruments from other telescopes. VO resources publishing, along with data access portals, implements the International Virtual Observatory Alliance (IVOA) protocols providing astronomers with new ways of analyzing data. Given the large variety of data flavours and IVOA standards, the need for tools to easily accomplish data ingestion and data publishing arises. This paper describes the VO-Dance tool, that IA2 started developing to address VO resources publishing in a dynamical way from already existent database tables or views. The tool consists in a Java web application, potentially DBMS and platform independent, that stores internally the services' metadata and information, exposes restful endpoints to accept VO queries for these services and dynamically translates calls to these endpoints to SQL queries coherent with the published table or view. In response to the call VO-Dance translates back the database answer in a VO compliant way.

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.

PubMed

Lizio, Marina; Harshbarger, Jayson; Abugessaisa, Imad; Noguchi, Shuei; Kondo, Atsushi; Severin, Jessica; Mungall, Chris; Arenillas, David; Mathelier, Anthony; Medvedeva, Yulia A; Lennartsson, Andreas; Drabløs, Finn; Ramilowski, Jordan A; Rackham, Owen; Gough, Julian; Andersson, Robin; Sandelin, Albin; Ienasescu, Hans; Ono, Hiromasa; Bono, Hidemasa; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Kasukawa, Takeya; Kawaji, Hideya

2017-01-04

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Development of a Data Citations Database for an Interdisciplinary Data Center

NASA Astrophysics Data System (ADS)

Chen, R. S.; Downs, R. R.; Schumacher, J.; Gerard, A.

2017-12-01

The scientific community has long depended on consistent citation of the scientific literature to enable traceability, support replication, and facilitate analysis and debate about scientific hypotheses, theories, assumptions, and conclusions. However, only in the past few years has the community focused on consistent citation of scientific data, e.g., through the application of Digital Object Identifiers (DOIs) to data, the development of peer-reviewed data publications, community principles and guidelines, and other mechanisms. This means that, moving ahead, it should be easier to identify and track data citations and conduct systematic bibliometric studies. However, this still leaves the problem that many legacy datasets and past citations lack DOIs, making it difficult to develop a historical baseline or assess trends. With this in mind, the NASA Socioeconomic Data and Applications Center (SEDAC) has developed a searchable citations database, containing more than 3,400 citations of SEDAC data and information products over the past 20 years. These citations were collected through various indices and search tools and in some cases through direct contacts with authors. The citations come from a range of natural, social, health, and engineering science journals, books, reports, and other media. The database can be used to find and extract citations filtered by a range of criteria, enabling quantitative analysis of trends, intercomparisons between data collections, and categorization of citations by type. We present a preliminary analysis of citations for selected SEDAC data collections, in order to establish a baseline and assess options for ongoing metrics to track the impact of SEDAC data on interdisciplinary science. We also present an analysis of the uptake of DOIs within data citations reported in published studies that used SEDAC data.

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.

PubMed

Ribeiro, António J M; Holliday, Gemma L; Furnham, Nicholas; Tyzack, Jonathan D; Ferris, Katherine; Thornton, Janet M

2018-01-04

M-CSA (Mechanism and Catalytic Site Atlas) is a database of enzyme active sites and reaction mechanisms that can be accessed at www.ebi.ac.uk/thornton-srv/m-csa. Our objectives with M-CSA are to provide an open data resource for the community to browse known enzyme reaction mechanisms and catalytic sites, and to use the dataset to understand enzyme function and evolution. M-CSA results from the merging of two existing databases, MACiE (Mechanism, Annotation and Classification in Enzymes), a database of enzyme mechanisms, and CSA (Catalytic Site Atlas), a database of catalytic sites of enzymes. We are releasing M-CSA as a new website and underlying database architecture. At the moment, M-CSA contains 961 entries, 423 of these with detailed mechanism information, and 538 with information on the catalytic site residues only. In total, these cover 81% (195/241) of third level EC numbers with a PDB structure, and 30% (840/2793) of fourth level EC numbers with a PDB structure, out of 6028 in total. By searching for close homologues, we are able to extend M-CSA coverage of PDB and UniProtKB to 51 993 structures and to over five million sequences, respectively, of which about 40% and 30% have a conserved active site. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.

PubMed

Slenter, Denise N; Kutmon, Martina; Hanspers, Kristina; Riutta, Anders; Windsor, Jacob; Nunes, Nuno; Mélius, Jonathan; Cirillo, Elisa; Coort, Susan L; Digles, Daniela; Ehrhart, Friederike; Giesbertz, Pieter; Kalafati, Marianthi; Martens, Marvin; Miller, Ryan; Nishida, Kozo; Rieswijk, Linda; Waagmeester, Andra; Eijssen, Lars M T; Evelo, Chris T; Pico, Alexander R; Willighagen, Egon L

2018-01-04

WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation. Recent curation efforts focused on improving the annotation of metabolism and metabolic pathways by associating unmapped metabolites with database identifiers and providing more detailed interaction knowledge. Here, we report the outcomes of the continued growth and curation efforts, such as a doubling of the number of annotated metabolite nodes in WikiPathways. Furthermore, we introduce an OpenAPI documentation of our web services and the FAIR (Findable, Accessible, Interoperable and Reusable) annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data. New search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Clinical Uncertainties, Health Service Challenges, and Ethical Complexities of HIV “Test-and-Treat”: A Systematic Review

PubMed Central

Shah, Kavita R.; Sarma, Karthik V.; Mahajan, Anish P.

2013-01-01

Despite the HIV “test-and-treat” strategy’s promise, questions about its clinical rationale, operational feasibility, and ethical appropriateness have led to vigorous debate in the global HIV community. We performed a systematic review of the literature published between January 2009 and May 2012 using PubMed, SCOPUS, Global Health, Web of Science, BIOSIS, Cochrane CENTRAL, EBSCO Africa-Wide Information, and EBSCO CINAHL Plus databases to summarize clinical uncertainties, health service challenges, and ethical complexities that may affect the test-and-treat strategy’s success. A thoughtful approach to research and implementation to address clinical and health service questions and meaningful community engagement regarding ethical complexities may bring us closer to safe, feasible, and effective test-and-treat implementation. PMID:23597344

Towards a standards-compliant genomic and metagenomic publication record

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

Fenner, Marsha W; Garrity, George M.; Field, Dawn

2008-04-01

Increasingly we are aware as a community of the growing need to manage the avalanche of genomic and metagenomic data, in addition to related data types like ribosomal RNA and barcode sequences, in a way that tightly integrates contextual data with traditional literature in a machine-readable way. It is for this reason that the Genomic Standards Consortium (GSC) formed in 2005. Here we suggest that we move beyond the development of standards and tackle standards-compliance and improved data capture at the level of the scientific publication. We are supported in this goal by the fact that the scientific community ismore » in the midst of a publishing revolution. This revolution is marked by a growing shift away from a traditional dichotomy between 'journal articles' and 'database entries' and an increasing adoption of hybrid models of collecting and disseminating scientific information. With respect to genomes and metagenomes and related data types, we feel the scientific community would be best served by the immediate launch of a central repository of short, highly structured 'Genome Notes' that must be standards-compliant. This could be done in the context of an existing journal, but we also suggest the more radical solution of launching a new journal. Such a journal could be designed to cater to a wide range of standards-related content types that are not currently centralized in the published literature. It could also support the demand for centralizing aspects of the 'gray literature' (documents developed by institutions or communities) such as the call by the GSCl for a central repository of Standard Operating Procedures describing the genomic annotation pipelines of the major sequencing centers. We argue that such an 'eJournal', published under the Open Access paradigm by the GSC, could be an attractive publishing forum for a broader range of standardization initiatives within, and beyond, the GSC and thereby fill an unoccupied yet increasingly important niche within the current research landscape.« less

Astronaut Demographic Database: Everything You Want to Know About Astronauts and More

NASA Technical Reports Server (NTRS)

Keeton, Kathryn; Patterson, Holly

2011-01-01

A wealth of information regarding the astronaut population is available that could be especially useful to researchers. However, until now, it has been difficult to obtain that information in a systematic way. Therefore, this "astronaut database" began as a way for researchers within the Behavioral Health and Performance Group to keep track of the ever growing astronaut corps population. Before our effort, compilation of such data could be found, but not in a way that was easily acquired or accessible. One would have to use internet search engines, read through lengthy and potentially inaccurate informational sites, or read through astronaut biographies compiled by NASA. Astronauts are a unique class of individuals and, by examining such information, which we dubbed "Demographics," we hoped to find some commonalities that may be useful for other research areas and future research topics. By organizing the information pertaining to astronauts1 in a formal, unified catalog, we believe we have made the information more easily accessible, readily useable, and user friendly. Our end goal is to provide this database to others as a highly functional resource within the research community. Perhaps the database can eventually be an official, published document for researchers to gain full access.

The igmspec database of public spectra probing the intergalactic medium

NASA Astrophysics Data System (ADS)

Prochaska, J. X.

2017-04-01

We describe v02 of igmspec, a database of publicly available ultraviolet, optical, and near-infrared spectra that probe the intergalactic medium (IGM). This database, a child of the specdb repository in the specdb github organization, comprises 403 277 unique sources and 434 686 spectra obtained with the world's greatest observatories. All of these data are distributed in a single ≈ 25GB HDF5 file maintained at the University of California Observatories and the University of California, Santa Cruz. The specdb software package includes Python scripts and modules for searching the source catalog and spectral datasets, and software links to the linetools package for spectral analysis. The repository also includes software to generate private spectral datasets that are compliant with International Virtual Observatory Alliance (IVOA) protocols and a Python-based interface for IVOA Simple Spectral Access queries. Future versions of igmspec will ingest other sources (e.g. gamma-ray burst afterglows) and other surveys as they become publicly available. The overall goal is to include every spectrum that effectively probes the IGM. Future databases of specdb may include publicly available galaxy spectra (exgalspec) and published supernovae spectra (snspec). The community is encouraged to join the effort on github: https://github.com/specdb.

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.

Systematic review of qualitative evaluations of reentry programs addressing problematic drug use and mental health disorders amongst people transitioning from prison to communities.

PubMed

Kendall, Sacha; Redshaw, Sarah; Ward, Stephen; Wayland, Sarah; Sullivan, Elizabeth

2018-03-02

The paper presents a systematic review and metasynthesis of findings from qualitative evaluations of community reentry programs. The programs sought to engage recently released adult prison inmates with either problematic drug use or a mental health disorder. Seven biomedical and social science databases, Cinahl, Pubmed, Scopus, Proquest, Medline, Sociological abstracts and Web of Science and publisher database Taylor and Francis were searched in 2016 resulting in 2373 potential papers. Abstract reviews left 140 papers of which 8 were included after detailed review. Major themes and subthemes were identified through grounded theory inductive analysis of results from the eight papers. Of the final eight papers the majority (6) were from the United States. In total, the papers covered 405 interviews and included 121 (30%) females and 284 (70%) males. Findings suggest that the interpersonal skills of case workers; access to social support and housing; and continuity of case worker relationships throughout the pre-release and post-release period are key social and structural factors in program success. Evaluation of community reentry programs requires qualitative data to contextualize statistical findings and identify social and structural factors that impact on reducing incarceration and improving participant health. These aspects of program efficacy have implications for reentry program development and staff training and broader social and health policy and services.

"Balkan journal of medical genetics"--facts, editorial policies, practices and challenges.

PubMed

Plaseska Karanfilska, Dijana; Sukarova Stefanovska, Emilija

2014-01-01

The Balkan Journal of Medical Genetics (BJMG) is an international, open access journal that publishes scientific papers covering different aspects of medical genetics. It is published by the Macedonian Academy of Sciences and Arts twice a year in both printed and electronic versions. BJMG is covered by many abstracting and indexing databases, including PubMed Central and Thomson Reuters. Although there are many journals in the field of medical genetics, only a few come from regions outside Western Europe and North America. Being one of these few journals, BJMG aims to promote genetics and research on this topic in the Balkan countries and beyond. BJMG's ultimate goal is to raise the scientific quality and metrics of the journal and provide a better place for BJMG in the community of scientific journals.

A Multipronged, Adaptive Approach for the Recruitment of Diverse Community-Residing Elders with Memory Impairment: The MIND at Home Experience.

PubMed

Samus, Quincy M; Amjad, Halima; Johnston, Deirdre; Black, Betty S; Bartels, Stephen J; Lyketsos, Constantine G

2015-07-01

To provide a critical review of a multipronged recruitment approach used to identify, recruit, and enroll a diverse community-based sample of persons with memory disorders into an 18-month randomized, controlled dementia care coordination trial. Descriptive analysis of a recruitment approach comprised five strategies: community liaison ("gatekeepers") method, letters sent from trusted community organizations, display and distribution of study materials in the community, research registries, and general community outreach and engagement activities. Participants were 55 community organizations and 63 staff of community organizations in Baltimore, Maryland. Participant referral sources, eligibility, enrollment status, demographics, and loss to follow-up were tracked in a relational access database. In total, 1,275 referrals were received and 303 socioeconomically, cognitively, and racially diverse community-dwelling persons with cognitive disorders were enrolled. Most referrals came from letters sent from community organizations directly to clients on the study's behalf (39%) and referrals from community liaison organizations (29%). African American/black enrollees were most likely to come from community liaison organizations. A multipronged, adaptive approach led to the successful recruitment of diverse community-residing elders with memory impairment for an intervention trial. Key factors for success included using a range of evidence-supported outreach strategies, forming key strategic community partnerships, seeking regular stakeholder input through all research phases, and obtaining "buy-in" from community stakeholders by aligning study objectives with perceived unmet community needs. Copyright © 2015 American Association for Geriatric Psychiatry. Published by Elsevier Inc. All rights reserved.

SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.

PubMed

Silva, Genivaldo Gueiros Z; Green, Kevin T; Dutilh, Bas E; Edwards, Robert A

2016-02-01

Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools. SUPER-FOCUS was implemented in Python, and its source code and the tool website are freely available at https://edwards.sdsu.edu/SUPERFOCUS. redwards@mail.sdsu.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Hospital and Community Characteristics Associated With Pediatric Direct Admission to Hospital.

PubMed

Leyenaar, JoAnna K; Shieh, Meng-Shiou; Lagu, Tara; Pekow, Penelope S; Lindenauer, Peter K

2017-10-27

One quarter of pediatric hospitalizations begin as direct admissions, defined as hospitalization without receiving care in the hospital's emergency department (ED). Direct admission rates are highly variable across hospitals, yet previous studies have not examined reasons for this variation. We aimed to determine the relationships between hospital and community factors and pediatric direct admission rates, and to evaluate the degree to which these characteristics explain variation in risk-adjusted direct admission rates. We conducted a cross-sectional study of the Healthcare Cost and Utilization Project's Kids Inpatient Database, American Hospital Association Database, and Area Health Resource File, including children <18 years of age who were admitted for a medical hospitalization in states contributing data to all data sets. Using hierarchical generalized linear modeling, we generated risk-adjusted direct admission rates and used generalized linear models to assess the association of hospital and community characteristics with these risk-adjusted rates. We included 211,458 children discharged from 933 hospitals and 26 states; 20.2% were admitted directly. One-fifth of the variance in risk-adjusted direct admission rates was attributed to observed hospital and community factors. The greatest proportion of this explained variance was related to ED volume (37%), volume of pediatric hospitalizations (27%), and size of the pediatrician workforce (12%). Direct admission rates were associated with several hospital and community characteristics, but the majority of variation in hospitals' direct admission rates was not explained by these factors. These findings suggest opportunities for diverse hospital types to develop the infrastructure and communication systems necessary to support pediatric direct admissions. Copyright © 2017 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures

PubMed Central

Culhane, Aedín C.; Schröder, Markus S.; Sultana, Razvan; Picard, Shaita C.; Martinelli, Enzo N.; Kelly, Caroline; Haibe-Kains, Benjamin; Kapushesky, Misha; St Pierre, Anne-Alyssa; Flahive, William; Picard, Kermshlise C.; Gusenleitner, Daniel; Papenhausen, Gerald; O'Connor, Niall; Correll, Mick; Quackenbush, John

2012-01-01

GeneSigDB (http://www.genesigdb.org or http://compbio.dfci.harvard.edu/genesigdb/) is a database of gene signatures that have been extracted and manually curated from the published literature. It provides a standardized resource of published prognostic, diagnostic and other gene signatures of cancer and related disease to the community so they can compare the predictive power of gene signatures or use these in gene set enrichment analysis. Since GeneSigDB release 1.0, we have expanded from 575 to 3515 gene signatures, which were collected and transcribed from 1604 published articles largely focused on gene expression in cancer, stem cells, immune cells, development and lung disease. We have made substantial upgrades to the GeneSigDB website to improve accessibility and usability, including adding a tag cloud browse function, facetted navigation and a ‘basket’ feature to store genes or gene signatures of interest. Users can analyze GeneSigDB gene signatures, or upload their own gene list, to identify gene signatures with significant gene overlap and results can be viewed on a dynamic editable heatmap that can be downloaded as a publication quality image. All data in GeneSigDB can be downloaded in numerous formats including .gmt file format for gene set enrichment analysis or as a R/Bioconductor data file. GeneSigDB is available from http://www.genesigdb.org. PMID:22110038

Enhancing AstroInformatics and Science Discovery from Data in Journal Articles

NASA Astrophysics Data System (ADS)

Mazzarella, Joseph

2011-05-01

Traditional methods of publishing scientific data and metadata in journal articles are in need of major upgrades to reach the full potential of astronomical databases and astroinformatics techniques to facilitate semi-automated, and eventually autonomous, methods of science discovery. I will review a growing collaboration involving the NASA/IPAC Extragalactic Database (NED), the Astrophysics Data System (ADS), the Virtual Astronomical Observatory (VAO), the AAS Journals and IOP, and the Data Conservancy that is aimed toward transforming the methodology used to publish, capture and link data associated with astrophysics journal articles. We are planning a web-based workflow to assist astronomers during the publication of journal articles. The primary goals are to facilitate the application of structure and standards to (meta)data, reduce errors, remove ambiguities in the identification of astrophysical objects and regions of sky, capture and preserve the images and spectral data files used to make plots, and accelerate the ingestion of the data into relevant repositories, search engines and integration services. The outcome of this community wide effort will address a recent public policy mandate to publish scientific data in open formats to allow reproducibility of results and to facilitate new discoveries. Equally important, this work has the potential to usher in a new wave of science discovery based on seamless connectivity between data relationships that are continuously growing in size and complexity, and increasingly sophisticated data visualization and analysis applications.

The community and consumer food environment and children's diet: a systematic review.

PubMed

Engler-Stringer, Rachel; Le, Ha; Gerrard, Angela; Muhajarine, Nazeem

2014-05-29

While there is a growing body of research on food environments for children, there has not been a published comprehensive review to date evaluating food environments outside the home and school and their relationship with diet in children. The purpose of this paper is to review evidence on the influence of the community and consumer nutrition environments on the diet of children under the age of 18 years. Our search strategy included a combination of both subject heading searching as well as natural language, free-text searching. We searched nine databases (MEDLINE, Web of Science, CINAHL, Embase, Scopus, ProQuest Public Health, PsycINFO, Sociological Abstracts, and GEOBASE) for papers published between 1995 and July 2013. Study designs were included if they were empirically-based, published scholarly research articles, were focused on children as the population of interest, fit within the previously mentioned date range, included at least one diet outcome, and exposures within the community nutrition environment (e.g., location and accessibility of food outlets), and consumer nutrition environment (e.g., price, promotion, and placement of food choices). After applying exclusion and inclusion criteria, a total of 26 articles were included in our review. The vast majority of the studies were cross-sectional in design, except for two articles reporting on longitudinal studies. The food environment exposure(s) included aspects of the community nutrition environments, except for three that focused on the consumer nutrition environment. The community nutrition environment characterization most often used Geographic Information Systems to geolocate participants' homes (and/or schools) and then one or more types of food outlets in relation to these. The children included were all of school age. Twenty-two out of 26 studies showed at least one positive association between the food environment exposure and diet outcome. Four studies reported only null associations. This review found moderate evidence of the relationship between the community and consumer nutrition environments and dietary intake in children up to 18 years of age. There is wide variation in measures used to characterize both the community and consumer nutrition environments and diet, and future research should work to decrease this heterogeneity.

The community and consumer food environment and children’s diet: a systematic review

PubMed Central

2014-01-01

Background While there is a growing body of research on food environments for children, there has not been a published comprehensive review to date evaluating food environments outside the home and school and their relationship with diet in children. The purpose of this paper is to review evidence on the influence of the community and consumer nutrition environments on the diet of children under the age of 18 years. Methods Our search strategy included a combination of both subject heading searching as well as natural language, free-text searching. We searched nine databases (MEDLINE, Web of Science, CINAHL, Embase, Scopus, ProQuest Public Health, PsycINFO, Sociological Abstracts, and GEOBASE) for papers published between 1995 and July 2013. Study designs were included if they were empirically-based, published scholarly research articles, were focused on children as the population of interest, fit within the previously mentioned date range, included at least one diet outcome, and exposures within the community nutrition environment (e.g., location and accessibility of food outlets), and consumer nutrition environment (e.g., price, promotion, and placement of food choices). Results After applying exclusion and inclusion criteria, a total of 26 articles were included in our review. The vast majority of the studies were cross-sectional in design, except for two articles reporting on longitudinal studies. The food environment exposure(s) included aspects of the community nutrition environments, except for three that focused on the consumer nutrition environment. The community nutrition environment characterization most often used Geographic Information Systems to geolocate participants’ homes (and/or schools) and then one or more types of food outlets in relation to these. The children included were all of school age. Twenty-two out of 26 studies showed at least one positive association between the food environment exposure and diet outcome. Four studies reported only null associations. Conclusions This review found moderate evidence of the relationship between the community and consumer nutrition environments and dietary intake in children up to 18 years of age. There is wide variation in measures used to characterize both the community and consumer nutrition environments and diet, and future research should work to decrease this heterogeneity. PMID:24884443

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.

Maximizing the use of Special Olympics International's Healthy Athletes database: A call to action.

PubMed

Lloyd, Meghann; Foley, John T; Temple, Viviene A

2018-02-01

There is a critical need for high-quality population-level data related to the health of individuals with intellectual disabilities. For more than 15 years Special Olympics International has been conducting free Healthy Athletes screenings at local, national and international events. The Healthy Athletes database is the largest known international database specifically on the health of people with intellectual disabilities; however, it is relatively under-utilized by the research community. A consensus meeting with two dozen North American researchers, stakeholders, clinicians and policymakers took place in Toronto, Canada. The purpose of the meeting was to: 1) establish the perceived utility of the database, and 2) to identify and prioritize 3-5 specific priorities related to using the Healthy Athletes database to promote the health of individuals with intellectual disabilities. There was unanimous agreement from the meeting participants that this database represents an immense opportunity both from the data already collected, and data that will be collected in the future. The 3 top priorities for the database were deemed to be: 1) establish the representativeness of data collected on Special Olympics athletes compared to the general population with intellectual disabilities, 2) create a scientific advisory group for Special Olympics International, and 3) use the data to improve Special Olympics programs around the world. The Special Olympics Healthy Athletes database includes data not found in any other source and should be used, in partnership with Special Olympics International, by researchers to significantly increase our knowledge and understanding of the health of individuals with intellectual disabilities. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Systematic review of mental health and well-being outcomes following community-based obesity prevention interventions among adolescents.

PubMed

Hoare, Erin; Fuller-Tyszkiewicz, Matthew; Skouteris, Helen; Millar, Lynne; Nichols, Melanie; Allender, Steven

2015-01-05

This paper aimed to systematically evaluate the mental health and well-being outcomes observed in previous community-based obesity prevention interventions in adolescent populations. Systematic review of literature from database inception to October 2014. Articles were sourced from CINAHL, Global Health, Health Source: Nursing and Academic Edition, MEDLINE, PsycARTICLES and PsycINFO, all of which were accessed through EBSCOhost. The Cochrane Database was also searched to identify all eligible articles. PRISMA guidelines were followed and search terms and search strategy ensured all possible studies were identified for review. Intervention studies were eligible for inclusion if they were: focused on overweight or obesity prevention, community-based, targeted adolescents (aged 10-19 years), reported a mental health or well-being measure, and included a comparison or control group. Studies that focused on specific adolescent groups or were treatment interventions were excluded from review. Quality of evidence was assessed using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) guidelines. Primary outcomes were measures of mental health and well-being, including diagnostic and symptomatic measures. Secondary outcomes included adiposity or weight-related measures. Seven studies met the inclusion criteria; one reported anxiety/depressive outcomes, two reported on self-perception well-being measures such as self-esteem and self-efficacy, and four studies reported outcomes of quality of life. Positive mental health outcomes demonstrated that following obesity prevention, interventions included a decrease in anxiety and improved health-related quality of life. Quality of evidence was graded as very low. Although positive outcomes for mental health and well-being do exist, controlled evaluations of community-based obesity prevention interventions have not often included mental health measures (n=7). It is recommended that future interventions incorporate mental health and well-being measures to identify any potential mechanisms influencing adolescent weight-related outcomes, and equally to ensure interventions are not causing harm to adolescent mental health. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Epidemiology of balance symptoms and disorders in the community: a systematic review.

PubMed

Murdin, Louisa; Schilder, Anne G M

2015-03-01

Balance disorders presenting with symptoms of dizziness or vertigo may have significant impact on quality of life and are a recognized risk factor for falls. The objective of this review was to systematically synthesize the published literature on the epidemiology of balance symptoms and disorders in the adult community population. A search was carried out across PubMed, Medline, and Cochrane databases to identify suitable studies. Studies were eligible for inclusion if they contained data on the epidemiology of symptoms of balance disorders (dizziness and vertigo) or balance disorders sampled from community-based adult populations. Data were collected on prevalence and incidence of balance symptoms and on specific balance disorders. A validated risk-of-bias assessment was carried out. Twenty eligible studies were identified. The lifetime prevalence estimates of significant dizziness ranged between 17 and 30%, and for vertigo between 3 and 10%. Published point prevalence data exist for Ménière's disease (0.12-0.5%) and for vestibular migraine (0.98%). For benign paroxysmal positional vertigo, 1-year incidence estimates range from 0.06 to 0.6%. There are no community-based studies on the prevalence or incidence of chronic uncompensated peripheral vestibular disorders or vestibular neuritis. Symptoms of dizziness and vertigo are common in the adult population, and data give a coherent picture of community epidemiology. These data can inform rational service planning and much-needed clinical trials in this field. There are insufficient data on specific balance disorders, especially peripheral vestibular disorders such as vestibular neuritis and its long-term sequelae.

SpecDB: The AAVSO’s Public Repository for Spectra of Variable Stars

NASA Astrophysics Data System (ADS)

Kafka, Stella; Weaver, John; Silvis, George; Beck, Sara

2018-01-01

SpecDB is the American Association of Variable Star Observers (AAVSO) spectral database. Accessible to any astronomer with the capability to perform spectroscopy, SpecDB provides an unprecedented scientific opportunity for amateur and professional astronomers around the globe. Backed by the Variable Star Index, one of the most utilized variable star catalogs, SpecDB is expected to become one of the world leading databases of its kind. Once verified by a team of expert spectroscopists, an observer can upload spectra of variable stars target easily and efficiently. Uploaded spectra can then be searched for, previewed, and downloaded for inclusion in publications. Close community development and involvement will ensure a user-friendly and versatile database, compatible with the needs of 21st century astrophysics. Observations of 1D spectra are submitted as FITS files. All spectra are required to be preprocessed for wavelength calibration and dark subtraction; Bias and flat are strongly recommended. First time observers are required to submit a spectrum of a standard (non-variable) star to be checked for errors in technique or equipment. Regardless of user validation, FITS headers must include several value cards detailing the observation, as well as information regarding the observer, equipment, and observing site in accordance with existing AAVSO records. This enforces consistency and provides necessary details for follow up analysis. Requirements are provided to users in a comprehensive guidebook and accompanying technical manual. Upon submission, FITS headers are automatically checked for errors and any anomalies are immediately fed back to the user. Successful candidates can then submit at will, including multiple simultaneous submissions. All published observations can be searched and interactively previewed. Community involvement will be enhanced by an associated forum where users can discuss observation techniques and suggest improvements to the database.

Teleform scannable data entry: an efficient method to update a community-based medical record? Community care coordination network Database Group.

PubMed Central

Guerette, P.; Robinson, B.; Moran, W. P.; Messick, C.; Wright, M.; Wofford, J.; Velez, R.

1995-01-01

Community-based multi-disciplinary care of chronically ill individuals frequently requires the efforts of several agencies and organizations. The Community Care Coordination Network (CCCN) is an effort to establish a community-based clinical database and electronic communication system to facilitate the exchange of pertinent patient data among primary care, community-based and hospital-based providers. In developing a primary care based electronic record, a method is needed to update records from the field or remote sites and agencies and yet maintain data quality. Scannable data entry with fixed fields, optical character recognition and verification was compared to traditional keyboard data entry to determine the relative efficiency of each method in updating the CCCN database. PMID:8563414

The BioMart community portal: an innovative alternative to large, centralized data repositories

USDA-ARS?s Scientific Manuscript database

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biologi...

International Soil Carbon Network (ISCN) Database v3-1

DOE Data Explorer

Nave, Luke [University of Michigan] (ORCID:0000000182588335); Johnson, Kris [USDA-Forest Service; van Ingen, Catharine [Microsoft Research; Agarwal, Deborah [Lawrence Berkeley National Laboratory] (ORCID:0000000150452396); Humphrey, Marty [University of Virginia; Beekwilder, Norman [University of Virginia

2016-01-01

The ISCN is an international scientific community devoted to the advancement of soil carbon research. The ISCN manages an open-access, community-driven soil carbon database. This is version 3-1 of the ISCN Database, released in December 2015. It gathers 38 separate dataset contributions, totalling 67,112 sites with data from 71,198 soil profiles and 431,324 soil layers. For more information about the ISCN, its scientific community and resources, data policies and partner networks visit: http://iscn.fluxdata.org/.

Database on Demand: insight how to build your own DBaaS

NASA Astrophysics Data System (ADS)

Gaspar Aparicio, Ruben; Coterillo Coz, Ignacio

2015-12-01

At CERN, a number of key database applications are running on user-managed MySQL, PostgreSQL and Oracle database services. The Database on Demand (DBoD) project was born out of an idea to provide CERN user community with an environment to develop and run database services as a complement to the central Oracle based database service. The Database on Demand empowers the user to perform certain actions that had been traditionally done by database administrators, providing an enterprise platform for database applications. It also allows the CERN user community to run different database engines, e.g. presently three major RDBMS (relational database management system) vendors are offered. In this article we show the actual status of the service after almost three years of operations, some insight of our new redesign software engineering and near future evolution.

NGS Catalog: A Database of Next Generation Sequencing Studies in Humans

PubMed Central

Xia, Junfeng; Wang, Qingguo; Jia, Peilin; Wang, Bing; Pao, William; Zhao, Zhongming

2015-01-01

Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research since its advent only a few years ago, and they are expected to advance at an unprecedented pace in the following years. To provide the research community with a comprehensive NGS resource, we have developed the database Next Generation Sequencing Catalog (NGS Catalog, http://bioinfo.mc.vanderbilt.edu/NGS/index.html), a continually updated database that collects, curates and manages available human NGS data obtained from published literature. NGS Catalog deposits publication information of NGS studies and their mutation characteristics (SNVs, small insertions/deletions, copy number variations, and structural variants), as well as mutated genes and gene fusions detected by NGS. Other functions include user data upload, NGS general analysis pipelines, and NGS software. NGS Catalog is particularly useful for investigators who are new to NGS but would like to take advantage of these powerful technologies for their own research. Finally, based on the data deposited in NGS Catalog, we summarized features and findings from whole exome sequencing, whole genome sequencing, and transcriptome sequencing studies for human diseases or traits. PMID:22517761

The Saccharomyces Genome Database Variant Viewer.

PubMed

Sheppard, Travis K; Hitz, Benjamin C; Engel, Stacia R; Song, Giltae; Balakrishnan, Rama; Binkley, Gail; Costanzo, Maria C; Dalusag, Kyla S; Demeter, Janos; Hellerstedt, Sage T; Karra, Kalpana; Nash, Robert S; Paskov, Kelley M; Skrzypek, Marek S; Weng, Shuai; Wong, Edith D; Cherry, J Michael

2016-01-04

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data.

PubMed

Butyaev, Alexander; Mavlyutov, Ruslan; Blanchette, Mathieu; Cudré-Mauroux, Philippe; Waldispühl, Jérôme

2015-09-18

Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data (3DBG), and a 3D genome browser to visualize and explore 3D genome structures (3DGB). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Stigma Related Avoidance in People Living with Severe Mental Illness (SMI): Findings of an Integrative Review.

PubMed

Abiri, Sadat; Oakley, Linda Denise; Hitchcock, Mary E; Hall, Amanda

2016-04-01

The purpose of this integrative review is to synthesize primary evidence of the impact of internalized stigma on avoidance in adult community treatment patients living with SMI. A keyword database search of articles published through 2015 yielded 21 papers and a total of 4256 patients. Our analyses found that stigmatizing beliefs associated with avoidance are related to significant loss of self-esteem. Factors generally thought to reduce stigma internalized as self-stigmatizing beliefs, such as improved insight, increased self-awareness, and psycho-education to improve stigma coping skills, do not appear to improve self-esteem.

A review of instruments to measure interprofessional collaboration for chronic disease management for community-living older adults.

PubMed

Bookey-Bassett, Sue; Markle-Reid, Maureen; McKey, Colleen; Akhtar-Danesh, Noori

2016-01-01

It is acknowledged internationally that chronic disease management (CDM) for community-living older adults (CLOA) is an increasingly complex process. CDM for older adults, who are often living with multiple chronic conditions, requires coordination of various health and social services. Coordination is enabled through interprofessional collaboration (IPC) among individual providers, community organizations, and health sectors. Measuring IPC is complicated given there are multiple conceptualisations and measures of IPC. A literature review of several healthcare, psychological, and social science electronic databases was conducted to locate instruments that measure IPC at the team level and have published evidence of their reliability and validity. Five instruments met the criteria and were critically reviewed to determine their strengths and limitations as they relate to CDM for CLOA. A comparison of the characteristics, psychometric properties, and overall concordance of each instrument with salient attributes of IPC found the Collaborative Practice Assessment Tool to be the most appropriate instrument for measuring IPC for CDM in CLOA.

16 CFR 1102.28 - Publication of reports of harm.

Code of Federal Regulations, 2012 CFR

2012-01-01

... REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102.28... publish reports of harm that meet the requirements for publication in the Database. The Commission will... Commission may publish a report of harm that meets the requirements of § 1102.10(d) in the Database beyond...

16 CFR 1102.28 - Publication of reports of harm.

Code of Federal Regulations, 2014 CFR

2014-01-01

... REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102.28... publish reports of harm that meet the requirements for publication in the Database. The Commission will... Commission may publish a report of harm that meets the requirements of § 1102.10(d) in the Database beyond...

Academic Journal Embargoes and Full Text Databases.

ERIC Educational Resources Information Center

Brooks, Sam

2003-01-01

Documents the reasons for embargoes of academic journals in full text databases (i.e., publisher-imposed delays on the availability of full text content) and provides insight regarding common misconceptions. Tables present data on selected journals covering a cross-section of subjects and publishers and comparing two full text business databases.…

Analysis and Evaluation of Databases on Business and Management Training Schemes for Small and Medium-Sized Enterprises in the European Community.

ERIC Educational Resources Information Center

Allesch, Jurgen; Preiss-Allesch, Dagmar

This report describes a study that identified major databases in operation in the 12 European Community countries that provide small- and medium-sized enterprises with information on opportunities for obtaining training and continuing education. Thirty-five databases were identified through information obtained from telephone interviews or…

MaizeGDB update: New tools, data, and interface for the maize model organism database

USDA-ARS?s Scientific Manuscript database

MaizeGDB is a highly curated, community-oriented database and informatics service to researchers focused on the crop plant and model organism Zea mays ssp. mays. Although some form of the maize community database has existed over the last 25 years, there have only been two major releases. In 1991, ...

The Future of the ASP Conference Series

NASA Astrophysics Data System (ADS)

Jensen, Joseph B.; Barnes, Jonathan; Moody, J. Ward; Szkody, Paula

The Astronomical Society of the Pacific (ASP) has been publishing the proceedings of conferences in astronomy and astrophysics for more than 20 years. The ASP Conference Series (ASPCS) is widely known for its affordable and high quality printed volumes. The ASPCS is adapting to the changing market by making electronically published volumes available to subscribers around the world, including papers in the Astrophysics Data System (ADS) database, and allowing authors to post papers on e-print archives. We discuss the role of the printed book in our future plans, and how electronic publishing affects the types of products and services we offer. Recently there has been increasing pressure in the academic world for open access (electronic copies of scholarly publications made freely-available immediately after publication), and we discuss how the ASPCS is responding to the needs of the professional astronomical community, the ASP, and humanity at large. While we cannot yet provide full open access and stay in business, we are actively pursuing several initiatives to improve the quality of our product and the impact of the papers we publish.

MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups

PubMed Central

McIlroy, Simon Jon; Kirkegaard, Rasmus Hansen; McIlroy, Bianca; Nierychlo, Marta; Kristensen, Jannie Munk; Karst, Søren Michael; Albertsen, Mads

2017-01-01

Abstract Wastewater is increasingly viewed as a resource, with anaerobic digester technology being routinely implemented for biogas production. Characterising the microbial communities involved in wastewater treatment facilities and their anaerobic digesters is considered key to their optimal design and operation. Amplicon sequencing of the 16S rRNA gene allows high-throughput monitoring of these systems. The MiDAS field guide is a public resource providing amplicon sequencing protocols and an ecosystem-specific taxonomic database optimized for use with wastewater treatment facility samples. The curated taxonomy endeavours to provide a genus-level-classification for abundant phylotypes and the online field guide links this identity to published information regarding their ecology, function and distribution. This article describes the expansion of the database resources to cover the organisms of the anaerobic digester systems fed primary sludge and surplus activated sludge. The updated database includes descriptions of the abundant genus-level-taxa in influent wastewater, activated sludge and anaerobic digesters. Abundance information is also included to allow assessment of the role of emigration in the ecology of each phylotype. MiDAS is intended as a collaborative resource for the progression of research into the ecology of wastewater treatment, by providing a public repository for knowledge that is accessible to all interested in these biotechnologically important systems. Database URL: http://www.midasfieldguide.org PMID:28365734

VO-Dance an IVOA tools to easy publish data into VO and it's extension on planetology request

NASA Astrophysics Data System (ADS)

Smareglia, R.; Capria, M. T.; Molinaro, M.

2012-09-01

Data publishing through the self standing portals can be joined to VO resource publishing, i.e. astronomical resources deployed through VO compliant services. Since the IVOA (International Virtual Observatory Alliance) provides many protocols and standards for the various data flavors (images, spectra, catalogues … ), and since the data center has as a goal to grow up in number of hosted archives and services providing, the idea arose to find a way to easily deploy and maintain VO resources. VO-Dance is a java web application developed at IA2 that addresses this idea creating, in a dynamical way, VO resources out of database tables or views. It is structured to be potentially DBMS and platform independent and consists of 3 main tokens, an internal DB to store resources description and model metadata information, a restful web application to deploy the resources to the VO community. It's extension to planetology request is under study to best effort INAF software development and archive efficiency.

16 CFR § 1102.28 - Publication of reports of harm.

Code of Federal Regulations, 2013 CFR

2013-01-01

... REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102.28... publish reports of harm that meet the requirements for publication in the Database. The Commission will... Commission may publish a report of harm that meets the requirements of § 1102.10(d) in the Database beyond...

Novel statistical tools for management of public databases facilitate community-wide replicability and control of false discovery.

PubMed

Rosset, Saharon; Aharoni, Ehud; Neuvirth, Hani

2014-07-01

Issues of publication bias, lack of replicability, and false discovery have long plagued the genetics community. Proper utilization of public and shared data resources presents an opportunity to ameliorate these problems. We present an approach to public database management that we term Quality Preserving Database (QPD). It enables perpetual use of the database for testing statistical hypotheses while controlling false discovery and avoiding publication bias on the one hand, and maintaining testing power on the other hand. We demonstrate it on a use case of a replication server for GWAS findings, underlining its practical utility. We argue that a shift to using QPD in managing current and future biological databases will significantly enhance the community's ability to make efficient and statistically sound use of the available data resources. © 2014 WILEY PERIODICALS, INC.

Filling a missing link between biogeochemical, climate and ecosystem studies: a global database of atmospheric water-soluble organic nitrogen

NASA Astrophysics Data System (ADS)

Cornell, Sarah

2015-04-01

It is time to collate a global community database of atmospheric water-soluble organic nitrogen deposition. Organic nitrogen (ON) has long been known to be globally ubiquitous in atmospheric aerosol and precipitation, with implications for air and water quality, climate, biogeochemical cycles, ecosystems and human health. The number of studies of atmospheric ON deposition has increased steadily in recent years, but to date there is no accessible global dataset, for either bulk ON or its major components. Improved qualitative and quantitative understanding of the organic nitrogen component is needed to complement the well-established knowledge base pertaining to other components of atmospheric deposition (cf. Vet et al 2014). Without this basic information, we are increasingly constrained in addressing the current dynamics and potential interactions of atmospheric chemistry, climate and ecosystem change. To see the full picture we need global data synthesis, more targeted data gathering, and models that let us explore questions about the natural and anthropogenic dynamics of atmospheric ON. Collectively, our research community already has a substantial amount of atmospheric ON data. Published reports extend back over a century and now have near-global coverage. However, datasets available from the literature are very piecemeal and too often lack crucially important information that would enable aggregation or re-use. I am initiating an open collaborative process to construct a community database, so we can begin to systematically synthesize these datasets (generally from individual studies at a local and temporally limited scale) to increase their scientific usability and statistical power for studies of global change and anthropogenic perturbation. In drawing together our disparate knowledge, we must address various challenges and concerns, not least about the comparability of analysis and sampling methodologies, and the known complexity of composition of ON. We need to discuss and develop protocols that work for diverse research needs. The database will need to be harmonized or merged into existing global N data initiatives. This presentation therefore launches a standing invitation for experts to contribute and share rain and aerosol ON and chemical composition data, and jointly refine the preliminary database structure and metadata requirements for optimal mutual use. Reference: Vet et al. (2014) A global assessment of precipitation chemistry… Atmos Environ 93: 3-100

Social media and patient health outcomes. Findings from the yearbook 2014 section on consumer health informatics.

PubMed

Staccini, P; Douali, N

2014-08-15

To provide a review of the current excellent research published in the field of Consumer Health Informatics. We searched MEDLINE® and WEB OF SCIENCE® databases for papers published in 2013 in relation with Consumer Health Informatics. The authors identified 16 candidate best papers, which were then reviewed by four reviewers. Five out of the 16 candidate papers were selected as best papers. One paper presents the key features of a system to automate the collection of web-based social media content for subsequent semantic annotation. This paper emphasizes the importance of mining social media to collect novel data from which new findings in drug abuse research were uncovered. The second paper presents a practical method to predict how a community structure would impact the spreading of information within the community. The third paper presents a method for improving the quality of online health communities. The fourth presents a new social network to allow the monitoring of the evolution of individuals' health status and diagnostic deficiencies, difficulties or barriers in rehabilitation. The last paper reports on teenage patients' perception on privacy and social media. Selected papers not only show the value of using social media in the medical field but how to use these media to detect emergent diseases or risks, inform patients, promote disease prevention, and follow patients' opinion on healthcare resources.

Social Media and Patient Health Outcomes

PubMed Central

2014-01-01

Summary Objectives To provide a review of the current excellent research published in the field of Consumer Health Informatics. Method We searched MEDLINE® and WEB OF SCIENCE® databases for papers published in 2013 in relation with Consumer Health Informatics. The authors identified 16 candidate best papers, which were then reviewed by four reviewers. Results Five out of the 16 candidate papers were selected as best papers. One paper presents the key features of a system to automate the collection of web-based social media content for subsequent semantic annotation. This paper emphasizes the importance of mining social media to collect novel data from which new findings in drug abuse research were uncovered. The second paper presents a practical method to predict how a community structure would impact the spreading of information within the community. The third paper presents a method for improving the quality of online health communities. The fourth presents a new social network to allow the monitoring of the evolution of individuals’ health status and diagnostic deficiencies, difficulties or barriers in rehabilitation. The last paper reports on teenage patients’ perception on privacy and social media. Conclusion Selected papers not only show the value of using social media in the medical field but how to use these media to detect emergent diseases or risks, inform patients, promote disease prevention, and follow patients’ opinion on healthcare resources. PMID:25123742

Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database.

PubMed

Wang, Shur-Jen; Laulederkind, Stanley J F; Hayman, G Thomas; Petri, Victoria; Smith, Jennifer R; Tutaj, Marek; Nigam, Rajni; Dwinell, Melinda R; Shimoyama, Mary

2016-08-01

Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuration at RGD, including disease, genetic, and pathway data. The RGD curation team uses controlled vocabularies/ontologies to organize data curated from the published literature or imported from disease and pathway databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to genome objects. Screen shots from the web pages are used to demonstrate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually curated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other databases enriches the collection of disease genes not only in quantity but also in quality. Copyright © 2016 the American Physiological Society.

Open Clients for Distributed Databases

NASA Astrophysics Data System (ADS)

Chayes, D. N.; Arko, R. A.

2001-12-01

We are actively developing a collection of open source example clients that demonstrate use of our "back end" data management infrastructure. The data management system is reported elsewhere at this meeting (Arko and Chayes: A Scaleable Database Infrastructure). In addition to their primary goal of being examples for others to build upon, some of these clients may have limited utility in them selves. More information about the clients and the data infrastructure is available on line at http://data.ldeo.columbia.edu. The available examples to be demonstrated include several web-based clients including those developed for the Community Review System of the Digital Library for Earth System Education, a real-time watch standers log book, an offline interface to use log book entries, a simple client to search on multibeam metadata and others are Internet enabled and generally web-based front ends that support searches against one or more relational databases using industry standard SQL queries. In addition to the web based clients, simple SQL searches from within Excel and similar applications will be demonstrated. By defining, documenting and publishing a clear interface to the fully searchable databases, it becomes relatively easy to construct client interfaces that are optimized for specific applications in comparison to building a monolithic data and user interface system.

The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database.

PubMed

Hayman, G Thomas; Laulederkind, Stanley J F; Smith, Jennifer R; Wang, Shur-Jen; Petri, Victoria; Nigam, Rajni; Tutaj, Marek; De Pons, Jeff; Dwinell, Melinda R; Shimoyama, Mary

2016-01-01

The Rat Genome Database (RGD;http://rgd.mcw.edu/) provides critical datasets and software tools to a diverse community of rat and non-rat researchers worldwide. To meet the needs of the many users whose research is disease oriented, RGD has created a series of Disease Portals and has prioritized its curation efforts on the datasets important to understanding the mechanisms of various diseases. Gene-disease relationships for three species, rat, human and mouse, are annotated to capture biomarkers, genetic associations, molecular mechanisms and therapeutic targets. To generate gene-disease annotations more effectively and in greater detail, RGD initially adopted the MEDIC disease vocabulary from the Comparative Toxicogenomics Database and adapted it for use by expanding this framework with the addition of over 1000 terms to create the RGD Disease Ontology (RDO). The RDO provides the foundation for, at present, 10 comprehensive disease area-related dataset and analysis platforms at RGD, the Disease Portals. Two major disease areas are the focus of data acquisition and curation efforts each year, leading to the release of the related Disease Portals. Collaborative efforts to realize a more robust disease ontology are underway. Database URL:http://rgd.mcw.edu. © The Author(s) 2016. Published by Oxford University Press.

Making proteomics data accessible and reusable: current state of proteomics databases and repositories.

PubMed

Perez-Riverol, Yasset; Alpi, Emanuele; Wang, Rui; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-03-01

Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Immediate dissemination of student discoveries to a model organism database enhances classroom-based research experiences.

PubMed

Wiley, Emily A; Stover, Nicholas A

2014-01-01

Use of inquiry-based research modules in the classroom has soared over recent years, largely in response to national calls for teaching that provides experience with scientific processes and methodologies. To increase the visibility of in-class studies among interested researchers and to strengthen their impact on student learning, we have extended the typical model of inquiry-based labs to include a means for targeted dissemination of student-generated discoveries. This initiative required: 1) creating a set of research-based lab activities with the potential to yield results that a particular scientific community would find useful and 2) developing a means for immediate sharing of student-generated results. Working toward these goals, we designed guides for course-based research aimed to fulfill the need for functional annotation of the Tetrahymena thermophila genome, and developed an interactive Web database that links directly to the official Tetrahymena Genome Database for immediate, targeted dissemination of student discoveries. This combination of research via the course modules and the opportunity for students to immediately "publish" their novel results on a Web database actively used by outside scientists culminated in a motivational tool that enhanced students' efforts to engage the scientific process and pursue additional research opportunities beyond the course.

Proteogenomics approaches for studying cancer biology and their potential in the identification of acute myeloid leukemia biomarkers.

PubMed

Hernandez-Valladares, Maria; Vaudel, Marc; Selheim, Frode; Berven, Frode; Bruserud, Øystein

2017-08-01

Mass spectrometry (MS)-based proteomics has become an indispensable tool for the characterization of the proteome and its post-translational modifications (PTM). In addition to standard protein sequence databases, proteogenomics strategies search the spectral data against the theoretical spectra obtained from customized protein sequence databases. Up to date, there are no published proteogenomics studies on acute myeloid leukemia (AML) samples. Areas covered: Proteogenomics involves the understanding of genomic and proteomic data. The intersection of both datatypes requires advanced bioinformatics skills. A standard proteogenomics workflow that could be used for the study of AML samples is described. The generation of customized protein sequence databases as well as bioinformatics tools and pipelines commonly used in proteogenomics are discussed in detail. Expert commentary: Drawing on evidence from recent cancer proteogenomics studies and taking into account the public availability of AML genomic data, the interpretation of present and future MS-based AML proteomic data using AML-specific protein sequence databases could discover new biological mechanisms and targets in AML. However, proteogenomics workflows including bioinformatics guidelines can be challenging for the wide AML research community. It is expected that further automation and simplification of the bioinformatics procedures might attract AML investigators to adopt the proteogenomics strategy.

Tools for knowledge acquisition within the NeuroScholar system and their application to anatomical tract-tracing data

PubMed Central

Burns, Gully APC; Cheng, Wei-Cheng

2006-01-01

Background Knowledge bases that summarize the published literature provide useful online references for specific areas of systems-level biology that are not otherwise supported by large-scale databases. In the field of neuroanatomy, groups of small focused teams have constructed medium size knowledge bases to summarize the literature describing tract-tracing experiments in several species. Despite years of collation and curation, these databases only provide partial coverage of the available published literature. Given that the scientists reading these papers must all generate the interpretations that would normally be entered into such a system, we attempt here to provide general-purpose annotation tools to make it easy for members of the community to contribute to the task of data collation. Results In this paper, we describe an open-source, freely available knowledge management system called 'NeuroScholar' that allows straightforward structured markup of the PDF files according to a well-designed schema to capture the essential details of this class of experiment. Although, the example worked through in this paper is quite specific to neuroanatomical connectivity, the design is freely extensible and could conceivably be used to construct local knowledge bases for other experiment types. Knowledge representations of the experiment are also directly linked to the contributing textual fragments from the original research article. Through the use of this system, not only could members of the community contribute to the collation task, but input data can be gathered for automated approaches to permit knowledge acquisition through the use of Natural Language Processing (NLP). Conclusion We present a functional, working tool to permit users to populate knowledge bases for neuroanatomical connectivity data from the literature through the use of structured questionnaires. This system is open-source, fully functional and available for download from [1]. PMID:16895608

BioCarian: search engine for exploratory searches in heterogeneous biological databases.

PubMed

Zaki, Nazar; Tennakoon, Chandana

2017-10-02

There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search on previously published viral integration data and were able to deduce the main conclusions of the original publication. BioCarian is accessible via http://www.biocarian.com . We have developed a search engine to explore RDF databases that can be used by both novice and advanced users.

A systematic review on the effectiveness of school and community-based injury prevention programmes on risk behaviour and injury risk in 8-12 year old children.

PubMed

Nauta, Joske; van Mechelen, Willem; Otten, René H J; Verhagen, Evert A L M

2014-03-01

To review existing literature on the effectiveness of community-based and school-based physical activity related injury prevention programmes implemented to increase safety behaviour and decrease injury risk in 8-12 year old children, considering the methodological quality of the studies. A systematic review with quality assessment. A systematic search was performed using the CINAHL, Cochrane, EMBASE, PubMed and Sportdiscus databases. Inclusion criteria included the following: children aged 8-12 years; school- or community-based injury prevention programmes; an outcome defined as number of injuries, injury incidence or safety behaviour; published in an English language journal. Methodological quality was assessed for all included studies. The search yielded 5377 records, of which 11 were included in the review; four studies were considered as being of high quality. The focus of studies that were included was on the use of safety devices (8), pedestrian safety (2) and physical activity-related injury prevention (1). For safety device use, short term effects of school- and community-based interventions are promising for 8-12 year olds. Results regarding sustainability of the effect are inconsistent. A mediating effect on the distribution of safety devices was observed. Both financial and non-financial barriers seemed to prevent participants from purchasing a safety device. The short term effects for school- and community-based interventions using safety devices for 8-12 year olds are promising. More high quality research is, however warranted, preferably shifting focus from safety behaviour change to actual physical activity injury reduction. Copyright © 2013 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

HIV prevention interventions to reduce sexual risk for African Americans: the influence of community-level stigma and psychological processes.

PubMed

Reid, Allecia E; Dovidio, John F; Ballester, Estrellita; Johnson, Blair T

2014-02-01

Interventions to improve public health may benefit from consideration of how environmental contexts can facilitate or hinder their success. We examined the extent to which efficacy of interventions to improve African Americans' condom use practices was moderated by two indicators of structural stigma-Whites' attitudes toward African Americans and residential segregation in the communities where interventions occurred. A previously published meta-analytic database was re-analyzed to examine the interplay of community-level stigma with the psychological processes implied by intervention content in influencing intervention efficacy. All studies were conducted in the United States and included samples that were at least 50% African American. Whites' attitudes were drawn from the American National Election Studies, which collects data from nationally representative samples. Residential segregation was drawn from published reports. Results showed independent effects of Whites' attitudes and residential segregation on condom use effect sizes. Interventions were most successful when Whites' attitudes were more positive or when residential segregation was low. These two structural factors interacted: Interventions improved condom use only when communities had both relatively positive attitudes toward African Americans and lower levels of segregation. The effect of Whites' attitudes was more pronounced at longer follow-up intervals and for younger samples and those samples with more African Americans. Tailoring content to participants' values and needs, which may reduce African Americans' mistrust of intervention providers, buffered against the negative influence of Whites' attitudes on condom use. The structural factors uniquely accounted for variance in condom use effect sizes over and above intervention-level features and community-level education and poverty. Results highlight the interplay of social identity and environment in perpetuating intergroup disparities. Potential mechanisms for these effects are discussed along with public health implications. Copyright © 2013 Elsevier Ltd. All rights reserved.

HIV Prevention Interventions to Reduce Sexual Risk for African Americans: The Influence of Community-Level Stigma and Psychological Processes

PubMed Central

Reid, Allecia E.; Dovidio, John F.; Ballester, Estrellita; Johnson, Blair T.

2013-01-01

Interventions to improve public health may benefit from consideration of how environmental contexts can facilitate or hinder their success. We examined the extent to which efficacy of interventions to improve African Americans’ condom use practices was moderated by two indicators of structural stigma—Whites’ attitudes toward African Americans and residential segregation in the communities where interventions occurred. A previously published meta-analytic database was re-analyzed to examine the interplay of community-level stigma with the psychological processes implied by intervention content in influencing intervention efficacy. All studies were conducted in the United States and included samples that were at least 50% African American. Whites’ attitudes were drawn from the American National Election Studies, which collects data from nationally representative samples. Residential segregation was drawn from published reports. Results showed independent effects of Whites’ attitudes and residential segregation on condom use effect sizes. Interventions were most successful when Whites’ attitudes were more positive or when residential segregation was low. These two structural factors interacted: Interventions improved condom use only when communities had both relatively positive attitudes toward African Americans and lower levels of segregation. The effect of Whites’ attitudes was more pronounced at longer follow-up intervals and for younger samples and those samples with more African Americans. Tailoring content to participants’ values and needs, which may reduce African Americans’ mistrust of intervention providers, buffered against the negative influence of Whites’ attitudes on condom use. The structural factors uniquely accounted for variance in condom use effect sizes over and above intervention-level features and community-level education and poverty. Results highlight the interplay of social identity and environment in perpetuating intergroup disparities. Potential mechanisms for these effects are discussed along with public health implications. PMID:24507916

Global systematic review of Indigenous community-led legal interventions to control alcohol.

PubMed

Muhunthan, Janani; Angell, Blake; Hackett, Maree L; Wilson, Andrew; Latimer, Jane; Eades, Anne-Marie; Jan, Stephen

2017-03-27

The national and subnational governments of most developed nations have adopted cost-effective regulatory and legislative controls over alcohol supply and consumption with great success. However, there has been a lack of scrutiny of the effectiveness and appropriateness of these laws in shaping the health-related behaviours of Indigenous communities, who disproportionately experience alcohol-related harm. Further, such controls imposed unilaterally without Indigenous consultation have often been discriminatory and harmful in practice. In this systematic review of quantitative evaluations of Indigenous-led alcohol controls, we aim to investigate how regulatory responses have been developed and implemented by Indigenous communities worldwide, and evaluate their effectiveness in improving health and social outcomes. We included articles from electronic databases MEDLINE, EMBASE, CINAHL, PsycINFO and Web of Science from inception to December 2015. Our search yielded 1489 articles from which 18 met the inclusion criteria. Controls were implemented in rural and remote populations of high-income nations. Communities employed a range of regulatory options including alcohol rationing, prohibition of sale, importation or possession, restrictions on liquor sold, times of sale or mode of sale, Indigenous-controlled liquor licensing, sin tax and traditional forms of control. 11 studies reported interventions that were effective in reducing crime, injury deaths, injury, hospitalisations or lowering per capita consumption. In six studies interventions were found to be ineffective or harmful. The results were inconclusive in one. Indigenous-led policies that are developed or implemented by communities can be effective in improving health and social outcomes. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

A systematic review of community-based interventions for emerging zoonotic infectious diseases in Southeast Asia

PubMed Central

Halton, Kate; Sarna, Mohinder; Barnett, Adrian; Leonardo, Lydia; Graves, Nicholas

2013-01-01

Executive Summary Background Southeast Asia has been at the epicentre of recent epidemics of emerging and re-emerging zoonotic diseases. Community-based surveillance and control interventions have been heavily promoted but the most effective interventions have not been identified. Objectives This review evaluated evidence for the effectiveness of community-based surveillance interventions at monitoring and identifying emerging infectious disease; the effectiveness of community-based control interventions at reducing rates of emerging infectious disease; and contextual factors that influence intervention effectiveness. Inclusion criteria Participants Communities in Brunei, Cambodia, Indonesia, Laos, Malaysia, Myanmar, the Philippines, Singapore, Thailand and Viet Nam. Types of intervention(s) Non-pharmaceutical, non-vaccine, and community-based surveillance or prevention and control interventions targeting rabies, Nipah virus, dengue, SARS or avian influenza. Types of outcomes Primary outcomes: measures: of infection or disease; secondary outcomes: measures of intervention function. Types of studies Original quantitative studies published in English. Search strategy Databases searched (1980 to 2011): PubMed, CINAHL, ProQuest, EBSCOhost, Web of Science, Science Direct, Cochrane database of systematic reviews, WHOLIS, British Development Library, LILACS, World Bank (East Asia), Asian Development Bank. Methodological quality Two independent reviewers critically appraised studies using standard Joanna Briggs Institute instruments. Disagreements were resolved through discussion. Data extraction A customised tool was used to extract quantitative data on intervention(s), populations, study methods, and primary and secondary outcomes; and qualitative contextual information or narrative evidence about interventions. Data synthesis Data was synthesised in a narrative summary with the aid of tables. Meta-analysis was used to statistically pool quantitative results. Results Fifty-seven studies were included. Vector control interventions using copepods, environmental cleanup and education are effective and sustainable at reducing dengue in rural and urban communities, whilst insecticide spraying is effective in urban outbreak situations. Community-based surveillance interventions can effectively identify avian influenza in backyard flocks, but have not been broadly applied. Outbreak control interventions for Nipah virus and SARS are effective but may not be suitable for ongoing control. Canine vaccination and education is more acceptable than culling, but still fails to reach coverage levels required to effectively control rabies. Contextual factors were identified that influence community engagement with, and ultimately effectiveness of, interventions. Conclusion Despite investment in community-based disease control and surveillance in Southeast Asia, published evidence evaluating interventions is limited in quantity and quality. Nonetheless this review identified a number of effective interventions, and several contextual factors influencing effectiveness. Identification of the best programs will require comparative evidence of effectiveness acceptability, cost-effectiveness and sustainability. Implications for practice Interventions are more effective if there are high levels of community ownership and engagement. Linkages between veterinary and public health surveillance systems are essential. Interventions are not well accepted when they fail to acknowledge the importance of animals for economic activity in communities. Implications for research Evidence is needed on functioning and outcomes of current surveillance systems and novel low-cost methods of surveillance. Evaluations of control interventions should control for confounding and report measures of disease, cost and sustainability. Translational research is needed to assess generalisability and evaluate roll-out of effective interventions as regional or national programs.

Does cessation of community water fluoridation lead to an increase in tooth decay? A systematic review of published studies.

PubMed

McLaren, Lindsay; Singhal, Sonica

2016-09-01

Cessation of community water fluoridation (CWF) appears to be occurring with increasing frequency in some regions. Our objective was to comprehensively review published research on the impact of CWF cessation on dental caries. We searched 13 multidisciplinary databases. Results were synthesised qualitatively and quantitatively. We identified 15 instances of CWF cessation ('intervention') in 13 countries, which covered a broad time frame (1956-2003) and diverse geographical and political/economic contexts. Overall, results were mixed, but pointed more to an increase in caries postcessation than otherwise. For example, of the 9 studies with at least moderate methodological quality based on criteria we developed for this review, 5 showed an increase in caries postcessation. 3 studies did not show an increase in caries postcessation; however, important postcessation changes (eg, implementation of alternative fluoride delivery programmes) and/or large-scale social change may have contributed to those effects. Of the 3 study groupings that permitted quantitative synthesis, 2 showed statistically significant mean overall increase in caries postcessation; however, quantitative synthesis results must be interpreted cautiously. Overall, the published research points more to an increase in dental caries post-CWF cessation than otherwise. However, the literature is highly diverse and variable in methodological quality. To build this literature, it is important to exploit research opportunities presented by CWF cessation. Remaining knowledge gaps include the impact of CWF cessation on the distribution of dental caries (ie, equitable or not) and understanding the decision-making circumstances around CWF cessation. 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/

Exploring human disease using the Rat Genome Database.

PubMed

Shimoyama, Mary; Laulederkind, Stanley J F; De Pons, Jeff; Nigam, Rajni; Smith, Jennifer R; Tutaj, Marek; Petri, Victoria; Hayman, G Thomas; Wang, Shur-Jen; Ghiasvand, Omid; Thota, Jyothi; Dwinell, Melinda R

2016-10-01

Rattus norvegicus, the laboratory rat, has been a crucial model for studies of the environmental and genetic factors associated with human diseases for over 150 years. It is the primary model organism for toxicology and pharmacology studies, and has features that make it the model of choice in many complex-disease studies. Since 1999, the Rat Genome Database (RGD; http://rgd.mcw.edu) has been the premier resource for genomic, genetic, phenotype and strain data for the laboratory rat. The primary role of RGD is to curate rat data and validate orthologous relationships with human and mouse genes, and make these data available for incorporation into other major databases such as NCBI, Ensembl and UniProt. RGD also provides official nomenclature for rat genes, quantitative trait loci, strains and genetic markers, as well as unique identifiers. The RGD team adds enormous value to these basic data elements through functional and disease annotations, the analysis and visual presentation of pathways, and the integration of phenotype measurement data for strains used as disease models. Because much of the rat research community focuses on understanding human diseases, RGD provides a number of datasets and software tools that allow users to easily explore and make disease-related connections among these datasets. RGD also provides comprehensive human and mouse data for comparative purposes, illustrating the value of the rat in translational research. This article introduces RGD and its suite of tools and datasets to researchers - within and beyond the rat community - who are particularly interested in leveraging rat-based insights to understand human diseases. © 2016. Published by The Company of Biologists Ltd.

SeedStor: A Germplasm Information Management System and Public Database.

PubMed

Horler, R S P; Turner, A S; Fretter, P; Ambrose, M

2018-01-01

SeedStor (https://www.seedstor.ac.uk) acts as the publicly available database for the seed collections held by the Germplasm Resources Unit (GRU) based at the John Innes Centre, Norwich, UK. The GRU is a national capability supported by the Biotechnology and Biological Sciences Research Council (BBSRC). The GRU curates germplasm collections of a range of temperate cereal, legume and Brassica crops and their associated wild relatives, as well as precise genetic stocks, near-isogenic lines and mapping populations. With >35,000 accessions, the GRU forms part of the UK's plant conservation contribution to the Multilateral System (MLS) of the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA) for wheat, barley, oat and pea. SeedStor is a fully searchable system that allows our various collections to be browsed species by species through to complicated multipart phenotype criteria-driven queries. The results from these searches can be downloaded for later analysis or used to order germplasm via our shopping cart. The user community for SeedStor is the plant science research community, plant breeders, specialist growers, hobby farmers and amateur gardeners, and educationalists. Furthermore, SeedStor is much more than a database; it has been developed to act internally as a Germplasm Information Management System that allows team members to track and process germplasm requests, determine regeneration priorities, handle cost recovery and Material Transfer Agreement paperwork, manage the Seed Store holdings and easily report on a wide range of the aforementioned tasks. © The Author(s) 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

How does the media portray drinking water security in Indigenous communities in Canada? An analysis of Canadian newspaper coverage from 2000-2015.

PubMed

Lam, Steven; Cunsolo, Ashlee; Sawatzky, Alexandra; Ford, James; Harper, Sherilee L

2017-03-27

Drinking water insecurity and related health outcomes often disproportionately impact Indigenous communities internationally. Understanding media coverage of these water-related issues can provide insight into the ways in which public perceptions are shaped, with potential implications for decision-making and action. This study aimed to examine the extent, range, and nature of newspaper coverage of drinking water security in Canadian Indigenous communities. Using ProQuest database, we systematically searched for and screened newspaper articles published from 2000 to 2015 from Canadian newspapers: Windspeaker, Toronto Star, The Globe and Mail, and National Post. We conducted descriptive quantitative analysis and thematic qualitative analysis on relevant articles to characterize framing and trends in coverage. A total of 1382 articles were returned in the search, of which 256 articles were identified as relevant. There was limited coverage of water challenges for Canadian Indigenous communities, especially for Métis (5%) and Inuit (3%) communities. Most stories focused on government responses to water-related issues, and less often covered preventative measures such as source water protection. Overall, Indigenous peoples were quoted the most often. Double-standards of water quality between Indigenous and non-Indigenous communities, along with conflict and cooperation efforts between stakeholders were emphasized in many articles. Limited media coverage could undermine public and stakeholder interest in addressing water-related issues faced by many Canadian Indigenous communities.

Community pharmacies as sites of adult vaccination: A systematic review.

PubMed

Burson, Randall C; Buttenheim, Alison M; Armstrong, Allison; Feemster, Kristen A

2016-12-01

Vaccine-preventable deaths among adults remain a major public health concern, despite continued efforts to increase vaccination rates in this population. Alternative approaches to immunization delivery may help address under-vaccination among adults. This systematic review assesses the feasibility, acceptability, and effectiveness of community pharmacies as sites for adult vaccination. We searched 5 electronic databases (PubMed, EMBASE, Scopus, Cochrane, LILACS) for studies published prior to June 2016 and identified 47 relevant articles. We found that pharmacy-based immunization services (PBIS) have been facilitated by state regulatory changes and training programs that allow pharmacists to directly provide vaccinations. These services are widely accepted by both patients and pharmacy staff, and are capable of improving access and increasing vaccination rates. However, political and organizational barriers limit the feasibility and effectiveness of vaccine delivery in pharmacies. These studies provide evidence to inform policy and organizational efforts that promote the efficacy and sustainability of PBIS.

Community pharmacies as sites of adult vaccination: A systematic review

PubMed Central

Burson, Randall C.; Buttenheim, Alison M.; Armstrong, Allison; Feemster, Kristen A.

2016-01-01

ABSTRACT Vaccine-preventable deaths among adults remain a major public health concern, despite continued efforts to increase vaccination rates in this population. Alternative approaches to immunization delivery may help address under-vaccination among adults. This systematic review assesses the feasibility, acceptability, and effectiveness of community pharmacies as sites for adult vaccination. We searched 5 electronic databases (PubMed, EMBASE, Scopus, Cochrane, LILACS) for studies published prior to June 2016 and identified 47 relevant articles. We found that pharmacy-based immunization services (PBIS) have been facilitated by state regulatory changes and training programs that allow pharmacists to directly provide vaccinations. These services are widely accepted by both patients and pharmacy staff, and are capable of improving access and increasing vaccination rates. However, political and organizational barriers limit the feasibility and effectiveness of vaccine delivery in pharmacies. These studies provide evidence to inform policy and organizational efforts that promote the efficacy and sustainability of PBIS. PMID:27715409

Community-Supported Data Repositories in Paleobiology: A 'Middle Tail' Between the Geoscientific and Informatics Communities

NASA Astrophysics Data System (ADS)

Williams, J. W.; Ashworth, A. C.; Betancourt, J. L.; Bills, B.; Blois, J.; Booth, R.; Buckland, P.; Charles, D.; Curry, B. B.; Goring, S. J.; Davis, E.; Grimm, E. C.; Graham, R. W.; Smith, A. J.

2015-12-01

Community-supported data repositories (CSDRs) in paleoecology and paleoclimatology have a decades-long tradition and serve multiple critical scientific needs. CSDRs facilitate synthetic large-scale scientific research by providing open-access and curated data that employ community-supported metadata and data standards. CSDRs serve as a 'middle tail' or boundary organization between information scientists and the long-tail community of individual geoscientists collecting and analyzing paleoecological data. Over the past decades, a distributed network of CSDRs has emerged, each serving a particular suite of data and research communities, e.g. Neotoma Paleoecology Database, Paleobiology Database, International Tree Ring Database, NOAA NCEI for Paleoclimatology, Morphobank, iDigPaleo, and Integrated Earth Data Alliance. Recently, these groups have organized into a common Paleobiology Data Consortium dedicated to improving interoperability and sharing best practices and protocols. The Neotoma Paleoecology Database offers one example of an active and growing CSDR, designed to facilitate research into ecological and evolutionary dynamics during recent past global change. Neotoma combines a centralized database structure with distributed scientific governance via multiple virtual constituent data working groups. The Neotoma data model is flexible and can accommodate a variety of paleoecological proxies from many depositional contests. Data input into Neotoma is done by trained Data Stewards, drawn from their communities. Neotoma data can be searched, viewed, and returned to users through multiple interfaces, including the interactive Neotoma Explorer map interface, REST-ful Application Programming Interfaces (APIs), the neotoma R package, and the Tilia stratigraphic software. Neotoma is governed by geoscientists and provides community engagement through training workshops for data contributors, stewards, and users. Neotoma is engaged in the Paleobiological Data Consortium and other efforts to improve interoperability among cyberinfrastructure in the paleogeosciences.

Towards BioDBcore: a community-defined information specification for biological databases

PubMed Central

Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K.; Bateman, Alex; Blake, Judith A.; Bult, Carol J.; Cherry, J. Michael; Chisholm, Rex L.; Cochrane, Guy; Cook, Charles E.; Eppig, Janan T.; Galperin, Michael Y.; Gentleman, Robert; Goble, Carole A.; Gojobori, Takashi; Hancock, John M.; Howe, Douglas G.; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E.; Mizrachi, Ilene Karsch; Orchard, Sandra; Ouellette, B. F. Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N.; Smedley, Damian; Southan, Christopher; Tan, Tin Wee; Tatusova, Tatiana; Whetzel, Patricia L.; White, Owen; Yamasaki, Chisato

2011-01-01

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21097465

Towards BioDBcore: a community-defined information specification for biological databases

PubMed Central

Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K.; Bateman, Alex; Blake, Judith A.; Bult, Carol J.; Cherry, J. Michael; Chisholm, Rex L.; Cochrane, Guy; Cook, Charles E.; Eppig, Janan T.; Galperin, Michael Y.; Gentleman, Robert; Goble, Carole A.; Gojobori, Takashi; Hancock, John M.; Howe, Douglas G.; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E.; Karsch Mizrachi, Ilene; Orchard, Sandra; Ouellette, B.F. Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N.; Smedley, Damian; Southan, Christopher; Tan, Tin W.; Tatusova, Tatiana; Whetzel, Patricia L.; White, Owen; Yamasaki, Chisato

2011-01-01

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources; and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21205783

Publishing scientific papers based on Master's and Ph.D. theses from a small scientific community: case study of Croatian medical schools.

PubMed

Frković, Vedran; Skender, Tomislav; Dojćinović, Bojan; Bilić-Zulle, Lidija

2003-02-01

To evaluate publishing activity of medical doctors after they have obtained Master's or Ph.D. degree at the Rijeka and Zagreb University Schools of Medicine in Croatia, and establish the number of journal articles based on these theses. Data on Master's and Ph.D. theses defended at the Rijeka and Zagreb University Schools of Medicine in the 1990-1999 period were collected by hand-search of the archive. MEDLINE and Current Contents databases were searched for journal articles resulting from the theses. During the 10-year period, 1,535 Master's and 634 Ph.D. theses were defended at the Rijeka and Zagreb University Schools of Medicine (253 Master's and 138 Ph.D. theses from Rijeka and 1,282 Master's and 496 Ph.D. theses from Zagreb). There were 201 (14%) Master's and 218 (34%) Ph.D. theses that resulted in articles published in journals indexed in MEDLINE (13% of Master's and 11% of Ph.D. theses from Rijeka, and 14% of Master's and 41% of Ph.D. theses from Zagreb). Also, 97 (6%) Master's and 129 (20%) Ph.D. theses that resulted in articles published in Current Contents journals (8% of Master's and 6% of Ph.D. theses from Rijeka, and 6% of Master's and 24% of Ph.D. theses from Zagreb). There was no significant difference between the two Universities with respect to published articles based on Master's theses, but there were significantly more articles from Ph.D. theses in Zagreb (p<0.001). Most of the theses resulted in a single publication (95%), 19 (5%) in 2, and 2 in 3 publications. Out of all 453 journal articles, 31% were published in Croatian and 69% in international journals. Most Croatian Master's and Ph.D. theses are not made available to the scientific community. There should be more institutional effort directed at the stimulation of postgraduate students to publish their scientific work.

Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life

PubMed Central

Smith, Vincent S; Rycroft, Simon D; Harman, Kehan T; Scott, Ben; Roberts, David

2009-01-01

Background Natural History science is characterised by a single immense goal (to document, describe and synthesise all facets pertaining to the diversity of life) that can only be addressed through a seemingly infinite series of smaller studies. The discipline's failure to meaningfully connect these small studies with natural history's goal has made it hard to demonstrate the value of natural history to a wider scientific community. Digital technologies provide the means to bridge this gap. Results We describe the system architecture and template design of "Scratchpads", a data-publishing framework for groups of people to create their own social networks supporting natural history science. Scratchpads cater to the particular needs of individual research communities through a common database and system architecture. This is flexible and scalable enough to support multiple networks, each with its own choice of features, visual design, and constituent data. Our data model supports web services on standardised data elements that might be used by related initiatives such as GBIF and the Encyclopedia of Life. A Scratchpad allows users to organise data around user-defined or imported ontologies, including biological classifications. Automated semantic annotation and indexing is applied to all content, allowing users to navigate intuitively and curate diverse biological data, including content drawn from third party resources. A system of archiving citable pages allows stable referencing with unique identifiers and provides credit to contributors through normal citation processes. Conclusion Our framework currently serves more than 1,100 registered users across 100 sites, spanning academic, amateur and citizen-science audiences. These users have generated more than 130,000 nodes of content in the first two years of use. The template of our architecture may serve as a model to other research communities developing data publishing frameworks outside biodiversity research. PMID:19900302

Volcanoes of the World: Reconfiguring a scientific database to meet new goals and expectations

NASA Astrophysics Data System (ADS)

Venzke, Edward; Andrews, Ben; Cottrell, Elizabeth

2015-04-01

The Smithsonian Global Volcanism Program's (GVP) database of Holocene volcanoes and eruptions, Volcanoes of the World (VOTW), originated in 1971, and was largely populated with content from the IAVCEI Catalog of Volcanoes of Active Volcanoes and some independent datasets. Volcanic activity reported by Smithsonian's Bulletin of the Global Volcanism Network and USGS/SI Weekly Activity Reports (and their predecessors), published research, and other varied sources has expanded the database significantly over the years. Three editions of the VOTW were published in book form, creating a catalog with new ways to display data that included regional directories, a gazetteer, and a 10,000-year chronology of eruptions. The widespread dissemination of the data in electronic media since the first GVP website in 1995 has created new challenges and opportunities for this unique collection of information. To better meet current and future goals and expectations, we have recently transitioned VOTW into a SQL Server database. This process included significant schema changes to the previous relational database, data auditing, and content review. We replaced a disparate, confusing, and changeable volcano numbering system with unique and permanent volcano numbers. We reconfigured structures for recording eruption data to allow greater flexibility in describing the complexity of observed activity, adding in the ability to distinguish episodes within eruptions (in time and space) and events (including dates) rather than characteristics that take place during an episode. We have added a reference link field in multiple tables to enable attribution of sources at finer levels of detail. We now store and connect synonyms and feature names in a more consistent manner, which will allow for morphological features to be given unique numbers and linked to specific eruptions or samples; if the designated overall volcano name is also a morphological feature, it is then also listed and described as that feature. One especially significant audit involved re-evaluating the categories of evidence used to include a volcano in the Holocene list, and reviewing in detail the entries in low-certainty categories. Concurrently, we developed a new data entry system that may in the future allow trusted users outside of Smithsonian to input data into VOTW. A redesigned website now provides new search tools and data download options. We are collaborating with organizations that manage volcano and eruption databases, physical sample databases, and geochemical databases to allow real-time connections and complex queries. VOTW serves the volcanological community by providing a clear and consistent core database of distinctly identified volcanoes and eruptions to advance goals in research, civil defense, and public outreach.

Community-deliverable exercise and anxiety in adults with arthritis and other rheumatic diseases: a protocol for a systematic review and meta-analysis of randomised controlled trials.

PubMed

Kelley, George A; Kelley, Kristi S; Callahan, Leigh F

2017-03-06

While anxiety is a major public health problem in adults with arthritis and other rheumatic diseases (AORD), the effects of exercise on anxiety in adults are not well established despite numerous studies on this topic. The purpose of this study is to conduct a systematic review with an aggregate data meta-analysis to determine the effects of community-deliverable exercise interventions (aerobic, strength training or both) on anxiety in adults with AORD. Randomised controlled exercise intervention trials ≥4 weeks and published in any language up to 31 December 2016 will be included. Studies will be retrieved by searching 8 electronic databases, cross-referencing and expert review. Dual selection and abstraction of data will occur. The primary outcome will be changes in anxiety. Risk of bias will be assessed using the Cochrane risk of bias assessment instrument while confidence in the cumulative evidence will be assessed using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) instrument. Standardised effect sizes for anxiety will be calculated from each study and then pooled using the inverse variance heterogeneity (IVhet) model. Meta-regression based on the IVhet model will be used to examine the relationship between changes in anxiety and selected covariates. The results of this study will be presented at a professional conference and published in a peer-reviewed journal. CRD42016048728. 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/.

Tobacco control funding for low-income and middle-income countries in a time of economic hardship.

PubMed

Stoklosa, Michal; Ross, Hana

2014-11-01

To assess how levels of tobacco control funding for low-income and middle-income countries (LMIC) changed following the 2008-2009 global economic downturn. In order to estimate the amount of tobacco control funding in LMICs, we created an integrated database of Development Assistance to Control Tobacco (DACT). This database includes data on funding from bilateral and multilateral donors, non-governmental organisations, private foundations and the corporate sector. The database contains information on 1389 disbursements awarded by 30 entities between 2000 and 2012. DACT declined only marginally from US$68.8 million (US$0.016 per adult) in 2009 to US$68.2 million (US$0.016 per adult) in 2011, but deviated significantly from its 2000 to 2009 trend. The sources of funding remain highly concentrated, with nearly a half of the money coming from the Bloomberg Initiative and the Bill & Melinda Gates Foundation in 2011. The relative importance of institutional and research grants has declined. Our findings are consistent with the patterns in general levels of development assistance for health: after a decade of rapid growth, funding for tobacco control activities in LMICs has levelled off. Just as the tobacco control community is beginning to envision the endgame for tobacco, the funding remains erratic, inadequate, and highly vulnerable due to its level of concentration. Innovative financing mechanisms might help to increase the funding pool. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

The psychosocial impact of natural disasters among adult survivors: an integrative review.

PubMed

Warsini, Sri; West, Caryn; Ed Tt, Grad Dip; Res Meth, Grad Cert; Mills, Jane; Usher, Kim

2014-06-01

The aim of this review was to identify the psychosocial impact of natural disasters on adult (over the age of 18 years) survivors. Databases searched included PsycInfo, CINAHL, Proquest, Ovid SP, Scopus, and Science Direct. The search was limited to articles written in English and published between 2002 and 2012. A total of 1,642 abstracts and articles were obtained during the first search; 39 articles were retained. The results indicate that PTSD is the most-studied psychosocial impact after a disaster. Mental health nurses have a significant role to play in supporting survivors and can assist with the development of resilience in community members.

Efficacy of Transcranial Magnetic Stimulation (TMS) in the Treatment of Schizophrenia: A Review of the Literature to Date.

PubMed

Cole, Jonathan C; Green Bernacki, Carolyn; Helmer, Amanda; Pinninti, Narsimha; O'reardon, John P

2015-01-01

We reviewed the literature on transcranial magnetic stimulation and its uses and efficacy in schizophrenia. Multiple sources were examined on transcranial magnetic stimulation efficacy in relieving positive and negative symptoms of schizophrenia. Literature review was conducted via Ovid Medline and PubMed databases. We found multiple published studies and metaanalyses that give evidence that repetitive transcranial magnetic stimulation can have benefit in relieving positive and negative symptoms of schizophrenia, particularly auditory hallucinations. These findings should encourage the psychiatric community to expand research into other applications for which transcranial magnetic stimulation may be used to treat patients with psychiatric disability.

[Matematical modeling of antibiotic resistance: perspectives from a meta-analysys].

PubMed

Fresnadillo-Martínez, M J; García-Sánchez, E; García-Merino, E; Martín-Del-Rey, A; Rodríguez-Encinas, A; Rodríguez-Sánchez, G; García-Sánchez, J E

2012-09-01

The antibiotic resistance is one of the greatest challenges of the international health community. The study of antibiotic resistance must be a multidisciplinary task and, in this sense, the main goal of this work is to analyze the role that Mathematical Modeling can play in this scenario. A qualitative and cuantitative analysis of the works published in the scientific literature is done by means of a search in the most important databases: MEDLINE, SCOPUS and ISI Web of Science. Consequently, there are few papers related to our topic but the existing works have been published in high-quality and impact international journals. Moreover, we can state that mathematical models are a very important and useful tool to analyze and study both the treatments protocols for resistance prevention and the assesment of control strategies in hospital environtment, or the prediction of the evolution of diseases due to resistant strains.

Methane Yield Database: Online infrastructure and bioresource for methane yield data and related metadata.

PubMed

Murovec, Boštjan; Kolbl, Sabina; Stres, Blaž

2015-01-01

The aim of this study was to develop and validate a community supported online infrastructure and bioresource for methane yield data and accompanying metadata collected from published literature. In total, 1164 entries described by 15,749 data points were assembled. Analysis of data collection showed little congruence in reporting of methodological approaches. The largest identifiable source of variation in reported methane yields was represented by authorship (i.e. substrate batches within particular substrate class) within which experimental scales (volumes (0.02-5l), incubation temperature (34-40 °C) and % VS of substrate played an important role (p < 0.05, npermutations = 999) as well. The largest fraction of variability, however, remained unaccounted for and thus unexplained (> 63%). This calls for reconsideration of accepted approaches to reporting data in currently published literature to increase capacity to service industrial decision making to a greater extent. Copyright © 2015 Elsevier Ltd. All rights reserved.

Protocol for developing a Database of Zoonotic disease Research in India (DoZooRI).

PubMed

Chatterjee, Pranab; Bhaumik, Soumyadeep; Chauhan, Abhimanyu Singh; Kakkar, Manish

2017-12-10

Zoonotic and emerging infectious diseases (EIDs) represent a public health threat that has been acknowledged only recently although they have been on the rise for the past several decades. On an average, every year since the Second World War, one pathogen has emerged or re-emerged on a global scale. Low/middle-income countries such as India bear a significant burden of zoonotic and EIDs. We propose that the creation of a database of published, peer-reviewed research will open up avenues for evidence-based policymaking for targeted prevention and control of zoonoses. A large-scale systematic mapping of the published peer-reviewed research conducted in India will be undertaken. All published research will be included in the database, without any prejudice for quality screening, to broaden the scope of included studies. Structured search strategies will be developed for priority zoonotic diseases (leptospirosis, rabies, anthrax, brucellosis, cysticercosis, salmonellosis, bovine tuberculosis, Japanese encephalitis and rickettsial infections), and multiple databases will be searched for studies conducted in India. The database will be managed and hosted on a cloud-based platform called Rayyan. Individual studies will be tagged based on key preidentified parameters (disease, study design, study type, location, randomisation status and interventions, host involvement and others, as applicable). The database will incorporate already published studies, obviating the need for additional ethical clearances. The database will be made available online, and in collaboration with multisectoral teams, domains of enquiries will be identified and subsequent research questions will be raised. The database will be queried for these and resulting evidence will be analysed and published in peer-reviewed journals. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Updated Palaeotsunami Database for Aotearoa/New Zealand

NASA Astrophysics Data System (ADS)

Gadsby, M. R.; Goff, J. R.; King, D. N.; Robbins, J.; Duesing, U.; Franz, T.; Borrero, J. C.; Watkins, A.

2016-12-01

The updated configuration, design, and implementation of a national palaeotsunami (pre-historic tsunami) database for Aotearoa/New Zealand (A/NZ) is near completion. This tool enables correlation of events along different stretches of the NZ coastline, provides information on frequency and extent of local, regional and distant-source tsunamis, and delivers detailed information on the science and proxies used to identify the deposits. In A/NZ a plethora of data, scientific research and experience surrounds palaeotsunami deposits, but much of this information has been difficult to locate, has variable reporting standards, and lacked quality assurance. The original database was created by Professor James Goff while working at the National Institute of Water & Atmospheric Research in A/NZ, but has subsequently been updated during his tenure at the University of New South Wales. The updating and establishment of the national database was funded by the Ministry of Civil Defence and Emergency Management (MCDEM), led by Environment Canterbury Regional Council, and supported by all 16 regions of A/NZ's local government. Creation of a single database has consolidated a wide range of published and unpublished research contributions from many science providers on palaeotsunamis in A/NZ. The information is now easily accessible and quality assured and allows examination of frequency, extent and correlation of events. This provides authoritative scientific support for coastal-marine planning and risk management. The database will complement the GNS New Zealand Historical Database, and contributes to a heightened public awareness of tsunami by being a "one-stop-shop" for information on past tsunami impacts. There is scope for this to become an international database, enabling the pacific-wide correlation of large events, as well as identifying smaller regional ones. The Australian research community has already expressed an interest, and the database is also compatible with a similar one currently under development in Japan. Expressions of interest in collaborating with the A/NZ team to expand the database are invited from other Pacific nations.

Multicenter neonatal databases: Trends in research uses.

PubMed

Creel, Liza M; Gregory, Sean; McNeal, Catherine J; Beeram, Madhava R; Krauss, David R

2017-01-13

In the US, approximately 12.7% of all live births are preterm, 8.2% of live births were low birth weight (LBW), and 1.5% are very low birth weight (VLBW). Although technological advances have improved mortality rates among preterm and LBW infants, improving overall rates of prematurity and LBW remains a national priority. Monitoring short- and long-term outcomes is critical for advancing medical treatment and minimizing morbidities associated with prematurity or LBW; however, studying these infants can be challenging. Several large, multi-center neonatal databases have been developed to improve research and quality improvement of treatments for and outcomes of premature and LBW infants. The purpose of this systematic review was to describe three multi-center neonatal databases. We conducted a literature search using PubMed and Google Scholar over the period 1990 to August 2014. Studies were included in our review if one of the databases was used as a primary source of data or comparison. Included studies were categorized by year of publication; study design employed, and research focus. A total of 343 studies published between 1991 and 2014 were included. Studies of premature and LBW infants using these databases have increased over time, and provide evidence for both neonatology and community-based pediatric practice. Research into treatment and outcomes of premature and LBW infants is expanding, partially due to the availability of large, multicenter databases. The consistency of clinical conditions and neonatal outcomes studied since 1990 demonstrates that there are dedicated research agendas and resources that allow for long-term, and potentially replicable, studies within this population.

Is methicillin-resistant Staphylococcus aureus an emerging community pathogen? A review of the literature

PubMed Central

Gardam, Michael A

2000-01-01

OBJECTIVES: To discuss the historical epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) and review the literature suggesting that MRSA has become a community pathogen. DATA SOURCES: A search of the MEDLINE database was performed, encompassing all English or French language citations from 1966 to 1999 and containing the subjects and/or text words: 'Staphylococcus aureus', 'methicillin resistance', 'endocarditis', 'cellulites', 'pneumonia' and 'community-acquired'. Articles published in other languages that provided English or French abstracts were included. All relevant references cited in articles obtained from the MEDLINE database and book chapters were also included. DATA EXTRACTION: All articles obtained from the above sources were examined and were included in the review if a laboratory or epidemiological study of community-acquired MRSA was presented. DATA SYNTHESIS AND CONCLUSIONS: MRSA has emerged over the past 30 years to become a worldwide nosocomial pathogen and has recently been reported as a cause of community-acquired infections. The changing epidemiology of MRSA is likely because of two mechanisms: the movement of nosocomial MRSA strains into the community and the de novo appearance of community strains resulting from the transfer of genetic material from methicillin-resistant Gram-positive organisms to sensitive S aureus strains. The emergence of MRSA as a community pathogen has occurred at a slower rate than it did for penicillin-resistant S aureus (PRSA) in the 1950s and 1960s, possibly because the mechanism of methicillin resistance does not exhibit the same ease of transferability as that of penicillin resistance. Four case reports, seven case series, 10 case-control studies and two cohort studies on community-acquired MRSA were analyzed. Determining whether these reports involve new community-acquired strains rather than previously acquired nosocomial strains can be problematic. It appears, however, that MRSA strains of both nosocomial and community origin are now endemic in certain communities in different parts of the world. Few surveillance studies of nonhospitalized patient populations have been performed to date; thus, the true prevalence of MRSA in the community at large is essentially unknown, although it appears to be low. At present, the empirical treatment of community-acquired S aureus infections with a beta-lactamase-stable beta-lactam antibiotic is appropriate for most populations. However, empirical vancomycin therapy for serious S aureus infections should be strongly considered for patients with significant risk factors for previously-acquired nosocomial MRSA or for patients belonging to outpatient populations with a proven high prevalence of MRSA. Increasing vancomycin use will likely have a significant impact on the development of resistance in Gram-positive organisms. PMID:18159291

Profile and scientific output analysis of physical therapy researchers with research productivity fellowship from the Brazilian National Council for Scientific and Technological Development.

PubMed

Sturmer, Giovani; Viero, Carolina C M; Silveira, Matheus N; Lukrafka, Janice L; Plentz, Rodrigo D M

2013-01-01

To describe the profile and the scientific output of physical therapists researchers holding a research productivity fellowship (PQ) from the Brazilian National Council of Scientific and Technological Development (Conselho Nacional de Desenvolvimento Científico e Tecnológico-CNPq). This is a cross-sectional study, which has evaluated the Lattes Curriculum of all PQ physiotherapy researchers registered at CNPq holding a research productivity fellowship in the period of 2010. The variables analyzed were: gender, geographic and institutional distribution, duration since doctorate defense, research productivity fellowship level, scientific output until 2010 and the H index in Scopus(®) and ISI databases. A total of 55 PQ from the CNPq were identified in the area of knowledge of Physical Therapy and Occupational Therapy, being 81.8% from the Southeast region of Brazil. They were predominantly female (61.8%), with research productivity fellowship level PQ2 (74.5%), and with average time since doctorate defense of 10.1 (±4.1) years. A total of 2.381 articles were published, with average of 42.5 (±18.9) articles/researcher. The average of articles published after doctorate defense was 39.40 (±18.9) articles/researchers with a mean output of 4.2 (±2.0) articles/year. We found 304 articles indexed in the Scopus(®) database with 2.463 citations, and 222 articles indexed in the Web of Science with 1.805 citations. The articles were published in 481 journals, being 244 (50.7%) of them listed on JCR-web. The researchers presented a median 5 of the H index in the Scopus(®) database, and a median 3 in ISI. The scientific output of the researchers with research productivity fellowship in the field of physical therapy stands out in their indicators, since the figures are very promising for a relatively young area and as it can be observed by the amount of published articles and citations obtained by the national and international research community.

Using Hospitalization and Mortality Data to Identify Areas at Risk for Adolescent Suicide.

PubMed

Chen, Kun; Aseltine, Robert H

2017-08-01

The purpose of this study is to use statewide data on inpatient hospitalizations for suicide attempts and suicide mortality to identify communities and school districts at risk for adolescent suicide. Five years of data (2010-2014) from the Office of the Connecticut Medical Examiner and the Connecticut Hospital Inpatient Discharge Database were analyzed. A mixed-effects Poisson regression model was used to assess whether suicide attempt/mortality rates in the state's 119 school districts were significantly better or worse than expected after adjusting for 10 community-level characteristics. Ten districts were at significantly higher risk for suicidal behavior, with suicide mortality/hospitalization rates ranging from 154% to 241% of their expected rates, after accounting for their community characteristics. Four districts were identified as having significantly lower risk for suicide attempts than expected after accounting for community-level advantages and disadvantages. Data capturing hospitalization for suicide attempts and suicide deaths can inform prevention activities by identifying high-risk areas to which resources should be allocated, as well as low-risk areas that may provide insight into the best practices in suicide prevention. Copyright © 2017 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Cholesterol Point-of-Care Testing for Community Pharmacies: A Review of the Current Literature.

PubMed

Haggerty, Lauren; Tran, Deanna

2017-08-01

To summarize the literature on cholesterol point-of-care tests (POCTs). This article would serve as a resource to assist community pharmacists in developing cholesterol point-of-care (POC) pharmacy services. A literature search was performed in MEDLINE Ovid, PubMed, EMBASE, and Cochrane database using the following medical subject headings (MeSH) terms: point-of-care test, cholesterol, blood chemical analysis, rapid testing, collaborative practice, community pharmacy, and ambulatory care. Additional resources including device manufacturer web sites were summarized to supplement the current literature. All human research articles, review articles, meta-analyses, and abstracts published in English through September 1, 2014, were considered. A total of 36 articles were applicable for review. Information was divided into the following categories to be summarized: devices, pharmacists' impact, and operational cost for the pharmacy. The current literature suggests that POCTs in community pharmacies assist with patient outcomes by providing screenings and referring patients with dyslipidemia for further evaluation. The majority of studies on cholesterol POC devices focused on accuracy, revealing the need for further studies to develop best practices and practice models with successful reimbursement. Accuracy, device specifications, required supplies, and patient preference should be considered when selecting a POC device for purchase.

Community Health Workers in Low- and Middle-Income Countries: What Do We Know About Scaling Up and Sustainability?

PubMed Central

Minhas, Dilpreet; Pérez-Escamilla, Rafael; Taylor, Lauren; Curry, Leslie; Bradley, Elizabeth H.

2013-01-01

Objectives. We sought to provide a systematic review of the determinants of success in scaling up and sustaining community health worker (CHW) programs in low- and middle-income countries (LMICs). Methods. We searched 11 electronic databases for academic literature published through December 2010 (n = 603 articles). Two independent reviewers applied exclusion criteria to identify articles that provided empirical evidence about the scale-up or sustainability of CHW programs in LMICs, then extracted data from each article by using a standardized form. We analyzed the resulting data for determinants and themes through iterated categorization. Results. The final sample of articles (n = 19) present data on CHW programs in 16 countries. We identified 23 enabling factors and 15 barriers to scale-up and sustainability, which were grouped into 3 thematic categories: program design and management, community fit, and integration with the broader environment. Conclusions. Scaling up and sustaining CHW programs in LMICs requires effective program design and management, including adequate training, supervision, motivation, and funding; acceptability of the program to the communities served; and securing support for the program from political leaders and other health care providers. PMID:23678926

Molecular Imaging and Contrast Agent Database (MICAD): evolution and progress.

PubMed

Chopra, Arvind; Shan, Liang; Eckelman, W C; Leung, Kam; Latterner, Martin; Bryant, Stephen H; Menkens, Anne

2012-02-01

The purpose of writing this review is to showcase the Molecular Imaging and Contrast Agent Database (MICAD; www.micad.nlm.nih.gov ) to students, researchers, and clinical investigators interested in the different aspects of molecular imaging. This database provides freely accessible, current, online scientific information regarding molecular imaging (MI) probes and contrast agents (CA) used for positron emission tomography, single-photon emission computed tomography, magnetic resonance imaging, X-ray/computed tomography, optical imaging and ultrasound imaging. Detailed information on >1,000 agents in MICAD is provided in a chapter format and can be accessed through PubMed. Lists containing >4,250 unique MI probes and CAs published in peer-reviewed journals and agents approved by the United States Food and Drug Administration as well as a comma separated values file summarizing all chapters in the database can be downloaded from the MICAD homepage. Users can search for agents in MICAD on the basis of imaging modality, source of signal/contrast, agent or target category, pre-clinical or clinical studies, and text words. Chapters in MICAD describe the chemical characteristics (structures linked to PubChem), the in vitro and in vivo activities, and other relevant information regarding an imaging agent. All references in the chapters have links to PubMed. A Supplemental Information Section in each chapter is available to share unpublished information regarding an agent. A Guest Author Program is available to facilitate rapid expansion of the database. Members of the imaging community registered with MICAD periodically receive an e-mail announcement (eAnnouncement) that lists new chapters uploaded to the database. Users of MICAD are encouraged to provide feedback, comments, or suggestions for further improvement of the database by writing to the editors at micad@nlm.nih.gov.

Molecular Imaging and Contrast Agent Database (MICAD): Evolution and Progress

PubMed Central

Chopra, Arvind; Shan, Liang; Eckelman, W. C.; Leung, Kam; Latterner, Martin; Bryant, Stephen H.; Menkens, Anne

2011-01-01

The purpose of writing this review is to showcase the Molecular Imaging and Contrast Agent Database (MICAD; www.micad.nlm.nih.gov) to students, researchers and clinical investigators interested in the different aspects of molecular imaging. This database provides freely accessible, current, online scientific information regarding molecular imaging (MI) probes and contrast agents (CA) used for positron emission tomography, single-photon emission computed tomography, magnetic resonance imaging, x-ray/computed tomography, optical imaging and ultrasound imaging. Detailed information on >1000 agents in MICAD is provided in a chapter format and can be accessed through PubMed. Lists containing >4250 unique MI probes and CAs published in peer-reviewed journals and agents approved by the United States Food and Drug Administration (FDA) as well as a CSV file summarizing all chapters in the database can be downloaded from the MICAD homepage. Users can search for agents in MICAD on the basis of imaging modality, source of signal/contrast, agent or target category, preclinical or clinical studies, and text words. Chapters in MICAD describe the chemical characteristics (structures linked to PubChem), the in vitro and in vivo activities and other relevant information regarding an imaging agent. All references in the chapters have links to PubMed. A Supplemental Information Section in each chapter is available to share unpublished information regarding an agent. A Guest Author Program is available to facilitate rapid expansion of the database. Members of the imaging community registered with MICAD periodically receive an e-mail announcement (eAnnouncement) that lists new chapters uploaded to the database. Users of MICAD are encouraged to provide feedback, comments or suggestions for further improvement of the database by writing to the editors at: micad@nlm.nih.gov PMID:21989943

The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud.

PubMed

Karimi, Kamran; Vize, Peter D

2014-01-01

As a model organism database, Xenbase has been providing informatics and genomic data on Xenopus (Silurana) tropicalis and Xenopus laevis frogs for more than a decade. The Xenbase database contains curated, as well as community-contributed and automatically harvested literature, gene and genomic data. A GBrowse genome browser, a BLAST+ server and stock center support are available on the site. When this resource was first built, all software services and components in Xenbase ran on a single physical server, with inherent reliability, scalability and inter-dependence issues. Recent advances in networking and virtualization techniques allowed us to move Xenbase to a virtual environment, and more specifically to a private cloud. To do so we decoupled the different software services and components, such that each would run on a different virtual machine. In the process, we also upgraded many of the components. The resulting system is faster and more reliable. System maintenance is easier, as individual virtual machines can now be updated, backed up and changed independently. We are also experiencing more effective resource allocation and utilization. Database URL: www.xenbase.org. © The Author(s) 2014. Published by Oxford University Press.

"Utstein style" spreadsheet and database programs based on Microsoft Excel and Microsoft Access software for CPR data management of in-hospital resuscitation.

PubMed

Adams, Bruce D; Whitlock, Warren L

2004-04-01

In 1997, The American Heart Association in association with representatives of the International Committee on Resuscitation (ILCOR) published recommended guidelines for reviewing, reporting and conducting in-hospital cardiopulmonary resuscitation (CPR) outcomes using the "Utstein style". Using these guidelines, we developed two Microsoft Office based database management programs that may be useful to the resuscitation community. We developed a user-friendly spreadsheet based on MS Office Excel. The user enters patient variables such as name, age, and diagnosis. Then, event resuscitation variables such as time of collapse and CPR team arrival are entered from a "code flow sheet". Finally, outcome variables such as patient condition at different time points are recorded. The program then makes automatic calculations of average response times, survival rates and other important outcome measurements. Also using the Utstein style, we developed a database program based on MS Office Access. To promote free public access to these programs, we established at a website. These programs will help hospitals track, analyze, and present their CPR outcomes data. Clinical CPR researchers might also find the programs useful because they are easily modified and have statistical functions.

PDS: A Performance Database Server

DOE PAGES

Berry, Michael W.; Dongarra, Jack J.; Larose, Brian H.; ...

1994-01-01

The process of gathering, archiving, and distributing computer benchmark data is a cumbersome task usually performed by computer users and vendors with little coordination. Most important, there is no publicly available central depository of performance data for all ranges of machines from personal computers to supercomputers. We present an Internet-accessible performance database server (PDS) that can be used to extract current benchmark data and literature. As an extension to the X-Windows-based user interface (Xnetlib) to the Netlib archival system, PDS provides an on-line catalog of public domain computer benchmarks such as the LINPACK benchmark, Perfect benchmarks, and the NAS parallelmore » benchmarks. PDS does not reformat or present the benchmark data in any way that conflicts with the original methodology of any particular benchmark; it is thereby devoid of any subjective interpretations of machine performance. We believe that all branches (research laboratories, academia, and industry) of the general computing community can use this facility to archive performance metrics and make them readily available to the public. PDS can provide a more manageable approach to the development and support of a large dynamic database of published performance metrics.« less

ProtaBank: A repository for protein design and engineering data.

PubMed

Wang, Connie Y; Chang, Paul M; Ary, Marie L; Allen, Benjamin D; Chica, Roberto A; Mayo, Stephen L; Olafson, Barry D

2018-03-25

We present ProtaBank, a repository for storing, querying, analyzing, and sharing protein design and engineering data in an actively maintained and updated database. ProtaBank provides a format to describe and compare all types of protein mutational data, spanning a wide range of properties and techniques. It features a user-friendly web interface and programming layer that streamlines data deposition and allows for batch input and queries. The database schema design incorporates a standard format for reporting protein sequences and experimental data that facilitates comparison of results across different data sets. A suite of analysis and visualization tools are provided to facilitate discovery, to guide future designs, and to benchmark and train new predictive tools and algorithms. ProtaBank will provide a valuable resource to the protein engineering community by storing and safeguarding newly generated data, allowing for fast searching and identification of relevant data from the existing literature, and exploring correlations between disparate data sets. ProtaBank invites researchers to contribute data to the database to make it accessible for search and analysis. ProtaBank is available at https://protabank.org. © 2018 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Occupational exposure to silica in construction workers: a literature-based exposure database.

PubMed

Beaudry, Charles; Lavoué, Jérôme; Sauvé, Jean-François; Bégin, Denis; Senhaji Rhazi, Mounia; Perrault, Guy; Dion, Chantal; Gérin, Michel

2013-01-01

We created an exposure database of respirable crystalline silica levels in the construction industry from the literature. We extracted silica and dust exposure levels in publications reporting silica exposure levels or quantitative evaluations of control effectiveness published in or after 1990. The database contains 6118 records (2858 of respirable crystalline silica) extracted from 115 sources, summarizing 11,845 measurements. Four hundred and eighty-eight records represent summarized exposure levels instead of individual values. For these records, the reported summary parameters were standardized into a geometric mean and a geometric standard deviation. Each record is associated with 80 characteristics, including information on trade, task, materials, tools, sampling strategy, analytical methods, and control measures. Although the database was constructed in French, 38 essential variables were standardized and translated into English. The data span the period 1974-2009, with 92% of the records corresponding to personal measurements. Thirteen standardized trades and 25 different standardized tasks are associated with at least five individual silica measurements. Trade-specific respirable crystalline silica geometric means vary from 0.01 (plumber) to 0.30 mg/m³ (tunnel construction skilled labor), while tasks vary from 0.01 (six categories, including sanding and electrical maintenance) to 1.59 mg/m³ (abrasive blasting). Despite limitations associated with the use of literature data, this database can be analyzed using meta-analytical and multivariate techniques and currently represents the most important source of exposure information about silica exposure in the construction industry. It is available on request to the research community.

Citation classics in radiology journals: the 100 top-cited articles, 1945-2012.

PubMed

Yoon, Dae Young; Yun, Eun Joo; Ku, You Jin; Baek, Sora; Lim, Kyoung Ja; Seo, Young Lan; Yie, Miyeon

2013-09-01

The number of citations an article receives after its publication reflects its impact in the scientific community. The aim of this study was to identify and characterize the 100 top-cited articles published in radiology journals. The top-cited articles published in 12 radiology journals were identified using the database of Science Citation Index Expanded (1945-2012). The 100 top-cited articles were selected and analyzed with regard to the number of citations, year of publication, publishing journal, authorship, institution and country of origin, type of article, radiologic subspecialty, main topic, and radiologic technique. The 100 top-cited articles were published in eight radiology journals, led by Radiology (n=67) and followed by the American Journal of Roentgenology (n=11). These articles were published between 1939 and 2006 with a mean of 664.3 citations per article (range, 371-6931). Seventy-eight articles were published after 1979, 57 originated from the United States, and 69 were original articles. The most common subspecialties of study were interventional radiology (n=19), neuroradiology (n=15), and breast imaging (n=11). The main topics of articles were radiofrequency ablation of hepatic tumors (n=9), followed by receiver operating characteristic curves (n=6). Our study presents a detailed list and analysis of the 100 top-cited articles published in radiology journals, which provides insight into historical developments in the field of radiology.

Development of the Community Health Improvement Navigator Database of Interventions.

PubMed

Roy, Brita; Stanojevich, Joel; Stange, Paul; Jiwani, Nafisa; King, Raymond; Koo, Denise

2016-02-26

With the passage of the Patient Protection and Affordable Care Act, the requirements for hospitals to achieve tax-exempt status include performing a triennial community health needs assessment and developing a plan to address identified needs. To address community health needs, multisector collaborative efforts to improve both health care and non-health care determinants of health outcomes have been the most effective and sustainable. In 2015, CDC released the Community Health Improvement Navigator to facilitate the development of these efforts. This report describes the development of the database of interventions included in the Community Health Improvement Navigator. The database of interventions allows the user to easily search for multisector, collaborative, evidence-based interventions to address the underlying causes of the greatest morbidity and mortality in the United States: tobacco use and exposure, physical inactivity, unhealthy diet, high cholesterol, high blood pressure, diabetes, and obesity.

Development of the Community Health Improvement Navigator Database of Interventions

PubMed Central

Roy, Brita; Stanojevich, Joel; Stange, Paul; Jiwani, Nafisa; King, Raymond; Koo, Denise

2016-01-01

Summary With the passage of the Patient Protection and Affordable Care Act, the requirements for hospitals to achieve tax-exempt status include performing a triennial community health needs assessment and developing a plan to address identified needs. To address community health needs, multisector collaborative efforts to improve both health care and non–health care determinants of health outcomes have been the most effective and sustainable. In 2015, CDC released the Community Health Improvement Navigator to facilitate the development of these efforts. This report describes the development of the database of interventions included in the Community Health Improvement Navigator. The database of interventions allows the user to easily search for multisector, collaborative, evidence-based interventions to address the underlying causes of the greatest morbidity and mortality in the United States: tobacco use and exposure, physical inactivity, unhealthy diet, high cholesterol, high blood pressure, diabetes, and obesity. PMID:26917110

Aging in community nutrition, diet therapy, and nutrition and aging textbooks.

PubMed

O'Neill, Peggy Schafer; Wellman, Nancy S; Himburg, Susan P; Johnson, Paulette; Elfenbien, Pamela

2005-01-01

Using content analysis, this study evaluated the aging content and context in 11 nutrition sub-specialty textbooks: community nutrition (n = 3), diet therapy (n = 4), and nutrition and aging (n = 4). Pages with paragraphs on aging were identified in community nutrition and diet therapy textbooks, and 10% random samples of pages were evaluated in nutrition and aging textbooks. Paragraphs were assigned to one of four categories: gerontology, nutrition as primary, nutrition as secondary, or tertiary prevention. A total of 310 pages was qualitatively analyzed using NUD*IST 5 software and quantitatively with percentages. Only 7% of community nutrition and 2% of diet therapy pages were devoted to aging. There was little integration of aging beyond the chapters on aging. Community nutrition had the most gerontology (30%) and primary prevention (43%) content. Diet therapy and nutrition and aging had more secondary prevention (33% and 42%, respectively) and tertiary prevention (27% each) content. Some important databases and studies were absent. Of the 1,239 ageism words, 10% were positive, 53% neutral, and 36% negative. Photographs were generally positive. Women, but not minorities, reflected current older adult demographics. Future textbook editions should address aging more comprehensively and positively to better prepare dietitians for the job market. Recommendations for authors, course instructors, and publishers are given.

Community Game Day: Using an End-of-Life Conversation Game to Encourage Advance Care Planning.

PubMed

Van Scoy, Lauren J; Reading, Jean M; Hopkins, Margaret; Smith, Brandi; Dillon, Judy; Green, Michael J; Levi, Benjamin H

2017-11-01

Advance care planning (ACP) is an important process that involves discussing and documenting one's values and preferences for medical care, particularly end-of-life treatments. This convergent, mixed-methods study assessed whether an end-of-life conversation card game is an acceptable and effective means for performing ACP for patients with chronic illness and/or their caregivers when deployed in a community setting. Twenty-two games (n = 93 participants) were held in community settings surrounding Hershey, PA in 2016. Participants were recruited using random sampling from patient databases and also convenience sampling (i.e., flyers). Quantitative questionnaires and qualitative focus group interviews were administered to assess the game experience and subsequent performance of ACP behaviors. Both quantitative and qualitative data found that Community Game Day was a well-received, positive experience for participants and 75% of participants performed ACP within three months post-intervention. These findings suggest that using a conversation game during community outreach is a useful approach for engaging patients and caregivers in ACP. The convergence of quantitative and qualitative data strongly supports the continued investigation of the game in randomized controlled trials. Copyright © 2017 American Academy of Hospice and Palliative Medicine. Published by Elsevier Inc. All rights reserved.

A community-based partnership to promote information infrastructure for bleeding disorders.

PubMed

Aschman, Diane J; Abshire, Thomas C; Shapiro, Amy D; Lusher, Jeanne M; Forsberg, Ann D; Kulkarni, Roshni

2011-12-01

Specialists in rare disorders often face challenges in collecting surveillance and research data. As movement toward more fully realizing the potential of electronic health information gains momentum, practitioners who treat individuals with rare disorders are in need of public-private support to tap into the advantages offered by the developing electronic information technologies and the interoperability standards promulgated by the USDHHS. The not-for-profit American Thrombosis and Hemostasis Network (ATHN) was created in 2006 to provide stewardship of a secure, national, web-based database to support federally funded hemophilia treatment centers (HTCs) across the country. In pursuit of its mission to support clinical outcomes analysis, research, advocacy, and public health reporting in the hemostasis and thrombosis community, ATHN has established a spectrum of community-based partnerships. This paper describes the process and public health benefits of creating formal relationships with 127 of the 134 HTCs from 12 regional networks across the U.S., government agencies such as the CDC, Health Resources and Services Administration, and NIH; consumer-based organizations; and industry leaders. This community-based partnership model can be applied to other rare disorders communities with high economic and public health impact. Copyright © 2011 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

Design of Community Resource Inventories as a Component of Scalable Earth Science Infrastructure: Experience of the Earthcube CINERGI Project

NASA Astrophysics Data System (ADS)

Zaslavsky, I.; Richard, S. M.; Valentine, D. W., Jr.; Grethe, J. S.; Hsu, L.; Malik, T.; Bermudez, L. E.; Gupta, A.; Lehnert, K. A.; Whitenack, T.; Ozyurt, I. B.; Condit, C.; Calderon, R.; Musil, L.

2014-12-01

EarthCube is envisioned as a cyberinfrastructure that fosters new, transformational geoscience by enabling sharing, understanding and scientifically-sound and efficient re-use of formerly unconnected data resources, software, models, repositories, and computational power. Its purpose is to enable science enterprise and workforce development via an extensible and adaptable collaboration and resource integration framework. A key component of this vision is development of comprehensive inventories supporting resource discovery and re-use across geoscience domains. The goal of the EarthCube CINERGI (Community Inventory of EarthCube Resources for Geoscience Interoperability) project is to create a methodology and assemble a large inventory of high-quality information resources with standard metadata descriptions and traceable provenance. The inventory is compiled from metadata catalogs maintained by geoscience data facilities, as well as from user contributions. The latter mechanism relies on community resource viewers: online applications that support update and curation of metadata records. Once harvested into CINERGI, metadata records from domain catalogs and community resource viewers are loaded into a staging database implemented in MongoDB, and validated for compliance with ISO 19139 metadata schema. Several types of metadata defects detected by the validation engine are automatically corrected with help of several information extractors or flagged for manual curation. The metadata harvesting, validation and processing components generate provenance statements using W3C PROV notation, which are stored in a Neo4J database. Thus curated metadata, along with the provenance information, is re-published and accessed programmatically and via a CINERGI online application. This presentation focuses on the role of resource inventories in a scalable and adaptable information infrastructure, and on the CINERGI metadata pipeline and its implementation challenges. Key project components are described at the project's website (http://workspace.earthcube.org/cinergi), which also provides access to the initial resource inventory, the inventory metadata model, metadata entry forms and a collection of the community resource viewers.

An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant.

PubMed

Ortseifen, Vera; Stolze, Yvonne; Maus, Irena; Sczyrba, Alexander; Bremges, Andreas; Albaum, Stefan P; Jaenicke, Sebastian; Fracowiak, Jochen; Pühler, Alfred; Schlüter, Andreas

2016-08-10

To study the metaproteome of a biogas-producing microbial community, fermentation samples were taken from an agricultural biogas plant for microbial cell and protein extraction and corresponding metagenome analyses. Based on metagenome sequence data, taxonomic community profiling was performed to elucidate the composition of bacterial and archaeal sub-communities. The community's cytosolic metaproteome was represented in a 2D-PAGE approach. Metaproteome databases for protein identification were compiled based on the assembled metagenome sequence dataset for the biogas plant analyzed and non-corresponding biogas metagenomes. Protein identification results revealed that the corresponding biogas protein database facilitated the highest identification rate followed by other biogas-specific databases, whereas common public databases yielded insufficient identification rates. Proteins of the biogas microbiome identified as highly abundant were assigned to the pathways involved in methanogenesis, transport and carbon metabolism. Moreover, the integrated metagenome/-proteome approach enabled the examination of genetic-context information for genes encoding identified proteins by studying neighboring genes on the corresponding contig. Exemplarily, this approach led to the identification of a Methanoculleus sp. contig encoding 16 methanogenesis-related gene products, three of which were also detected as abundant proteins within the community's metaproteome. Thus, metagenome contigs provide additional information on the genetic environment of identified abundant proteins. Copyright © 2016 Elsevier B.V. All rights reserved.

Online communities of practice and their role in educational development: a systematic appraisal.

PubMed

Swift, Lynn

2014-04-01

Practice teachers and academics have a role in developing knowledge and promoting evidence-based practice with their students in a supportive and creative learning environment. Recent advances in technology are enabling communities of practice' (CoPs) to be developed online and may present a valuable opportunity to form greater connections between educators. To explore this idea, the author conducted a systematic appraisal of published evidence relating to the impact of using an online CoP (OCoP) to develop knowledge among healthcare educators. Three academic databases were targeted for articles and the search retrieved nine articles that were analysed for quality. The findings identified that an OCoP offers a 'polycontextual' environment that can enhance knowledge development, strengthen social ties and build social capital. Communities that support tacit knowledge development, information sharing and problem solving are most valued and existing information and communication technology (ICT) tools can be used to promote usability and accessibility. Recognising the value of tacit knowledge and using ICT for educational development within workload hours will require a shift in cultural thinking at both an individual and organisational level.

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update.

PubMed

Tian, Tian; Liu, Yue; Yan, Hengyu; You, Qi; Yi, Xin; Du, Zhou; Xu, Wenying; Su, Zhen

2017-07-03

The agriGO platform, which has been serving the scientific community for >10 years, specifically focuses on gene ontology (GO) enrichment analyses of plant and agricultural species. We continuously maintain and update the databases and accommodate the various requests of our global users. Here, we present our updated agriGO that has a largely expanded number of supporting species (394) and datatypes (865). In addition, a larger number of species have been classified into groups covering crops, vegetables, fish, birds and insects closely related to the agricultural community. We further improved the computational efficiency, including the batch analysis and P-value distribution (PVD), and the user-friendliness of the web pages. More visualization features were added to the platform, including SEACOMPARE (cross comparison of singular enrichment analysis), direct acyclic graph (DAG) and Scatter Plots, which can be merged by choosing any significant GO term. The updated platform agriGO v2.0 is now publicly accessible at http://systemsbiology.cau.edu.cn/agriGOv2/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

ZikaBase: An integrated ZIKV- Human Interactome Map database.

PubMed

Gurumayum, Sanathoi; Brahma, Rahul; Naorem, Leimarembi Devi; Muthaiyan, Mathavan; Gopal, Jeyakodi; Venkatesan, Amouda

2018-01-15

Re-emergence of ZIKV has caused infections in more than 1.5 million people. The molecular mechanism and pathogenesis of ZIKV is not well explored due to unavailability of adequate model and lack of publically accessible resources to provide information of ZIKV-Human protein interactome map till today. This study made an attempt to curate the ZIKV-Human interaction proteins from published literatures and RNA-Seq data. 11 direct interaction, 12 associated genes are retrieved from literatures and 3742 Differentially Expressed Genes (DEGs) are obtained from RNA-Seq analysis. The genes have been analyzed to construct the ZIKV-Human Interactome Map. The importance of the study has been illustrated by the enrichment analysis and observed that direct interaction and associated genes are enriched in viral entry into host cell. Also, ZIKV infection modulates 32% signal and 27% immune system pathways. The integrated database, ZikaBase has been developed to help the virology research community and accessible at https://test5.bicpu.edu.in. Copyright © 2017 Elsevier Inc. All rights reserved.

FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca

PubMed Central

Naithani, Sushma; Partipilo, Christina M.; Raja, Rajani; Elser, Justin L.; Jaiswal, Pankaj

2016-01-01

FragariaCyc is a strawberry-specific cellular metabolic network based on the annotated genome sequence of Fragaria vesca L. ssp. vesca, accession Hawaii 4. It was built on the Pathway-Tools platform using MetaCyc as the reference. The experimental evidences from published literature were used for supporting/editing existing entities and for the addition of new pathways, enzymes, reactions, compounds, and small molecules in the database. To date, FragariaCyc comprises 66 super-pathways, 488 unique pathways, 2348 metabolic reactions, 3507 enzymes, and 2134 compounds. In addition to searching and browsing FragariaCyc, researchers can compare pathways across various plant metabolic networks and analyze their data using Omics Viewer tool. We view FragariaCyc as a resource for the community of researchers working with strawberry and related fruit crops. It can help understanding the regulation of overall metabolism of strawberry plant during development and in response to diseases and abiotic stresses. FragariaCyc is available online at http://pathways.cgrb.oregonstate.edu. PMID:26973684

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability

PubMed Central

Vita, Randi; Overton, James A; Mungall, Christopher J; Sette, Alessandro

2018-01-01

Abstract The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings. We here examine how the IEDB complies with these principles and identify broad areas of success, but also areas for improvement. We describe short-term improvements to the IEDB that are being implemented now, as well as a long-term vision of true ‘machine-actionable interoperability’, which we believe will require community agreement on standardization of knowledge representation that can be built on top of the shared use of ontologies. PMID:29688354

How to measure the internationality of scientific publications.

PubMed

Buela-Casal, Gualberto; Zych, Izabela

2012-01-01

Although the term "internationality" has never been defined by consensus, it is commonly used as a synonym of quality. Even though its meaning has never been established, internationality is frequently used to evaluate scientists, publications, or universities in many different countries. The present investigation is based on the opinion about the meaning of the concept "internationality" of the members of scientific community, represented by a broad sample of 16,056 scientists from 109 countries working in all the fields of knowledge defined by UNESCO. The sample was randomly selected from the Web of Science database from the scientists who have published at least one article in one of the journals indexed by the database. A questionnaire based on eleven criteria was designed for the purpose of the study. As a result, the first measure of internationality has been obtained. The most important criteria of internationality are: the publication language, online access, and international publication standards. There are significant differences among geographic zones and fields of knowledge.

BioMart Central Portal: an open database network for the biological community

PubMed Central

Guberman, Jonathan M.; Ai, J.; Arnaiz, O.; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J.; Di Génova, A.; Forbes, Simon; Fujisawa, T.; Gadaleta, E.; Goodstein, D. M.; Gundem, Gunes; Haggarty, Bernard; Haider, Syed; Hall, Matthew; Harris, Todd; Haw, Robin; Hu, S.; Hubbard, Simon; Hsu, Jack; Iyer, Vivek; Jones, Philip; Katayama, Toshiaki; Kinsella, R.; Kong, Lei; Lawson, Daniel; Liang, Yong; Lopez-Bigas, Nuria; Luo, J.; Lush, Michael; Mason, Jeremy; Moreews, Francois; Ndegwa, Nelson; Oakley, Darren; Perez-Llamas, Christian; Primig, Michael; Rivkin, Elena; Rosanoff, S.; Shepherd, Rebecca; Simon, Reinhard; Skarnes, B.; Smedley, Damian; Sperling, Linda; Spooner, William; Stevenson, Peter; Stone, Kevin; Teague, J.; Wang, Jun; Wang, Jianxin; Whitty, Brett; Wong, D. T.; Wong-Erasmus, Marie; Yao, L.; Youens-Clark, Ken; Yung, Christina; Zhang, Junjun; Kasprzyk, Arek

2011-01-01

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities. Database URL: http://central.biomart.org. PMID:21930507

Database resources for the Tuberculosis community

PubMed Central

Lew, Jocelyne M.; Mao, Chunhong; Shukla, Maulik; Warren, Andrew; Will, Rebecca; Kuznetsov, Dmitry; Xenarios, Ioannis; Robertson, Brian D.; Gordon, Stephen V.; Schnappinger, Dirk; Cole, Stewart T.; Sobral, Bruno

2013-01-01

Summary Access to online repositories for genomic and associated “-omics” datasets is now an essential part of everyday research activity. It is important therefore that the Tuberculosis community is aware of the databases and tools available to them online, as well as for the database hosts to know what the needs of the research community are. One of the goals of the Tuberculosis Annotation Jamboree, held in Washington DC on March 7th–8th 2012, was therefore to provide an overview of the current status of three key Tuberculosis resources, TubercuList (tuberculist.epfl.ch), TB Database (www.tbdb.org), and Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org). Here we summarize some key updates and upcoming features in TubercuList, and provide an overview of the PATRIC site and its online tools for pathogen RNA-Seq analysis. PMID:23332401

Collection and storage of HLA NGS genotyping data for the 17th International HLA and Immunogenetics Workshop.

PubMed

Chang, Chia-Jung; Osoegawa, Kazutoyo; Milius, Robert P; Maiers, Martin; Xiao, Wenzhong; Fernandez-Viňa, Marcelo; Mack, Steven J

2018-02-01

For over 50 years, the International HLA and Immunogenetics Workshops (IHIW) have advanced the fields of histocompatibility and immunogenetics (H&I) via community sharing of technology, experience and reagents, and the establishment of ongoing collaborative projects. Held in the fall of 2017, the 17th IHIW focused on the application of next generation sequencing (NGS) technologies for clinical and research goals in the H&I fields. NGS technologies have the potential to allow dramatic insights and advances in these fields, but the scope and sheer quantity of data associated with NGS raise challenges for their analysis, collection, exchange and storage. The 17th IHIW adopted a centralized approach to these issues, and we developed the tools, services and systems to create an effective system for capturing and managing these NGS data. We worked with NGS platform and software developers to define a set of distinct but equivalent NGS typing reports that record NGS data in a uniform fashion. The 17th IHIW database applied our standards, tools and services to collect, validate and store those structured, multi-platform data in an automated fashion. We have created community resources to enable exploration of the vast store of curated sequence and allele-name data in the IPD-IMGT/HLA Database, with the goal of creating a long-term community resource that integrates these curated data with new NGS sequence and polymorphism data, for advanced analyses and applications. Copyright © 2017 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

The Influence of Community Health Resources on Effectiveness and Sustainability of Community and Lay Health Worker Programs in Lower-Income Countries: A Systematic Review.

PubMed

de Vries, Daniel H; Pool, Robert

2017-01-01

Despite the availability of practical knowledge and effective interventions required to reduce priority health problems in low-income countries, poor and vulnerable populations are often not reached. One possible solution to this problem is the use of Community or Lay Health Workers (CLHWs). So far, however, the development of sustainability in CLHW programs has failed and high attrition rates continue to pose a challenge. We propose that the roles and interests which support community health work should emerge directly from the way in which health is organized at community level. This review explores the evidence available to assess if increased levels of integration of community health resources in CLHW programs indeed lead to higher program effectiveness and sustainability. This review includes peer-reviewed articles which meet three eligibility criteria: 1) specific focus on CLHWs or equivalent; 2) randomized, quasi-randomized, before/after methodology or substantial descriptive assessment; and 3) description of a community or peer intervention health program located in a low- or middle-income country. Literature searches using various article databases led to 2930 hits, of which 359 articles were classified. Of these, 32 articles were chosen for extensive review, complemented by analysis of the results of 15 other review studies. Analysis was conducted using an excel based data extraction form. Because results showed that no quantitative data was published, a descriptive synthesis was conducted. The review protocol was not proactively registered. Findings show minimal inclusion of even basic community level indicators, such as the degree to which the program is a community initiative, community input in the program or training, the background and history of CLHW recruits, and the role of the community in motivation and retention. Results show that of the 32 studies, only one includes one statistical measure of community integration. As a result of this lack of data we are unable to derive an evidence-based conclusion to our propositions. Instead, our results indicate a larger problem, namely the complete absence of indicators measuring community relationships with the programs studied. Studies pay attention only to gender and peer roles, along with limited demographic information about the recruits. The historicity of the health worker and the community s/he belongs to is absent in most studies reviewed. None of the studies discuss or test for the possibility that motivation emanates from the community. Only a few studies situate attrition and retention as an issue enabled by the community. The results were limited by a focus on low-income countries and English, peer-reviewed published articles only. Published, peer-reviewed studies evaluating the effectiveness and sustainability of CLHW interventions in health programs have not yet adequately tested for the potential of utilizing existing community health roles or social networks for the development of effective and sustainable (retentive) CLHW programs. Community relationships are generally seen as a "black box" represented by an interchangeable CLHW labor unit. This disconnect from community relationships and resources may have led to a systematic and chronic undervaluing of community agency in explanations of programmatic effectiveness and sustainability.

Data quality scoring system for microcosm and mesocosm studies used to derive a level of concern for atrazine.

PubMed

Giddings, Jeffrey M; Campana, David; Nair, Shyam; Brain, Richard

2018-04-16

The US Environmental Protection Agency (USEPA) has historically used different methods to derive an aquatic level of concern (LoC) for atrazine, though all have generally relied on an expanding set of mesocosm and microcosm ("cosm") studies for calibration. The database of results from ecological effects studies with atrazine in cosms now includes 108 data points from 39 studies and forms the basis for assessing atrazine's potential to impact aquatic plant communities. Inclusion of the appropriate cosm studies and accurate interpretation of each data point-delineated as binary scores of "effect" (effect score 1) or "no effect" (effect score 0) of a specific atrazine exposure profile on plant communities in a single study-is critical to USEPA's approach to determining the LoC. We reviewed the atrazine cosm studies in detail and carefully interpreted their results in terms of the binary effect scores. The cosm database includes a wide range of experimental systems and study designs, some of which are more relevant to natural plant communities than others. Moreover, the studies vary in the clarity and consistency of their results. We therefore evaluated each study against objective criteria for relevance and reliability to produce a weighting score that can be applied to the effect scores when calculating the LoC. This approach is useful because studies that are more relevant and reliable have greater influence on the LoC than studies with lower weighting scores. When the current iteration of USEPA's LoC approach, referred to as the plant assemblage toxicity index (PATI), was calibrated with the weighted cosm data set, the result was a 60-day LoC of 21.2 μg/L. Integr Environ Assess Manag 2018;00:000-000. © 2018 The Authors. Integrated Environmental Assessment and Management Published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC). © 2018 The Authors. Integrated Environmental Assessment and Management Published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Special Section: The USMARC Community Information Format.

ERIC Educational Resources Information Center

Lutz, Marilyn; And Others

1992-01-01

Five papers discuss topics related to the USMARC Community Information Format (CIF), including using CIF to create a public service resource network; development of a CIF-based database of materials relating to multicultural and differently-abled populations; background on CIF; development of an information and referral database; and CIF and…

The CHOICES Project: Piloting a Secondary Transition Planning Database

ERIC Educational Resources Information Center

Campbell, Dennis; Baxter, Abigail; Ellis, David; Pardue, Harold

2013-01-01

The CHOICES Project funded by the Institute of Education Sciences (IES), U.S. Department of Education, addresses the need for ready access to information for parents, students, school, and community agency personnel regarding transitional and community support programs. At this time we have created two databases (student information and community…

Community engagement strategies for genomic studies in Africa: a review of the literature.

PubMed

Tindana, Paulina; de Vries, Jantina; Campbell, Megan; Littler, Katherine; Seeley, Janet; Marshall, Patricia; Troyer, Jennifer; Ogundipe, Morisola; Alibu, Vincent Pius; Yakubu, Aminu; Parker, Michael

2015-04-12

Community engagement has been recognised as an important aspect of the ethical conduct of biomedical research, especially when research is focused on ethnically or culturally distinct populations. While this is a generally accepted tenet of biomedical research, it is unclear what components are necessary for effective community engagement, particularly in the context of genomic research in Africa. We conducted a review of the published literature to identify the community engagement strategies that can support the successful implementation of genomic studies in Africa. Our search strategy involved using online databases, Pubmed (National Library of Medicine), Medline and Google scholar. Search terms included a combination of the following: community engagement, community advisory boards, community consultation, community participation, effectiveness, genetic and genomic research, Africa, developing countries. A total of 44 articles and 1 thesis were retrieved of which 38 met the selection criteria. Of these, 21 were primary studies on community engagement, while the rest were secondary reports on community engagement efforts in biomedical research studies. 34 related to biomedical research generally, while 4 were specific to genetic and genomic research in Africa. We concluded that there were several community engagement strategies that could support genomic studies in Africa. While many of the strategies could support the early stages of a research project such as the recruitment of research participants, further research is needed to identify effective strategies to engage research participants and their communities beyond the participant recruitment stage. Research is also needed to address how the views of local communities should be incorporated into future uses of human biological samples. Finally, studies evaluating the impact of CE on genetic research are lacking. Systematic evaluation of CE strategies is essential to determine the most effective models of CE for genetic and genomic research conducted in African settings.

First Nuclear DNA Amounts in more than 300 Angiosperms

PubMed Central

ZONNEVELD, B. J. M.; LEITCH, I. J.; BENNETT, M. D.

2005-01-01

• Background and Aims Genome size (DNA C-value) data are key biodiversity characters of fundamental significance used in a wide variety of biological fields. Since 1976, Bennett and colleagues have made scattered published and unpublished genome size data more widely accessible by assembling them into user-friendly compilations. Initially these were published as hard copy lists, but since 1997 they have also been made available electronically (see the Plant DNA C-values database www.kew.org/cval/homepage.html). Nevertheless, at the Second Plant Genome Size Meeting in 2003, Bennett noted that as many as 1000 DNA C-value estimates were still unpublished and hence unavailable. Scientists were strongly encouraged to communicate such unpublished data. The present work combines the databasing experience of the Kew-based authors with the unpublished C-values produced by Zonneveld to make a large body of valuable genome size data available to the scientific community. • Methods C-values for angiosperm species, selected primarily for their horticultural interest, were estimated by flow cytometry using the fluorochrome propidium iodide. The data were compiled into a table whose form is similar to previously published lists of DNA amounts by Bennett and colleagues. • Key Results and Conclusions The present work contains C-values for 411 taxa including first values for 308 species not listed previously by Bennett and colleagues. Based on a recent estimate of the global published output of angiosperm DNA C-value data (i.e. 200 first C-value estimates per annum) the present work equals 1·5 years of average global published output; and constitutes over 12 % of the latest 5-year global target set by the Second Plant Genome Size Workshop (see www.kew.org/cval/workshopreport.html). Hopefully, the present example will encourage others to unveil further valuable data which otherwise may lie forever unpublished and unavailable for comparative analyses. PMID:15905300

ORENZA: a web resource for studying ORphan ENZyme activities

PubMed Central

Lespinet, Olivier; Labedan, Bernard

2006-01-01

Background Despite the current availability of several hundreds of thousands of amino acid sequences, more than 36% of the enzyme activities (EC numbers) defined by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) are not associated with any amino acid sequence in major public databases. This wide gap separating knowledge of biochemical function and sequence information is found for nearly all classes of enzymes. Thus, there is an urgent need to explore these sequence-less EC numbers, in order to progressively close this gap. Description We designed ORENZA, a PostgreSQL database of ORphan ENZyme Activities, to collate information about the EC numbers defined by the NC-IUBMB with specific emphasis on orphan enzyme activities. Complete lists of all EC numbers and of orphan EC numbers are available and will be periodically updated. ORENZA allows one to browse the complete list of EC numbers or the subset associated with orphan enzymes or to query a specific EC number, an enzyme name or a species name for those interested in particular organisms. It is possible to search ORENZA for the different biochemical properties of the defined enzymes, the metabolic pathways in which they participate, the taxonomic data of the organisms whose genomes encode them, and many other features. The association of an enzyme activity with an amino acid sequence is clearly underlined, making it easy to identify at once the orphan enzyme activities. Interactive publishing of suggestions by the community would provide expert evidence for re-annotation of orphan EC numbers in public databases. Conclusion ORENZA is a Web resource designed to progressively bridge the unwanted gap between function (enzyme activities) and sequence (dataset present in public databases). ORENZA should increase interactions between communities of biochemists and of genomicists. This is expected to reduce the number of orphan enzyme activities by allocating gene sequences to the relevant enzymes. PMID:17026747

Cited Brazilian papers in general surgery between 1970 and 2009

PubMed Central

Heldwein, Flavio L.; Hartmann, Antonio A.; Kalil, Antonio N.; Neves, Bruno V. D.; Ratti, Giorigo S. B.; Beber, Moises C.; Souza, Rafael M.; d’Acampora, Armando J.

2010-01-01

OBJECTIVES To identify the most cited articles in general surgery published by Brazilian authors. INTRODUCTION There are several ways for the international community to recognize the quality of a scientific article. Although controversial, the most widely used and reliable methodology to identify the importance of an article is citation analysis. METHODS A search using the Institute for Scientific Information citation database (Science Citation Index Expanded) was performed to identify highly cited Brazilian papers published in twenty-six highly cited general surgery journals, selected based on their elevated impact factors, from 1970 to 2009. Further analysis was done on the 65 most-cited papers. RESULTS We identified 1,713 Brazilian articles, from which nine papers emerged as classics (more than 100 citations received). For the Brazilian contributions, a total increase of about 21-fold was evident between 1970 and 2009. Although several topics were covered, articles covering trauma, oncology and organ transplantation were the most cited. The majority of classic studies were done with international cooperation. CONCLUSIONS This study identified the most influential Brazilian articles published in internationally renowned general surgery journals. PMID:20535371

GLOFs in the WOS: bibliometrics, geographies and global trends of research on glacial lake outburst floods (Web of Science, 1979-2016)

NASA Astrophysics Data System (ADS)

Emmer, Adam

2018-03-01

Research on glacial lake outburst floods (GLOFs) - specific low-frequency, high-magnitude floods originating in glacial lakes, including jökulhlaups - is well justified in the context of glacier ice loss and glacial lake evolution in glacierized areas all over the world. Increasing GLOF research activities, which are documented by the increasing number of published research items, have been observed in the past few decades; however, comprehensive insight into the GLOF research community, its global bibliometrics, geographies and trends in research is missing. To fill this gap, a set of 892 GLOF research items published in the Web of Science database covering the period 1979-2016 was analysed. General bibliometric characteristics, citations and references were analysed, revealing a certain change in the publishing paradigm over time. Furthermore, the global geographies of research on GLOFs were studied, focusing on (i) where GLOFs are studied, (ii) who studies GLOFs, (iii) the export of research on GLOFs and (iv) international collaboration. The observed trends and links to the challenges ahead are discussed and placed in a broader context.

Cited Brazilian papers in general surgery between 1970 and 2009.

PubMed

Heldwein, Flavio L; Hartmann, Antonio A; Kalil, Antonio N; Neves, Bruno V D; Ratti, Giorigo S B; Beber, Moises C; Souza, Rafael M; d'Acampora, Armando J

2010-05-01

To identify the most cited articles in general surgery published by Brazilian authors. There are several ways for the international community to recognize the quality of a scientific article. Although controversial, the most widely used and reliable methodology to identify the importance of an article is citation analysis. A search using the Institute for Scientific Information citation database (Science Citation Index Expanded) was performed to identify highly cited Brazilian papers published in twenty-six highly cited general surgery journals, selected based on their elevated impact factors, from 1970 to 2009. Further analysis was done on the 65 most-cited papers. We identified 1,713 Brazilian articles, from which nine papers emerged as classics (more than 100 citations received). For the Brazilian contributions, a total increase of about 21-fold was evident between 1970 and 2009. Although several topics were covered, articles covering trauma, oncology and organ transplantation were the most cited. The majority of classic studies were done with international cooperation. This study identified the most influential Brazilian articles published in internationally renowned general surgery journals.

Predicting tuberculosis risk in the foreign-born population of British Columbia, Canada: study protocol for a retrospective population-based cohort study.

PubMed

Ronald, Lisa A; Campbell, Jonathon R; Balshaw, Robert F; Roth, David Z; Romanowski, Kamila; Marra, Fawziah; Cook, Victoria J; Johnston, James C

2016-11-25

Improved understanding of risk factors for developing active tuberculosis (TB) will better inform decisions about diagnostic testing and treatment for latent TB infection (LTBI) in migrant populations in low-incidence regions. We aim to examine TB risk factors among the foreign-born population in British Columbia (BC), Canada, and to create and validate a clinically relevant multivariate risk score to predict active TB. This retrospective population-based cohort study will include all foreign-born individuals who acquired permanent resident status in Canada between 1 January 1985 and 31 December 2013 and acquired healthcare coverage in BC at any point during this period. Multiple administrative databases and disease registries will be linked, including a National Immigration Database, BC Provincial Health Insurance Registration, physician billings, hospitalisations, drugs dispensed from community pharmacies, vital statistics, HIV testing and notifications, cancer, chronic kidney disease and dialysis treatment, and all TB and LTBI testing and treatment data in BC. Extended proportional hazards regression will be used to estimate risk factors for TB and to create a prognostic TB risk score. Ethical approval for this study has been obtained from the University of British Columbia Clinical Ethics Review Board. Once completed, study findings will be presented at conferences and published in peer-reviewed journals. An online TB risk score calculator will also be created. 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/.

The effectiveness of community-based loan funds for transport during obstetric emergencies in developing countries: a systematic review.

PubMed

Nwolise, Chidiebere Hope; Hussein, Julia; Kanguru, Lovney; Bell, Jacqueline; Patel, Purvi

2015-09-01

Scarcity and costs of transport have been implicated as key barriers to accessing care when obstetric emergencies occur in community settings. Community-based loans have been used to increase utilization of health facilities and potentially reduce maternal mortality by providing funding at community level to provide emergency transport. This review aimed to provide evidence of the effect of community-based loan funds on utilization of health facilities and reduction of maternal mortality in developing countries. Electronic databases of published literature and websites were searched for relevant literature using a pre-defined set of search terms, inclusion and exclusion criteria. Screening of titles, abstracts and full-text articles were done by at least two reviewers independently. Quality assessment was carried out on the selected papers. Data related to deliveries and obstetric complications attended at facilities, maternal deaths and live births were extracted to measure and compare the effects of community-based loan funds using odds ratios (ORs) and reductions in maternal mortality ratio. Forest plots are presented where possible. The results of the review show that groups where community-based loan funds were implemented (alongside other interventions) generally recorded increases in utilization of health facilities for deliveries, with ORs of 3.5 (0.97-15.48) and 3.55 (1.56-8.05); and an increase in utilization of emergency obstetric care with ORs of 2.22 (0.51-10.38) and 3.37 (1.78-6.37). Intervention groups also experienced a positive effect on met need for complications and a reduction in maternal mortality. There is some evidence to suggest that community-based loan funds as part of a multifaceted intervention have positive effects. Conclusions are limited by challenges of study design and bias. Further studies which strengthen the evidence of the effects of loan funds, and mechanism for their functionality, are recommended. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine © The Author 2014; all rights reserved.

New mutations and an updated database for the patched-1 (PTCH1) gene.

PubMed

Reinders, Marie G; van Hout, Antonius F; Cosgun, Betûl; Paulussen, Aimée D; Leter, Edward M; Steijlen, Peter M; Mosterd, Klara; van Geel, Michel; Gille, Johan J

2018-05-01

Basal cell nevus syndrome (BCNS) is an autosomal dominant disorder characterized by multiple basal cell carcinomas (BCCs), maxillary keratocysts, and cerebral calcifications. BCNS most commonly is caused by a germline mutation in the patched-1 (PTCH1) gene. PTCH1 mutations are also described in patients with holoprosencephaly. We have established a locus-specific database for the PTCH1 gene using the Leiden Open Variation Database (LOVD). We included 117 new PTCH1 variations, in addition to 331 previously published unique PTCH1 mutations. These new mutations were found in 141 patients who had a positive PTCH1 mutation analysis in either the VU University Medical Centre (VUMC) or Maastricht University Medical Centre (MUMC) between 1995 and 2015. The database contains 331 previously published unique PTCH1 mutations and 117 new PTCH1 variations. We have established a locus-specific database for the PTCH1 gene using the Leiden Open Variation Database (LOVD). The database provides an open collection for both clinicians and researchers and is accessible online at http://www.lovd.nl/PTCH1. © 2018 The Authors. Molecular Genetics & Genomic Medicine published by Wiley Periodicals, Inc.

Use of a German longitudinal prescription database (LRx) in pharmacoepidemiology.

PubMed

Richter, Hartmut; Dombrowski, Silvia; Hamer, Hajo; Hadji, Peyman; Kostev, Karel

2015-01-01

Large epidemiological databases are often used to examine matters pertaining to drug utilization, health services, and drug safety. The major strength of such databases is that they include large sample sizes, which allow precise estimates to be made. The IMS® LRx database has in recent years been used as a data source for epidemiological research. The aim of this paper is to review a number of recent studies published with the aid of this database and compare these with the results of similar studies using independent data published in the literature. In spite of being somewhat limited to studies for which comparative independent results were available, it was possible to include a wide range of possible uses of the LRx database in a variety of therapeutic fields: prevalence/incidence rate determination (diabetes, epilepsy), persistence analyses (diabetes, osteoporosis), use of comedication (diabetes), drug utilization (G-CSF market) and treatment costs (diabetes, G-CSF market). In general, the results of the LRx studies were found to be clearly in line with previously published reports. In some cases, noticeable discrepancies between the LRx results and the literature data were found (e.g. prevalence in epilepsy, persistence in osteoporosis) and these were discussed and possible reasons presented. Overall, it was concluded that the IMS® LRx database forms a suitable database for pharmacoepidemiological studies.

Real-time magnetic resonance imaging and electromagnetic articulography database for speech production research (TC)

PubMed Central

Narayanan, Shrikanth; Toutios, Asterios; Ramanarayanan, Vikram; Lammert, Adam; Kim, Jangwon; Lee, Sungbok; Nayak, Krishna; Kim, Yoon-Chul; Zhu, Yinghua; Goldstein, Louis; Byrd, Dani; Bresch, Erik; Ghosh, Prasanta; Katsamanis, Athanasios; Proctor, Michael

2014-01-01

USC-TIMIT is an extensive database of multimodal speech production data, developed to complement existing resources available to the speech research community and with the intention of being continuously refined and augmented. The database currently includes real-time magnetic resonance imaging data from five male and five female speakers of American English. Electromagnetic articulography data have also been presently collected from four of these speakers. The two modalities were recorded in two independent sessions while the subjects produced the same 460 sentence corpus used previously in the MOCHA-TIMIT database. In both cases the audio signal was recorded and synchronized with the articulatory data. The database and companion software are freely available to the research community. PMID:25190403

neXtA5: accelerating annotation of articles via automated approaches in neXtProt.

PubMed

Mottin, Luc; Gobeill, Julien; Pasche, Emilie; Michel, Pierre-André; Cusin, Isabelle; Gaudet, Pascale; Ruch, Patrick

2016-01-01

The rapid increase in the number of published articles poses a challenge for curated databases to remain up-to-date. To help the scientific community and database curators deal with this issue, we have developed an application, neXtA5, which prioritizes the literature for specific curation requirements. Our system, neXtA5, is a curation service composed of three main elements. The first component is a named-entity recognition module, which annotates MEDLINE over some predefined axes. This report focuses on three axes: Diseases, the Molecular Function and Biological Process sub-ontologies of the Gene Ontology (GO). The automatic annotations are then stored in a local database, BioMed, for each annotation axis. Additional entities such as species and chemical compounds are also identified. The second component is an existing search engine, which retrieves the most relevant MEDLINE records for any given query. The third component uses the content of BioMed to generate an axis-specific ranking, which takes into account the density of named-entities as stored in the Biomed database. The two ranked lists are ultimately merged using a linear combination, which has been specifically tuned to support the annotation of each axis. The fine-tuning of the coefficients is formally reported for each axis-driven search. Compared with PubMed, which is the system used by most curators, the improvement is the following: +231% for Diseases, +236% for Molecular Functions and +3153% for Biological Process when measuring the precision of the top-returned PMID (P0 or mean reciprocal rank). The current search methods significantly improve the search effectiveness of curators for three important curation axes. Further experiments are being performed to extend the curation types, in particular protein-protein interactions, which require specific relationship extraction capabilities. In parallel, user-friendly interfaces powered with a set of JSON web services are currently being implemented into the neXtProt annotation pipeline.Available on: http://babar.unige.ch:8082/neXtA5Database URL: http://babar.unige.ch:8082/neXtA5/fetcher.jsp. © The Author(s) 2016. Published by Oxford University Press.

Database resources for the tuberculosis community.

PubMed

Lew, Jocelyne M; Mao, Chunhong; Shukla, Maulik; Warren, Andrew; Will, Rebecca; Kuznetsov, Dmitry; Xenarios, Ioannis; Robertson, Brian D; Gordon, Stephen V; Schnappinger, Dirk; Cole, Stewart T; Sobral, Bruno

2013-01-01

Access to online repositories for genomic and associated "-omics" datasets is now an essential part of everyday research activity. It is important therefore that the Tuberculosis community is aware of the databases and tools available to them online, as well as for the database hosts to know what the needs of the research community are. One of the goals of the Tuberculosis Annotation Jamboree, held in Washington DC on March 7th-8th 2012, was therefore to provide an overview of the current status of three key Tuberculosis resources, TubercuList (tuberculist.epfl.ch), TB Database (www.tbdb.org), and Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org). Here we summarize some key updates and upcoming features in TubercuList, and provide an overview of the PATRIC site and its online tools for pathogen RNA-Seq analysis. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

PubMed

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

1998-01-01

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

Community Education for Family Planning in the U.S.

PubMed Central

Carter, Marion W.; Tregear, Michelle L.; Moskosky, Susan B.

2015-01-01

Context Community education may involve activities that seek to raise awareness and promote behavior change, using mass media, social media, and other media or interpersonal methods in community settings. This systematic review evaluated the evidence of the effects of community education on select short- and medium-term family planning outcomes. Evidence acquisition Using an analytic approach drawn from the U.S. Preventive Services Task Force, multiple databases were searched for articles published from January 1985 through February 2011 describing studies of community education related to family planning in the U.S. Included articles were reviewed and assessed for potential bias using a standardized process in 2011. An updated, targeted review for the 2011–2014 period was conducted in early 2015. Evidence synthesis Seventeen papers were identified. Most (nine) related to mass media interventions; three involved targeted print media, two involved text messaging or e-mail, two described outcome workers conducting community education, and one involved community theater. Study designs, strength of evidence, and levels of possible bias varied widely. Twelve of 15 studies that addressed outcomes such as increased awareness found positive associations with those outcomes, with six also reporting null findings. Seven of eight studies that addressed use of services reported positive associations, with two also reporting null findings. The targeted, additional review identified two other studies. Conclusions Evidence related to community education for family planning purposes is limited and highly variable. As goals of community education are usually limited to shorter-term outcomes, the evidence suggests that a range of approaches may be effective. PMID:26190841

A systematic review of a functional assessment Tool: UCSD Performance-based skill assessment (UPSA).

PubMed

Becattini-Oliveira, Ana Claudia; Dutra, Douglas de Farias; Spenciere de Oliveira Campos, Bárbara; de Araujo, Verônica Carvalho; Charchat-Fichman, Helenice

2018-05-18

Performance based assessment instruments have been employed in functional capacity measurement of mental disorders. The aim of this systematic review was to identify the psychometric properties of the UCSD Performance-based Skill Assessment (UPSA). A search was conducted using the PRISMA protocol and 'UPSA' as key word term on electronic databases, with a date range for articles published from 2001-2017. Published studies involving community-dwelling adults were included. Pharmacological and/or clinical interventions involving clinical outcomes and/or institutionalized samples were excluded. Data related to construct validity, test-retest reliability and sensitivity/specificity were extracted, summarized and analyzed according to UPSA versions and psychiatric disorders. Fifty-eight studies including 8782 Community-dwelling adults met selection criteria. Data supporting the construct and known-groups validity were extracted from 41 studies involving Schizophrenia and schizoaffective disorders and 17 studies involving other metal illness. The UPSA was culturally adapted to 8 different languages and employed in 17 countries. Few studies reported sensitivity and specificity and the cut-off points could not be generalized. Moderate to strong evidence of construct validity and test-retest reliability was found. Few studies proposed cut-off points. The UPSA showed good psychometric properties in different versions including those culturally adapted. Copyright © 2018 Elsevier B.V. All rights reserved.

Ethical, Legal, and Social Implications of Personalized Genomic Medicine Research: Current Literature and Suggestions for the Future.

PubMed

Callier, Shawneequa L; Abudu, Rachel; Mehlman, Maxwell J; Singer, Mendel E; Neuhauser, Duncan; Caga-Anan, Charlisse; Wiesner, Georgia L

2016-11-01

This review identifies the prominent topics in the literature pertaining to the ethical, legal, and social issues (ELSI) raised by research investigating personalized genomic medicine (PGM). The abstracts of 953 articles extracted from scholarly databases and published during a 5-year period (2008-2012) were reviewed. A total of 299 articles met our research criteria and were organized thematically to assess the representation of ELSI issues for stakeholders, health specialties, journals, and empirical studies. ELSI analyses were published in both scientific and ethics journals. Investigational research comprised 45% of the literature reviewed (135 articles) and the remaining 55% (164 articles) comprised normative analyses. Traditional ELSI concerns dominated the discourse including discussions about disclosure of research results. In fact, there was a dramatic increase in the number of articles focused on the disclosure of research results and incidental findings to research participants. Few papers focused on particular disorders, the use of racial categories in research, international communities, or special populations (e.g., adolescents, elderly patients, or ethnic groups). Considering that strategies in personalized medicine increasingly target individuals' unique health conditions, environments, and ancestries, further analysis is needed on how ELSI scholarship can better serve the increasingly global, interdisciplinary, and diverse PGM research community. © 2016 John Wiley & Sons Ltd.

Understanding the productive author who published papers in medicine using National Health Insurance Database: A systematic review and meta-analysis.

PubMed

Chien, Tsair-Wei; Chang, Yu; Wang, Hsien-Yi

2018-02-01

Many researchers used National Health Insurance database to publish medical papers which are often retrospective, population-based, and cohort studies. However, the author's research domain and academic characteristics are still unclear.By searching the PubMed database (Pubmed.com), we used the keyword of [Taiwan] and [National Health Insurance Research Database], then downloaded 2913 articles published from 1995 to 2017. Social network analysis (SNA), Gini coefficient, and Google Maps were applied to gather these data for visualizing: the most productive author; the pattern of coauthor collaboration teams; and the author's research domain denoted by abstract keywords and Pubmed MESH (medical subject heading) terms.Utilizing the 2913 papers from Taiwan's National Health Insurance database, we chose the top 10 research teams shown on Google Maps and analyzed one author (Dr. Kao) who published 149 papers in the database in 2015. In the past 15 years, we found Dr. Kao had 2987 connections with other coauthors from 13 research teams. The cooccurrence abstract keywords with the highest frequency are cohort study and National Health Insurance Research Database. The most coexistent MESH terms are tomography, X-ray computed, and positron-emission tomography. The strength of the author research distinct domain is very low (Gini < 0.40).SNA incorporated with Google Maps and Gini coefficient provides insight into the relationships between entities. The results obtained in this study can be applied for a comprehensive understanding of other productive authors in the field of academics.

Update on terrestrial ecological classification in the highlands of West Virginia

Treesearch

James P. Vanderhorst

2010-01-01

The West Virginia Natural Heritage Program (WVNHP) maintains databases on the biological diversity of the state, including species and natural communities, to help focus conservation efforts by agencies and organizations. Information on terrestrial communities (also called vegetation, or habitat, depending on user or audience focus) is maintained in two databases. The...

Do We Really Know how Much it Costs to Construct High Performance Buildings?

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

Livingston, Olga V.; Dillon, Heather E.; Halverson, Mark A.

2012-08-31

Understanding the cost of energy efficient construction is critical to decision makers in building design, code development, and energy analysis. How much does it cost to upgrade from R-13 to R-19 in a building wall? How much do low-e windows really cost? Can we put a dollar figure on commissioning? Answers to these questions have a fuzzy nature, based on educated guesses and industry lore. The response depends on location, perspective, bulk buying, and hand waving. This paper explores the development of a web tool intended to serve as a publicly available repository of building component costs. In 2011 themore » U.S. Department of Energy (DOE) funded the launch of a web tool called the Building Component Cost Community (BC3), dedicated to publishing building component costs from documented sources, actively gathering verifiable cost data from the users, and collecting feedback from a wide range of participants on the quality of the posted cost data. The updated BC3 database, available at http://bc3.pnnl.gov, went live on April 30, 2012. BC3 serves as the ultimate source of the energy-related component costs for DOE’s residential code development activities, including cost-effectiveness analyses. The paper discusses BC3 objectives, structure, functionality and the current content of the database. It aims to facilitate a dialog about the lack of verifiable transparent cost data, as well as introduce a web tool that helps to address the problem. The questions posed above will also be addressed by this paper, but they have to be resolved by the user community by providing feedback and cost data to the BC3 database, thus increasing transparency and removing information asymmetry.« less

The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease.

PubMed

Eppig, Janan T; Blake, Judith A; Bult, Carol J; Kadin, James A; Richardson, Joel E

2015-01-01

The Mouse Genome Database (MGD, http://www.informatics.jax.org) serves the international biomedical research community as the central resource for integrated genomic, genetic and biological data on the laboratory mouse. To facilitate use of mouse as a model in translational studies, MGD maintains a core of high-quality curated data and integrates experimentally and computationally generated data sets. MGD maintains a unified catalog of genes and genome features, including functional RNAs, QTL and phenotypic loci. MGD curates and provides functional and phenotype annotations for mouse genes using the Gene Ontology and Mammalian Phenotype Ontology. MGD integrates phenotype data and associates mouse genotypes to human diseases, providing critical mouse-human relationships and access to repositories holding mouse models. MGD is the authoritative source of nomenclature for genes, genome features, alleles and strains following guidelines of the International Committee on Standardized Genetic Nomenclature for Mice. A new addition to MGD, the Human-Mouse: Disease Connection, allows users to explore gene-phenotype-disease relationships between human and mouse. MGD has also updated search paradigms for phenotypic allele attributes, incorporated incidental mutation data, added a module for display and exploration of genes and microRNA interactions and adopted the JBrowse genome browser. MGD resources are freely available to the scientific community. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Correlates of picky eating and food neophobia in young children: a systematic review and meta-analysis.

PubMed

Cole, Natasha Chong; An, Ruopeng; Lee, Soo-Yeun; Donovan, Sharon M

2017-07-01

Picky eating behavior is prevalent among toddlers and may negatively impact their growth and development. This article summarizes the correlates of picky eating and food neophobia in young children, which were identified using a socio-ecological framework. A literature search was conducted in 4 electronic databases. Inclusion criteria were English-language peer-reviewed publications that investigated correlate(s) of picky eating or food neophobia in children aged ≤30 months. Correlates were categorized into 4 levels: cell, child, clan (family), and community/country. Thirty-two studies, which examined 89 correlates, were identified from the keyword searches of the databases and manual searches of the reference lists of included articles. The most examined correlates were characteristics related to the child (sex, weight, and dietary intake) and parent (feeding beliefs and practices). A meta-analysis estimated the prevalence of picky eating to be 22%. Each additional month of a child's age was associated with a 0.06 U increase in the Children's Eating Behavior Questionnaire food fussiness score. This review highlights the importance of investigating child-parent dyads and bidirectional feeding interactions and draws attention to the lack of picky eating research at the level of the cell and the community/country. © The Author(s) 2017. Published by Oxford University Press on behalf of the International Life Sciences Institute. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

78 FR 65644 - Privacy Act of 1974; System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-01

... Files Database. FHFA-OIG-2: FHFA-OIG Investigative & Evaluative Files Database. FHFA-OIG-3: FHFA-OIG Investigative & Evaluative MIS Database. FHFA-OIG-4: FHFA-OIG Hotline Database. FHFA-OIG-5: FHFA-OIG... & Evaluative Files Database, published at 76 FR 11465 (March 2, 2011), is being amended to eliminate all...

Development of a Dependency Theory Toolbox for Database Design.

DTIC Science & Technology

1987-12-01

published algorithms and theorems , and hand simulating these algorithms can be a tedious and error prone chore. Additionally, since the process of...to design and study relational databases exists in the form of published algorithms and theorems . However, hand simulating these algorithms can be a...published algorithms and theorems . Hand simulating these algorithms can be a tedious and error prone chore. Therefore, a toolbox of algorithms and

Automatic categorization of diverse experimental information in the bioscience literature

PubMed Central

2012-01-01

Background Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such as C. elegans and D. melanogaster to identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance. Results We successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction. Conclusions Our methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort. PMID:22280404

Automatic categorization of diverse experimental information in the bioscience literature.

PubMed

Fang, Ruihua; Schindelman, Gary; Van Auken, Kimberly; Fernandes, Jolene; Chen, Wen; Wang, Xiaodong; Davis, Paul; Tuli, Mary Ann; Marygold, Steven J; Millburn, Gillian; Matthews, Beverley; Zhang, Haiyan; Brown, Nick; Gelbart, William M; Sternberg, Paul W

2012-01-26

Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such as C. elegans and D. melanogaster to identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance. We successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction. Our methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort.

Rolling Deck to Repository (R2R): Collaborative Development of Linked Data for Oceanographic Research

NASA Astrophysics Data System (ADS)

Arko, Robert; Chandler, Cynthia; Stocks, Karen; Smith, Shawn; Clark, Paul; Shepherd, Adam; Moore, Carla; Beaulieu, Stace

2013-04-01

The Rolling Deck to Repository (R2R) program is developing infrastructure to ensure the underway sensor data from U.S. academic oceanographic research vessels are routinely and consistently documented, preserved in long-term archives, and disseminated to the science community. The entire R2R Catalog is published online as a Linked Data collection, making it easily accessible to encourage discovery and integration with data at other repositories. We are developing the R2R Linked Data collection with specific goals in mind: 1.) We facilitate data access and reuse by publishing the richest possible collection of resources to describe vessels, cruises, instruments, and datasets from the U.S. academic fleet, including data quality assessment results and clean trackline navigation; 2.) We facilitate data citation through the entire lifecycle from field acquisition to shoreside archiving to journal articles and global syntheses, by publishing Digital Object Identifiers (DOIs) for datasets and encoding them directly into our Linked Data resources; and 3.) We facilitate federation with other repositories such as the Biological and Chemical Oceanography Data Management Office (BCO-DMO), InterRidge Vents Database, and Index to Marine and Lacustrine Geological Samples (IMLGS), by reciprocal linking between RDF resources and supporting the RDF Query Language. R2R participates in the Ocean Data Interoperability Platform (ODIP), a joint European-U.S.-Australian partnership to facilitate the sharing of data and documentation across international borders. We publish our controlled vocabularies as a Simple Knowledge Organization System (SKOS) concept collection, and are working toward alignment with SeaDataNet and other community-standard terms using the NERC Vocabulary Server (NVS). http://rvdata.us/

CLSI-based transference of the CALIPER database of pediatric reference intervals from Abbott to Beckman, Ortho, Roche and Siemens Clinical Chemistry Assays: direct validation using reference samples from the CALIPER cohort.

PubMed

Estey, Mathew P; Cohen, Ashley H; Colantonio, David A; Chan, Man Khun; Marvasti, Tina Binesh; Randell, Edward; Delvin, Edgard; Cousineau, Jocelyne; Grey, Vijaylaxmi; Greenway, Donald; Meng, Qing H; Jung, Benjamin; Bhuiyan, Jalaluddin; Seccombe, David; Adeli, Khosrow

2013-09-01

The CALIPER program recently established a comprehensive database of age- and sex-stratified pediatric reference intervals for 40 biochemical markers. However, this database was only directly applicable for Abbott ARCHITECT assays. We therefore sought to expand the scope of this database to biochemical assays from other major manufacturers, allowing for a much wider application of the CALIPER database. Based on CLSI C28-A3 and EP9-A2 guidelines, CALIPER reference intervals were transferred (using specific statistical criteria) to assays performed on four other commonly used clinical chemistry platforms including Beckman Coulter DxC800, Ortho Vitros 5600, Roche Cobas 6000, and Siemens Vista 1500. The resulting reference intervals were subjected to a thorough validation using 100 reference specimens (healthy community children and adolescents) from the CALIPER bio-bank, and all testing centers participated in an external quality assessment (EQA) evaluation. In general, the transferred pediatric reference intervals were similar to those established in our previous study. However, assay-specific differences in reference limits were observed for many analytes, and in some instances were considerable. The results of the EQA evaluation generally mimicked the similarities and differences in reference limits among the five manufacturers' assays. In addition, the majority of transferred reference intervals were validated through the analysis of CALIPER reference samples. This study greatly extends the utility of the CALIPER reference interval database which is now directly applicable for assays performed on five major analytical platforms in clinical use, and should permit the worldwide application of CALIPER pediatric reference intervals. Copyright © 2013 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Troubleshooting Public Data Archiving: Suggestions to Increase Participation

PubMed Central

Roche, Dominique G.; Lanfear, Robert; Binning, Sandra A.; Haff, Tonya M.; Schwanz, Lisa E.; Cain, Kristal E.; Kokko, Hanna; Jennions, Michael D.; Kruuk, Loeske E. B.

2014-01-01

An increasing number of publishers and funding agencies require public data archiving (PDA) in open-access databases. PDA has obvious group benefits for the scientific community, but many researchers are reluctant to share their data publicly because of real or perceived individual costs. Improving participation in PDA will require lowering costs and/or increasing benefits for primary data collectors. Small, simple changes can enhance existing measures to ensure that more scientific data are properly archived and made publicly available: (1) facilitate more flexible embargoes on archived data, (2) encourage communication between data generators and re-users, (3) disclose data re-use ethics, and (4) encourage increased recognition of publicly archived data. PMID:24492920

Factors Influencing Suicide Behaviours in Immigrant and Ethno-Cultural Minority Groups: A Systematic Review.

PubMed

Lai, Daniel W L; Li, Lun; Daoust, Gabrielle D

2017-06-01

This paper reviews recent literature on factors influencing suicide behaviours, including thoughts, plans, and attempts, in immigrant and ethno-cultural minority groups, to inform a more comprehensive understanding of suicide behaviours in increasingly culturally diverse populations. Thirty-three studies published between 2002 and 2013 were identified through digital databases searches and included in this review. Analysis of study findings focused on impacts of ethno-cultural identity and acculturation, other cultural and immigration influences, and family and community supports on suicide behaviours. Policy, practice, and research recommendations are identified, to inform relevant suicide prevention efforts and enhance mental health supports for immigrant and ethno-cultural minority populations.

Arbuscular mycorrhizal symbiosis for sustainable cultivation of Chinese medicinal plants: a promising research direction.

PubMed

Zeng, Yan; Guo, Lan-Ping; Chen, Bao-Dong; Hao, Zhi-Peng; Wang, Ji-Yong; Huang, Lu-Qi; Yang, Guang; Cui, Xiu-Ming; Yang, Li; Wu, Zhao-Xiang; Chen, Mei-Lan; Zhang, Yan

2013-01-01

Arbuscular mycorrhizal (AM) are symbiotic systems in nature and have great significance in promoting the growth and stress resistance of medicinal plants. During our literature search from the Chinese Scientific Information Database (Chinese National Knowledge Infrastructure, CNKI) we obtained 65 articles with "AM fungi" and "medicinal plant" as the key words, which indicates that in China, research efforts on these topics have been increasing. The main purposes of this review are to discuss the effects of mycorrhiza on the active ingredients of Chinese medicinal plants in comparison with results obtained in other plants in studies conducted by the international research community, and to introduce works published in Chinese journals to international colleagues.

Community integration after traumatic brain injury: a systematic review of the clinical implications of measurement and service provision for older adults.

PubMed

Ritchie, Linda; Wright-St Clair, Valerie A; Keogh, Justin; Gray, Marion

2014-01-01

To explore the scope, reliability, and validity of community integration measures for older adults after traumatic brain injury (TBI). A search of peer-reviewed articles in English from 1990 to April 2011 was conducted using the EBSCO Health and Scopus databases. Search terms included were community integration, traumatic brain injury or TBI, 65 plus or older adults, and assessment. Forty-three eligible articles were identified, with 11 selected for full review using a standardized critical review method. Common community integration measures were identified and ranked for relevance and psychometric properties. Of the 43 eligible articles, studies reporting community integration outcomes post-TBI were identified and critically reviewed. Older adults' community integration needs post-TBI from high quality studies were summarized. There is a relative lack of evidence pertaining to older adults post-TBI, but indicators are that older adults have poorer outcomes than their younger counterparts. The Community Integration Questionnaire (CIQ) is the most widely used community integration measurement tool used in research for people with TBI. Because of some limitations, many studies have used the CIQ in conjunction with other measures to better quantify and/or monitor changes in community integration. Enhancing integration of older adults after TBI into their community of choice, with particular emphasis on social integration and quality of life, should be a primary rehabilitation goal. However, more research is needed to inform best practice guidelines to meet the needs of this growing TBI population. It is recommended that subjective tools, such as quality of life measures, are used in conjunction with well-established community integration measures, such as the CIQ, during the assessment process. Copyright © 2014 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Outcomes, costs and stakeholders' perspectives associated with the incorporation of community pharmacy services into the National Health Insurance System in Thailand: a systematic review.

PubMed

Asayut, Narong; Sookaneknun, Phayom; Chaiyasong, Surasak; Saramunee, Kritsanee

2018-02-01

Identify costs, outcomes and stakeholders' perspectives associated with incorporation of community pharmacy services into the Thai National Health Insurance System and their values to all stakeholders. Using a combination of search terms, a comprehensive literature search was performed using the Thai Journal Citation Index Centre, Health System Research Institute database, PubMed and references from recent reviews. Identified studies were published between January 2000 and December 2014. The review included publications in English and Thai on primary research undertaken in community pharmacies associated with the National Health Insurance System. Two independent authors performed study selection, data extraction and quality assessment. The literature search yielded 251 titles, with 18 satisfying the inclusion criteria. Clinical outcomes of community pharmacy services included control and reduction in blood pressure and blood sugar, improved adherence to medications, an increase in acceptance of interventions, and an increase in healthy behaviours. Thirty-three percentage of those at risk of diabetes and hypertension achieved normal blood sugar and blood pressure levels after being followed for 2-6 months by a community pharmacist. The cost of collaborative screening by community pharmacies and primary care units was US$ 4.5. Diabetes management costs were US$ 5.1-30.7. Community pharmacists reported high satisfaction rates. Stakeholders' perspectives revealed support for the community pharmacists' roles and the inclusion of community pharmacies as partners with the National Health Insurance System. Community pharmacy services improved outcomes for diabetic and hypertensive patients. This review supports the feasibility of incorporating community pharmacies into the Thai National Health System. © 2017 Royal Pharmaceutical Society.

Comparison of published and unpublished phase I clinical cancer trials: an analysis of the CliniclTrials.gov database.

PubMed

Shepshelovich, D; Goldvaser, H; Wang, L; Abdul Razak, A R

2017-12-13

Introduction The role of phase I cancer trials is constantly evolving and they are increasingly being used in 'go/no' decisions in drug development. As a result, there is a growing need to ensure trials are published when completed. There are limited data on the publication rate and the factors associated with publication in phase I trials. Methods The ClinicalTrials.gov database was searched for completed adult phase I cancer trials with reported results. PubMed was searched for matching publications published prior to April 1, 2017. Logistic regression was used to identify factors associated with unpublished trials. Linear regression was used to explore factors associated with time lag from study database lock to publication for published trials. Results The study cohort included 319 trials. 95 (30%) trials had no matching publication. Thirty (9%) trials were not published in abstract form as well. On multivariable analysis, the most significant factor associated with unpublished trials was industry funding (odds ratio 3.3, 95% confidence interval 1.7-6.6, p=0.019). For published trials, time lag between database lock and publication was longer by 10.9 months (standard error 3.6, p<0.001) for industry funded trials compared with medical center funded trials. Conclusions Timely publishing of early cancer clinical trials results remains unsatisfactory. Industry funded phase I cancer trials were more likely to remain unpublished, and were associated with a longer time lag from database lock to publication. Policies that promote transparency and data sharing in clinical trial research might improve accountability among industry and investigators and improve timely results publication.

Ménière's Disease: A CHEER Database Study of Local and Regional Patient Encounter and Procedure Patterns.

PubMed

Crowson, Matthew G; Schulz, Kristine; Parham, Kourosh; Vambutas, Andrea; Witsell, David; Lee, Walter T; Shin, Jennifer J; Pynnonen, Melissa A; Nguyen-Huynh, Anh; Ryan, Sheila E; Langman, Alan

2016-07-01

(1) Integrate practice-based patient encounters using the Dartmouth Atlas Medicare database to understand practice treatments for Ménière's disease (MD). (2) Describe differences in the practice patterns between academic and community providers for MD. Practice-based research database review. CHEER (Creating Healthcare Excellence through Education and Research) network academic and community providers. MD patient data were identified with ICD-9 and CPT codes. Demographics, unique visits, and procedures per patient were tabulated. The Dartmouth Atlas of Health Care was used to reference regional health care utilization. Statistical analysis included 1-way analyses of variance, bivariate linear regression, and Student's t tests, with significance set at P < .05. A total of 2071 unique patients with MD were identified from 8 academic and 10 community otolaryngology-head and neck surgery provider centers nationally. Average age was 56.5 years; 63.9% were female; and 91.4% self-reported white ethnicity. There was an average of 3.2 visits per patient. Western providers had the highest average visits per patient. Midwest providers had the highest average procedures per patient. Community providers had more visits per site and per patient than did academic providers. Academic providers had significantly more operative procedures per site (P = .0002) when compared with community providers. Health care service areas with higher total Medicare reimbursements per enrollee did not report significantly more operative procedures being performed. This is the first practice-based clinical research database study to describe MD practice patterns. We demonstrate that academic otolaryngology-head and neck surgery providers perform significantly more operative procedures than do community providers for MD, and we validate these data with an independent Medicare spending database. © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2015.

Filling the gap in functional trait databases: use of ecological hypotheses to replace missing data.

PubMed

Taugourdeau, Simon; Villerd, Jean; Plantureux, Sylvain; Huguenin-Elie, Olivier; Amiaud, Bernard

2014-04-01

Functional trait databases are powerful tools in ecology, though most of them contain large amounts of missing values. The goal of this study was to test the effect of imputation methods on the evaluation of trait values at species level and on the subsequent calculation of functional diversity indices at community level using functional trait databases. Two simple imputation methods (average and median), two methods based on ecological hypotheses, and one multiple imputation method were tested using a large plant trait database, together with the influence of the percentage of missing data and differences between functional traits. At community level, the complete-case approach and three functional diversity indices calculated from grassland plant communities were included. At the species level, one of the methods based on ecological hypothesis was for all traits more accurate than imputation with average or median values, but the multiple imputation method was superior for most of the traits. The method based on functional proximity between species was the best method for traits with an unbalanced distribution, while the method based on the existence of relationships between traits was the best for traits with a balanced distribution. The ranking of the grassland communities for their functional diversity indices was not robust with the complete-case approach, even for low percentages of missing data. With the imputation methods based on ecological hypotheses, functional diversity indices could be computed with a maximum of 30% of missing data, without affecting the ranking between grassland communities. The multiple imputation method performed well, but not better than single imputation based on ecological hypothesis and adapted to the distribution of the trait values for the functional identity and range of the communities. Ecological studies using functional trait databases have to deal with missing data using imputation methods corresponding to their specific needs and making the most out of the information available in the databases. Within this framework, this study indicates the possibilities and limits of single imputation methods based on ecological hypothesis and concludes that they could be useful when studying the ranking of communities for their functional diversity indices.

Filling the gap in functional trait databases: use of ecological hypotheses to replace missing data

PubMed Central

Taugourdeau, Simon; Villerd, Jean; Plantureux, Sylvain; Huguenin-Elie, Olivier; Amiaud, Bernard

2014-01-01

Functional trait databases are powerful tools in ecology, though most of them contain large amounts of missing values. The goal of this study was to test the effect of imputation methods on the evaluation of trait values at species level and on the subsequent calculation of functional diversity indices at community level using functional trait databases. Two simple imputation methods (average and median), two methods based on ecological hypotheses, and one multiple imputation method were tested using a large plant trait database, together with the influence of the percentage of missing data and differences between functional traits. At community level, the complete-case approach and three functional diversity indices calculated from grassland plant communities were included. At the species level, one of the methods based on ecological hypothesis was for all traits more accurate than imputation with average or median values, but the multiple imputation method was superior for most of the traits. The method based on functional proximity between species was the best method for traits with an unbalanced distribution, while the method based on the existence of relationships between traits was the best for traits with a balanced distribution. The ranking of the grassland communities for their functional diversity indices was not robust with the complete-case approach, even for low percentages of missing data. With the imputation methods based on ecological hypotheses, functional diversity indices could be computed with a maximum of 30% of missing data, without affecting the ranking between grassland communities. The multiple imputation method performed well, but not better than single imputation based on ecological hypothesis and adapted to the distribution of the trait values for the functional identity and range of the communities. Ecological studies using functional trait databases have to deal with missing data using imputation methods corresponding to their specific needs and making the most out of the information available in the databases. Within this framework, this study indicates the possibilities and limits of single imputation methods based on ecological hypothesis and concludes that they could be useful when studying the ranking of communities for their functional diversity indices. PMID:24772273

dSED: A database tool for modeling sediment early diagenesis

NASA Astrophysics Data System (ADS)

Katsev, S.; Rancourt, D. G.; L'Heureux, I.

2003-04-01

Sediment early diagenesis reaction transport models (RTMs) are becoming powerful tools in providing kinetic descriptions of the metal and nutrient diagenetic cycling in marine, lacustrine, estuarine, and other aquatic sediments, as well as of exchanges with the water column. Whereas there exist several good database/program combinations for thermodynamic equilibrium calculations in aqueous systems, at present there exist no database tools for classification and analysis of the kinetic data essential to RTM development. We present a database tool that is intended to serve as an online resource for information about chemical reactions, solid phase and solute reactants, sorption reactions, transport mechanisms, and kinetic and equilibrium parameters that are relevant to sediment diagenesis processes. The list of reactive substances includes but is not limited to organic matter, Fe and Mn oxides and oxyhydroxides, sulfides and sulfates, calcium, iron, and manganese carbonates, phosphorus-bearing minerals, and silicates. Aqueous phases include dissolved carbon dioxide, oxygen, methane, hydrogen sulfide, sulfate, nitrate, phosphate, some organic compounds, and dissolved metal species. A number of filters allow extracting information according to user-specified criteria, e.g., about a class of substances contributing to the cycling of iron. The database also includes bibliographic information about published diagenetic models and the reactions and processes that they consider. At the time of preparing this abstract, dSED contained 128 reactions and 12 pre-defined filters. dSED is maintained by the Lake Sediment Structure and Evolution (LSSE) group at the University of Ottawa (www.science.uottawa.ca/LSSE/dSED) and we invite input from the geochemical community.

Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain.

PubMed

Matthes, Michaela; Preusse, Martin; Zhang, Jingzhong; Schechter, Julia; Mayer, Daniela; Lentes, Bernd; Theis, Fabian; Prakash, Nilima; Wurst, Wolfgang; Trümbach, Dietrich

2014-01-01

The study of developmental processes in the mouse and other vertebrates includes the understanding of patterning along the anterior-posterior, dorsal-ventral and medial- lateral axis. Specifically, neural development is also of great clinical relevance because several human neuropsychiatric disorders such as schizophrenia, autism disorders or drug addiction and also brain malformations are thought to have neurodevelopmental origins, i.e. pathogenesis initiates during childhood and adolescence. Impacts during early neurodevelopment might also predispose to late-onset neurodegenerative disorders, such as Parkinson's disease. The neural tube develops from its precursor tissue, the neural plate, in a patterning process that is determined by compartmentalization into morphogenetic units, the action of local signaling centers and a well-defined and locally restricted expression of genes and their interactions. While public databases provide gene expression data with spatio-temporal resolution, they usually neglect the genetic interactions that govern neural development. Here, we introduce Mouse IDGenes, a reference database for genetic interactions in the developing mouse brain. The database is highly curated and offers detailed information about gene expressions and the genetic interactions at the developing mid-/hindbrain boundary. To showcase the predictive power of interaction data, we infer new Wnt/β-catenin target genes by machine learning and validate one of them experimentally. The database is updated regularly. Moreover, it can easily be extended by the research community. Mouse IDGenes will contribute as an important resource to the research on mouse brain development, not exclusively by offering data retrieval, but also by allowing data input. http://mouseidgenes.helmholtz-muenchen.de. © The Author(s) 2014. Published by Oxford University Press.

Transportation-markings database : composite categories, classification & index. Part I 5, Volume 3, additional studies

DOT National Transportation Integrated Search

2006-01-01

The Transportation-Markings Database project (within the T-M Monograph Series) began in 1997 with the publishing of the initial component, Transportation-Markings Database: Marine. That study was joined by T-M Database: Traffic Control Devices (1998)...

Development of a Publicly Available, Comprehensive Database of Fiber and Health Outcomes: Rationale and Methods

PubMed Central

Livingston, Kara A.; Chung, Mei; Sawicki, Caleigh M.; Lyle, Barbara J.; Wang, Ding Ding; Roberts, Susan B.; McKeown, Nicola M.

2016-01-01

Background Dietary fiber is a broad category of compounds historically defined as partially or completely indigestible plant-based carbohydrates and lignin with, more recently, the additional criteria that fibers incorporated into foods as additives should demonstrate functional human health outcomes to receive a fiber classification. Thousands of research studies have been published examining fibers and health outcomes. Objectives (1) Develop a database listing studies testing fiber and physiological health outcomes identified by experts at the Ninth Vahouny Conference; (2) Use evidence mapping methodology to summarize this body of literature. This paper summarizes the rationale, methodology, and resulting database. The database will help both scientists and policy-makers to evaluate evidence linking specific fibers with physiological health outcomes, and identify missing information. Methods To build this database, we conducted a systematic literature search for human intervention studies published in English from 1946 to May 2015. Our search strategy included a broad definition of fiber search terms, as well as search terms for nine physiological health outcomes identified at the Ninth Vahouny Fiber Symposium. Abstracts were screened using a priori defined eligibility criteria and a low threshold for inclusion to minimize the likelihood of rejecting articles of interest. Publications then were reviewed in full text, applying additional a priori defined exclusion criteria. The database was built and published on the Systematic Review Data Repository (SRDR™), a web-based, publicly available application. Conclusions A fiber database was created. This resource will reduce the unnecessary replication of effort in conducting systematic reviews by serving as both a central database archiving PICO (population, intervention, comparator, outcome) data on published studies and as a searchable tool through which this data can be extracted and updated. PMID:27348733

Publishing with a Purpose: Caring for Our Community.

ERIC Educational Resources Information Center

Ruggieri, Colleen A.

2001-01-01

Describes lessons and units that allow the author's high school English students to make important connections with members of their community, publish their efforts, and thus bridge the gap between young adults and their communities. Describes a "literary cookbook" (published and distributed in their community) in which each student wrote one…

The Influence of Community Health Resources on Effectiveness and Sustainability of Community and Lay Health Worker Programs in Lower-Income Countries: A Systematic Review

PubMed Central

Pool, Robert

2017-01-01

Background Despite the availability of practical knowledge and effective interventions required to reduce priority health problems in low-income countries, poor and vulnerable populations are often not reached. One possible solution to this problem is the use of Community or Lay Health Workers (CLHWs). So far, however, the development of sustainability in CLHW programs has failed and high attrition rates continue to pose a challenge. We propose that the roles and interests which support community health work should emerge directly from the way in which health is organized at community level. This review explores the evidence available to assess if increased levels of integration of community health resources in CLHW programs indeed lead to higher program effectiveness and sustainability. Methods and Findings This review includes peer-reviewed articles which meet three eligibility criteria: 1) specific focus on CLHWs or equivalent; 2) randomized, quasi-randomized, before/after methodology or substantial descriptive assessment; and 3) description of a community or peer intervention health program located in a low- or middle-income country. Literature searches using various article databases led to 2930 hits, of which 359 articles were classified. Of these, 32 articles were chosen for extensive review, complemented by analysis of the results of 15 other review studies. Analysis was conducted using an excel based data extraction form. Because results showed that no quantitative data was published, a descriptive synthesis was conducted. The review protocol was not proactively registered. Findings show minimal inclusion of even basic community level indicators, such as the degree to which the program is a community initiative, community input in the program or training, the background and history of CLHW recruits, and the role of the community in motivation and retention. Results show that of the 32 studies, only one includes one statistical measure of community integration. As a result of this lack of data we are unable to derive an evidence-based conclusion to our propositions. Instead, our results indicate a larger problem, namely the complete absence of indicators measuring community relationships with the programs studied. Studies pay attention only to gender and peer roles, along with limited demographic information about the recruits. The historicity of the health worker and the community s/he belongs to is absent in most studies reviewed. None of the studies discuss or test for the possibility that motivation emanates from the community. Only a few studies situate attrition and retention as an issue enabled by the community. The results were limited by a focus on low-income countries and English, peer-reviewed published articles only. Conclusion Published, peer-reviewed studies evaluating the effectiveness and sustainability of CLHW interventions in health programs have not yet adequately tested for the potential of utilizing existing community health roles or social networks for the development of effective and sustainable (retentive) CLHW programs. Community relationships are generally seen as a “black box” represented by an interchangeable CLHW labor unit. This disconnect from community relationships and resources may have led to a systematic and chronic undervaluing of community agency in explanations of programmatic effectiveness and sustainability. PMID:28095475

Feasibility of combining two aquatic benthic macroinvertebrate community databases for water-quality assessment

USGS Publications Warehouse

Lenz, Bernard N.

1997-01-01

An important part of the U.S. Geological Survey's (USGS) National Water-Quality Assessment (NAWQA) Program is the analysis of existing data in each of the NAWQA study areas. The Wisconsin Department of Natural Resources (WDNR) has an extensive aquatic benthic macroinvertebrate communities in streams (benthic invertebrates) database maintained by the University of Wisconsin-Stevens Point. This database has data which date back to 1984 and includes data from streams within the Western Lake Michigan Drainages (WMIC) study area (fig. 1). This report looks at the feasibility of USGS scientists supplementing the data they collect with data from the WDNR database when assessing water quality in the study area.

WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions.

PubMed

Karr, Jonathan R; Phillips, Nolan C; Covert, Markus W

2014-01-01

Mechanistic 'whole-cell' models are needed to develop a complete understanding of cell physiology. However, extracting biological insights from whole-cell models requires running and analyzing large numbers of simulations. We developed WholeCellSimDB, a database for organizing whole-cell simulations. WholeCellSimDB was designed to enable researchers to search simulation metadata to identify simulations for further analysis, and quickly slice and aggregate simulation results data. In addition, WholeCellSimDB enables users to share simulations with the broader research community. The database uses a hybrid relational/hierarchical data format architecture to efficiently store and retrieve both simulation setup metadata and results data. WholeCellSimDB provides a graphical Web-based interface to search, browse, plot and export simulations; a JavaScript Object Notation (JSON) Web service to retrieve data for Web-based visualizations; a command-line interface to deposit simulations; and a Python API to retrieve data for advanced analysis. Overall, we believe WholeCellSimDB will help researchers use whole-cell models to advance basic biological science and bioengineering. http://www.wholecellsimdb.org SOURCE CODE REPOSITORY: URL: http://github.com/CovertLab/WholeCellSimDB. © The Author(s) 2014. Published by Oxford University Press.

CoCoMac 2.0 and the future of tract-tracing databases

PubMed Central

Bakker, Rembrandt; Wachtler, Thomas; Diesmann, Markus

2012-01-01

The CoCoMac database contains the results of several hundred published axonal tract-tracing studies in the macaque monkey brain. The combined results are used for constructing the macaque macro-connectome. Here we discuss the redevelopment of CoCoMac and compare it to six connectome-related projects: two online resources that provide full access to raw tracing data in rodents, a connectome viewer for advanced 3D graphics, a partial but highly detailed rat connectome, a brain data management system that generates custom connectivity matrices, and a software package that covers the complete pipeline from connectivity data to large-scale brain simulations. The second edition of CoCoMac features many enhancements over the original. For example, a search wizard is provided for full access to all tables and their nested dependencies. Connectivity matrices can be computed on demand in a user-selected nomenclature. A new data entry system is available as a preview, and is to become a generic solution for community-driven data entry in manually collated databases. We conclude with the question whether neuronal tracing will remain the gold standard to uncover the wiring of brains, thereby highlighting developments in human connectome construction, tracer substances, polarized light imaging, and serial block-face scanning electron microscopy. PMID:23293600

CoCoMac 2.0 and the future of tract-tracing databases.

PubMed

Bakker, Rembrandt; Wachtler, Thomas; Diesmann, Markus

2012-01-01

The CoCoMac database contains the results of several hundred published axonal tract-tracing studies in the macaque monkey brain. The combined results are used for constructing the macaque macro-connectome. Here we discuss the redevelopment of CoCoMac and compare it to six connectome-related projects: two online resources that provide full access to raw tracing data in rodents, a connectome viewer for advanced 3D graphics, a partial but highly detailed rat connectome, a brain data management system that generates custom connectivity matrices, and a software package that covers the complete pipeline from connectivity data to large-scale brain simulations. The second edition of CoCoMac features many enhancements over the original. For example, a search wizard is provided for full access to all tables and their nested dependencies. Connectivity matrices can be computed on demand in a user-selected nomenclature. A new data entry system is available as a preview, and is to become a generic solution for community-driven data entry in manually collated databases. We conclude with the question whether neuronal tracing will remain the gold standard to uncover the wiring of brains, thereby highlighting developments in human connectome construction, tracer substances, polarized light imaging, and serial block-face scanning electron microscopy.

PlasmoGEM, a database supporting a community resource for large-scale experimental genetics in malaria parasites.

PubMed

Schwach, Frank; Bushell, Ellen; Gomes, Ana Rita; Anar, Burcu; Girling, Gareth; Herd, Colin; Rayner, Julian C; Billker, Oliver

2015-01-01

The Plasmodium Genetic Modification (PlasmoGEM) database (http://plasmogem.sanger.ac.uk) provides access to a resource of modular, versatile and adaptable vectors for genome modification of Plasmodium spp. parasites. PlasmoGEM currently consists of >2000 plasmids designed to modify the genome of Plasmodium berghei, a malaria parasite of rodents, which can be requested by non-profit research organisations free of charge. PlasmoGEM vectors are designed with long homology arms for efficient genome integration and carry gene specific barcodes to identify individual mutants. They can be used for a wide array of applications, including protein localisation, gene interaction studies and high-throughput genetic screens. The vector production pipeline is supported by a custom software suite that automates both the vector design process and quality control by full-length sequencing of the finished vectors. The PlasmoGEM web interface allows users to search a database of finished knock-out and gene tagging vectors, view details of their designs, download vector sequence in different formats and view available quality control data as well as suggested genotyping strategies. We also make gDNA library clones and intermediate vectors available for researchers to produce vectors for themselves. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

mirPub: a database for searching microRNA publications.

PubMed

Vergoulis, Thanasis; Kanellos, Ilias; Kostoulas, Nikos; Georgakilas, Georgios; Sellis, Timos; Hatzigeorgiou, Artemis; Dalamagas, Theodore

2015-05-01

Identifying, amongst millions of publications available in MEDLINE, those that are relevant to specific microRNAs (miRNAs) of interest based on keyword search faces major obstacles. References to miRNA names in the literature often deviate from standard nomenclature for various reasons, since even the official nomenclature evolves. For instance, a single miRNA name may identify two completely different molecules or two different names may refer to the same molecule. mirPub is a database with a powerful and intuitive interface, which facilitates searching for miRNA literature, addressing the aforementioned issues. To provide effective search services, mirPub applies text mining techniques on MEDLINE, integrates data from several curated databases and exploits data from its user community following a crowdsourcing approach. Other key features include an interactive visualization service that illustrates intuitively the evolution of miRNA data, tag clouds summarizing the relevance of publications to particular diseases, cell types or tissues and access to TarBase 6.0 data to oversee genes related to miRNA publications. mirPub is freely available at http://www.microrna.gr/mirpub/. vergoulis@imis.athena-innovation.gr or dalamag@imis.athena-innovation.gr Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

The BIG Data Center: from deposition to integration to translation.

PubMed

2017-01-04

Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centralized resource housing genome-scale data with particular focus on economically important animals and plants, (v) Methylation Bank, an integrated database of whole-genome single-base resolution methylomes and (vi) Science Wikis, a central access point for biological wikis developed for community annotations. The BIG Data Center is dedicated to constructing and maintaining biological databases through big data integration and value-added curation, conducting basic research to translate big data into big knowledge and providing freely open access to a variety of data resources in support of worldwide research activities in both academia and industry. All of these resources are publicly available and can be found at http://bigd.big.ac.cn. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

CHOmine: an integrated data warehouse for CHO systems biology and modeling

PubMed Central

Hanscho, Michael; Ruckerbauer, David E.; Zanghellini, Jürgen; Borth, Nicole

2017-01-01

Abstract The last decade has seen a surge in published genome-scale information for Chinese hamster ovary (CHO) cells, which are the main production vehicles for therapeutic proteins. While a single access point is available at www.CHOgenome.org, the primary data is distributed over several databases at different institutions. Currently research is frequently hampered by a plethora of gene names and IDs that vary between published draft genomes and databases making systems biology analyses cumbersome and elaborate. Here we present CHOmine, an integrative data warehouse connecting data from various databases and links to other ones. Furthermore, we introduce CHOmodel, a web based resource that provides access to recently published CHO cell line specific metabolic reconstructions. Both resources allow to query CHO relevant data, find interconnections between different types of data and thus provides a simple, standardized entry point to the world of CHO systems biology. Database URL: http://www.chogenome.org PMID:28605771

Palaeo sea-level and ice-sheet databases: problems, strategies and perspectives

NASA Astrophysics Data System (ADS)

Rovere, Alessio; Düsterhus, André; Carlson, Anders; Barlow, Natasha; Bradwell, Tom; Dutton, Andrea; Gehrels, Roland; Hibbert, Fiona; Hijma, Marc; Horton, Benjamin; Klemann, Volker; Kopp, Robert; Sivan, Dorit; Tarasov, Lev; Törnqvist, Torbjorn

2016-04-01

Databases of palaeoclimate data have driven many major developments in understanding the Earth system. The measurement and interpretation of palaeo sea-level and ice-sheet data that form such databases pose considerable challenges to the scientific communities that use them for further analyses. In this paper, we build on the experience of the PALSEA (PALeo constraints on SEA level rise) community, which is a working group inside the PAGES (Past Global Changes) project, to describe the challenges and best strategies that can be adopted to build a self-consistent and standardised database of geological and geochemical data related to palaeo sea levels and ice sheets. Our aim in this paper is to identify key points that need attention and subsequent funding when undertaking the task of database creation. We conclude that any sea-level or ice-sheet database must be divided into three instances: i) measurement; ii) interpretation; iii) database creation. Measurement should include postion, age, description of geological features, and quantification of uncertainties. All must be described as objectively as possible. Interpretation can be subjective, but it should always include uncertainties and include all the possible interpretations, without unjustified a priori exclusions. We propose that, in the creation of a database, an approach based on Accessibility, Transparency, Trust, Availability, Continued updating, Completeness and Communication of content (ATTAC3) must be adopted. Also, it is essential to consider the community structure that creates and benefits of a database. We conclude that funding sources should consider to address not only the creation of original data in specific research-question oriented projects, but also include the possibility to use part of the funding for IT-related and database creation tasks, which are essential to guarantee accessibility and maintenance of the collected data.

[German general and visceral surgery: positioning within the international scientific community].

PubMed

Welsch, T; Wente, M N; Dralle, H; Neuhaus, P; Schumpelick, V; Siewert, J R; Büchler, M W

2010-04-01

Assessment of scientific performance is critical for selection committees and research funding. The present work evaluated the standing of German surgical research within the international community. A database analysis was performed in December 2009 using the ISI Web of Science. The highest impact factor of surgical journals is currently 8.460 with a median impact of all journals of 1.369. Leading academic surgeons have an h-index of more than 60. German surgeons are within the top five leading researchers in the fields of surgery for esophageal and pancreatic cancer, thyroid, hernia, and liver/kidney transplantation. Among the 50 institutions with most publications on a particular topic, 4-5 German centers are mostly represented. The top positions are in total decisively occupied by leading universities in the USA. On the basis of scientific parameters German surgical research can compete with leading international centers in certain fields, but should aim to increase the overall impact of research by publishing more in journals with above average impact factors.

[Tendencies of studies addressing the eldest individuals of aged population in the community: a (inter)national systematic review].

PubMed

Rosset, Idiane; Pedrazzi, Elizandra Cristina; Roriz-Cruz, Matheus; de Morais, Eliane Pinheiro; Rodrigues, Rosalina Aparecida Partezani

2011-03-01

The purpose of this study was to identify and analyze the tendencies and types of studies published in Brazil and abroad, involving elders aged>80 years, living in the community. A systematic review of national literature was performed using the LILACS and SciELO databases, and PUBMED and EMBASE for international literature, covering publications of the last two decades. Twelve national and 162 international references were selected. Biological sciences were the prevalent area both at the national (50%) and international (74.1%) levels. All national studies were observational, 91.7% of which were cross-sectional. Of the international studies, 93.3% were observational, 48.1% of which were cross-sectional and 37.6% were cohort studies. The United States were the country responsible for 41.4% of all international publications. Brazil and China were the only developing countries with international publications. Despite the significant number of international scientific publications as of 2005, this fact has not been observed at the national level.

Municipal solid waste management: identification and analysis of engineering indexes representing demand and costs generated in virtuous Italian communities.

PubMed

Gamberini, R; Del Buono, D; Lolli, F; Rimini, B

2013-11-01

The definition and utilisation of engineering indexes in the field of Municipal Solid Waste Management (MSWM) is an issue of interest for technicians and scientists, which is widely discussed in literature. Specifically, the availability of consolidated engineering indexes is useful when new waste collection services are designed, along with when their performance is evaluated after a warm-up period. However, most published works in the field of MSWM complete their study with an analysis of isolated case studies. Conversely, decision makers require tools for information collection and exchange in order to trace the trends of these engineering indexes in large experiments. In this paper, common engineering indexes are presented and their values analysed in virtuous Italian communities, with the aim of contributing to the creation of a useful database whose data could be used during experiments, by indicating examples of MSWM demand profiles and the costs required to manage them. Copyright © 2013 Elsevier Ltd. All rights reserved.

CD-ROMS Step by Step.

ERIC Educational Resources Information Center

Nath, Herbert

This manual consists of sets of guides for six CD-ROM databases: (1) ABI/INFORM, a business administration CD-ROM published by UMI; (2) Books in Print (an outstanding tool for compiling bibliographies on any subject); (3) ERIC (Educational Resources Information Center), an education database in the version published by SilverPlatter; (4) MLA, a…

Open resource metagenomics: a model for sharing metagenomic libraries.

PubMed

Neufeld, J D; Engel, K; Cheng, J; Moreno-Hagelsieb, G; Rose, D R; Charles, T C

2011-11-30

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM(2)BL [1]). The CM(2)BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project.

Open resource metagenomics: a model for sharing metagenomic libraries

PubMed Central

Neufeld, J.D.; Engel, K.; Cheng, J.; Moreno-Hagelsieb, G.; Rose, D.R.; Charles, T.C.

2011-01-01

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM2BL [1]). The CM2BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project. PMID:22180823

Roles, responsibilities and characteristics of lay community health workers involved in diabetes prevention programmes: A systematic review

PubMed Central

Oldenburg, Brian

2017-01-01

Aim To examine the characteristics of community health workers (CHWs) involved in diabetes prevention programmes (DPPs) and their contributions to expected outcomes. Methods Electronic databases including PubMed-MEDLINE, EBSCOHost, and SCOPUS/EMBASE were searched for studies published between January 2000 and March 2016. All studies that used CHWs to implement DPP in ≥18-year-old participants without diabetes but at high risk for developing the condition, irrespective of the study design, setting or outcomes measured, were included. Results were synthesized narratively. Results Forty papers of 30 studies were identified. Studies were mainly community-based and conducted in minority populations in USA. Sample sizes ranged from 20 participants in a single community to 2369 participants in 46 communities. Although CHWs were generally from the local community, their qualifications, work experience and training received differed across studies. Overall the training was culturally sensitive and/or appropriate, covering topics such as the importance of good nutrition and the benefits of increased physical activity, communication and leadership. CHWs delivered a variety of interventions and also screened or recruited participants. The shared culture and language between CHWs and participants likely contributed to better programme implementation and successful outcomes. Conclusions The complexity of DPPs and the diverse CHW roles preclude attributing specific outcomes to CHW involvement. Nevertheless, documenting potential CHW roles and the relevant training required may optimise CHW contributions and facilitate their involvement in DPPs in the future. PMID:29216263

Roles, responsibilities and characteristics of lay community health workers involved in diabetes prevention programmes: A systematic review.

PubMed

Hill, Jillian; Peer, Nasheeta; Oldenburg, Brian; Kengne, Andre Pascale

2017-01-01

To examine the characteristics of community health workers (CHWs) involved in diabetes prevention programmes (DPPs) and their contributions to expected outcomes. Electronic databases including PubMed-MEDLINE, EBSCOHost, and SCOPUS/EMBASE were searched for studies published between January 2000 and March 2016. All studies that used CHWs to implement DPP in ≥18-year-old participants without diabetes but at high risk for developing the condition, irrespective of the study design, setting or outcomes measured, were included. Results were synthesized narratively. Forty papers of 30 studies were identified. Studies were mainly community-based and conducted in minority populations in USA. Sample sizes ranged from 20 participants in a single community to 2369 participants in 46 communities. Although CHWs were generally from the local community, their qualifications, work experience and training received differed across studies. Overall the training was culturally sensitive and/or appropriate, covering topics such as the importance of good nutrition and the benefits of increased physical activity, communication and leadership. CHWs delivered a variety of interventions and also screened or recruited participants. The shared culture and language between CHWs and participants likely contributed to better programme implementation and successful outcomes. The complexity of DPPs and the diverse CHW roles preclude attributing specific outcomes to CHW involvement. Nevertheless, documenting potential CHW roles and the relevant training required may optimise CHW contributions and facilitate their involvement in DPPs in the future.

Empowered genome community: leveraging a bioinformatics platform as a citizen-scientist collaboration tool.

PubMed

Wendelsdorf, Katherine; Shah, Sohela

2015-09-01

There is on-going effort in the biomedical research community to leverage Next Generation Sequencing (NGS) technology to identify genetic variants that affect our health. The main challenge facing researchers is getting enough samples from individuals either sick or healthy - to be able to reliably identify the few variants that are causal for a phenotype among all other variants typically seen among individuals. At the same time, more and more individuals are having their genome sequenced either out of curiosity or to identify the cause of an illness. These individuals may benefit from of a way to view and understand their data. QIAGEN's Ingenuity Variant Analysis is an online application that allows users with and without extensive bioinformatics training to incorporate information from published experiments, genetic databases, and a variety of statistical models to identify variants, from a long list of candidates, that are most likely causal for a phenotype as well as annotate variants with what is already known about them in the literature and databases. Ingenuity Variant Analysis is also an information sharing platform where users may exchange samples and analyses. The Empowered Genome Community (EGC) is a new program in which QIAGEN is making this on-line tool freely available to any individual who wishes to analyze their own genetic sequence. EGC members are then able to make their data available to other Ingenuity Variant Analysis users to be used in research. Here we present and describe the Empowered Genome Community in detail. We also present a preliminary, proof-of-concept study that utilizes the 200 genomes currently available through the EGC. The goal of this program is to allow individuals to access and understand their own data as well as facilitate citizen-scientist collaborations that can drive research forward and spur quality scientific dialogue in the general public.

EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.

PubMed

Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra; Pereira, Emiliano; Schnetzer, Julia; Arvanitidis, Christos; Jensen, Lars Juhl

2016-01-01

The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have therefore developed an interactive annotation tool, EXTRACT, which helps curators identify and extract standard-compliant terms for annotation of metagenomic records and other samples. Behind its web-based user interface, the system combines published methods for named entity recognition of environment, organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, well documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Comparison of fully manual and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15-25% and helps curators to detect terms that would otherwise have been missed. Database URL: https://extract.hcmr.gr/. © The Author(s) 2016. Published by Oxford University Press.

PCDDB: new developments at the Protein Circular Dichroism Data Bank.

PubMed

Whitmore, Lee; Miles, Andrew John; Mavridis, Lazaros; Janes, Robert W; Wallace, B A

2017-01-04

The Protein Circular Dichroism Data Bank (PCDDB) has been in operation for more than 5 years as a public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. Since its inception, many improvements and new developments have been made in data display, searching algorithms, data formats, data content, auxillary information, and validation techniques, as well as, of course, an increase in the number of holdings. It provides a site (http://pcddb.cryst.bbk.ac.uk) for authors to deposit experimental data as well as detailed information on methods and calculations associated with published work. It also includes links for each entry to bioinformatics databases. The data are freely available to accessors either as single files or as complete data bank downloads. The PCDDB has found broad usage by the structural biology, bioinformatics, analytical and pharmaceutical communities, and has formed the basis for new software and methods developments. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Primary care teams in Ireland: a qualitative mapping review of Irish grey and published literature.

PubMed

O'Sullivan, M; Cullen, W; MacFarlane, A

2015-03-01

The Irish government published its primary care strategy, Primary Care: A New Direction in 2001. Progress with the implementation of Primary care teams is modest. The aim of this paper is to map the Irish grey literature and peer-reviewed publications to determine what research has been carried out in relation to primary care teams, the reform process and interdisciplinary working in primary care in Ireland. This scoping review employed three methods: a review of Web of Science, Medline and Embase databases, an email survey of researchers across academic institutions, the HSE and independent researchers and a review of Lenus and the Health Well repository. N = 123 outputs were identified. N = 14 were selected for inclusion. A thematic analysis was undertaken. Common themes identified were resources, GP participation, leadership, clarity regarding roles in primary care teams, skills and knowledge for primary care team working, communication and community. There is evidence of significant problems that disrupt team formation and functioning that warrants more comprehensive research.

Spirituality, religion, and health: over the last 15 years of field research (1999-2013).

PubMed

Lucchetti, Giancarlo; Lucchetti, Alessandra Lamas Granero

2014-01-01

Although several studies have examined the contribution of specific countries, journals, and authors in different scientific disciplines, little is known about the contribution of different world countries, journals, and authors to scientific research in the field of "Spirituality, religion, and health" (S/R). The present study aims to analyze the last 15 years of research in the field of spirituality and religiousness (S/R) through a bibliometric analysis. Using the Pubmed database, we retrieved all articles related to S/R field for the period 1999-2013. We then estimated the total number of publications, number of articles published per year, articles published per country, journals with most publications in S/R field, most productive authors, and most used keywords. We found a growth of publications in the last years, most from the United States and the United Kingdom and published in the English language. Noteworthy, some developing countries such as India, Brazil, Israel, and Iran are at higher positions in this list. The S/R articles were published in journals embracing all fields of research, including high impact journals. In the present study, we took a closer look at the field of "Spirituality, religion, and health," showing that this field of research has been constantly growing and consolidating in the scientific community.

Health effects of training laypeople to deliver emergency care in underserviced populations: a systematic review protocol.

PubMed

Orkin, Aaron M; Curran, Jeffrey D; Fortune, Melanie K; McArthur, Allison; Mew, Emma J; Ritchie, Stephen D; Van de Velde, Stijn; VanderBurgh, David

2016-05-18

The Disease Control Priorities Project recommends emergency care training for laypersons in low-resource settings, but evidence for these interventions has not yet been systematically reviewed. This review will identify the individual and community health effects of educating laypeople to deliver prehospital emergency care interventions in low-resource settings. This systematic review addresses the following question: in underserviced populations and low-resource settings (P), does first aid or emergency care training or education for laypeople (I) confer any individual or community health benefit for emergency health conditions (O), in comparison with no training or other forms of education (C)? We restrict this review to studies reporting quantitatively measurable outcomes, and search 12 electronic bibliographic databases and grey literature sources. A team of expert content and methodology reviewers will conduct title and abstract screening and full-text review, using a custom-built online platform. Two investigators will independently extract methodological variables and outcomes related to patient-level morbidity and mortality and community-level effects on resilience or emergency care capacity. Two investigators will independently assess external validity, selection bias, performance bias, measurement bias, attrition bias and confounding. We will summarise the findings using a narrative approach to highlight similarities and differences between the gathered studies. Formal ethical approval is not required. The results will be disseminated through a peer-reviewed publication and knowledge translation strategy. CRD42014009685. 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/

Spectral information (gas, liquid and solid phase from EUV-VUV-UV-Vis-NIR) and related data (e.g. information concerning publications on quantum yield studies or photolysis studies) from published papers

NASA Astrophysics Data System (ADS)

Noelle, A.; Hartmann, G. K.; Martin-Torres, F. J.

2010-05-01

The science-softCon "UV/Vis+ Spectra Data Base" is a non-profit project established in August 2000 and is operated in accordance to the "Open Access" definitions and regulations of the CSPR Assessment Panel on Scientific Data and Information (International Council for Science, 2004, HYPERLINK "http://www.science-softcon.de/spectra/cspr.pdf" ICSU Report of the CSPR Assessment Panel on Data and Information; ISBN 0-930357-60-4). The on-line database contains currently about 5600 spectra (from low to very high resolution, at different temperatures and pressures) and datasheets (metadata) of about 850 substances. Additional spectra/datasheets will be added continuously. In addition more than 250 links to on-line free available original publications are provided. The interdisciplinary of this photochemistry database provides a good interaction between different research areas. So, this database is an excellent tool for scientists who investigate on different fields such as atmospheric chemistry, astrophysics, agriculture, analytical chemistry, environmental chemistry, medicine, remote sensing, etc. To ensure the high quality standard of the fast growing UV/Vis+ Spectra Data Base an international "Scientific Advisory Group" (SAG) has been established in 2004. Because of the importance of maintenance of the database the support of the scientific community is crucial. Therefore we would like to encourage all scientists to support this data compilation project thru the provision of new or missing spectral data and information.

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information

NASA Astrophysics Data System (ADS)

Sushko, Iurii; Novotarskyi, Sergii; Körner, Robert; Pandey, Anil Kumar; Rupp, Matthias; Teetz, Wolfram; Brandmaier, Stefan; Abdelaziz, Ahmed; Prokopenko, Volodymyr V.; Tanchuk, Vsevolod Y.; Todeschini, Roberto; Varnek, Alexandre; Marcou, Gilles; Ertl, Peter; Potemkin, Vladimir; Grishina, Maria; Gasteiger, Johann; Schwab, Christof; Baskin, Igor I.; Palyulin, Vladimir A.; Radchenko, Eugene V.; Welsh, William J.; Kholodovych, Vladyslav; Chekmarev, Dmitriy; Cherkasov, Artem; Aires-de-Sousa, Joao; Zhang, Qing-You; Bender, Andreas; Nigsch, Florian; Patiny, Luc; Williams, Antony; Tkachenko, Valery; Tetko, Igor V.

2011-06-01

The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records. The OCHEM database is based on the wiki principle and focuses primarily on the quality and verifiability of the data. The database is tightly integrated with the modeling framework, which supports all the steps required to create a predictive model: data search, calculation and selection of a vast variety of molecular descriptors, application of machine learning methods, validation, analysis of the model and assessment of the applicability domain. As compared to other similar systems, OCHEM is not intended to re-implement the existing tools or models but rather to invite the original authors to contribute their results, make them publicly available, share them with other users and to become members of the growing research community. Our intention is to make OCHEM a widely used platform to perform the QSPR/QSAR studies online and share it with other users on the Web. The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://www.ochem.eu.

A mapping review of the literature on UK-focused health and social care databases.

PubMed

Cooper, Chris; Rogers, Morwenna; Bethel, Alison; Briscoe, Simon; Lowe, Jenny

2015-03-01

Bibliographic databases are a day-to-day tool of the researcher: they offer the researcher easy and organised access to knowledge, but how much is actually known about the databases on offer? The focus of this paper is UK health and social care databases. These databases are often small, specialised by topic, and provide a complementary literature to the large, international databases. There is, however, good evidence that these databases are overlooked in systematic reviews, perhaps because little is known about what they can offer. To systematically locate and map, published and unpublished literature on the key UK health and social care bibliographic databases. Systematic searching and mapping. Two hundred and forty-two items were identified which specifically related to the 24 of the 34 databases under review. There is little published or unpublished literature specifically analysing the key UK health and social care databases. Since several UK databases have closed, others are at risk, and some are overlooked in reviews, better information is required to enhance our knowledge. Further research on UK health and social care databases is required. This paper suggests the need to develop the evidence base through a series of case studies on each of the databases. © 2014 The authors. Health Information and Libraries Journal © 2014 Health Libraries Journal.

Comparison of Conflicts of Interest among Published Hernia Researchers Self-Reported with the Centers for Medicare and Medicaid Services Open Payments Database.

PubMed

Olavarria, Oscar A; Holihan, Julie L; Cherla, Deepa; Perez, Cristina A; Kao, Lillian S; Ko, Tien C; Liang, Mike K

2017-05-01

Many healthcare providers have financial interests and relationships with healthcare companies. To maintain transparency, investigators are expected to disclose their conflicts of interest (COIs). Recently, the Centers for Medicare and Medicaid Services developed the Open Payment database of COIs reported by industry. We hypothesize that there is discordance between industry-reported and physician self-reported COIs in ventral hernia publications. PubMed was searched for ventral hernia studies accepted for publication between June 2013 and October 2015 and published by authors from the US. Conflicts of interest were defined as payments received as honoraria, consulting fees, compensation for serving as faculty or as a speaker at a venue, research funding payments, or having ownerships/partnerships in companies. Conflicts of interest disclosed on the published articles were compared with the financial relationships in the Open Payments database. A total of 100 studies were selected with 497 participating authors. Information was available from the Open Payments database for 245 (49.2%) authors, of which 134 (26.9%) met the definition for COI. When comparing COIs disclosed by authors and data in the Open Payments database, 81 (16.3%) authors had at least 1 COI but did not declare any, 35 (7.0%) authors had COIs other than what they declared, and 20 (4.0%) declared a COI not listed in the Open Payments database, for a combined discordance rate of 27.3%. There is substantial discordance between self-reported COI in published articles compared with those in the Centers for Medicare and Medicaid Services Open Payments database. Additional studies are needed to determine the reasons for these differences, as COI can influence the validity of the design, conduct, and results of a study. Copyright © 2017 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

The BioMart community portal: an innovative alternative to large, centralized data repositories

PubMed Central

Smedley, Damian; Haider, Syed; Durinck, Steffen; Pandini, Luca; Provero, Paolo; Allen, James; Arnaiz, Olivier; Awedh, Mohammad Hamza; Baldock, Richard; Barbiera, Giulia; Bardou, Philippe; Beck, Tim; Blake, Andrew; Bonierbale, Merideth; Brookes, Anthony J.; Bucci, Gabriele; Buetti, Iwan; Burge, Sarah; Cabau, Cédric; Carlson, Joseph W.; Chelala, Claude; Chrysostomou, Charalambos; Cittaro, Davide; Collin, Olivier; Cordova, Raul; Cutts, Rosalind J.; Dassi, Erik; Genova, Alex Di; Djari, Anis; Esposito, Anthony; Estrella, Heather; Eyras, Eduardo; Fernandez-Banet, Julio; Forbes, Simon; Free, Robert C.; Fujisawa, Takatomo; Gadaleta, Emanuela; Garcia-Manteiga, Jose M.; Goodstein, David; Gray, Kristian; Guerra-Assunção, José Afonso; Haggarty, Bernard; Han, Dong-Jin; Han, Byung Woo; Harris, Todd; Harshbarger, Jayson; Hastings, Robert K.; Hayes, Richard D.; Hoede, Claire; Hu, Shen; Hu, Zhi-Liang; Hutchins, Lucie; Kan, Zhengyan; Kawaji, Hideya; Keliet, Aminah; Kerhornou, Arnaud; Kim, Sunghoon; Kinsella, Rhoda; Klopp, Christophe; Kong, Lei; Lawson, Daniel; Lazarevic, Dejan; Lee, Ji-Hyun; Letellier, Thomas; Li, Chuan-Yun; Lio, Pietro; Liu, Chu-Jun; Luo, Jie; Maass, Alejandro; Mariette, Jerome; Maurel, Thomas; Merella, Stefania; Mohamed, Azza Mostafa; Moreews, Francois; Nabihoudine, Ibounyamine; Ndegwa, Nelson; Noirot, Céline; Perez-Llamas, Cristian; Primig, Michael; Quattrone, Alessandro; Quesneville, Hadi; Rambaldi, Davide; Reecy, James; Riba, Michela; Rosanoff, Steven; Saddiq, Amna Ali; Salas, Elisa; Sallou, Olivier; Shepherd, Rebecca; Simon, Reinhard; Sperling, Linda; Spooner, William; Staines, Daniel M.; Steinbach, Delphine; Stone, Kevin; Stupka, Elia; Teague, Jon W.; Dayem Ullah, Abu Z.; Wang, Jun; Ware, Doreen; Wong-Erasmus, Marie; Youens-Clark, Ken; Zadissa, Amonida; Zhang, Shi-Jian; Kasprzyk, Arek

2015-01-01

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations. PMID:25897122

BioMart Central Portal: an open database network for the biological community.

PubMed

Guberman, Jonathan M; Ai, J; Arnaiz, O; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J; Di Génova, A; Forbes, Simon; Fujisawa, T; Gadaleta, E; Goodstein, D M; Gundem, Gunes; Haggarty, Bernard; Haider, Syed; Hall, Matthew; Harris, Todd; Haw, Robin; Hu, S; Hubbard, Simon; Hsu, Jack; Iyer, Vivek; Jones, Philip; Katayama, Toshiaki; Kinsella, R; Kong, Lei; Lawson, Daniel; Liang, Yong; Lopez-Bigas, Nuria; Luo, J; Lush, Michael; Mason, Jeremy; Moreews, Francois; Ndegwa, Nelson; Oakley, Darren; Perez-Llamas, Christian; Primig, Michael; Rivkin, Elena; Rosanoff, S; Shepherd, Rebecca; Simon, Reinhard; Skarnes, B; Smedley, Damian; Sperling, Linda; Spooner, William; Stevenson, Peter; Stone, Kevin; Teague, J; Wang, Jun; Wang, Jianxin; Whitty, Brett; Wong, D T; Wong-Erasmus, Marie; Yao, L; Youens-Clark, Ken; Yung, Christina; Zhang, Junjun; Kasprzyk, Arek

2011-01-01

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities.

Three decades of disasters: a review of disaster-specific literature from 1977-2009.

PubMed

Smith, Erin; Wasiak, Jason; Sen, Ayan; Archer, Frank; Burkle, Frederick M

2009-01-01

The potential for disasters exists in all communities. To mitigate the potential catastrophes that confront humanity in the new millennium, an evidence-based approach to disaster management is required urgently. This study moves toward such an evidence-based approach by identifying peer-reviewed publications following a range of disasters and events over the past three decades. Peer-reviewed, event-specific literature was identified using a comprehensive search of the electronically indexed database, MEDLINE (1956-January 2009). An extended comprehensive search was conducted for one event to compare the event-specific literature indexed in MEDLINE to other electronic databases (EMBASE, CINAHL, AMED, CENTRAL, Psych Info, Maternity and Infant Care, EBM Reviews). Following 25 individual disasters or overwhelming crises, a total of 2,098 peer-reviewed, event-specific publications were published in 789 journals (652 publications following disasters/events caused by natural hazards, 966 following human-made/technological disasters/events, and 480 following conflict/complex humanitarian events).The event with the greatest number of peer-reviewed, event-specific publications was the 11 September 2001 terrorist attacks (686 publications). Prehospital and Disaster Medicine published the greatest number of peer-reviewed, event-specific publications (54), followed by Journal of Traumatic Stress (42), Military Medicine (40), and Psychiatric Services (40). The primary topics of event-specific publications were mental health, medical health, and response. When an extended, comprehensive search was conducted for one event, 75% of all peer-reviewed, event-specific publications were indexed in MEDLINE. A broad range of multi-disciplinary journals publish peer reviewed, event-specific publications. While the majority of peer-reviewed, event-specific literature is indexed in MEDLINE, comprehensive search strategies should include EMBASE to increase yield.

Solving the challenges of data preprocessing, uploading, archiving, retrieval, analysis and visualization for large heterogeneous paleo- and rock magnetic datasets

NASA Astrophysics Data System (ADS)

Minnett, R.; Koppers, A. A.; Tauxe, L.; Constable, C.; Jarboe, N. A.

2011-12-01

The Magnetics Information Consortium (MagIC) provides an archive for the wealth of rock- and paleomagnetic data and interpretations from studies on natural and synthetic samples. As with many fields, most peer-reviewed paleo- and rock magnetic publications only include high level results. However, access to the raw data from which these results were derived is critical for compilation studies and when updating results based on new interpretation and analysis methods. MagIC provides a detailed metadata model with places for everything from raw measurements to their interpretations. Prior to MagIC, these raw data were extremely cumbersome to collect because they mostly existed in a lab's proprietary format on investigator's personal computers or undigitized in field notebooks. MagIC has developed a suite of offline and online tools to enable the paleomagnetic, rock magnetic, and affiliated scientific communities to easily contribute both their previously published data and data supporting an article undergoing peer-review, to retrieve well-annotated published interpretations and raw data, and to analyze and visualize large collections of published data online. Here we present the technology we chose (including VBA in Excel spreadsheets, Python libraries, FastCGI JSON webservices, Oracle procedures, and jQuery user interfaces) and how we implemented it in order to serve the scientific community as seamlessly as possible. These tools are now in use in labs worldwide, have helped archive many valuable legacy studies and datasets, and routinely enable new contributions to the MagIC Database (http://earthref.org/MAGIC/).

47 CFR 15.713 - TV bands database.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 1 2014-10-01 2014-10-01 false TV bands database. 15.713 Section 15.713... TV bands database. Link to an amendment published at 79 FR 48536, August 15, 2014. (a) Purpose. The TV bands database serves the following functions: (1) To determine and provide to a TVBD, upon...

16 CFR 1102.28 - Publication of reports of harm.

Code of Federal Regulations, 2011 CFR

2011-01-01

... REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011) Procedural..., the Commission will publish reports of harm that meet the requirements for publication in the Database...(d) in the Database beyond the 10-business-day time frame set forth in paragraph (a) of this section...

Interactive bibliographical database on color

NASA Astrophysics Data System (ADS)

Caivano, Jose L.

2002-06-01

The paper describes the methodology and results of a project under development, aimed at the elaboration of an interactive bibliographical database on color in all fields of application: philosophy, psychology, semiotics, education, anthropology, physical and natural sciences, biology, medicine, technology, industry, architecture and design, arts, linguistics, geography, history. The project is initially based upon an already developed bibliography, published in different journals, updated in various opportunities, and now available at the Internet, with more than 2,000 entries. The interactive database will amplify that bibliography, incorporating hyperlinks and contents (indexes, abstracts, keywords, introductions, or eventually the complete document), and devising mechanisms for information retrieval. The sources to be included are: books, doctoral dissertations, multimedia publications, reference works. The main arrangement will be chronological, but the design of the database will allow rearrangements or selections by different fields: subject, Decimal Classification System, author, language, country, publisher, etc. A further project is to develop another database, including color-specialized journals or newsletters, and articles on color published in international journals, arranged in this case by journal name and date of publication, but allowing also rearrangements or selections by author, subject and keywords.

[Presence of the biomedical periodicals of Hungarian editions in international databases].

PubMed

Vasas, Lívia; Hercsel, Imréné

2006-01-15

Presence of the biomedical periodicals of Hungarian editions in international databases. The majority of Hungarian scientific results in medical and related sciences are published in scientific periodicals of foreign edition with high impact factor (IF) values, and they appear in international scientific literature in foreign languages. In this study the authors dealt with the presence and registered citation in international databases of those periodicals only, which had been published in Hungary and/or in cooperation with foreign publishing companies. The examination went back to year 1980 and covered a 25-year long period. 110 periodicals were selected for more detailed examination. The authors analyzed the situation of the current periodicals in the three most often visited databases (MEDLINE, EMBASE, Web of Science), and discovered, that the biomedical scientific periodicals of Hungarian interests were not represented with reasonable emphasis in the relevant international bibliographic databases. Because of the great number of data the scientific literature of medicine and related sciences could not be represented in its entirety, this publication, however, might give useful information for the inquirers, and call the attention of the competent people.

Central Appalachian basin natural gas database: distribution, composition, and origin of natural gases

USGS Publications Warehouse

Román Colón, Yomayra A.; Ruppert, Leslie F.

2015-01-01

The U.S. Geological Survey (USGS) has compiled a database consisting of three worksheets of central Appalachian basin natural gas analyses and isotopic compositions from published and unpublished sources of 1,282 gas samples from Kentucky, Maryland, New York, Ohio, Pennsylvania, Tennessee, Virginia, and West Virginia. The database includes field and reservoir names, well and State identification number, selected geologic reservoir properties, and the composition of natural gases (methane; ethane; propane; butane, iso-butane [i-butane]; normal butane [n-butane]; iso-pentane [i-pentane]; normal pentane [n-pentane]; cyclohexane, and hexanes). In the first worksheet, location and American Petroleum Institute (API) numbers from public or published sources are provided for 1,231 of the 1,282 gas samples. A second worksheet of 186 gas samples was compiled from published sources and augmented with public location information and contains carbon, hydrogen, and nitrogen isotopic measurements of natural gas. The third worksheet is a key for all abbreviations in the database. The database can be used to better constrain the stratigraphic distribution, composition, and origin of natural gas in the central Appalachian basin.

[Safe school].

PubMed

Liberal, Edson Ferreira; Aires, Roberto Tschoepke; Aires, Mariana Tschoepke; Osório, Ana Carla de Albuquerque

2005-11-01

To review the strategies to make school a safe environment. The paper first addresses the social context of accidents and violence in the school environment, and makes recommendations, based on the literature data, for the implementation of safe schools. Articles published between 1993 and 2005 in the MEDLINE database. Brazilian epidemiological and literature data have also been searched. There is growing evidence that intervention has multiple components, focusing on health education practices, with the participation of the whole community. The aim of those interventions is to help students and community members to adopt healthy and safe behaviors. Schools are taking on an increasing role in health promotion, disease prevention, and injury prevention. In the context of prevention of external causes of morbidity and mortality, it is important to recognize a risky environment, places, and risk behaviors as favorable to injury and violence, as well as the concept of accident as something one can avoid. Implementation of safe schools represents a promising new direction for school-based preventive work. It is important to note that a safe school should intervene not only in its physical structure, but it should also make it as safe as possible by gathering the school community through health education, and mainly encouraging healthy behavior.

Effective nursing leadership of older persons in the community - a systematic review.

PubMed

Holm, Anne Lise; Severinsson, Elisabeth

2014-03-01

The aim of this systematic review was to increase the knowledge of developing effective nursing leadership and management in order to improve the outcomes of older persons in the community. There is a need for increased knowledge of nursing leadership and management in order to improve the outcomes of older persons in the community. A review of the literature published in different databases between January 2000 and May 2012 was conducted. Eleven articles met the inclusion criteria and were evaluated by means of thematic content analysis. Six themes were identified: Ability to change the attitudes towards older persons; Building trust; Ensuring efficacy in management decisions; Lack of knowledge about how to overcome relational challenges; Health system collaboration to achieve goals and visions; and Staff members' experiences of the meaning of and possibility to influence their work, all of which are of importance for effective nursing leadership and management in the care of older persons. Advanced nursing knowledge is necessary in order to improve the work and vision involved in nursing leadership and management. Findings indicate that relational and organisational abilities are necessary components of effective nursing leadership and management. © 2013 John Wiley & Sons Ltd.

An analysis of orthopaedic theses in Turkey: Evidence levels and publication rates.

PubMed

Koca, Kenan; Ekinci, Safak; Akpancar, Serkan; Gemci, Muhammed Hanifi; Erşen, Ömer; Akyıldız, Faruk

2016-10-01

The aim of this study was to present characteristics and publication patterns of studies arise from orthopedic theses obtained from National Thesis Center; database in terms of publication years, study types, topics, level of evidence between 1974 and 2014. Firstly, National Thesis Center database was searched for orthopedics and Traumatology theses. The theses, which their summary or full text were available were included in the study. The topics, study types and quality of study designs were reviewed. Then theses were searched in the PubMed database. Journals of published theses were classified according to category, scope and impact factors of the year 2014. 1508 theses were included into the study. Clinical studies comprised 71,7% of the theses, while 25,6% of the theses were non-clinical experimental and 2,7% of the theses were observational studies. Clinical studies were Level I in 8,6% (n = 93) and Level II in 5,8% of the theses (n = 63). A total of 224 theses (14,9%) were published in the journals indexed in PubMed database from 1974 to 2012. Fifty-two (23,2%) were published in SCI; 136 theses (60,7%) were published in SCI-E journals and 36 theses (16%) were published in other Journals indexed in PubMed. The quantity and quality of published theses need to be improved and effective measures should be taken to promote quality of theses. Theses from universities and Training hospitals which did not allow open access, and; incomplete records of the National Thesis Center database were major limitations of this study. Copyright © 2016 Turkish Association of Orthopaedics and Traumatology. Production and hosting by Elsevier B.V. All rights reserved.

The eNanoMapper database for nanomaterial safety information

PubMed Central

Chomenidis, Charalampos; Doganis, Philip; Fadeel, Bengt; Grafström, Roland; Hardy, Barry; Hastings, Janna; Hegi, Markus; Jeliazkov, Vedrin; Kochev, Nikolay; Kohonen, Pekka; Munteanu, Cristian R; Sarimveis, Haralambos; Smeets, Bart; Sopasakis, Pantelis; Tsiliki, Georgia; Vorgrimmler, David; Willighagen, Egon

2015-01-01

Summary Background: The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. Results: The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms. Conclusion: We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the “representational state transfer” (REST) API enables building user friendly interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure–activity relationships for nanomaterials (NanoQSAR). PMID:26425413

The eNanoMapper database for nanomaterial safety information.

PubMed

Jeliazkova, Nina; Chomenidis, Charalampos; Doganis, Philip; Fadeel, Bengt; Grafström, Roland; Hardy, Barry; Hastings, Janna; Hegi, Markus; Jeliazkov, Vedrin; Kochev, Nikolay; Kohonen, Pekka; Munteanu, Cristian R; Sarimveis, Haralambos; Smeets, Bart; Sopasakis, Pantelis; Tsiliki, Georgia; Vorgrimmler, David; Willighagen, Egon

2015-01-01

The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms. We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the "representational state transfer" (REST) API enables building user friendly interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure-activity relationships for nanomaterials (NanoQSAR).

The HydroServer Platform for Sharing Hydrologic Data

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Horsburgh, J. S.; Schreuders, K.; Maidment, D. R.; Zaslavsky, I.; Valentine, D. W.

2010-12-01

The CUAHSI Hydrologic Information System (HIS) is an internet based system that supports sharing of hydrologic data. HIS consists of databases connected using the Internet through Web services, as well as software for data discovery, access, and publication. The HIS system architecture is comprised of servers for publishing and sharing data, a centralized catalog to support cross server data discovery and a desktop client to access and analyze data. This paper focuses on HydroServer, the component developed for sharing and publishing space-time hydrologic datasets. A HydroServer is a computer server that contains a collection of databases, web services, tools, and software applications that allow data producers to store, publish, and manage the data from an experimental watershed or project site. HydroServer is designed to permit publication of data as part of a distributed national/international system, while still locally managing access to the data. We describe the HydroServer architecture and software stack, including tools for managing and publishing time series data for fixed point monitoring sites as well as spatially distributed, GIS datasets that describe a particular study area, watershed, or region. HydroServer adopts a standards based approach to data publication, relying on accepted and emerging standards for data storage and transfer. CUAHSI developed HydroServer code is free with community code development managed through the codeplex open source code repository and development system. There is some reliance on widely used commercial software for general purpose and standard data publication capability. The sharing of data in a common format is one way to stimulate interdisciplinary research and collaboration. It is anticipated that the growing, distributed network of HydroServers will facilitate cross-site comparisons and large scale studies that synthesize information from diverse settings, making the network as a whole greater than the sum of its parts in advancing hydrologic research. Details of the CUAHSI HIS can be found at http://his.cuahsi.org, and HydroServer codeplex site http://hydroserver.codeplex.com.

An Overview to Research on Education Technology Based on Constructivist Learning Approach

ERIC Educational Resources Information Center

Asiksoy, Gulsum; Ozdamli, Fezile

2017-01-01

The aim of this research is to determine the trends of education technology researches on Constructivist Learning Approach, which were published on database of ScienceDirect between 2010 and 2016. It also aims to guide researchers who will do studies in this field. After scanning the database, 81 articles published on ScienceDirect's data base…

Elsevier's Vanishing Act: To the Dismay of Scholars, the Publishing Giant Quietly Purges Articles from Its Database.

ERIC Educational Resources Information Center

Foster, Andrea L.

2003-01-01

Elsevier, the largest publisher of scientific journals, has removed journal articles from its database, often without providing reasons. The usual reason for removing an article is fear of copyright litigation, but critics of the policy fear that information gaps or misleading lack of data will develop. (SLD)

Nutrition-Related Policy and Environmental Strategies to Prevent Obesity in Rural Communities: A Systematic Review of the Literature, 2002–2013

PubMed Central

Leeman, Jennifer; Jilcott Pitts, Stephanie B.; Khan, Laura Kettel; Fleischhacker, Sheila; Evenson, Kelly R.; Schreiner, Michelle; Byker, Carmen; Owens, Clint; McGuirt, Jared; Barnidge, Ellen; Dean, Wesley; Johnson, Donna; Kolodinsky, Jane; Piltch, Emily; Pinard, Courtney; Quinn, Emilee; Whetstone, Lauren; Ammerman, Alice

2015-01-01

Introduction Residents of rural communities in the United States are at higher risk for obesity than their urban and suburban counterparts. Policy and environmental-change strategies supporting healthier dietary intake can prevent obesity and promote health equity. Evidence in support of these strategies is based largely on urban and suburban studies; little is known about use of these strategies in rural communities. The purpose of this review was to synthesize available evidence on the adaptation, implementation, and effectiveness of policy and environmental obesity-prevention strategies in rural settings. Methods The review was guided by a list of Centers for Disease Control and Prevention Recommended Community Strategies and Measurements to Prevent Obesity in the United States, commonly known as the “COCOMO” strategies. We searched PubMed, Cumulative Index of Nursing and Allied Health Literature, Public Affairs Information Service, and Cochrane databases for articles published from 2002 through 2013 that reported findings from research on nutrition-related policy and environmental strategies in rural communities in the United States and Canada. Two researchers independently abstracted data from each article, and resolved discrepancies by consensus. Results Of the 663 articles retrieved, 33 met inclusion criteria. The interventions most commonly focused on increasing access to more nutritious foods and beverages or decreasing access to less nutritious options. Rural adaptations included accommodating distance to food sources, tailoring to local food cultures, and building community partnerships. Conclusions Findings from this literature review provide guidance on adapting and implementing policy and environmental strategies in rural communities. PMID:25927605

Making your database available through Wikipedia: the pros and cons.

PubMed

Finn, Robert D; Gardner, Paul P; Bateman, Alex

2012-01-01

Wikipedia, the online encyclopedia, is the most famous wiki in use today. It contains over 3.7 million pages of content; with many pages written on scientific subject matters that include peer-reviewed citations, yet are written in an accessible manner and generally reflect the consensus opinion of the community. In this, the 19th Annual Database Issue of Nucleic Acids Research, there are 11 articles that describe the use of a wiki in relation to a biological database. In this commentary, we discuss how biological databases can be integrated with Wikipedia, thereby utilising the pre-existing infrastructure, tools and above all, large community of authors (or Wikipedians). The limitations to the content that can be included in Wikipedia are highlighted, with examples drawn from articles found in this issue and other wiki-based resources, indicating why other wiki solutions are necessary. We discuss the merits of using open wikis, like Wikipedia, versus other models, with particular reference to potential vandalism. Finally, we raise the question about the future role of dedicated database biocurators in context of the thousands of crowdsourced, community annotations that are now being stored in wikis.

Making your database available through Wikipedia: the pros and cons

PubMed Central

Finn, Robert D.; Gardner, Paul P.; Bateman, Alex

2012-01-01

Wikipedia, the online encyclopedia, is the most famous wiki in use today. It contains over 3.7 million pages of content; with many pages written on scientific subject matters that include peer-reviewed citations, yet are written in an accessible manner and generally reflect the consensus opinion of the community. In this, the 19th Annual Database Issue of Nucleic Acids Research, there are 11 articles that describe the use of a wiki in relation to a biological database. In this commentary, we discuss how biological databases can be integrated with Wikipedia, thereby utilising the pre-existing infrastructure, tools and above all, large community of authors (or Wikipedians). The limitations to the content that can be included in Wikipedia are highlighted, with examples drawn from articles found in this issue and other wiki-based resources, indicating why other wiki solutions are necessary. We discuss the merits of using open wikis, like Wikipedia, versus other models, with particular reference to potential vandalism. Finally, we raise the question about the future role of dedicated database biocurators in context of the thousands of crowdsourced, community annotations that are now being stored in wikis. PMID:22144683

The radiopurity.org material database

NASA Astrophysics Data System (ADS)

Cooley, J.; Loach, J. C.; Poon, A. W. P.

2018-01-01

The database at http://www.radiopurity.org is the world's largest public database of material radio-purity mea-surements. These measurements are used by members of the low-background physics community to build experiments that search for neutrinos, neutrinoless double-beta decay, WIMP dark matter, and other exciting physics. This paper summarizes the current status and the future plan of this database.

A practice-based information system for multi-disciplinary care of chronically ill patients: what information do we need? The Community Care Coordination Network Database Group.

PubMed Central

Moran, W. P.; Messick, C.; Guerette, P.; Anderson, R.; Bradham, D.; Wofford, J. L.; Velez, R.

1994-01-01

Primary care physicians provide longitudinal care for chronically ill individuals in concert with many other community-based disciplines. The care management of these individuals requires data not traditionally collected during the care of well, or acutely ill individuals. These data not only concern the patient, in the form of patient functional status, mental status and affect, but also pertain to the caregiver, home environment, and the formal community health and social service system. The goal of the Community Care Coordination Network is to build a primary care-based information system to share patient data and communicate patient related information among the community-based multi-disciplinary teams. One objective of the Community Care Coordination Network is to create a Community Care Database for chronically ill individuals by identifying those data elements necessary for efficient multi-disciplinary care. PMID:7949995

The DrugAge database of aging-related drugs.

PubMed

Barardo, Diogo; Thornton, Daniel; Thoppil, Harikrishnan; Walsh, Michael; Sharifi, Samim; Ferreira, Susana; Anžič, Andreja; Fernandes, Maria; Monteiro, Patrick; Grum, Tjaša; Cordeiro, Rui; De-Souza, Evandro Araújo; Budovsky, Arie; Araujo, Natali; Gruber, Jan; Petrascheck, Michael; Fraifeld, Vadim E; Zhavoronkov, Alexander; Moskalev, Alexey; de Magalhães, João Pedro

2017-06-01

Aging is a major worldwide medical challenge. Not surprisingly, identifying drugs and compounds that extend lifespan in model organisms is a growing research area. Here, we present DrugAge (http://genomics.senescence.info/drugs/), a curated database of lifespan-extending drugs and compounds. At the time of writing, DrugAge contains 1316 entries featuring 418 different compounds from studies across 27 model organisms, including worms, flies, yeast and mice. Data were manually curated from 324 publications. Using drug-gene interaction data, we also performed a functional enrichment analysis of targets of lifespan-extending drugs. Enriched terms include various functional categories related to glutathione and antioxidant activity, ion transport and metabolic processes. In addition, we found a modest but significant overlap between targets of lifespan-extending drugs and known aging-related genes, suggesting that some but not most aging-related pathways have been targeted pharmacologically in longevity studies. DrugAge is freely available online for the scientific community and will be an important resource for biogerontologists. © 2017 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

Public health and epidemiology journals published in Brazil and other Portuguese speaking countries

PubMed Central

Barreto, Mauricio L; Barata, Rita Barradas

2008-01-01

It is well known that papers written in languages other than English have a great risk of being ignored simply because these languages are not accessible to the international scientific community. The objective of this paper is to facilitate the access to the public health and epidemiology literature available in Portuguese speaking countries. It was found that it is particularly concentrated in Brazil, with some few examples in Portugal and none in other Portuguese speaking countries. This literature is predominantly written in Portuguese, but also in other languages such as English or Spanish. The paper describes the several journals, as well as the bibliographic databases that index these journals and how to access them. Most journals provide open-access with direct links in the indexing databases. The importance of this scientific production for the development of epidemiology as a scientific discipline and as a basic discipline for public health practice is discussed. To marginalize these publications has implications for a more balanced knowledge and understanding of the health problems and their determinants at a world-wide level. PMID:18826592

Consortia for Engineering, Science and Technology Libraries in India: A Case Study of INDEST Consortium

NASA Astrophysics Data System (ADS)

Pathak, S. K.; Deshpande, N. J.

2007-10-01

The present scenario of the INDEST Consortium among engineering, science and technology (including astronomy and astrophysics) libraries in India is discussed. The Indian National Digital Library in Engineering Sciences & Technology (INDEST) Consortium is a major initiative of the Ministry of Human Resource Development, Government of India. The INDEST Consortium provides access to 16 full text e-resources and 7 bibliographic databases for 166 institutions as members who are taking advantage of cost effective access to premier resources in engineering, science and technology, including astronomy and astrophysics. Member institutions can access over 6500 e-journals from 1092 publishers. Out of these, over 150 e-journals are exclusively for the astronomy and physics community. The current study also presents a comparative analysis of the key features of nine major services, viz. ACM Digital Library, ASCE Journals, ASME Journals, EBSCO Databases (Business Source Premier), Elsevier's Science Direct, Emerald Full Text, IEEE/IEE Electronic Library Online (IEL), ProQuest ABI/INFORM and Springer Verlag's Link. In this paper, the limitations of this consortium are also discussed.

ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species.

PubMed

Zeng, Victor; Extavour, Cassandra G

2012-01-01

The increased throughput and decreased cost of next-generation sequencing (NGS) have shifted the bottleneck genomic research from sequencing to annotation, analysis and accessibility. This is particularly challenging for research communities working on organisms that lack the basic infrastructure of a sequenced genome, or an efficient way to utilize whatever sequence data may be available. Here we present a new database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository and search engine for transcriptomic data from arthropods that are of high interest to multiple research communities but currently lack sequenced genomes. We demonstrate the functionality and utility of ASGARD using de novo assembled transcriptomes from the milkweed bug Oncopeltus fasciatus, the cricket Gryllus bimaculatus and the amphipod crustacean Parhyale hawaiensis. We have annotated these transcriptomes to assign putative orthology, coding region determination, protein domain identification and Gene Ontology (GO) term annotation to all possible assembly products. ASGARD allows users to search all assemblies by orthology annotation, GO term annotation or Basic Local Alignment Search Tool. User-friendly features of ASGARD include search term auto-completion suggestions based on database content, the ability to download assembly product sequences in FASTA format, direct links to NCBI data for predicted orthologs and graphical representation of the location of protein domains and matches to similar sequences from the NCBI non-redundant database. ASGARD will be a useful repository for transcriptome data from future NGS studies on these and other emerging model arthropods, regardless of sequencing platform, assembly or annotation status. This database thus provides easy, one-stop access to multi-species annotated transcriptome information. We anticipate that this database will be useful for members of multiple research communities, including developmental biology, physiology, evolutionary biology, ecology, comparative genomics and phylogenomics. Database URL: asgard.rc.fas.harvard.edu.

Community-acquired methicillin-resistant Staphylococcus aureus: a global problem.

PubMed

Evangelista, Síntia de Souza; de Oliveira, Adriana Cristina

2015-01-01

To describe the epidemiology of CA-MRSA cases in Brazil order to understand its occurrence, risk factors and forms of management in the country compared with the worldwide situation. Literature review and for articles selection considering the databases: Scopus, Science Direct, Isi Web of Knowledge, PubMed and BVS. Ten national articles describing 21 cases of CA-MRSA were identified, mostly in children, adolescents and adults with skin and soft tissue infection progressing to severe infections related to Oceania Southwest Pacific Clone (OSPC) leading to hospitalization. Conclusión: Although CA-MRSA is considered a global important microorganism we found a lack of published data about its epidemiology in Brazil, which hinder the design of the reality of the country against CA-MRSA.

Relational Database Design in Information Science Education.

ERIC Educational Resources Information Center

Brooks, Terrence A.

1985-01-01

Reports on database management system (dbms) applications designed by library school students for university community at University of Iowa. Three dbms design issues are examined: synthesis of relations, analysis of relations (normalization procedure), and data dictionary usage. Database planning prior to automation using data dictionary approach…

Scientific Communication of Geochemical Data and the Use of Computer Databases.

ERIC Educational Resources Information Center

Le Bas, M. J.; Durham, J.

1989-01-01

Describes a scheme in the United Kingdom that coordinates geochemistry publications with a computerized geochemistry database. The database comprises not only data published in the journals but also the remainder of the pertinent data set. The discussion covers the database design; collection, storage and retrieval of data; and plans for future…

49 CFR 837.3 - Published reports, material contained in the public accident investigation dockets, and accident...

Code of Federal Regulations, 2014 CFR

2014-10-01

... public accident investigation dockets, and accident database data. 837.3 Section 837.3 Transportation... investigation dockets, and accident database data. (a) Demands for material contained in the NTSB's official public docket files of its accident investigations, or its computerized accident database(s) shall be...

49 CFR 837.3 - Published reports, material contained in the public accident investigation dockets, and accident...

Code of Federal Regulations, 2012 CFR

2012-10-01

... public accident investigation dockets, and accident database data. 837.3 Section 837.3 Transportation... investigation dockets, and accident database data. (a) Demands for material contained in the NTSB's official public docket files of its accident investigations, or its computerized accident database(s) shall be...

49 CFR 837.3 - Published reports, material contained in the public accident investigation dockets, and accident...

Code of Federal Regulations, 2010 CFR

2010-10-01

... public accident investigation dockets, and accident database data. 837.3 Section 837.3 Transportation... investigation dockets, and accident database data. (a) Demands for material contained in the NTSB's official public docket files of its accident investigations, or its computerized accident database(s) shall be...

49 CFR 837.3 - Published reports, material contained in the public accident investigation dockets, and accident...

Code of Federal Regulations, 2013 CFR

2013-10-01

... public accident investigation dockets, and accident database data. 837.3 Section 837.3 Transportation... investigation dockets, and accident database data. (a) Demands for material contained in the NTSB's official public docket files of its accident investigations, or its computerized accident database(s) shall be...

49 CFR 837.3 - Published reports, material contained in the public accident investigation dockets, and accident...

Code of Federal Regulations, 2011 CFR

2011-10-01

... public accident investigation dockets, and accident database data. 837.3 Section 837.3 Transportation... investigation dockets, and accident database data. (a) Demands for material contained in the NTSB's official public docket files of its accident investigations, or its computerized accident database(s) shall be...

A 1.4-Billion Pixel Map of the Seafloor: BOEM's Mission to Visualize Dynamic Geology and Identify Natural Seep Sites in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Kramer, K.; Shedd, W. W.

2017-12-01

In May, 2017, the U.S. Department of the Interior's Bureau of Ocean Energy Management (BOEM) published a high-resolution seafloor map of the northern Gulf of Mexico region. The new map, derived from 3-D seismic surveys, provides the scientific community with enhanced resolution and reveals previously undiscovered and poorly resolved geologic features of the continental slope, salt minibasin province, abyssal plain, Mississippi Fan, and the Florida Shelf and Escarpment. It becomes an even more powerful scientific tool when paired with BOEM's public database of 35,000 seafloor features, identifying natural hydrocarbon seeps, hard grounds, mud volcanoes, sediment flows, pockmarks, slumps, and many others. BOEM has mapped the Gulf of Mexico seafloor since 1998 in a regulatory mission to identify natural oil and gas seeps and protect the coral and chemosynthetic communities growing at those sites. The nineteen-year mapping effort, still ongoing, resulted in the creation of the 1.4-billion pixel map and the seafloor features database. With these tools and continual collaboration with academia, professional scientific institutions, and the offshore energy industry, BOEM will continue to incorporate new data to update and expand these two resources on a regular basis. They can be downloaded for free from BOEM's website at https://www.boem.gov/Gulf-of-Mexico-Deepwater-Bathymetry/ and https://www.boem.gov/Seismic-Water-Bottom-Anomalies-Map-Gallery/.

Smoking in Correctional Settings Worldwide: Prevalence, Bans, and Interventions.

PubMed

Spaulding, Anne C; Eldridge, Gloria D; Chico, Cynthia E; Morisseau, Nancy; Drobeniuc, Ana; Fils-Aime, Rebecca; Day, Carolyn; Hopkins, Robyn; Jin, Xingzhong; Chen, Junyu; Dolan, Kate A

2018-06-01

Smoking tobacco contributes to 11.5% of deaths worldwide and, in some countries, more hospitalizations than alcohol and drugs combined. Globally in 2015, 25% of men and 5% of women smoked. In the United States, a higher proportion of people in prison smoke than do community-dwelling individuals. To determine smoking prevalence in prisons worldwide, we systematically reviewed the literature using Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines; we also examined whether prisons banned smoking or treated smokers. We searched databases for articles published between 2012 and 2016 and located 85 relevant articles with data representing 73.5% of all incarcerated persons from 50 countries. In 35 of 36 nations (97%) with published prevalence data, smoking for the incarcerated exceeded community rates 1.04- to 62.6-fold. Taking a conservative estimate of a 2-fold increase, we estimated that, globally, 14.5 million male and 26,000 female smokers pass through prisons annually. Prison authorities' responses include permitting, prohibiting, or treating tobacco use. Bans may temporarily improve health and reduce in-prison health care costs but have negligible effect after prison release. Evidence-based interventions for smoking cessation effective outside prisons are effective inside; effects persist after release. Because smoking prevalence is heightened in prisons, offering evidence-based interventions to nearly 15 million smokers passing through yearly would improve global health.

Measuring capacity building in communities: a review of the literature

PubMed Central

2011-01-01

Background Although communities have long been exhorted to make efforts to enhance their own health, such approaches have often floundered and resulted in little or no health benefits when the capacity of the community has not been adequately strengthened. Thus being able to assess the capacity building process is paramount in facilitating action in communities for social and health improvement. The current review aims to i) identify all domains used in systematically documented frameworks developed by other authors to assess community capacity building; and ii) to identify the dimensions and attributes of each of the domains as ascribed by these authors and reassemble them into a comprehensive compilation. Methods Relevant published articles were identified through systematic electronic searches of selected databases and the examination of the bibliographies of retrieved articles. Studies assessing capacity building or community development or community participation were selected and assessed for methodological quality, and quality in relation to the development and application of domains which were identified as constituents of community capacity building. Data extraction and analysis were undertaken using a realist synthesis approach. Results Eighteen articles met the criteria for this review. The various domains to assess community capacity building were identified and reassembled into nine comprehensive domains: "learning opportunities and skills development", "resource mobilization", "partnership/linkages/networking", "leadership", "participatory decision-making", "assets-based approach", "sense of community", "communication", and "development pathway". Six sub-domains were also identified: "shared vision and clear goals", "community needs assessment", "process and outcome monitoring", "sustainability", "commitment to action" and "dissemination". Conclusions The set of domains compiled in this review serve as a foundation for community-based work by those in the field seeking to support and nurture the development of competent communities. Further research is required to examine the robustness of capacity domains over time and to examine capacity development in association with health or other social outcomes. PMID:22067213

Seismic Search Engine: A distributed database for mining large scale seismic data

NASA Astrophysics Data System (ADS)

Liu, Y.; Vaidya, S.; Kuzma, H. A.

2009-12-01

The International Monitoring System (IMS) of the CTBTO collects terabytes worth of seismic measurements from many receiver stations situated around the earth with the goal of detecting underground nuclear testing events and distinguishing them from other benign, but more common events such as earthquakes and mine blasts. The International Data Center (IDC) processes and analyzes these measurements, as they are collected by the IMS, to summarize event detections in daily bulletins. Thereafter, the data measurements are archived into a large format database. Our proposed Seismic Search Engine (SSE) will facilitate a framework for data exploration of the seismic database as well as the development of seismic data mining algorithms. Analogous to GenBank, the annotated genetic sequence database maintained by NIH, through SSE, we intend to provide public access to seismic data and a set of processing and analysis tools, along with community-generated annotations and statistical models to help interpret the data. SSE will implement queries as user-defined functions composed from standard tools and models. Each query is compiled and executed over the database internally before reporting results back to the user. Since queries are expressed with standard tools and models, users can easily reproduce published results within this framework for peer-review and making metric comparisons. As an illustration, an example query is “what are the best receiver stations in East Asia for detecting events in the Middle East?” Evaluating this query involves listing all receiver stations in East Asia, characterizing known seismic events in that region, and constructing a profile for each receiver station to determine how effective its measurements are at predicting each event. The results of this query can be used to help prioritize how data is collected, identify defective instruments, and guide future sensor placements.

ForC: a global database of forest carbon stocks and fluxes

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

Anderson-Teixeira, Kristina J.; Wang, Maria M. H.; McGarvey, Jennifer C.

Forests play an influential role in the global carbon (C) cycle, storing roughly half of terrestrial C and annually exchanging with the atmosphere more than ten times the carbon dioxide (CO 2) emitted by anthropogenic activities. Yet, scaling up from ground-based measurements of forest C stocks and fluxes to understand global scale C cycling and its climate sensitivity remains an important challenge. Tens of thousands of forest C measurements have been made, but these data have yet to be integrated into a single database that makes them accessible for integrated analyses. Here we present an open-access global Forest Carbon databasemore » (ForC) containing records of ground-based measurements of ecosystem-level C stocks and annual fluxes, along with disturbance history and methodological information. ForC expands upon the previously published tropical portion of this database, TropForC (DOI: 10.5061/dryad.t516f), now including 17,538 records (previously 3568) representing 2,731 plots (previously 845) in 826 geographically distinct areas (previously 178). The database covers all forested biogeographic and climate zones, represents forest stands of all ages, and includes 89 C cycle variables collected between 1934 and 2015. We expect that ForC will prove useful for macroecological analyses of forest C cycling, for evaluation of model predictions or remote sensing products, for quantifying the contribution of forests to the global C cycle, and for supporting international efforts to inventory forest carbon and greenhouse gas exchange. A dynamic version of ForC-db is maintained at https://github.com/forc-db, and we encourage the research community to collaborate in updating, correcting, expanding, and utilizing this database.« less

DAMIT: a database of asteroid models

NASA Astrophysics Data System (ADS)

Durech, J.; Sidorin, V.; Kaasalainen, M.

2010-04-01

Context. Apart from a few targets that were directly imaged by spacecraft, remote sensing techniques are the main source of information about the basic physical properties of asteroids, such as the size, the spin state, or the spectral type. The most widely used observing technique - time-resolved photometry - provides us with data that can be used for deriving asteroid shapes and spin states. In the past decade, inversion of asteroid lightcurves has led to more than a hundred asteroid models. In the next decade, when data from all-sky surveys are available, the number of asteroid models will increase. Combining photometry with, e.g., adaptive optics data produces more detailed models. Aims: We created the Database of Asteroid Models from Inversion Techniques (DAMIT) with the aim of providing the astronomical community access to reliable and up-to-date physical models of asteroids - i.e., their shapes, rotation periods, and spin axis directions. Models from DAMIT can be used for further detailed studies of individual objects, as well as for statistical studies of the whole set. Methods: Most DAMIT models were derived from photometric data by the lightcurve inversion method. Some of them have been further refined or scaled using adaptive optics images, infrared observations, or occultation data. A substantial number of the models were derived also using sparse photometric data from astrometric databases. Results: At present, the database contains models of more than one hundred asteroids. For each asteroid, DAMIT provides the polyhedral shape model, the sidereal rotation period, the spin axis direction, and the photometric data used for the inversion. The database is updated when new models are available or when already published models are updated or refined. We have also released the C source code for the lightcurve inversion and for the direct problem (updates and extensions will follow).

Global Inventory of Gas Geochemistry Data from Fossil Fuel, Microbial and Burning Sources, version 2017

NASA Astrophysics Data System (ADS)

Sherwood, Owen A.; Schwietzke, Stefan; Arling, Victoria A.; Etiope, Giuseppe

2017-08-01

The concentration of atmospheric methane (CH4) has more than doubled over the industrial era. To help constrain global and regional CH4 budgets, inverse (top-down) models incorporate data on the concentration and stable carbon (δ13C) and hydrogen (δ2H) isotopic ratios of atmospheric CH4. These models depend on accurate δ13C and δ2H end-member source signatures for each of the main emissions categories. Compared with meticulous measurement and calibration of isotopic CH4 in the atmosphere, there has been relatively less effort to characterize globally representative isotopic source signatures, particularly for fossil fuel sources. Most global CH4 budget models have so far relied on outdated source signature values derived from globally nonrepresentative data. To correct this deficiency, we present a comprehensive, globally representative end-member database of the δ13C and δ2H of CH4 from fossil fuel (conventional natural gas, shale gas, and coal), modern microbial (wetlands, rice paddies, ruminants, termites, and landfills and/or waste) and biomass burning sources. Gas molecular compositional data for fossil fuel categories are also included with the database. The database comprises 10 706 samples (8734 fossil fuel, 1972 non-fossil) from 190 published references. Mean (unweighted) δ13C signatures for fossil fuel CH4 are significantly lighter than values commonly used in CH4 budget models, thus highlighting potential underestimation of fossil fuel CH4 emissions in previous CH4 budget models. This living database will be updated every 2-3 years to provide the atmospheric modeling community with the most complete CH4 source signature data possible. Database digital object identifier (DOI): https://doi.org/10.15138/G3201T.

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV).

PubMed

Lefkowitz, Elliot J; Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-04

The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Publication trend, resource utilization, and impact of the US National Cancer Database: A systematic review.

PubMed

Su, Chang; Peng, Cuiying; Agbodza, Ena; Bai, Harrison X; Huang, Yuqian; Karakousis, Giorgos; Zhang, Paul J; Zhang, Zishu

2018-03-01

The utilization and impact of the studies published using the National Cancer Database (NCDB) is currently unclear. In this study, we aim to characterize the published studies, and identify relatively unexplored areas for future investigations. A literature search was performed using PubMed in January 2017 to identify all papers published using NCDB data. Characteristics of the publications were extracted. Citation frequencies were obtained through the Web of Science. Three hundred 2 articles written by 230 first authors met the inclusion criteria. The number of publications grew exponentially since 2013, with 108 articles published in 2016. Articles were published in 86 journals. The majority of the published papers focused on digestive system cancer, while bone and joints, eye and orbit, myeloma, mesothelioma, and Kaposi Sarcoma were never studied. Thirteen institutions in the United States were associated with more than 5 publications. The papers have been cited for a total of 9858 times since the publication of the first paper in 1992. Frequently appearing keywords congregated into 3 clusters: "demographics," "treatments and survival," and "statistical analysis method." Even though the main focuses of the articles captured a extremely wide range, they can be classified into 2 main categories: survival analysis and characterization. Other focuses include database(s) analysis and/or comparison, and hospital reporting. The surging interest in the use of NCDB is accompanied by unequal utilization of resources by individuals and institutions. Certain areas were relatively understudied and should be further explored.

Literature searches on Ayurveda: An update.

PubMed

Aggithaya, Madhur G; Narahari, Saravu R

2015-01-01

The journals that publish on Ayurveda are increasingly indexed by popular medical databases in recent years. However, many Eastern journals are not indexed biomedical journal databases such as PubMed. Literature searches for Ayurveda continue to be challenging due to the nonavailability of active, unbiased dedicated databases for Ayurvedic literature. In 2010, authors identified 46 databases that can be used for systematic search of Ayurvedic papers and theses. This update reviewed our previous recommendation and identified current and relevant databases. To update on Ayurveda literature search and strategy to retrieve maximum publications. Author used psoriasis as an example to search previously listed databases and identify new. The population, intervention, control, and outcome table included keywords related to psoriasis and Ayurvedic terminologies for skin diseases. Current citation update status, search results, and search options of previous databases were assessed. Eight search strategies were developed. Hundred and five journals, both biomedical and Ayurveda, which publish on Ayurveda, were identified. Variability in databases was explored to identify bias in journal citation. Five among 46 databases are now relevant - AYUSH research portal, Annotated Bibliography of Indian Medicine, Digital Helpline for Ayurveda Research Articles (DHARA), PubMed, and Directory of Open Access Journals. Search options in these databases are not uniform, and only PubMed allows complex search strategy. "The Researches in Ayurveda" and "Ayurvedic Research Database" (ARD) are important grey resources for hand searching. About 44/105 (41.5%) journals publishing Ayurvedic studies are not indexed in any database. Only 11/105 (10.4%) exclusive Ayurveda journals are indexed in PubMed. AYUSH research portal and DHARA are two major portals after 2010. It is mandatory to search PubMed and four other databases because all five carry citations from different groups of journals. The hand searching is important to identify Ayurveda publications that are not indexed elsewhere. Availability information of citations in Ayurveda libraries from National Union Catalogue of Scientific Serials in India if regularly updated will improve the efficacy of hand searching. A grey database (ARD) contains unpublished PG/Ph.D. theses. The AYUSH portal, DHARA (funded by Ministry of AYUSH), and ARD should be merged to form single larger database to limit Ayurveda literature searches.

DSSTOX: NEW ON-LINE RESOURCE FOR PUBLISHING AND INTEGRATING STANDARDIZED STRUCTURE-INCLUSIVE TOXICITY DATABASES

EPA Science Inventory

DSSTox: New On-line Resource for Publishing Structure-Standardized Toxicity Databases

Ann M Richard1, Jamie Burch2, ClarLynda Williams3
1Nat. Health and Environ. Effects Res. Lb, US EP& Ret Triangle Park, NC 27711; 2EPA-NC
Central Univ Student COOP, US EPA, lies. Tri...

Introducing a New Interface for the Online MagIC Database by Integrating Data Uploading, Searching, and Visualization

NASA Astrophysics Data System (ADS)

Jarboe, N.; Minnett, R.; Constable, C.; Koppers, A. A.; Tauxe, L.

2013-12-01

The Magnetics Information Consortium (MagIC) is dedicated to supporting the paleomagnetic, geomagnetic, and rock magnetic communities through the development and maintenance of an online database (http://earthref.org/MAGIC/), data upload and quality control, searches, data downloads, and visualization tools. While MagIC has completed importing some of the IAGA paleomagnetic databases (TRANS, PINT, PSVRL, GPMDB) and continues to import others (ARCHEO, MAGST and SECVR), further individual data uploading from the community contributes a wealth of easily-accessible rich datasets. Previously uploading of data to the MagIC database required the use of an Excel spreadsheet using either a Mac or PC. The new method of uploading data utilizes an HTML 5 web interface where the only computer requirement is a modern browser. This web interface will highlight all errors discovered in the dataset at once instead of the iterative error checking process found in the previous Excel spreadsheet data checker. As a web service, the community will always have easy access to the most up-to-date and bug free version of the data upload software. The filtering search mechanism of the MagIC database has been changed to a more intuitive system where the data from each contribution is displayed in tables similar to how the data is uploaded (http://earthref.org/MAGIC/search/). Searches themselves can be saved as a permanent URL, if desired. The saved search URL could then be used as a citation in a publication. When appropriate, plots (equal area, Zijderveld, ARAI, demagnetization, etc.) are associated with the data to give the user a quicker understanding of the underlying dataset. The MagIC database will continue to evolve to meet the needs of the paleomagnetic, geomagnetic, and rock magnetic communities.

Atomic and Molecular Databases, VAMDC (Virtual Atomic and Molecular Data Centre)

NASA Astrophysics Data System (ADS)

Dubernet, Marie-Lise; Zwölf, Carlo Maria; Moreau, Nicolas; Awa Ba, Yaya; VAMDC Consortium

2015-08-01

The "Virtual Atomic and Molecular Data Centre Consortium",(VAMDC Consortium, http://www.vamdc.eu) is a Consortium bound by an Memorandum of Understanding aiming at ensuring the sustainability of the VAMDC e-infrastructure. The current VAMDC e-infrastructure inter-connects about 30 atomic and molecular databases with the number of connected databases increasing every year: some databases are well-known databases such as CDMS, JPL, HITRAN, VALD,.., other databases have been created since the start of VAMDC. About 90% of our databases are used for astrophysical applications. The data can be queried, retrieved, visualized in a single format from a general portal (http://portal.vamdc.eu) and VAMDC is also developing standalone tools in order to retrieve and handle the data. VAMDC provides software and support in order to include databases within the VAMDC e-infrastructure. One current feature of VAMDC is the constrained environnement of description of data that ensures a higher quality for distribution of data; a future feature is the link of VAMDC with evaluation/validation groups. The talk will present the VAMDC Consortium and the VAMDC e infrastructure with its underlying technology, its services, its science use cases and its etension towards other communities than the academic research community.

Development and Uses of Offline and Web-Searchable Metabolism Databases - The Case of Benzo[a]pyrene.

PubMed

Rendic, Slobodan P; Guengerich, Frederick P

2018-01-01

The present work describes development of offline and web-searchable metabolism databases for drugs, other chemicals, and physiological compounds using human and model species, prompted by the large amount of data published after year 1990. The intent was to provide a rapid and accurate approach to published data to be applied both in science and to assist therapy. Searches for the data were done using the Pub Med database, accessing the Medline database of references and abstracts. In addition, data presented at scientific conferences (e.g., ISSX conferences) are included covering the publishing period beginning with the year 1976. Application of the data is illustrated by the properties of benzo[a]pyrene (B[a]P) and its metabolites. Analysis show higher activity of P450 1A1 for activation of the (-)- isomer of trans-B[a]P-7,8-diol, while P4501B1 exerts higher activity for the (+)- isomer. P450 1A2 showed equally low activity in the metabolic activation of both isomers. The information collected in the databases is applicable in prediction of metabolic drug-drug and/or drug-chemical interactions in clinical and environmental studies. The data on the metabolism of searched compound (exemplified by benzo[a]pyrene and its metabolites) also indicate toxicological properties of the products of specific reactions. The offline and web-searchable databases had wide range of applications (e.g. computer assisted drug design and development, optimization of clinical therapy, toxicological applications) and adjustment in everyday life styles. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

ENGAGING THE COMMUNITY IN HEALTH RESEARCH IN INDIA

PubMed Central

Wells, Kristen J.; Preuss, Charles; Pathak, Yashwant; Kosambiya, J. K.; Kumar, Ambuj

2013-01-01

Community-engaged research approaches involve members of the community in various aspects of a research endeavor to improve the health of populations. Engaging the community in research is important in the development, dissemination, and evaluation of new interventions, technologies, and other medical advancements to improve population health globally. A review of published community-engaged research studies conducted in India was performed. Fifteen published studies were identified and reviewed to evaluate the state of community-engaged research in India. The review indicated that community-engaged research in India is limited. Most published community-engaged research focused on health promotion, especially in the prevention or management of HIV/AIDS and other STIs. Community members were involved in a variety of aspects of the research, but there was not one published article indicating that community members had defined the disease of focus. Community-engaged research often led to valuable insights into the views, experiences, and behaviors of community members and also led to increased community participation in health initiatives. It is anticipated that future community-engaged research will lead to improvements in global health through increased empowerment of communities and a better ability to implement new and innovative medical advances, technologies, and interventions. PMID:24353757

Comprehensive review of the evidence regarding the effectiveness of community-based primary health care in improving maternal, neonatal and child health: 1. rationale, methods and database description.

PubMed

Perry, Henry B; Rassekh, Bahie M; Gupta, Sundeep; Wilhelm, Jess; Freeman, Paul A

2017-06-01

Community-based primary health care (CBPHC) is an approach used by health programs to extend preventive and curative health services beyond health facilities into communities and even down to households. Evidence of the effectiveness of CBPHC in improving maternal, neonatal and child health (MNCH) has been summarized by others, but our review gives particular attention to not only the effectiveness of specific interventions but also their delivery strategies at the community level along with their equity effects. This is the first article in a series that summarizes and analyzes the assessments of programs, projects, and research studies (referred to collectively as projects) that used CBPHC to improve MNCH in low- and middle-income countries. The review addresses the following questions: (1) What kinds of projects were implemented? (2) What were the outcomes of these projects? (3) What kinds of implementation strategies were used? (4) What are the implications of these findings? 12 166 reports were identified through a search of articles in the National Library of Medicine database (PubMed). In addition, reports in the gray literature (available online but not published in a peer-reviewed journal) were also reviewed. Reports that describe the implementation of one or more community-based interventions or an integrated project in which an assessment of the effectiveness of the project was carried out qualified for inclusion in the review. Outcome measures that qualified for inclusion in the review were population-based indicators that defined some aspect of health status: changes in population coverage of evidence-based interventions or changes in serious morbidity, in nutritional status, or in mortality. 700 assessments qualified for inclusion in the review. Two independent reviewers completed a data extraction form for each assessment. A third reviewer compared the two data extraction forms and resolved any differences. The maternal interventions assessed concerned education about warning signs of pregnancy and safe delivery; promotion and/or provision of antenatal care; promotion and/or provision of safe delivery by a trained birth attendant, screening and treatment for HIV infection and other maternal infections; family planning, and; HIV prevention and treatment. The neonatal and child health interventions that were assessed concerned promotion or provision of good nutrition and immunizations; promotion of healthy household behaviors and appropriate utilization of health services, diagnosis and treatment of acute neonatal and child illness; and provision and/or promotion of safe water, sanitation and hygiene. Two-thirds of assessments (63.0%) were for projects implementing three or fewer interventions in relatively small populations for relatively brief periods; half of the assessments involved fewer than 5000 women or children, and 62.9% of the assessments were for projects lasting less than 3 years. One-quarter (26.6%) of the projects were from three countries in South Asia: India, Bangladesh and Nepal. The number of reports has grown markedly during the past decade. A small number of funders supported most of the assessments, led by the United States Agency for International Development. The reviewers judged the methodology for 90% of the assessments to be adequate. The evidence regarding the effectiveness of community-based interventions to improve the health of mothers, neonates, and children younger than 5 years of age is growing rapidly. The database created for this review serves as the basis for a series of articles that follow this one on the effectiveness of CBPHC in improving MNCH published in the Journal of Global Health. These findings, together with recommendations provided by an Expert Panel which has guided this review, that are included as the last paper in this series, will help to provide the rationale for building stronger community-based platforms for delivering evidence-based interventions in high-mortality, resource-constrained settings.

Subject and authorship of records related to the Organization for Tropical Studies (OTS) in BINABITROP, a comprehensive database about Costa Rican biology.

PubMed

Monge-Nájera, Julián; Nielsen-Muñoz, Vanessa; Azofeifa-Mora, Ana Beatriz

2013-06-01

BINABITROP is a bibliographical database of more than 38000 records about the ecosystems and organisms of Costa Rica. In contrast with commercial databases, such as Web of Knowledge and Scopus, which exclude most of the scientific journals published in tropical countries, BINABITROP is a comprehensive record of knowledge on the tropical ecosystems and organisms of Costa Rica. We analyzed its contents in three sites (La Selva, Palo Verde and Las Cruces) and recorded scientific field, taxonomic group and authorship. We found that most records dealt with ecology and systematics, and that most authors published only one article in the study period (1963-2011). Most research was published in four journals: Biotropica, Revista de Biología Tropical/ International Journal of Tropical Biology and Conservation, Zootaxa and Brenesia. This may be the first study of a such a comprehensive database for any case of tropical biology literature.

Implementation of the CUAHSI information system for regional hydrological research and workflow

NASA Astrophysics Data System (ADS)

Bugaets, Andrey; Gartsman, Boris; Bugaets, Nadezhda; Krasnopeyev, Sergey; Krasnopeyeva, Tatyana; Sokolov, Oleg; Gonchukov, Leonid

2013-04-01

Environmental research and education have become increasingly data-intensive as a result of the proliferation of digital technologies, instrumentation, and pervasive networks through which data are collected, generated, shared, and analyzed. Over the next decade, it is likely that science and engineering research will produce more scientific data than has been created over the whole of human history (Cox et al., 2006). Successful using these data to achieve new scientific breakthroughs depends on the ability to access, organize, integrate, and analyze these large datasets. The new project of PGI FEB RAS (http://tig.dvo.ru), FERHRI (www.ferhri.org) and Primgidromet (www.primgidromet.ru) is focused on creation of an open unified hydrological information system according to the international standards to support hydrological investigation, water management and forecasts systems. Within the hydrologic science community, the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (http://his.cuahsi.org) has been developing a distributed network of data sources and functions that are integrated using web services and that provide access to data, tools, and models that enable synthesis, visualization, and evaluation of hydrologic system behavior. Based on the top of CUAHSI technologies two first template databases were developed for primary datasets of special observations on experimental basins in the Far East Region of Russia. The first database contains data of special observation performed on the former (1957-1994) Primorskaya Water-Balance Station (1500 km2). Measurements were carried out on 20 hydrological and 40 rain gauging station and were published as special series but only as hardcopy books. Database provides raw data from loggers with hourly and daily time support. The second database called «FarEastHydro» provides published standard daily measurement performed at Roshydromet observation network (200 hydrological and meteorological stations) for the period beginning 1930 through 1990. Both of the data resources are maintained in a test mode at the project site http://gis.dvo.ru:81/, which is permanently updated. After first success, the decision was made to use the CUAHSI technology as a basis for development of hydrological information system to support data publishing and workflow of Primgidromet, the regional office of Federal State Hydrometeorological Agency. At the moment, Primgidromet observation network is equipped with 34 automatic SEBA hydrological pressure sensor pneumatic gauges PS-Light-2 and 36 automatic SEBA weather stations. Large datasets generated by sensor networks are organized and stored within a central ODM database which allows to unambiguously interpret the data with sufficient metadata and provides traceable heritage from raw measurements to useable information. Organization of the data within a central CUAHSI ODM database was the most critical step, with several important implications. This technology is widespread and well documented, and it ensures that all datasets are publicly available and readily used by other investigators and developers to support additional analyses and hydrological modeling. Implementation of ODM within a Relational Database Management System eliminates the potential data manipulation errors and intermediate the data processing steps. Wrapping CUAHSI WaterOneFlow web-service into OpenMI 2.0 linkable component (www.openmi.org) allows a seamless integration with well-known hydrological modeling systems.

Data Sharing in Astrobiology: the Astrobiology Habitable Environments Database (AHED)

NASA Astrophysics Data System (ADS)

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

2016-12-01

Astrobiology is a multidisciplinary area of scientific research focused on studying the origins of life on Earth and the conditions under which life might have emerged elsewhere in the universe. The understanding of complex questions in astrobiology requires integration and analysis of data spanning a range of disciplines including biology, chemistry, geology, astronomy and planetary science. However, the lack of a centralized repository makes it difficult for astrobiology teams to share data and benefit from resultant synergies. Moreover, in recent years, federal agencies are requiring that results of any federally funded scientific research must be available and useful for the public and the science community. Astrobiology, as any other scientific discipline, needs to respond to these mandates. The Astrobiology Habitable Environments Database (AHED) is a central, high quality, long-term searchable repository designed to help the community by promoting the integration and sharing of all the data generated by these diverse disciplines. AHED provides public and open-access to astrobiology-related research data through a user-managed web portal implemented using the open-source software The Open Data Repository's (ODR) Data Publisher [1]. ODR-DP provides a user-friendly interface that research teams or individual scientists can use to design, populate and manage their own databases or laboratory notebooks according to the characteristics of their data. AHED is then a collection of databases housed in the ODR framework that store information about samples, along with associated measurements, analyses, and contextual information about field sites where samples were collected, the instruments or equipment used for analysis, and people and institutions involved in their collection. Advanced graphics are implemented together with advanced online tools for data analysis (e.g. R, MATLAB, Project Jupyter-http://jupyter.org). A permissions system will be put in place so that as data are being actively collected and interpreted, they will remain proprietary. A citation system will allow research data to be used and appropriately referenced by other researchers after the data are made public. This project is supported by SERA and NASA NNX11AP82A, MSL. [1] Stone et al. (2016) AGU, submitted.

16 CFR § 1102.4 - Scope.

Code of Federal Regulations, 2013 CFR

2013-01-01

... AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Background and Definitions § 1102.4 Scope. This part... Product Safety Information Database, including all information published therein. ...

PrimateLit: About the Project

Science.gov Websites

Info Center WI Regional Primate Resource Center About the Project The PrimateLit database provides communities. Coverage of the database spans 1940 to present and includes all publication categories (articles will also be found in a search of the whole database. Books Received includes review copies of books

A Review of Databases Used in Orthopaedic Surgery Research and an Analysis of Database Use in Arthroscopy: The Journal of Arthroscopic and Related Surgery.

PubMed

Weinreb, Jeffrey H; Yoshida, Ryu; Cote, Mark P; O'Sullivan, Michael B; Mazzocca, Augustus D

2017-01-01

The purpose of this study was to evaluate how database use has changed over time in Arthroscopy: The Journal of Arthroscopic and Related Surgery and to inform readers about available databases used in orthopaedic literature. An extensive literature search was conducted to identify databases used in Arthroscopy and other orthopaedic literature. All articles published in Arthroscopy between January 1, 2006, and December 31, 2015, were reviewed. A database was defined as a national, widely available set of individual patient encounters, applicable to multiple patient populations, used in orthopaedic research in a peer-reviewed journal, not restricted by encounter setting or visit duration, and with information available in English. Databases used in Arthroscopy included PearlDiver, the American College of Surgeons National Surgical Quality Improvement Program, the Danish Common Orthopaedic Database, the Swedish National Knee Ligament Register, the Hospital Episodes Statistics database, and the National Inpatient Sample. Database use increased significantly from 4 articles in 2013 to 11 articles in 2015 (P = .012), with no database use between January 1, 2006, and December 31, 2012. Database use increased significantly between January 1, 2006, and December 31, 2015, in Arthroscopy. Level IV, systematic review of Level II through IV studies. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Characteristics of Smartphone Applications for Nutrition Improvement in Community Settings: A Scoping Review1234

PubMed Central

Brimblecombe, Julie; Wycherley, Thomas Philip

2017-01-01

Smartphone applications are increasingly being used to support nutrition improvement in community settings. However, there is a scarcity of practical literature to support researchers and practitioners in choosing or developing health applications. This work maps the features, key content, theoretical approaches, and methods of consumer testing of applications intended for nutrition improvement in community settings. A systematic, scoping review methodology was used to map published, peer-reviewed literature reporting on applications with a specific nutrition-improvement focus intended for use in the community setting. After screening, articles were grouped into 4 categories: dietary self-monitoring trials, nutrition improvement trials, application description articles, and qualitative application development studies. For mapping, studies were also grouped into categories based on the target population and aim of the application or program. Of the 4818 titles identified from the database search, 64 articles were included. The broad categories of features found to be included in applications generally corresponded to different behavior change support strategies common to many classic behavioral change models. Key content of applications generally focused on food composition, with tailored feedback most commonly used to deliver educational content. Consumer testing before application deployment was reported in just over half of the studies. Collaboration between practitioners and application developers promotes an appropriate balance of evidence-based content and functionality. This work provides a unique resource for program development teams and practitioners seeking to use an application for nutrition improvement in community settings. PMID:28298274

[Producing know-how and making recommendations for promoting high blood pressure management in Colombia , 1998-2005].

PubMed

Ortega-Bolaños, Jesús

2008-01-01

Producing know-how and making recommendations concerning the most effective health promotion community interventions for managing high blood pressure in Colombia. A systematic review was made of the Cochrane, Lilacs, Ovid, Proquest and Pubmed databases, the main interest of the study lying within the framework of the most effective community interventions around the world for managing high blood pressure. The following search words were used: systematic review, community intervention, cost effectiveness, health promotion and high blood pressure. Studies published in Spanish, English and Portuguese were reviewed. The research strategies used were derived from defining the most pertinent methodological approach for involving individual, interpersonal and community levels in developing the project. 1,041 articles were obtained from the systematic review of the literature: 246 abstracts, 197 articles about educational interventions for preventing and controlling high blood pressure and 53 articles adopting different approaches regarding informative interventions and communication. Only 11 complete referenced articles from this world of information fulfilled the levels of evidence and evaluation criteria necessary for producing recommendations. The available evidence concerning effective, culturally-suitable programmes and for promoting a reduction in these risk factors is limited. Greater evidence regarding community interventions is required for reducing risk factors directed towards special population groups adapted to the cultural characteristics of the participating population. This must involve determinants of the social and physical context related to social practices, these being developed on a large scale within the daily settings in which the subjects and their families are living.

Characteristics of Smartphone Applications for Nutrition Improvement in Community Settings: A Scoping Review.

PubMed

Tonkin, Emma; Brimblecombe, Julie; Wycherley, Thomas Philip

2017-03-01

Smartphone applications are increasingly being used to support nutrition improvement in community settings. However, there is a scarcity of practical literature to support researchers and practitioners in choosing or developing health applications. This work maps the features, key content, theoretical approaches, and methods of consumer testing of applications intended for nutrition improvement in community settings. A systematic, scoping review methodology was used to map published, peer-reviewed literature reporting on applications with a specific nutrition-improvement focus intended for use in the community setting. After screening, articles were grouped into 4 categories: dietary self-monitoring trials, nutrition improvement trials, application description articles, and qualitative application development studies. For mapping, studies were also grouped into categories based on the target population and aim of the application or program. Of the 4818 titles identified from the database search, 64 articles were included. The broad categories of features found to be included in applications generally corresponded to different behavior change support strategies common to many classic behavioral change models. Key content of applications generally focused on food composition, with tailored feedback most commonly used to deliver educational content. Consumer testing before application deployment was reported in just over half of the studies. Collaboration between practitioners and application developers promotes an appropriate balance of evidence-based content and functionality. This work provides a unique resource for program development teams and practitioners seeking to use an application for nutrition improvement in community settings. © 2017 American Society for Nutrition.

16 CFR 1102.4 - Scope.

Code of Federal Regulations, 2011 CFR

2011-01-01

... CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011) Background and Definitions § 1102.4 Scope... Available Consumer Product Safety Information Database, including all information published therein. ...

Navigating from Publications to Astronomical Databases

NASA Astrophysics Data System (ADS)

Ochsenbein, François; Bertout, Claude; Lequeux, James; Genova, Françoise

The implementation of journals on the Web has opened new possibilities for the scientific usage of published results because it is now possible to link published articles to other types of information. The availability of published information in electronic form also allows for new types of content validation, complementary to the referee's validation, and to the layout performed by the publisher. For several years now, authors publishing in A&A are offered the possibility of quoting the astronomical objects they are studying directly in their latex manuscript (via the object macro). Since April 2001, this macro is being translated into an actual link from the article to the SIMBAD database. This experiment is still a prototype, and its various aspects are presented here.

Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation.

PubMed

Poos, Kathrin; Smida, Jan; Nathrath, Michaela; Maugg, Doris; Baumhoer, Daniel; Neumann, Anna; Korsching, Eberhard

2014-01-01

Osteosarcoma (OS) is the most common primary bone cancer exhibiting high genomic instability. This genomic instability affects multiple genes and microRNAs to a varying extent depending on patient and tumor subtype. Massive research is ongoing to identify genes including their gene products and microRNAs that correlate with disease progression and might be used as biomarkers for OS. However, the genomic complexity hampers the identification of reliable biomarkers. Up to now, clinico-pathological factors are the key determinants to guide prognosis and therapeutic treatments. Each day, new studies about OS are published and complicate the acquisition of information to support biomarker discovery and therapeutic improvements. Thus, it is necessary to provide a structured and annotated view on the current OS knowledge that is quick and easily accessible to researchers of the field. Therefore, we developed a publicly available database and Web interface that serves as resource for OS-associated genes and microRNAs. Genes and microRNAs were collected using an automated dictionary-based gene recognition procedure followed by manual review and annotation by experts of the field. In total, 911 genes and 81 microRNAs related to 1331 PubMed abstracts were collected (last update: 29 October 2013). Users can evaluate genes and microRNAs according to their potential prognostic and therapeutic impact, the experimental procedures, the sample types, the biological contexts and microRNA target gene interactions. Additionally, a pathway enrichment analysis of the collected genes highlights different aspects of OS progression. OS requires pathways commonly deregulated in cancer but also features OS-specific alterations like deregulated osteoclast differentiation. To our knowledge, this is the first effort of an OS database containing manual reviewed and annotated up-to-date OS knowledge. It might be a useful resource especially for the bone tumor research community, as specific information about genes or microRNAs is quick and easily accessible. Hence, this platform can support the ongoing OS research and biomarker discovery. Database URL: http://osteosarcoma-db.uni-muenster.de. © The Author(s) 2014. Published by Oxford University Press.

The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database

PubMed Central

Engel, Stacia R.; Cherry, J. Michael

2013-01-01

The first completed eukaryotic genome sequence was that of the yeast Saccharomyces cerevisiae, and the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the original model organism database. SGD remains the authoritative community resource for the S. cerevisiae reference genome sequence and its annotation, and continues to provide comprehensive biological information correlated with S. cerevisiae genes and their products. A diverse set of yeast strains have been sequenced to explore commercial and laboratory applications, and a brief history of those strains is provided. The publication of these new genomes has motivated the creation of new tools, and SGD will annotate and provide comparative analyses of these sequences, correlating changes with variations in strain phenotypes and protein function. We are entering a new era at SGD, as we incorporate these new sequences and make them accessible to the scientific community, all in an effort to continue in our mission of educating researchers and facilitating discovery. Database URL: http://www.yeastgenome.org/ PMID:23487186

Novel ITS1 Fungal Primers for Characterization of the Mycobiome

PubMed Central

Usyk, Mykhaylo; Zolnik, Christine P.; Patel, Hitesh; Levi, Michael H.

2017-01-01

ABSTRACT Studies of the human microbiome frequently omit characterization of fungal communities (the mycobiome), which limits our ability to investigate how fungal communities influence human health. The internal transcribed spacer 1 (ITS1) region of the eukaryotic ribosomal cluster has features allowing for wide taxonomic coverage and has been recognized as a suitable barcode region for species-level identification of fungal organisms. We developed custom ITS1 primer sets using iterative alignment refinement. Primer performance was evaluated using in silico testing and experimental testing of fungal cultures and human samples. Using an expanded novel reference database, SIS (18S-ITS1-5.8S), the newly designed primers showed an average in silico taxonomic coverage of 79.9% ± 7.1% compared to a coverage of 44.6% ± 13.2% using previously published primers (P = 0.05). The newly described primer sets recovered an average of 21,830 ± 225 fungal reads from fungal isolate culture samples, whereas the previously published primers had an average of 3,305 ± 1,621 reads (P = 0.03). Of note was an increase in the taxonomic coverage of the Candida genus, which went from a mean coverage of 59.5% ± 13% to 100.0% ± 0.0% (P = 0.0015) comparing the previously described primers to the new primers, respectively. The newly developed ITS1 primer sets significantly improve general taxonomic coverage of fungal communities infecting humans and increased read depth by an order of magnitude over the best-performing published primer set tested. The overall best-performing primer pair in terms of taxonomic coverage and read recovery, ITS1-30F/ITS1-217R, will aid in advancing research in the area of the human mycobiome. IMPORTANCE The mycobiome constitutes all the fungal organisms within an environment or biological niche. The fungi are eukaryotes, are extremely heterogeneous, and include yeasts and molds that colonize humans as part of the microbiome. In addition, fungi can also infect humans and cause disease. Characterization of the bacterial component of the microbiome was revolutionized by 16S rRNA gene fragment amplification, next-generation sequencing technologies, and bioinformatics pipelines. Characterization of the mycobiome has often not been included in microbiome studies because of limitations in amplification systems. This report revisited the selection of PCR primers that amplify the fungal ITS1 region. We have identified primers with superior identification of fungi present in the database. We have compared the new primer sets against those previously used in the literature and show a significant improvement in read count and taxon identification. These primers should facilitate the study of fungi in human physiology and disease states. PMID:29242834

Effect of environmental exposure to hydrogen sulfide on central nervous system and respiratory function: a systematic review of human studies

PubMed Central

Lim, Eunjung; Mbowe, Omar; Lee, Angela S. W.; Davis, James

2016-01-01

Background Assessment of the health effects of low-level exposure to hydrogen sulfide (H2S) on humans through experiments, industrial, and community studies has shown inconsistent results. Objective To critically appraise available studies investigating the effect of H2S on the central nervous system (CNS) and on respiratory function. Methods A search was conducted in 16 databases for articles published between January 1980 and July 2014. Two researchers independently evaluated potentially relevant papers based on a set of inclusion/exclusion criteria. Results Twenty-seven articles met the inclusion criteria: 6 experimental, 12 industry-based studies, and 10 community-based studies (one article included both experimental and industry-based studies). The results of the systematic review varied by study setting and quality. Several community-based studies reported associations between day-to-day variations in H2S levels and health outcomes among patients with chronic respiratory conditions. However, evidence from the largest and better-designed community-based studies did not support that chronic, ambient H2S exposure has health effects on the CNS or respiratory function. Results from industry-based studies varied, reflecting the diversity of settings and the broad range of H2S exposures. Most studies did not have individual measurements of H2S exposure. Discussion The results across studies were inconsistent, justifying the need for further research. PMID:27128692

Effect of environmental exposure to hydrogen sulfide on central nervous system and respiratory function: a systematic review of human studies.

PubMed

Lim, Eunjung; Mbowe, Omar; Lee, Angela S W; Davis, James

2016-01-01

Assessment of the health effects of low-level exposure to hydrogen sulfide (H2S) on humans through experiments, industrial, and community studies has shown inconsistent results. To critically appraise available studies investigating the effect of H2S on the central nervous system (CNS) and on respiratory function. A search was conducted in 16 databases for articles published between January 1980 and July 2014. Two researchers independently evaluated potentially relevant papers based on a set of inclusion/exclusion criteria. Twenty-seven articles met the inclusion criteria: 6 experimental, 12 industry-based studies, and 10 community-based studies (one article included both experimental and industry-based studies). The results of the systematic review varied by study setting and quality. Several community-based studies reported associations between day-to-day variations in H2S levels and health outcomes among patients with chronic respiratory conditions. However, evidence from the largest and better-designed community-based studies did not support that chronic, ambient H2S exposure has health effects on the CNS or respiratory function. Results from industry-based studies varied, reflecting the diversity of settings and the broad range of H2S exposures. Most studies did not have individual measurements of H2S exposure. The results across studies were inconsistent, justifying the need for further research.

More bark than bite: Comparative studies are needed to determine the importance of canine zoonoses in Aboriginal communities. A critical review of published research.

PubMed

Smout, F; Schrieber, L; Speare, R; Skerratt, L F

2017-11-01

The objective of this review was to identify and critique over forty years of peer-reviewed literature concerned with the transmission of canine zoonoses to Aboriginal people and determine the zoonotic organisms documented in dogs in Australian Aboriginal communities. A systematic literature search of public health, medical and veterinary databases identified 19 articles suitable for critical appraisal. Thirteen articles documented the occurrence of recognized zoonotic organisms in dogs in Aboriginal communities, including Toxocara canis, Dirofilaria immitis, Streptococcus dysgalactiae, Rickettsia felis, Sarcoptes scabiei and Giardia. Currently, there is definitive evidence indicating that dogs act as a reservoir for human scabies in Aboriginal communities. However, there is a need for large-scale, high-quality, comparative studies of dogs and humans from the same household to assess the occurrence and importance of transmission of S. scabiei and other diseases between dogs and humans. These studies should use current genetic and molecular techniques along with traditional techniques to identify and type organisms in order to better understand their epidemiology. This review has revealed that there is a lack of high-quality comparative studies to determine whether dogs are contributing to human disease by transmitting zoonoses. Our recommendations differ significantly from current public health policy and may have substantial implications for human and dog health. © 2017 Blackwell Verlag GmbH.

16 CFR 1102.10 - Reports of harm.

Code of Federal Regulations, 2012 CFR

2012-01-01

... AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.10 Reports of harm. (a... they have a public safety purpose. (b) Manner of submission. To be entered into the Database, reports... Commission will publish in the Publicly Available Consumer Product Safety Information Database reports of...

16 CFR 1102.10 - Reports of harm.

Code of Federal Regulations, 2014 CFR

2014-01-01

... AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.10 Reports of harm. (a... they have a public safety purpose. (b) Manner of submission. To be entered into the Database, reports... Commission will publish in the Publicly Available Consumer Product Safety Information Database reports of...

16 CFR 1102.10 - Reports of harm.

Code of Federal Regulations, 2011 CFR

2011-01-01

... AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011) Content Requirements § 1102.10... they have a public safety purpose. (b) Manner of submission. To be entered into the Database, reports... Commission will publish in the Publicly Available Consumer Product Safety Information Database reports of...

Database for High Throughput Screening Hits (dHITS): a simple tool to retrieve gene specific phenotypes from systematic screens done in yeast.

PubMed

Chuartzman, Silvia G; Schuldiner, Maya

2018-03-25

In the last decade several collections of Saccharomyces cerevisiae yeast strains have been created. In these collections every gene is modified in a similar manner such as by a deletion or the addition of a protein tag. Such libraries have enabled a diversity of systematic screens, giving rise to large amounts of information regarding gene functions. However, often papers describing such screens focus on a single gene or a small set of genes and all other loci affecting the phenotype of choice ('hits') are only mentioned in tables that are provided as supplementary material and are often hard to retrieve or search. To help unify and make such data accessible, we have created a Database of High Throughput Screening Hits (dHITS). The dHITS database enables information to be obtained about screens in which genes of interest were found as well as the other genes that came up in that screen - all in a readily accessible and downloadable format. The ability to query large lists of genes at the same time provides a platform to easily analyse hits obtained from transcriptional analyses or other screens. We hope that this platform will serve as a tool to facilitate investigation of protein functions to the yeast community. © 2018 The Authors Yeast Published by John Wiley & Sons Ltd.

Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data.

PubMed

Edwards, J D; Baldo, A M; Mueller, L A

2016-01-01

Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the United States.

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.

PubMed

Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C; Hoeng, Julia

2015-01-01

With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com © The Author(s) 2015. Published by Oxford University Press.

"Trust is not something you can reclaim easily": patenting in the field of direct-to-consumer genetic testing.

PubMed

Sterckx, Sigrid; Cockbain, Julian; Howard, Heidi; Huys, Isabelle; Borry, Pascal

2013-05-01

Recently, 23andMe announced that it had obtained its first patent, related to "polymorphisms associated with Parkinson's disease" (US-B-8187811). This announcement immediately sparked controversy in the community of 23andMe users and research participants, especially with regard to issues of transparency and trust. The purpose of this article was to analyze the patent portfolio of this prominent direct-to-consumer genetic testing company and discuss the potential ethical implications of patenting in this field for public participation in Web-based genetic research. We searched the publicly accessible patent database Espacenet as well as the commercially available database Micropatent for published patents and patent applications of 23andMe. Six patent families were identified for 23andMe. These included patent applications related to: genetic comparisons between grandparents and grandchildren, family inheritance, genome sharing, processing data from genotyping chips, gamete donor selection based on genetic calculations, finding relatives in a database, and polymorphisms associated with Parkinson disease. An important lesson to be drawn from this ongoing controversy seems to be that any (private or public) organization involved in research that relies on human participation, whether by providing information, body material, or both, needs to be transparent, not only about its research goals but also about its strategies and policies regarding commercialization.

[Scientific Evidence on Preventive Interventions in Childhood Obesity].

PubMed

Alba-Martín, Raquel

The increasing prevalence of obesity or overweight at all ages, their associated morbidity and mortality associated, and the increased perception of the problem by the society have generated several hypotheses in response to the scientific and the international community. Investigate the preventive interventions in childhood obesity so far. Integrative review during the study period from April 2013 to November 2014. The MEDLINE international database was used, including PubMed, the Cochrane Library (Issue 4 2002), the national database Isooc (CSIC) national database, as well as the Internet. The review included health articles published in Spanish and English between 1990 and 2014 that focused on or included education, prevention, diagnostic, and treatment of obesity interventions. Of the 726 articles identified, 34 of most relevant (peer reviewed) were selected. It was noted that there is limited generisable evidence on interventions that could be implemented in Primary Care or referral services available, although numerous studies suggest that improvements in the overweight are possible. Despite the abundant literature and that many institutions place childhood obesity as one of the priorities of Public Health, we face the paradox that the evidence on cost-effectiveness of prevention interventions is sparse. Knowing these gaps in knowledge should lead to filling them with rigorous and well-designed studies. Copyright © 2016 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Disbiome database: linking the microbiome to disease.

PubMed

Janssens, Yorick; Nielandt, Joachim; Bronselaer, Antoon; Debunne, Nathan; Verbeke, Frederick; Wynendaele, Evelien; Van Immerseel, Filip; Vandewynckel, Yves-Paul; De Tré, Guy; De Spiegeleer, Bart

2018-06-04

Recent research has provided fascinating indications and evidence that the host health is linked to its microbial inhabitants. Due to the development of high-throughput sequencing technologies, more and more data covering microbial composition changes in different disease types are emerging. However, this information is dispersed over a wide variety of medical and biomedical disciplines. Disbiome is a database which collects and presents published microbiota-disease information in a standardized way. The diseases are classified using the MedDRA classification system and the micro-organisms are linked to their NCBI and SILVA taxonomy. Finally, each study included in the Disbiome database is assessed for its reporting quality using a standardized questionnaire. Disbiome is the first database giving a clear, concise and up-to-date overview of microbial composition differences in diseases, together with the relevant information of the studies published. The strength of this database lies within the combination of the presence of references to other databases, which enables both specific and diverse search strategies within the Disbiome database, and the human annotation which ensures a simple and structured presentation of the available data.

Specialist Bibliographic Databases

PubMed Central

2016-01-01

Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls. PMID:27134485

Specialist Bibliographic Databases.

PubMed

Gasparyan, Armen Yuri; Yessirkepov, Marlen; Voronov, Alexander A; Trukhachev, Vladimir I; Kostyukova, Elena I; Gerasimov, Alexey N; Kitas, George D

2016-05-01

Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls.

CHOmine: an integrated data warehouse for CHO systems biology and modeling.

PubMed

Gerstl, Matthias P; Hanscho, Michael; Ruckerbauer, David E; Zanghellini, Jürgen; Borth, Nicole

2017-01-01

The last decade has seen a surge in published genome-scale information for Chinese hamster ovary (CHO) cells, which are the main production vehicles for therapeutic proteins. While a single access point is available at www.CHOgenome.org, the primary data is distributed over several databases at different institutions. Currently research is frequently hampered by a plethora of gene names and IDs that vary between published draft genomes and databases making systems biology analyses cumbersome and elaborate. Here we present CHOmine, an integrative data warehouse connecting data from various databases and links to other ones. Furthermore, we introduce CHOmodel, a web based resource that provides access to recently published CHO cell line specific metabolic reconstructions. Both resources allow to query CHO relevant data, find interconnections between different types of data and thus provides a simple, standardized entry point to the world of CHO systems biology. http://www.chogenome.org. © The Author(s) 2017. Published by Oxford University Press.

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

PubMed Central

Tripathi, Sushil; Vercruysse, Steven; Chawla, Konika; Christie, Karen R.; Blake, Judith A.; Huntley, Rachael P.; Orchard, Sandra; Hermjakob, Henning; Thommesen, Liv; Lægreid, Astrid; Kuiper, Martin

2016-01-01

A large gap remains between the amount of knowledge in scientific literature and the fraction that gets curated into standardized databases, despite many curation initiatives. Yet the availability of comprehensive knowledge in databases is crucial for exploiting existing background knowledge, both for designing follow-up experiments and for interpreting new experimental data. Structured resources also underpin the computational integration and modeling of regulatory pathways, which further aids our understanding of regulatory dynamics. We argue how cooperation between the scientific community and professional curators can increase the capacity of capturing precise knowledge from literature. We demonstrate this with a project in which we mobilize biological domain experts who curate large amounts of DNA binding transcription factors, and show that they, although new to the field of curation, can make valuable contributions by harvesting reported knowledge from scientific papers. Such community curation can enhance the scientific epistemic process. Database URL: http://www.tfcheckpoint.org PMID:27270715

CORE-Hom: a powerful and exhaustive database of clinical trials in homeopathy.

PubMed

Clausen, Jürgen; Moss, Sian; Tournier, Alexander; Lüdtke, Rainer; Albrecht, Henning

2014-10-01

The CORE-Hom database was created to answer the need for a reliable and publicly available source of information in the field of clinical research in homeopathy. As of May 2014 it held 1048 entries of clinical trials, observational studies and surveys in the field of homeopathy, including second publications and re-analyses. 352 of the trials referenced in the database were published in peer reviewed journals, 198 of which were randomised controlled trials. The most often used remedies were Arnica montana (n = 103) and Traumeel(®) (n = 40). The most studied medical conditions were respiratory tract infections (n = 126) and traumatic injuries (n = 110). The aim of this article is to introduce the database to the public, describing and explaining the interface, features and content of the CORE-Hom database. Copyright © 2014 The Faculty of Homeopathy. Published by Elsevier Ltd. All rights reserved.

Ownership, Access, and Authority: Publishing and Circulating Histories to (Re)Member Community

ERIC Educational Resources Information Center

Monberg, Terese Guinsatao

2017-01-01

In gathering and circulating histories, the Filipino American National Historical Society (FANHS) enacts both community publishing and self-publishing models, as they have been defined in literacy studies. As a community institution situated within a larger constellation of counterpublics and dominant publics that have often overlooked, erased,…

Assessment and Application of National Environmental Databases and Mapping Tools at the Local Level to Two Community Case Studies

EPA Science Inventory

Communities are concerned over pollution levels and seek methods to systematically identify and prioritize the environmental stressors in their communities. Geographic information system (GIS) maps of environmental information can be useful tools for communities in their assessm...

Effect of Reiki therapy on pain and anxiety in adults: an in-depth literature review of randomized trials with effect size calculations.

PubMed

Thrane, Susan; Cohen, Susan M

2014-12-01

The objective of this study was to calculate the effect of Reiki therapy for pain and anxiety in randomized clinical trials. A systematic search of PubMed, ProQuest, Cochrane, PsychInfo, CINAHL, Web of Science, Global Health, and Medline databases was conducted using the search terms pain, anxiety, and Reiki. The Center for Reiki Research also was examined for articles. Studies that used randomization and a control or usual care group, used Reiki therapy in one arm of the study, were published in 2000 or later in peer-reviewed journals in English, and measured pain or anxiety were included. After removing duplicates, 49 articles were examined and 12 articles received full review. Seven studies met the inclusion criteria: four articles studied cancer patients, one examined post-surgical patients, and two analyzed community dwelling older adults. Effect sizes were calculated for all studies using Cohen's d statistic. Effect sizes for within group differences ranged from d = 0.24 for decrease in anxiety in women undergoing breast biopsy to d = 2.08 for decreased pain in community dwelling adults. The between group differences ranged from d = 0.32 for decrease of pain in a Reiki versus rest intervention for cancer patients to d = 4.5 for decrease in pain in community dwelling adults. Although the number of studies is limited, based on the size Cohen's d statistics calculated in this review, there is evidence to suggest that Reiki therapy may be effective for pain and anxiety. Continued research using Reiki therapy with larger sample sizes, consistently randomized groups, and standardized treatment protocols is recommended. Copyright © 2014 American Society for Pain Management Nursing. Published by Elsevier Inc. All rights reserved.

The need for a juvenile fire setting database.

PubMed

Klein, Julianne J; Mondozzi, Mary A; Andrews, David A

2008-01-01

A juvenile fire setter can be classified as any youth setting a fire regardless of the reason. Many communities have programs to deal with this problem, most based on models developed by the United States Fire Administration. We reviewed our programs data to compare it with that published nationally. Currently there is not a nationwide database to compare fire setter data. A single institution, retrospective chart review of all fire setters between the years of January 1, 2003 and December 31, 2005 was completed. There were 133 participants ages 3 to 17. Information obtained included age, location, ignition source, court order and recidivism. Analysis from our data set found 26% of the peak ages for fire involvement to be 12 and 14. Location, ignition source, and court ordered participants were divided into two age groups: 3 to 10 (N = 58) and 11 to 17 (N = 75). Bedrooms ranked first for the younger population and schools for the latter. Fifty-four percentage of the 133 participants used lighters over matches. Twelve percentage of the 3- to 10-year-olds were court mandated, compared with 52% of the 11- to 17-year-olds. Recidivism rates were 4 to 10% with a 33 to 38% survey return rate. Currently there is no state or nationwide, time honored data base to compare facts from which conclusions can be drawn. Starting small with a statewide database could educe a stimulus for a national database. This could also enhance the information provided by the United States Fire Administration, National Fire Data Center beginning one juvenile firesetter program and State Fire Marshal's office at a time.

Classical Observations of Visual Binary and Multiple Stars

NASA Astrophysics Data System (ADS)

Mason, Brian D.

2007-08-01

The database of visual double star data has experienced tremendous changes, doubling in size during the last 25 years and growing at an ever increasing rate. Interferometric techniques have allowed the database to extend to much closer separation (and shorter periods), while longer timebases and higher-precision wide-field surveys have increased our knowledge of common proper motion pairs at the widest separations. These changes in the database are highlighted, describing the evolution of methods of observation (both historically and the past few years) and the effectiveness of these various methods in different regimes of separation/ period space. The various niches for wide- and narrow-field work as applied to double and multiple stars are examined and the different types of information which each can provide are also highlighted. After more than 20 years of successful work, speckle interferometry and conventional CCD astrometry have replaced filar micrometry and photography as the preferred classical techniques. Indeed, most work in filar micrometry is now being done by amateurs, although much of that community is also switching to CCDs and other electronic techniques. Despite the significant growth of the double star database, much still remains to be done, such as finding lost pairs, filling in missing parameters so that observing programs may be more efficient at observing stars appropriate to their capabilities, and providing at least approximate kinematic descriptions. Work on pairs described as neglected at the time of the last major WDS data release (2001) is given as a specific example of recent improvements, and finally the continued need to publish data using classical double star parameters is discussed.

Database Resources of the BIG Data Center in 2018.

PubMed

2018-01-04

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

myPhyloDB: a local web server for the storage and analysis of metagenomic data.

PubMed

Manter, Daniel K; Korsa, Matthew; Tebbe, Caleb; Delgado, Jorge A

2016-01-01

myPhyloDB v.1.1.2 is a user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of microbial community populations (e.g. 16S metagenomics data). MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all available data in the database. The data processing capabilities of myPhyloDB are also flexible enough to allow the upload and storage of pre-processed data, or use the built-in Mothur pipeline to automate the processing of raw sequencing data. myPhyloDB provides several analytical (e.g. analysis of covariance,t-tests, linear regression, differential abundance (DESeq2), and principal coordinates analysis (PCoA)) and normalization (rarefaction, DESeq2, and proportion) tools for the comparative analysis of taxonomic abundance, species richness and species diversity for projects of various types (e.g. human-associated, human gut microbiome, air, soil, and water) for any taxonomic level(s) desired. Finally, since myPhyloDB is a local web-server, users can quickly distribute data between colleagues and end-users by simply granting others access to their personal myPhyloDB database. myPhyloDB is available athttp://www.ars.usda.gov/services/software/download.htm?softwareid=472 and more information along with tutorials can be found on our websitehttp://www.myphylodb.org. Database URL:http://www.myphylodb.org. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the United States.

Development of a prototype system for statewide asthma surveillance.

PubMed

Deprez, Ronald D; Asdigian, Nancy L; Oliver, L Christine; Anderson, Norman; Caldwell, Edgar; Baggott, Lee Ann

2002-12-01

We developed and evaluated a statewide and community-level asthma surveillance system. Databases and measures included a community prevalence survey, hospital admissions data, emergency department/outpatient clinic visit records, and a physician survey of diagnosis and treatment practices. We evaluated the system in 5 Maine communities varying in population and income. Asthma hospitalizations were high in the rural/low-socioeconomic-status communities studied, although diagnosed asthma was low. Males were more likely than females to experience asthma symptoms, although they were less likely to have been diagnosed with asthma or to have used hospital-based asthma care. Databases were useful for estimating asthma burden and identifying service needs as well as high-risk groups. They were less useful in estimating severity or in identifying environmental risks.

Communicable diseases in rural and remote Australia: the need for improved understanding and action.

PubMed

Quinn, Emma K; Massey, Peter D; Speare, Rick

2015-01-01

Rural and remote communities of Australia, particularly those including Aboriginal people, experience greater morbidity and mortality across a range of health outcomes compared to urban communities. Previous national data have demonstrated that rural and remote communities experience a disproportionate burden of communicable diseases compared to their urban counterparts. This systematic review was undertaken to describe the types of research that have explored the epidemiology of communicable diseases in rural and remote communities in Australia, with particular reference to the social determinants of health. We conducted a keyword search of several databases (EMBASE, MEDLINE/PubMed, RURAL, Aboriginal and Torres Strait Islander Health Database, Web of Science Core Collection, and Google and Google Scholar websites) for peer-reviewed and grey literature that described or analysed the epidemiology of communicable diseases in rural and/or remote communities of Australia from 2004 to 2013. Exclusion criteria were applied to keep the review focused on rural and/or remote communities and the population-level epidemiological analysis of communicable diseases. From 2287 retrieved articles, a total of 50 remained after applying exclusion criteria. The majority of included articles were descriptive studies (41/50). Seven of the total 50 articles contained analytical studies; one systematic literature review and one experimental study were also identified. Due to the diversity of approaches in measuring disease burden, we performed a narrative synthesis of the articles according to the review objectives. Most of the articles investigated the disease burden in remote (n=37/50) and Aboriginal communities only (n=21/50). The studies highlighted a high prevalence or incidence of skin, eye and respiratory infections for remote Aboriginal communities, particularly children over the past decade. There was emerging evidence to suggest that housing and social conditions play an important role in determining the risk of skin, ear, respiratory and gastrointestinal infections in children. Other health service and sociocultural factors were also discussed by authors as influencing the epidemiology of communicable diseases in rural and remote communities. This systematic review identified several communicable diseases that continue to cause considerable morbidity in remote Aboriginal communities, including skin, eye and respiratory infections, particularly for children. Overall there is a substantial amount of descriptive epidemiology published, but few analytical or experimental studies. Despite a lack of empirical investigation into the social determinants of the burden of communicable disease, there is emerging evidence that has demonstrated a significant association between housing conditions and skin, ear, respiratory and gastrointestinal infections in children. There is also growing recognition of other social and environmental factors that can influence the burden of diseases in rural and remote communities. Further investment into higher quality community-based research that addresses the social determinants of communicable diseases in remote communities is warranted. The lack of research investigating zoonoses and tropical diseases was noted.

Introducing Scientific Writing as Mandatory Topic in Bachelor Nursing Program - Experience of the University of Dubrovnik, Croatia.

PubMed

Zidarić, Mihaela; Vičić-Hudorović, Višnja; Hudorović, Narcis

2016-06-01

One of the methods that have been used to encourage student reflection skills is scientific writing. The purpose of this article is to discuss implementation of obligatory study topic with the main objective to increase the skills of scientific writing among students of Bachelor Nursing Curriculum and its relation to scientific publishing volume of Bachelor degree students from the University of Dubrovnik. By searching the local rank database called HRČAK, data were collected on publication volume of the Bachelor course students at the University of Dubrovnik from 2010 to 2014. Articles published in the Croatian medical journals in Croatian language were identified. Sixty-six students published 35 articles, alone or with co-authors. Two (6%) articles were written by a single author. Among co-authors from the nursing profession, those with associate degree in nursing (20%) predominated, followed by medical doctors and anthropologists (25%). The total number of authors was 95, and the share of papers published in Croatian language was 100%. The body of published articles increased from 2012 to 2013 by 14%, and then from 2013 to 2014 by 113%. For future investigations, closer insight into novel approaches is needed to encourage nursing students to increase their scientific productivity, especially in English language. In order to enhance international visibility of Croatian nursing authors, academic members of the Croatian scientific nursing community should find additional tools to upgrade scientific productivity of the Croatian nursing authors.

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection.

PubMed

Rigden, Daniel J; Fernández, Xosé M

2018-01-04

The 2018 Nucleic Acids Research Database Issue contains 181 papers spanning molecular biology. Among them, 82 are new and 84 are updates describing resources that appeared in the Issue previously. The remaining 15 cover databases most recently published elsewhere. Databases in the area of nucleic acids include 3DIV for visualisation of data on genome 3D structure and RNArchitecture, a hierarchical classification of RNA families. Protein databases include the established SMART, ELM and MEROPS while GPCRdb and the newcomer STCRDab cover families of biomedical interest. In the area of metabolism, HMDB and Reactome both report new features while PULDB appears in NAR for the first time. This issue also contains reports on genomics resources including Ensembl, the UCSC Genome Browser and ENCODE. Update papers from the IUPHAR/BPS Guide to Pharmacology and DrugBank are highlights of the drug and drug target section while a number of proteomics databases including proteomicsDB are also covered. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been updated, reviewing 138 entries, adding 88 new resources and eliminating 47 discontinued URLs, bringing the current total to 1737 databases. It is available at http://www.oxfordjournals.org/nar/database/c/. © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.

A scientific database for real-time Neutron Monitor measurements - taking Neutron Monitors into the 21st century

NASA Astrophysics Data System (ADS)

Steigies, Christian

2012-07-01

The Neutron Monitor Database project, www.nmdb.eu, has been funded in 2008 and 2009 by the European Commission's 7th framework program (FP7). Neutron monitors (NMs) have been in use worldwide since the International Geophysical Year (IGY) in 1957 and cosmic ray data from the IGY and the improved NM64 NMs has been distributed since this time, but a common data format existed only for data with one hour resolution. This data was first distributed in printed books, later via the World Data Center ftp server. In the 1990's the first NM stations started to record data at higher resolutions (typically 1 minute) and publish in on their webpages. However, every NM station chose their own format, making it cumbersome to work with this distributed data. In NMDB all European and some neighboring NM stations came together to agree on a common format for high-resolution data and made this available via a centralized database. The goal of NMDB is to make all data from all NM stations available in real-time. The original NMDB network has recently been joined by the Bartol Research Institute (Newark DE, USA), the National Autonomous University of Mexico and the North-West University (Potchefstroom, South Africa). The data is accessible to everyone via an easy to use webinterface, but expert users can also directly access the database to build applications like real-time space weather alerts. Even though SQL databases are used today by most webservices (blogs, wikis, social media, e-commerce), the power of an SQL database has not yet been fully realized by the scientific community. In training courses, we are teaching how to make use of NMDB, how to join NMDB, and how to ensure the data quality. The present status of the extended NMDB will be presented. The consortium welcomes further data providers to help increase the scientific contributions of the worldwide neutron monitor network to heliospheric physics and space weather.

Electronic Publishing and Document Delivery; A Case Study of Commercial Information Services on the Internet.

ERIC Educational Resources Information Center

Abbott, Anthony

1992-01-01

Discusses the electronic publishing activities of Meckler Publishing on the Internet, including a publications catalog, an electronic journal, and tables of contents databases. Broader issues of commercial network publishing are also addressed, including changes in the research process, changes in publishing, bibliographic control,…

A systematic narrative review of consumer-directed care for older people: implications for model development.

PubMed

Ottmann, Goetz; Allen, Jacqui; Feldman, Peter

2013-11-01

Consumer-directed care is increasingly becoming a mainstream option in community-based aged care. However, a systematic review describing how the current evaluation research translates into practise has not been published to date. This review aimed to systematically establish an evidence base of user preferences for and satisfaction with services associated with consumer-directed care programmes for older people. Twelve databases were searched, including MedLine, BioMed Central, Cinahl, Expanded Academic ASAP, PsychInfo, ProQuest, Age Line, Science Direct, Social Citation Index, Sociological Abstracts, Web of Science and the Cochrane Library. Google Scholar and Google were also searched. Eligible studies were those reporting on choice, user preferences and service satisfaction outcomes regarding a programme or model of home-based care in the United States or United Kingdom. This systematic narrative review retrieved literature published from January 1992 to August 2011. A total of 277 references were identified. Of these 17 met the selection criteria and were reviewed. Findings indicate that older people report varying preferences for consumer-directed care with some demonstrating limited interest. Clients and carers reported good service satisfaction. However, research comparing user preferences across countries or investigating how ecological factors shape user preferences has received limited attention. Policy-makers and practitioners need to carefully consider the diverse contexts, needs and preferences of older adults in adopting consumer-directed care approaches in community aged care. The review calls for the development of consumer-directed care programmes offering a broad range of options that allow for personalisation and greater control over services without necessarily transferring the responsibility for administrative responsibilities to service users. Review findings suggest that consumer-directed care approaches have the potential to empower older people. © 2013 Blackwell Publishing Ltd.

16 CFR § 1102.10 - Reports of harm.

Code of Federal Regulations, 2013 CFR

2013-01-01

... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.10 Reports of... they have a public safety purpose. (b) Manner of submission. To be entered into the Database, reports... Commission will publish in the Publicly Available Consumer Product Safety Information Database reports of...

PHYTOTOX: DATABASE DEALING WITH THE EFFECT OF ORGANIC CHEMICALS ON TERRESTRIAL VASCULAR PLANTS

EPA Science Inventory

A new database, PHYTOTOX, dealing with the direct effects of exogenously supplied organic chemicals on terrestrial vascular plants is described. The database consists of two files, a Reference File and Effects File. The Reference File is a bibliographic file of published research...

Publication trend, resource utilization, and impact of the US National Cancer Database

PubMed Central

Su, Chang; Peng, Cuiying; Agbodza, Ena; Bai, Harrison X.; Huang, Yuqian; Karakousis, Giorgos; Zhang, Paul J.; Zhang, Zishu

2018-01-01

Abstract Background: The utilization and impact of the studies published using the National Cancer Database (NCDB) is currently unclear. In this study, we aim to characterize the published studies, and identify relatively unexplored areas for future investigations. Methods: A literature search was performed using PubMed in January 2017 to identify all papers published using NCDB data. Characteristics of the publications were extracted. Citation frequencies were obtained through the Web of Science. Results: Three hundred 2 articles written by 230 first authors met the inclusion criteria. The number of publications grew exponentially since 2013, with 108 articles published in 2016. Articles were published in 86 journals. The majority of the published papers focused on digestive system cancer, while bone and joints, eye and orbit, myeloma, mesothelioma, and Kaposi Sarcoma were never studied. Thirteen institutions in the United States were associated with more than 5 publications. The papers have been cited for a total of 9858 times since the publication of the first paper in 1992. Frequently appearing keywords congregated into 3 clusters: “demographics,” “treatments and survival,” and “statistical analysis method.” Even though the main focuses of the articles captured a extremely wide range, they can be classified into 2 main categories: survival analysis and characterization. Other focuses include database(s) analysis and/or comparison, and hospital reporting. Conclusion: The surging interest in the use of NCDB is accompanied by unequal utilization of resources by individuals and institutions. Certain areas were relatively understudied and should be further explored. PMID:29489679

Do community specialist palliative care services that provide home nursing increase rates of home death for people with life-limiting illnesses? A systematic review and meta-analysis of comparative studies.

PubMed

Luckett, Tim; Davidson, Patricia M; Lam, Lawrence; Phillips, Jane; Currow, David C; Agar, Meera

2013-02-01

Systematic reviews and meta-analyses suggest that community specialist palliative care services (SPCSs) can avoid hospitalizations and enable home deaths. But more information is needed regarding the relative efficacies of different models. Family caregivers highlight home nursing as the most important service, but it is also likely the most costly. To establish whether community SPCSs offering home nursing increase rates of home death compared with other models. We searched MEDLINE, AMED, Embase, CINAHL, the Cochrane Database of Systematic Reviews, and CENTRAL on March 2 and 3, 2011. To be eligible, articles had to be published in English-language peer-reviewed journals and report original research comparing the effect on home deaths of SPCSs providing home nursing vs. any alternative. Study quality was independently rated using Cochrane grades. Maximum likelihood estimation of heterogeneity was used to establish the method for meta-analysis (fixed or random effects). Potential biases were assessed. Of 1492 articles screened, 10 articles were found eligible, reporting nine studies that yielded data for 10 comparisons. Study quality was high in two cases, moderate in three and low in four. Meta-analysis indicated a significant effect for SPCSs with home nursing (odds ratio 4.45, 95% CI 3.24-6.11; P<0.001). However, the high-quality studies found no effect (odds ratio 1.40, 95% CI 0.97-2.02; P=0.071). Bias was minimal. A meta-analysis found evidence to be inconclusive that community SPCSs that offer home nursing increase home deaths without compromising symptoms or increasing costs. But a compelling trend warrants further confirmatory studies. Future trials should compare the relative efficacy of different models and intensities of SPCSs. Copyright © 2013 U.S. Cancer Pain Relief Committee. Published by Elsevier Inc. All rights reserved.

Frailty as a Predictor of Future Falls Among Community-Dwelling Older People: A Systematic Review and Meta-Analysis.

PubMed

Kojima, Gotaro

2015-12-01

Although multiple longitudinal studies have investigated frailty as a predictor of future falls, the results were mixed. Thus far, no systematic review or meta-analysis on this topic has been conducted. To review the evidence of frailty as a predictor of future falls among community-dwelling older people. Systematic review of literature and meta-analysis were performed using 6 electronic databases (Embase, Scopus, MEDLINE, CINAHL Plus, PsycINFO, and the Cochrane Library) searching for studies that prospectively examined risk of future fall risk according to frailty among community-dwelling older people published from 2010 to April 2015 with no language restrictions. Of 2245 studies identified through the systematic review, 11 studies incorporating 68,723 individuals were included in the meta-analysis. Among 7 studies reporting odds ratios (ORs), frailty and prefrailty were significantly associated with higher risk of future falls (pooled OR = 1.84, 95% confidence interval [95% CI] = 1.43-2.38, P < .001; pooled OR = 1.25, 95% CI = 1.01-1.53, P = .005, respectively). Among 4 studies reporting hazard ratios (HRs), whereas frailty was significantly associated with higher risk of future falls (pooled HR = 1.24, 95% CI = 1.10-1.41, P < .001), future fall risk according to prefrailty did not reach statistical significance (pooled HR = 1.14, 95% CI = 0.95-1·36, P = .15). High heterogeneity was noted among 7 studies reporting ORs and seemed attributed to difference in gender proportion of cohorts according to subgroup and meta-regression analyses. Frailty is demonstrated to be a significant predictor of future falls among community-dwelling older people despite various criteria used to define frailty. The future fall risk according to frailty seemed to be higher in men than in women. Copyright © 2015 AMDA – The Society for Post-Acute and Long-Term Care Medicine. Published by Elsevier Inc. All rights reserved.

Library of molecular associations: curating the complex molecular basis of liver diseases.

PubMed

Buchkremer, Stefan; Hendel, Jasmin; Krupp, Markus; Weinmann, Arndt; Schlamp, Kai; Maass, Thorsten; Staib, Frank; Galle, Peter R; Teufel, Andreas

2010-03-20

Systems biology approaches offer novel insights into the development of chronic liver diseases. Current genomic databases supporting systems biology analyses are mostly based on microarray data. Although these data often cover genome wide expression, the validity of single microarray experiments remains questionable. However, for systems biology approaches addressing the interactions of molecular networks comprehensive but also highly validated data are necessary. We have therefore generated the first comprehensive database for published molecular associations in human liver diseases. It is based on PubMed published abstracts and aimed to close the gap between genome wide coverage of low validity from microarray data and individual highly validated data from PubMed. After an initial text mining process, the extracted abstracts were all manually validated to confirm content and potential genetic associations and may therefore be highly trusted. All data were stored in a publicly available database, Library of Molecular Associations http://www.medicalgenomics.org/databases/loma/news, currently holding approximately 1260 confirmed molecular associations for chronic liver diseases such as HCC, CCC, liver fibrosis, NASH/fatty liver disease, AIH, PBC, and PSC. We furthermore transformed these data into a powerful resource for molecular liver research by connecting them to multiple biomedical information resources. Together, this database is the first available database providing a comprehensive view and analysis options for published molecular associations on multiple liver diseases.

A geographic information system analysis of the impact of a statewide acute stroke emergency medical services routing protocol on community hospital bypass.

PubMed

Asimos, Andrew W; Ward, Shana; Brice, Jane H; Enright, Dianne; Rosamond, Wayne D; Goldstein, Larry B; Studnek, Jonathan

2014-01-01

Our goal was to determine if a statewide Emergency Medical Services (EMSs) Stroke Triage and Destination Plan (STDP), specifying bypass of hospitals unable to routinely treat stroke patients with thrombolytics (community hospitals), changed bypass frequency of those hospitals. Using a statewide EMS database, we identified stroke patients eligible for community hospital bypass and compared bypass frequency 1-year before and after STDP implementation. Symptom onset time was missing for 48% of pre-STDP (n = 2385) and 29% of post-STDP (n = 1612) cases. Of the remaining cases with geocodable scene addresses, 58% (1301) in the pre-STDP group and 61% (2,078) in the post-STDP group were ineligible for bypass, because a community hospital was not the closest hospital to the stroke event location. Because of missing data records for some EMS agencies in 1 or both study periods, we included EMS agencies from only 49 of 100 North Carolina counties in our analysis. Additionally, we found conflicting hospital classifications by different EMS agencies for 35% of all hospitals (n = 38 of 108). Given these limitations, we found similar community hospital bypass rates before and after STDP implementation (64%, n = 332 of 520 vs. 63%, n = 345 of 552; P = .65). Missing symptom duration time and data records in our state's EMS data system, along with conflicting hospital classifications between EMS agencies limit the ability to study statewide stroke routing protocols. Bypass policies may apply to a minority of patients because a community hospital is not the closest hospital to most stroke events. Given these limitations, we found no difference in community hospital bypass rates after implementation of the STDP. Copyright © 2014 National Stroke Association. Published by Elsevier Inc. All rights reserved.

16 CFR § 1102.30 - Publication of manufacturer comments.

Code of Federal Regulations, 2013 CFR

2013-01-01

... SAFETY ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural....26, the Commission will publish in the Database manufacturer comments submitted in response to a...

An Interactive Online Database for Potato Varieties Evaluated in the Eastern U.S.

USDA-ARS?s Scientific Manuscript database

Online databases are no longer a novelty. However, for the potato growing and research community little effort has been put into collecting data from multiple states and provinces, and presenting it in a web-based database format for researchers and end users to utilize. The NE1031 regional potato v...

Health economic analyses in medical nutrition: a systematic literature review.

PubMed

Walzer, Stefan; Droeschel, Daniel; Nuijten, Mark; Chevrou-Séverac, Hélène

2014-01-01

Medical nutrition is a specific nutrition category either covering specific dietary needs and/or nutrient deficiency in patients or feeding patients unable to eat normally. Medical nutrition is regulated by a specific bill in Europe and in the US, with specific legislation and guidelines, and is provided to patients with special nutritional needs and indications for nutrition support. Therefore, medical nutrition products are delivered by medical prescription and supervised by health care professionals. Although these products have existed for more than 2 decades, health economic evidence of medical nutrition interventions is scarce. This research assesses the current published health economic evidence for medical nutrition by performing a systematic literature review related to health economic analysis of medical nutrition. A systematic literature search was done using standard literature databases, including PubMed, the Health Technology Assessment Database, and the National Health Service Economic Evaluation Database. Additionally, a free web-based search was conducted using the same search terms utilized in the systematic database search. The clinical background and basis of the analysis, health economic design, and results were extracted from the papers finally selected. The Drummond checklist was used to validate the quality of health economic modeling studies and the AMSTAR (A Measurement Tool to Assess Systematic Reviews) checklist was used for published systematic reviews. Fifty-three papers were identified and obtained via PubMed, or directly via journal webpages for further assessment. Thirty-two papers were finally included in a thorough data extraction procedure, including those identified by a "gray literature search" utilizing the Google search engine and cross-reference searches. Results regarding content of the studies showed that malnutrition was the underlying clinical condition in most cases (32%). In addition, gastrointestinal disorders (eg, surgery, cancer) were often analyzed. In terms of settings, 56% of papers covered inpatients, whereas 14 papers (44%) captured outpatients, including patients in community centers. Interestingly, in comparison with the papers identified overall, very few health economic models were found. Most of the articles were modeling analyses and economic trials in different design settings. Overall, only eight health economic models were published and were validated applying the Drummond checklist. In summary, most of the models included were carried out to quite a high standard, although some areas were identified for further improvement. Of the two systematic health economic reviews identified, one achieved the highest quality score when applying the AMSTAR checklist. The reasons for finding only a few modeling studies but quite a large number of clinical trials with health economic endpoints, might be different. Until recently, health economics has not been required for reimbursement or coverage decisions concerning medical nutrition interventions. Further, there might be specifics of medical nutrition which might not allow easy modeling and consequently explain the limited uptake so far. The health economic data on medical nutrition generated and published is quite ample. However, it has been primarily based on database analysis and clinical studies. Only a few modeling analyses have been carried out, indicating a need for further research to understand the specifics of medical nutrition and their applicability for health economic modeling.

The Multinational Arabidopsis Steering Subcommittee for Proteomics Assembles the Largest Proteome Database Resource for Plant Systems Biology

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

Weckwerth, Wolfram; Baginsky, Sacha; Van Wijk, Klass

2009-12-01

In the past 10 years, we have witnessed remarkable advances in the field of plant molecular biology. The rapid development of proteomic technologies and the speed with which these techniques have been applied to the field have altered our perception of how we can analyze proteins in complex systems. At nearly the same time, the availability of the complete genome for the model plant Arabidopsis thaliana was released; this effort provides an unsurpassed resource for the identification of proteins when researchers use MS to analyze plant samples. Recognizing the growth in this area, the Multinational Arabidopsis Steering Committee (MASC) establishedmore » a subcommittee for A. thaliana proteomics in 2006 with the objective of consolidating databases, technique standards, and experimentally validated candidate genes and functions. Since the establishment of the Multinational Arabidopsis Steering Subcommittee for Proteomics (MASCP), many new approaches and resources have become available. Recently, the subcommittee established a webpage to consolidate this information (www.masc-proteomics.org). It includes links to plant proteomic databases, general information about proteomic techniques, meeting information, a summary of proteomic standards, and other relevant resources. Altogether, this website provides a useful resource for the Arabidopsis proteomics community. In the future, the website will host discussions and investigate the cross-linking of databases. The subcommittee members have extensive experience in arabidopsis proteomics and collectively have produced some of the most extensive proteomics data sets for this model plant (Table S1 in the Supporting Information has a list of resources). The largest collection of proteomics data from a single study in A. thaliana was assembled into an accessible database (AtProteome; http://fgcz-atproteome.unizh.ch/index.php) and was recently published by the Baginsky lab.1 The database provides links to major Arabidopsis online resources, and raw data have been deposited in PRIDE and PRIDE BioMart. Included in this database is an Arabidopsis proteome map that provides evidence for the expression of {approx}50% of all predicted gene models, including several alternative gene models that are not represented in The Arabidopsis Information Resource (TAIR) protein database. A set of organ-specific biomarkers is provided, as well as organ-specific proteotypic peptides for 4105 proteins that can be used to facilitate targeted quantitative proteomic surveys. In the future, the AtProteome database will be linked to additional existing resources developed by MASCP members, such as PPDB, ProMEX, and SUBA. The most comprehensive study on the Arabidopsis chloroplast proteome, which includes information on chloroplast sorting signals, posttranslational modifications (PTMs), and protein abundances (analyzed by high-accuracy MS [Orbitrap]), was recently published by the van Wijk lab.2 These and previous data are available via the plant proteome database (PPDB; http://ppdb.tc.cornell.edu) for A. thaliana and maize. PPDB provides genome-wide experimental and functional characterization of the A. thaliana and maize proteomes, including PTMs and subcellular localization information, with an emphasis on leaf and plastid proteins. Maize and Arabidopsis proteome entries are directly linked via internal BLAST alignments within PPDB. Direct links for each protein to TAIR, SUBA, ProMEX, and other resources are also provided.« less

ClusterMine360: a database of microbial PKS/NRPS biosynthesis

PubMed Central

Conway, Kyle R.; Boddy, Christopher N.

2013-01-01

ClusterMine360 (http://www.clustermine360.ca/) is a database of microbial polyketide and non-ribosomal peptide gene clusters. It takes advantage of crowd-sourcing by allowing members of the community to make contributions while automation is used to help achieve high data consistency and quality. The database currently has >200 gene clusters from >185 compound families. It also features a unique sequence repository containing >10 000 polyketide synthase/non-ribosomal peptide synthetase domains. The sequences are filterable and downloadable as individual or multiple sequence FASTA files. We are confident that this database will be a useful resource for members of the polyketide synthases/non-ribosomal peptide synthetases research community, enabling them to keep up with the growing number of sequenced gene clusters and rapidly mine these clusters for functional information. PMID:23104377

Progress Toward an IRIS++ Database Open to the Helioseismological Community

NASA Astrophysics Data System (ADS)

Gelly, B.; Khalikov, S.; Pallé, P. L.; IRIS Team

The IRIS network is now fourteen years old, and has continuously been taking data since 1989. The data analysis, which produced some noticeable scientifical results, like the measurement of the ell = 1 rotationnal splitting or the measurement of the solar acoustic cut-off frequency, was mainly performed with the summer campaigns data of 1989 to 1992. P-mode frequency and width tables were recently published using the same subset of the IRIS data . We are now finishing the calibration and the timing of the whole set of IRIS data from 89 to 97, which will increase by a factor of 4 the amount of available data. The duty cycle of the IRIS network ranges from about 65% over 3 months of the summer campaigns to some 23% over one year in the worst case. To improve our duty cycle we developed several collaborations with other teams running similar instruments: (1) the Mark I instrument, ran at the IAC for many years, a potassium resonance single pixel device, also part of the BiSON network (Elsworth et al., 1988). (2) Alexandro Cacciani's MOF, ran at the JPL in Pasadena. Although this is a sodium resonance imaging instrument, it has been used in ``one pixel'' format for several summer seasons since 1989 (Cacciani et al., 1984). (3) the LOWL instrument is a Doppler imager also based on a Magneto-Optical Filter (MOF), operated at the Mauna Loa solar observatory since 1994 (Tomczyk et al., 1995). The merging of those 'alien' data has been carefully adressed at the calibration ands timing stages, and we can now present the advantages of such a-posteriori collaborations. We endeavour to set-up the corresponding database of 'one-pixel seismological data from ground-based intruments' in Nice and to open it to the scientific community of this meeting by the end of 1998. This database will soon have the potential to trace the spectral features of the solar signal over one 11-years cycle.

Creating a FIESTA (Framework for Integrated Earth Science and Technology Applications) with MagIC

NASA Astrophysics Data System (ADS)

Minnett, R.; Koppers, A. A. P.; Jarboe, N.; Tauxe, L.; Constable, C.

2017-12-01

The Magnetics Information Consortium (https://earthref.org/MagIC) has recently developed a containerized web application to considerably reduce the friction in contributing, exploring and combining valuable and complex datasets for the paleo-, geo- and rock magnetic scientific community. The data produced in this scientific domain are inherently hierarchical and the communities evolving approaches to this scientific workflow, from sampling to taking measurements to multiple levels of interpretations, require a large and flexible data model to adequately annotate the results and ensure reproducibility. Historically, contributing such detail in a consistent format has been prohibitively time consuming and often resulted in only publishing the highly derived interpretations. The new open-source (https://github.com/earthref/MagIC) application provides a flexible upload tool integrated with the data model to easily create a validated contribution and a powerful search interface for discovering datasets and combining them to enable transformative science. MagIC is hosted at EarthRef.org along with several interdisciplinary geoscience databases. A FIESTA (Framework for Integrated Earth Science and Technology Applications) is being created by generalizing MagIC's web application for reuse in other domains. The application relies on a single configuration document that describes the routing, data model, component settings and external services integrations. The container hosts an isomorphic Meteor JavaScript application, MongoDB database and ElasticSearch search engine. Multiple containers can be configured as microservices to serve portions of the application or rely on externally hosted MongoDB, ElasticSearch, or third-party services to efficiently scale computational demands. FIESTA is particularly well suited for many Earth Science disciplines with its flexible data model, mapping, account management, upload tool to private workspaces, reference metadata, image galleries, full text searches and detailed filters. EarthRef's Seamount Catalog of bathymetry and morphology data, EarthRef's Geochemical Earth Reference Model (GERM) databases, and Oregon State University's Marine and Geology Repository (http://osu-mgr.org) will benefit from custom adaptations of FIESTA.

Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes.

PubMed

Putman, Tim E; Burgstaller-Muehlbacher, Sebastian; Waagmeester, Andra; Wu, Chunlei; Su, Andrew I; Good, Benjamin M

2016-01-01

The last 20 years of advancement in sequencing technologies have led to sequencing thousands of microbial genomes, creating mountains of genetic data. While efficiency in generating the data improves almost daily, applying meaningful relationships between taxonomic and genetic entities on this scale requires a structured and integrative approach. Currently, knowledge is distributed across a fragmented landscape of resources from government-funded institutions such as National Center for Biotechnology Information (NCBI) and UniProt to topic-focused databases like the ODB3 database of prokaryotic operons, to the supplemental table of a primary publication. A major drawback to large scale, expert-curated databases is the expense of maintaining and extending them over time. No entity apart from a major institution with stable long-term funding can consider this, and their scope is limited considering the magnitude of microbial data being generated daily. Wikidata is an openly editable, semantic web compatible framework for knowledge representation. It is a project of the Wikimedia Foundation and offers knowledge integration capabilities ideally suited to the challenge of representing the exploding body of information about microbial genomics. We are developing a microbial specific data model, based on Wikidata's semantic web compatibility, which represents bacterial species, strains and the gene and gene products that define them. Currently, we have loaded 43,694 gene and 37,966 protein items for 21 species of bacteria, including the human pathogenic bacteriaChlamydia trachomatis.Using this pathogen as an example, we explore complex interactions between the pathogen, its host, associated genes, other microbes, disease and drugs using the Wikidata SPARQL endpoint. In our next phase of development, we will add another 99 bacterial genomes and their gene and gene products, totaling ∼900,000 additional entities. This aggregation of knowledge will be a platform for community-driven collaboration, allowing the networking of microbial genetic data through the sharing of knowledge by both the data and domain expert. © The Author(s) 2016. Published by Oxford University Press.

Top-100 Highest-Cited Original Articles in Ischemic Stroke: A Bibliometric Analysis.

PubMed

Malhotra, Konark; Saeed, Omar; Goyal, Nitin; Katsanos, Aristeidis H; Tsivgoulis, Georgios

2018-03-01

The total number of citations of a research article can be used to determine its impact on the scientific community. We aimed to identify the top-100 articles published on ischemic stroke and evaluate their characteristics. Based on the database of Journal Citation Reports, 934 journals were selected that published original ischemic stroke articles. We used Web of Science citation search tool to identify top-100 citation classics, i.e., articles with more than 400 citations, in the field of ischemic stroke. All original articles were evaluated for publication year, journal category, journal and its impact factor, number of total and annual citations, research topic, publishing country, and institutional affiliation. The top-100 citation classics in ischemic stroke were published from 1970 to 2015, with the decade of 1990-1999 contributing 47 articles of historical significance. Median of total citations and annual citations in our analysis were 625.0 (interquartile range [IQR] 851.3-494.5) and 35.7 (IQR 79.9-25.9), respectively. The majority of the articles originated from the United States (n = 57), focused over the medical management (n = 26), and were published in the New England Journal of Medicine or Stroke (n = 25 each) journals. The median impact factor for the journals that published top-100 ischemic stroke citation classics was 9.11 (IQR 21.49-6.11). Our list of top-100 citation classics specific to ischemic stroke provide a detailed insight into academic achievements, historical perspective and serves as a guide for the scientific progress in stroke. Copyright © 2017 Elsevier Inc. All rights reserved.

Adding glycaemic index and glycaemic load functionality to DietPLUS, a Malaysian food composition database and diet intake calculator.

PubMed

Shyam, Sangeetha; Wai, Tony Ng Kock; Arshad, Fatimah

2012-01-01

This paper outlines the methodology to add glycaemic index (GI) and glycaemic load (GL) functionality to food DietPLUS, a Microsoft Excel-based Malaysian food composition database and diet intake calculator. Locally determined GI values and published international GI databases were used as the source of GI values. Previously published methodology for GI value assignment was modified to add GI and GL calculators to the database. Two popular local low GI foods were added to the DietPLUS database, bringing up the total number of foods in the database to 838 foods. Overall, in relation to the 539 major carbohydrate foods in the Malaysian Food Composition Database, 243 (45%) food items had local Malaysian values or were directly matched to International GI database and another 180 (33%) of the foods were linked to closely-related foods in the GI databases used. The mean ± SD dietary GI and GL of the dietary intake of 63 women with previous gestational diabetes mellitus, calculated using DietPLUS version3 were, 62 ± 6 and 142 ± 45, respectively. These values were comparable to those reported from other local studies. DietPLUS version3, a simple Microsoft Excel-based programme aids calculation of diet GI and GL for Malaysian diets based on food records.

CrossCheck: an open-source web tool for high-throughput screen data analysis.

PubMed

Najafov, Jamil; Najafov, Ayaz

2017-07-19

Modern high-throughput screening methods allow researchers to generate large datasets that potentially contain important biological information. However, oftentimes, picking relevant hits from such screens and generating testable hypotheses requires training in bioinformatics and the skills to efficiently perform database mining. There are currently no tools available to general public that allow users to cross-reference their screen datasets with published screen datasets. To this end, we developed CrossCheck, an online platform for high-throughput screen data analysis. CrossCheck is a centralized database that allows effortless comparison of the user-entered list of gene symbols with 16,231 published datasets. These datasets include published data from genome-wide RNAi and CRISPR screens, interactome proteomics and phosphoproteomics screens, cancer mutation databases, low-throughput studies of major cell signaling mediators, such as kinases, E3 ubiquitin ligases and phosphatases, and gene ontological information. Moreover, CrossCheck includes a novel database of predicted protein kinase substrates, which was developed using proteome-wide consensus motif searches. CrossCheck dramatically simplifies high-throughput screen data analysis and enables researchers to dig deep into the published literature and streamline data-driven hypothesis generation. CrossCheck is freely accessible as a web-based application at http://proteinguru.com/crosscheck.

16 CFR 1102.30 - Publication of manufacturer comments.

Code of Federal Regulations, 2011 CFR

2011-01-01

... ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011....24, and 1102.26, the Commission will publish in the Database manufacturer comments submitted in...

Effectiveness of case management for homeless persons: a systematic review.

PubMed

de Vet, Renée; van Luijtelaar, Maurice J A; Brilleslijper-Kater, Sonja N; Vanderplasschen, Wouter; Beijersbergen, Mariëlle D; Wolf, Judith R L M

2013-10-01

We reviewed the literature on standard case management (SCM), intensive case management (ICM), assertive community treatment (ACT), and critical time intervention (CTI) for homeless adults. We searched databases for peer-reviewed English articles published from 1985 to 2011 and found 21 randomized controlled trials or quasi-experimental studies comparing case management to other services. We found little evidence for the effectiveness of ICM. SCM improved housing stability, reduced substance use, and removed employment barriers for substance users. ACT improved housing stability and was cost-effective for mentally ill and dually diagnosed persons. CTI showed promise for housing, psychopathology, and substance use and was cost-effective for mentally ill persons. More research is needed on how case management can most effectively support rapid-rehousing approaches to homelessness.

Effectiveness of Case Management for Homeless Persons: A Systematic Review

PubMed Central

de Vet, Renée; van Luijtelaar, Maurice J. A.; Brilleslijper-Kater, Sonja N.; Vanderplasschen, Wouter; Beijersbergen, Mariëlle D.

2013-01-01

We reviewed the literature on standard case management (SCM), intensive case management (ICM), assertive community treatment (ACT), and critical time intervention (CTI) for homeless adults. We searched databases for peer-reviewed English articles published from 1985 to 2011 and found 21 randomized controlled trials or quasi-experimental studies comparing case management to other services. We found little evidence for the effectiveness of ICM. SCM improved housing stability, reduced substance use, and removed employment barriers for substance users. ACT improved housing stability and was cost-effective for mentally ill and dually diagnosed persons. CTI showed promise for housing, psychopathology, and substance use and was cost-effective for mentally ill persons. More research is needed on how case management can most effectively support rapid-rehousing approaches to homelessness. PMID:23947309

Exploration of options for publishing databases and supplemental material in society journals

USDA-ARS?s Scientific Manuscript database

As scientific information becomes increasingly more abundant, there is increasing interest among members of our societies to share databases. These databases have great value, for example, in providing long-term perspectives of various scientific problems and for use by modelers to extend the inform...

DSSTOX STRUCTURE-SEARCHABLE PUBLIC TOXICITY DATABASE NETWORK: CURRENT PROGRESS AND NEW INITIATIVES TO IMPROVE CHEMO-BIOINFORMATICS CAPABILITIES

EPA Science Inventory

The EPA DSSTox website (http://www/epa.gov/nheerl/dsstox) publishes standardized, structure-annotated toxicity databases, covering a broad range of toxicity disciplines. Each DSSTox database features documentation written in collaboration with the source authors and toxicity expe...

Publications of Australian LIS Academics in Databases

ERIC Educational Resources Information Center

Wilson, Concepcion S.; Boell, Sebastian K.; Kennan, Mary Anne; Willard, Patricia

2011-01-01

This paper examines aspects of journal articles published from 1967 to 2008, located in eight databases, and authored or co-authored by academics serving for at least two years in Australian LIS programs from 1959 to 2008. These aspects are: inclusion of publications in databases, publications in journals, authorship characteristics of…

Graduation and Persistence Rates: University of Hawaii Community Colleges, Fall 1987-Fall 1995 Cohorts. A Summary of Selected Data from the NCHEMS/University of Hawaii System Longitudinal Database Project. Special Report.

ERIC Educational Resources Information Center

Hawaii Univ., Honolulu. Institutional Research Office.

This report details graduation and persistence rates for degree-seeking students at the seven University of Hawaii Community Colleges (UHCC) from Fall 1987-Fall 1995. The data are from the National Center for Higher Education Management Systems/University of Hawaii System Longitudinal Database Project. The report focuses on full-time and part-time…

Nonsuicidal self-injury in community adolescents: A systematic review of prospective predictors, mediators and moderators.

PubMed

Valencia-Agudo, Fatima; Burcher, Georgina Corbet; Ezpeleta, Lourdes; Kramer, Tami

2018-06-01

Nonsuicidal self-injury (NSSI) usually starts during adolescence and is associated with an array of psychological and psychiatric symptoms and future suicide attempts. The aim of this study is to determine prospective predictors, mediators and moderators of NSSI in adolescent community samples in order to target prevention and treatment strategies. Two team members searched online databases independently. Thirty-nine studies were included in the review. Several variables were seen to prospectively predict NSSI: female gender, family-related variables, peer victimisation, depression, previous NSSI and self-concept. Few studies analysed mediators and moderators. Low self-concept was highlighted as a relevant moderator in the relationship between intra/interpersonal variables and NSSI. Implications of these findings are discussed. The considerable heterogeneity between studies posed a limitation to determine robust predictors of NSSI. Further prospective studies using standardised measures of predictors and outcomes are needed to ascertain the most at risk individuals and develop prevention strategies. Copyright © 2018 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

Culturally competent evidence-based behavioral health services for the transgender community: Progress and challenges.

PubMed

Hope, Debra A; Mocarski, Richard; Bautista, Chandra L; Holt, Natalie R

2016-01-01

The presence of individuals who identify as transgender has emerged into public awareness in the United States in recent years. Celebrities who publicly transition have expanded the national conversation about gender variation beyond gender and women's studies classrooms and certain specialty health and mental health services. This increased public visibility has been accompanied by increased visibility in the mental health literature, including the publishing of competencies or guidelines for working with clients who identify as transgender by various professional organizations. However, rapid societal changes and increased understanding of the experience of being transgender in our society means literature can rapidly become dated. This commentary identifies key points that will move forward professional competency, both of the field and of individual practitioners, in the provision of psychological services. Topics discussed include (1) how mental health has contributed to trans stigma, (2) why more than good intentions are needed, (3) a research agenda for the development of high-quality evidence-based behavioral health care for the trans community, and (4) clinician recommendations. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

HopBase: a unified resource for Humulus genomics

PubMed Central

Hill, Steven T.; Sudarsanam, Ramcharan

2017-01-01

Abstract Hop (Humulus lupulus L. var lupulus) is a dioecious plant of worldwide significance, used primarily for bittering and flavoring in brewing beer. Studies on the medicinal properties of several unique compounds produced by hop have led to additional interest from pharmacy and healthcare industries as well as livestock production as a natural antibiotic. Genomic research in hop has resulted a published draft genome and transcriptome assemblies. As research into the genomics of hop has gained interest, there is a critical need for centralized online genomic resources. To support the growing research community, we report the development of an online resource "HopBase.org." In addition to providing a gene annotation to the existing Shinsuwase draft genome, HopBase makes available genome assemblies and annotations for both the cultivar “Teamaker” and male hop accession number USDA 21422M. These genome assemblies, gene annotations, along with other common data, coupled with a genome browser and BLAST database enable the hop community to enter the genomic age. The HopBase genomic resource is accessible at http://hopbase.org and http://hopbase.cgrb.oregonstate.edu. PMID:28415075

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.

PubMed

Druzinsky, Robert E; Balhoff, James P; Crompton, Alfred W; Done, James; German, Rebecca Z; Haendel, Melissa A; Herrel, Anthony; Herring, Susan W; Lapp, Hilmar; Mabee, Paula M; Muller, Hans-Michael; Mungall, Christopher J; Sternberg, Paul W; Van Auken, Kimberly; Vinyard, Christopher J; Williams, Susan H; Wall, Christine E

2016-01-01

In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required. Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar. Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.

Methamphetamine use and treatment in Iran: A systematic review from the most populated Persian Gulf country.

PubMed

Alam-mehrjerdi, Zahra; Mokri, Azarakhsh; Dolan, Kate

2015-08-01

Methamphetamine use is a new health concern in Iran, the most populated Persian Gulf country. However, there is no well-documented literature. The current study objectives were to systematically review all published English and Persian studies of the prevalence of methamphetamine use, the general physical and psychiatric-related harms and the availability of methamphetamine treatment and harm reduction services for adult users in Iran. A comprehensive search of the international peer-reviewed and gray literature was undertaken. Multiple electronic and scientific English and Persian databases were systematically searched from January 2002 to September 2014. Additionally, English and Persian gray literature on methamphetamine use was sought using online gray literature databases, library databases and general online searches over the same period of time. Nineteen thousand and two hundred and eight studies, reports and conference papers were identified but only 42 studies were relevant to the study objectives. They were mainly published in 2010-2014. The search results confirmed the seizures of methamphetamine (six studies), the prevalence of methamphetamine use among the general population (three studies), drug users (four studies), women (nine studies) and opiate users in opiate treatment programs (five studies). In addition, methamphetamine use had resulted in blood-borne viral infections (one study), psychosis and intoxication (ten studies). Different reasons had facilitated methamphetamine use. However, the Matrix Model, community therapy and harm reduction services (four studies) had been provided for methamphetamine users in some cities. The current situation of methamphetamine use necessitates more research on the epidemiology and health-related implications. These studies should help in identifying priorities for designing and implementing prevention and educational programs. More active models of engagement with Persian methamphetamine users and the provision of services that meet their specific treatment needs are required. Copyright © 2015 Elsevier B.V. All rights reserved.

Establishing a regional, multisite database for quality improvement and service planning in community-based palliative care and hospice.

PubMed

Bull, Janet; Zafar, S Yousuf; Wheeler, Jane L; Harker, Matthew; Gblokpor, Agbessi; Hanson, Laura; Hulihan, Deirdre; Nugent, Rikki; Morris, John; Abernethy, Amy P

2010-08-01

Outpatient palliative care, an evolving delivery model, seeks to improve continuity of care across settings and to increase access to services in hospice and palliative medicine (HPM). It can provide a critical bridge between inpatient palliative care and hospice, filling the gap in community-based supportive care for patients with advanced life-limiting illness. Low capacities for data collection and quantitative research in HPM have impeded assessment of the impact of outpatient palliative care. In North Carolina, a regional database for community-based palliative care has been created through a unique partnership between a HPM organization and academic medical center. This database flexibly uses information technology to collect patient data, entered at the point of care (e.g., home, inpatient hospice, assisted living facility, nursing home). HPM physicians and nurse practitioners collect data; data are transferred to an academic site that assists with analyses and data management. Reports to community-based sites, based on data they provide, create a better understanding of local care quality. The data system was developed and implemented over a 2-year period, starting with one community-based HPM site and expanding to four. Data collection methods were collaboratively created and refined. The database continues to grow. Analyses presented herein examine data from one site and encompass 2572 visits from 970 new patients, characterizing the population, symptom profiles, and change in symptoms after intervention. A collaborative regional approach to HPM data can support evaluation and improvement of palliative care quality at the local, aggregated, and statewide levels.

Identifying unprotected and potentially at risk plant communities in the western USA

USGS Publications Warehouse

Wright, R.G.; Scott, J.M.; Mann, S.; Murray, M.

2001-01-01

We analyzed the conservation status of 73 vegetation cover types distributed across a 1.76 million km2 region in 10 states of the western USA. We found that 25 vegetation cover types had at least 10% of their area in nature reserves. These were generally plant communities located at higher elevations and thus more commonly associated with national parks and wilderness areas. All but three of the remaining 48 cover types occurred with sufficient area on publically owned lands in the region to imply that transforming land management intent on these lands could also increase their protection. We also analyzed the level of protection afforded each cover type across its entire geographic distribution in the region. Most cover types that were at least minimally protected in total across the region were also at least minimally protected in most areas of their occurrence. Our results show that there is a realistic opportunity to design a system of biodiversity reserves in this region that represent the full range of environmental conditions in which the various plant communities occur. Conducting this type of broad-scale analysis is a necessary first step in that process and provides a database for others to work from. Published by Elsevier Science Ltd.

Prevalence of psychological distress and psychiatric disorders among homeless youth in Australia: a comparative review.

PubMed

Kamieniecki, G W

2001-06-01

To review the prevalence literature on psychological distress and psychiatric disorders among homeless youth in Australia, and to compare these rates with Australian youth as a whole. Computerized databases were utilized to access all published Australian studies on psychological distress (as measured by standardized symptom scales and suicidal behaviour) and psychiatric disorders among homeless youth; in addition, unpublished Australian studies were utilized whenever accessible. A total of 14 separate studies were located, only three of which have included non-homeless control groups. In the current review, prevalence data from uncontrolled youth homelessness studies are compared with data from Australian community and student surveys. Homeless youth have usually scored significantly higher on standardized measures of psychological distress than all domiciled control groups. Youth homelessness studies have also reported very high rates of suicidal behaviour, but methodological limitations in these studies make comparisons with community surveys difficult. Furthermore, rates of various psychiatric disorders are usually at least twice as high among homeless youth than among youth from community surveys. Homeless youth in Australia have extremely high rates of psychological distress and psychiatric disorders. As homeless youth are at risk of developing psychiatric disorders and possibly self-injurious behaviour the longer they are homeless, early intervention in relevant health facilities is required.

Bayesian mixture analysis for metagenomic community profiling.

PubMed

Morfopoulou, Sofia; Plagnol, Vincent

2015-09-15

Deep sequencing of clinical samples is now an established tool for the detection of infectious pathogens, with direct medical applications. The large amount of data generated produces an opportunity to detect species even at very low levels, provided that computational tools can effectively profile the relevant metagenomic communities. Data interpretation is complicated by the fact that short sequencing reads can match multiple organisms and by the lack of completeness of existing databases, in particular for viral pathogens. Here we present metaMix, a Bayesian mixture model framework for resolving complex metagenomic mixtures. We show that the use of parallel Monte Carlo Markov chains for the exploration of the species space enables the identification of the set of species most likely to contribute to the mixture. We demonstrate the greater accuracy of metaMix compared with relevant methods, particularly for profiling complex communities consisting of several related species. We designed metaMix specifically for the analysis of deep transcriptome sequencing datasets, with a focus on viral pathogen detection; however, the principles are generally applicable to all types of metagenomic mixtures. metaMix is implemented as a user friendly R package, freely available on CRAN: http://cran.r-project.org/web/packages/metaMix sofia.morfopoulou.10@ucl.ac.uk Supplementary data are available at Bionformatics online. © The Author 2015. Published by Oxford University Press.

dictyBase 2015: Expanding data and annotations in a new software environment.

PubMed

Basu, Siddhartha; Fey, Petra; Jimenez-Morales, David; Dodson, Robert J; Chisholm, Rex L

2015-08-01

dictyBase is the model organism database for the social amoeba Dictyostelium discoideum and related species. The primary mission of dictyBase is to provide the biomedical research community with well-integrated high quality data, and tools that enable original research. Data presented at dictyBase is obtained from sequencing centers, groups performing high throughput experiments such as large-scale mutagenesis studies, and RNAseq data, as well as a growing number of manually added functional gene annotations from the published literature, including Gene Ontology, strain, and phenotype annotations. Through the Dicty Stock Center we provide the community with an impressive amount of annotated strains and plasmids. Recently, dictyBase accomplished a major overhaul to adapt an outdated infrastructure to the current technological advances, thus facilitating the implementation of innovative tools and comparative genomics. It also provides new strategies for high quality annotations that enable bench researchers to benefit from the rapidly increasing volume of available data. dictyBase is highly responsive to its users needs, building a successful relationship that capitalizes on the vast efforts of the Dictyostelium research community. dictyBase has become the trusted data resource for Dictyostelium investigators, other investigators or organizations seeking information about Dictyostelium, as well as educators who use this model system. © 2015 Wiley Periodicals, Inc.

Culturally and linguistically diverse population health social marketing campaigns in Australia: a consideration of evidence and related evaluation issues.

PubMed

Milat, Andrew J; Carroll, Tom E; Taylor, Jennifer J

2005-04-01

This paper describes a review of population health social marketing campaigns targeting culturally and linguistically diverse (CLD) communities in Australia in order to identify characteristics of effective CLD campaigns. Literature on CLD population health social marketing was identified from electronic searches of databases in August 2004. At the same time, the grey literature was examined by searching the Internet and talking to Australian experts in the fields of CLD social marketing and CLD research. Eight studies met the search criteria, four from the published literature. Two studies that employed prepost evaluation designs provided tentative support for the potential efficacy of CLD social marketing strategies. The remaining studies did not allow for causal attribution as they used post-campaign only or process evaluations. Studies did, however, show that CLD communities access campaign-related information from both mainstream and ethnic media channels. In addition, Vietnamese respondents were more likely to access campaign messages through ethnic radio and Chinese respondents through ethnic press. There is insufficient evidence to clearly identify the characteristics of effective CLD campaigns. Campaign evaluation designs used to evaluate social marketing strategies targeting CLD communities in Australia are generally weak, but there is tentative evidence supporting the potential efficacy of these strategies in some Australian settings.

Tracking Community College Transfers Using National Student Clearinghouse Data.

ERIC Educational Resources Information Center

Romano, Richard M.; Wisniewski, Martin

This study shows how community colleges can track almost all of their own students who transfer into both public and private colleges and across state lines using the National Student Clearinghouse (NSC) database. It utilizes data from the student information systems of Broome Community College, New York; Cayuga Community College, New York; the…

Highlighting the Way Forward: A Review of Community Mental Health Research and Practice Published in AJCP and JCP.

PubMed

Townley, Greg; Terry, Rachel

2018-03-01

Articles published in the two most prominent journals of community psychology in North America, the American Journal of Community Psychology (AJCP) and Journal of Community Psychology (JCP), provide a clear indicator of trends in community research and practice. An examination of community psychology's history and scholarship suggests that the field has reduced its emphasis on promoting mental health, well-being, and liberation of individuals with serious mental illnesses over the past several decades. To further investigate this claim, the current review presents an analysis of articles relevant to community mental health (N = 307) published in the American Journal of Community Psychology (AJCP) and Journal of Community Psychology (JCP) from 1973 to 2015. The review focuses on article characteristics (e.g., type of article and methods employed), author characteristics, topic areas, and theoretical frameworks. Results document a downward trend in published articles from the mid-1980s to mid-2000s, with a substantial increase in published work between 2006 and 2015. A majority of articles were empirical and employed quantitative methods. The most frequent topic area was community mental health centers and services (n = 49), but the past three decades demonstrate a clear shift away from mental health service provision to address pressing social issues that impact community mental health, particularly homelessness (n = 42) and community integration of adults with serious mental illnesses (n = 40). Findings reflect both the past and present state of community psychology and suggest promising directions for re-engaging with community mental health and fostering well-being, inclusion, and liberation of adults experiencing serious mental health challenges. © Society for Community Research and Action 2017.

Ligandbook: an online repository for small and drug-like molecule force field parameters.

PubMed

Domanski, Jan; Beckstein, Oliver; Iorga, Bogdan I

2017-06-01

Ligandbook is a public database and archive for force field parameters of small and drug-like molecules. It is a repository for parameter sets that are part of published work but are not easily available to the community otherwise. Parameter sets can be downloaded and immediately used in molecular dynamics simulations. The sets of parameters are versioned with full histories and carry unique identifiers to facilitate reproducible research. Text-based search on rich metadata and chemical substructure search allow precise identification of desired compounds or functional groups. Ligandbook enables the rapid set up of reproducible molecular dynamics simulations of ligands and protein-ligand complexes. Ligandbook is available online at https://ligandbook.org and supports all modern browsers. Parameters can be searched and downloaded without registration, including access through a programmatic RESTful API. Deposition of files requires free user registration. Ligandbook is implemented in the PHP Symfony2 framework with TCL scripts using the CACTVS toolkit. oliver.beckstein@asu.edu or bogdan.iorga@cnrs.fr ; contact@ligandbook.org . Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Peer-reviewed public health journals from Arabic-speaking countries: An updated snapshot.

PubMed

Aboul-Enein, Basil H; Bernstein, Joshua; Bowser, Jacquelyn E

2017-02-01

There is a positive association between availability of regional peer-reviewed public health information systems and progressive change in community and population health. The objective of this brief report was to identify public health journals in Arabic-speaking countries actively publishing as of 2016. We conducted an electronic search in several electronic database records for public health journals using a combination of search terms. We excluded journals that focused on human medicine, veterinary medicine, nursing, and other discipline-specific or clinical health professions. We identified twenty-five public health journals for review. Five journals were interrupted or discontinued. Only three journals had a consistent, uninterrupted active publication history of greater than 20 years. Most journals were not in the regional native language. Introduction of regional public health-dedicated journals with in-print and electronic availability and also to be published in region-native languages may require interdisciplinary partnerships. Region-wide public health journals such as the Eastern Mediterranean Health Journal could serve as an ideal model for the establishment of additional local and regional public health journals in Arabic-speaking countries.

Improving the discoverability, accessibility, and citability of omics datasets: a case report.

PubMed

Darlington, Yolanda F; Naumov, Alexey; McOwiti, Apollo; Kankanamge, Wasula H; Becnel, Lauren B; McKenna, Neil J

2017-03-01

Although omics datasets represent valuable assets for hypothesis generation, model testing, and data validation, the infrastructure supporting their reuse lacks organization and consistency. Using nuclear receptor signaling transcriptomic datasets as proof of principle, we developed a model to improve the discoverability, accessibility, and citability of published omics datasets. Primary datasets were retrieved from archives, processed to extract data points, then subjected to metadata enrichment and gap filling. The resulting secondary datasets were exposed on responsive web pages to support mining of gene lists, discovery of related datasets, and single-click citation integration with popular reference managers. Automated processes were established to embed digital object identifier-driven links to the secondary datasets in associated journal articles, small molecule and gene-centric databases, and a dataset search engine. Our model creates multiple points of access to reprocessed and reannotated derivative datasets across the digital biomedical research ecosystem, promoting their visibility and usability across disparate research communities. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Electronic publishing and intelligent information retrieval

NASA Technical Reports Server (NTRS)

Heck, A.

1992-01-01

Europeans are now taking steps to homogenize policies and standardize procedures in electronic publishing (EP) in astronomy and space sciences. This arose from an open meeting organized in Oct. 1991 at Strasbourg Observatory (France) and another business meeting held late Mar. 1992 with the major publishers and journal editors in astronomy and space sciences. The ultimate aim of EP might be considered as the so-called 'intelligent information retrieval' (IIR) or better named 'advanced information retrieval' (AIR), taking advantage of the fact that the material to be published appears at some stage in a machine-readable form. It is obvious that the combination of desktop and electronic publishing with networking and new structuring of knowledge bases will profoundly reshape not only our ways of publishing, but also our procedures of communicating and retrieving information. It should be noted that a world-wide survey among astronomers and space scientists carried out before the October 1991 colloquium on the various packages and machines used, indicated that TEX-related packages were already in majoritarian use in our community. It has also been stressed at each meeting that the European developments should be carried out in collaboration with what is done in the US (STELLAR project, for instance). American scientists and journal editors actually attended both meetings mentioned above. The paper will offer a review of the status of electronic publishing in astronomy and its possible contribution to advanced information retrieval in this field. It will also report on recent meetings such as the 'Astronomy from Large Databases-2 (ALD-2)' conference dealing with the latest developments in networking, in data, information, and knowledge bases, as well as in the related methodologies.

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

PubMed Central

Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-01

Abstract The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. PMID:29040670

Development of the Nursing Community Apgar Questionnaire (NCAQ): a rural nurse recruitment and retention tool.

PubMed

Prengaman, M P; Bigbee, J L; Baker, E; Schmitz, D F

2014-01-01

Health professional shortages are a significant issue throughout the USA, particularly in rural communities. Filling nurse vacancies is a costly concern for many critical access hospitals (CAH), which serve as the primary source of health care for rural communities. CAHs and rural communities have strengths and weaknesses that affect their recruitment and retention of rural nurses. The purpose of this study was to develop a tool that rural communities and CAHs can utilize to assess their strengths and weaknesses related to nurse recruitment and retention. The Nursing Community Apgar Questionnaire (NCAQ) was developed based on an extensive literature review, visits to multiple rural sites, and consultations with rural nurses, rural nurse administrators and content experts. A quantitative interview tool consisting of 50 factors that affect rural nurse recruitment and retention was developed. The tool allows participants to rate each factor in terms of advantage and importance level. The tool also includes three open-ended questions for qualitative analysis. The NCAQ was designed to identify rural communities' and CAHs' strengths and challenges related to rural nurse recruitment and retention. The NCAQ will be piloted and a database developed for CAHs to compare their results with those in the database. Furthermore, the NCAQ results may be utilized to prioritize resource allocation and tailor rural nurse recruitment and retention efforts to highlight a community's strengths. The NCAQ will function as a useful real-time tool for CAHs looking to assess and improve their rural nurse recruitment and retention practices and compare their results with those of their peers. Longitudinal results will allow CAHs and their communities to evaluate their progress over time. As the database grows in size, state, regional, and national results can be compared, trends may be discovered and best practices identified.

The built environment and older adults: A literature review and an applied approach to engaging older adults in built environment improvements for health.

PubMed

Tuckett, Anthony G; Banchoff, Ann W; Winter, Sandra J; King, Abby C

2018-03-01

This paper presents a review of the literature about the built environment as it impacts the health of older people. It then introduces the gerontological nurse and researcher to the Our Voice framework for engaging older people as citizen scientists in order to empower them as agents of change in improving their local built environment and ultimately advancing community health. Community-level strategies to promote successful ageing in place are critical both to optimising health outcomes and containing healthcare costs. Such strategies must take into account the influence of the built environment both on individual health behaviours and on overall community health. At the same time, the perspectives and experiences of older people themselves ought to inform policies and practices in a systematic way. Integrative literature review. A wide scan of English language articles published in the EMBASE, PubMed and CINAHL bibliographic databases was conducted. Additional articles were sourced by mining relevant reference lists (i.e., snowball sampling). Papers included were published between 2005 and 2016. Three distinct components emerged from the review: the impact of the built environment on health-in particular the health of older persons; citizen science and its applicability for older people research; and the promise of the Our Voice citizen science framework to activate changes in the built environment that improve older peoples' health. The ageing of the world's population brings with it an increased population-level risk of chronic disease and disability. We present the Our Voice framework, developed by researchers at Stanford University, as a promising strategy for engaging and empowering older people as citizen scientists, as a framework to apply to gerontological nursing and improving community health. Gerontology nurses are encouraged to: (i) Recognise the impact of the built environment and other community-level factors on the health of their patients. (ii) Encourage older adults to take an active role in documenting features of their environments that promote or hinder healthy living. (iii) Support policies and programmes that promote healthy environments. © 2017 John Wiley & Sons Ltd.

Community pharmacy-delivered interventions for public health priorities: a systematic review of interventions for alcohol reduction, smoking cessation and weight management, including meta-analysis for smoking cessation.

PubMed

Brown, Tamara J; Todd, Adam; O'Malley, Claire; Moore, Helen J; Husband, Andrew K; Bambra, Clare; Kasim, Adetayo; Sniehotta, Falko F; Steed, Liz; Smith, Sarah; Nield, Lucie; Summerbell, Carolyn D

2016-02-29

To systematically review the effectiveness of community pharmacy-delivered interventions for alcohol reduction, smoking cessation and weight management. Systematic review and meta-analyses. 10 electronic databases were searched from inception to May 2014. randomised and non-randomised controlled trials; controlled before/after studies, interrupted times series. any relevant intervention set in a community pharmacy, delivered by the pharmacy team. No restrictions on duration, country, age, or language. 19 studies were included: 2 alcohol reduction, 12 smoking cessation and 5 weight management. Study quality rating: 6 'strong', 4 'moderate' and 9 'weak'. 8 studies were conducted in the UK, 4 in the USA, 2 in Australia, 1 each in 5 other countries. Evidence from 2 alcohol-reduction interventions was limited. Behavioural support and/or nicotine replacement therapy are effective and cost-effective for smoking cessation: pooled OR was 2.56 (95% CI 1.45 to 4.53) for active intervention vs usual care. Pharmacy-based interventions produced similar weight loss compared with active interventions in other primary care settings; however, weight loss was not sustained longer term in a range of primary care and commercial settings compared with control. Pharmacy-based weight management interventions have similar provider costs to those delivered in other primary care settings, which are greater than those delivered by commercial organisations. Very few studies explored if and how sociodemographic or socioeconomic variables moderated intervention effects. Insufficient information was available to examine relationships between effectiveness and behaviour change strategies, implementation factors, or organisation and delivery of interventions. Community pharmacy-delivered interventions are effective for smoking cessation, and demonstrate that the pharmacy is a feasible option for weight management interventions. Given the potential reach, effectiveness and associated costs of these interventions, commissioners should consider using community pharmacies to help deliver public health services. 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/

Zooplankton community analysis in the Changjiang River estuary by single-gene-targeted metagenomics

NASA Astrophysics Data System (ADS)

Cheng, Fangping; Wang, Minxiao; Li, Chaolun; Sun, Song

2014-07-01

DNA barcoding provides accurate identification of zooplankton species through all life stages. Single-gene-targeted metagenomic analysis based on DNA barcode databases can facilitate longterm monitoring of zooplankton communities. With the help of the available zooplankton databases, the zooplankton community of the Changjiang (Yangtze) River estuary was studied using a single-gene-targeted metagenomic method to estimate the species richness of this community. A total of 856 mitochondrial cytochrome oxidase subunit 1 (cox1) gene sequences were determined. The environmental barcodes were clustered into 70 molecular operational taxonomic units (MOTUs). Forty-two MOTUs matched barcoded marine organisms with more than 90% similarity and were assigned to either the species (similarity>96%) or genus level (similarity<96%). Sibling species could also be distinguished. Many species that were overlooked by morphological methods were identified by molecular methods, especially gelatinous zooplankton and merozooplankton that were likely sampled at different life history phases. Zooplankton community structures differed significantly among all of the samples. The MOTU spatial distributions were influenced by the ecological habits of the corresponding species. In conclusion, single-gene-targeted metagenomic analysis is a useful tool for zooplankton studies, with which specimens from all life history stages can be identified quickly and effectively with a comprehensive database.

NATIONAL URBAN DATABASE AND ACCESS PORTAL TOOL (NUDAPT): FACILITATING ADVANCEMENTS IN URBAN METEOROLOGY AND CLIMATE MODELING WITH COMMUNITY-BASED URBAN DATABASES

EPA Science Inventory

We discuss the initial design and application of the National Urban Database and Access Portal Tool (NUDAPT). This new project is sponsored by the USEPA and involves collaborations and contributions from many groups from federal and state agencies, and from private and academic i...

A systematic review of administrative and clinical databases of infants admitted to neonatal units.

PubMed

Statnikov, Yevgeniy; Ibrahim, Buthaina; Modi, Neena

2017-05-01

High quality information, increasingly captured in clinical databases, is a useful resource for evaluating and improving newborn care. We conducted a systematic review to identify neonatal databases, and define their characteristics. We followed a preregistered protocol using MesH terms to search MEDLINE, EMBASE, CINAHL, Web of Science and OVID Maternity and Infant Care Databases for articles identifying patient level databases covering more than one neonatal unit. Full-text articles were reviewed and information extracted on geographical coverage, criteria for inclusion, data source, and maternal and infant characteristics. We identified 82 databases from 2037 publications. Of the country-specific databases there were 39 regional and 39 national. Sixty databases restricted entries to neonatal unit admissions by birth characteristic or insurance cover; 22 had no restrictions. Data were captured specifically for 53 databases; 21 administrative sources; 8 clinical sources. Two clinical databases hold the largest range of data on patient characteristics, USA's Pediatrix BabySteps Clinical Data Warehouse and UK's National Neonatal Research Database. A number of neonatal databases exist that have potential to contribute to evaluating neonatal care. The majority is created by entering data specifically for the database, duplicating information likely already captured in other administrative and clinical patient records. This repetitive data entry represents an unnecessary burden in an environment where electronic patient records are increasingly used. Standardisation of data items is necessary to facilitate linkage within and between countries. 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/.

Herpes zoster surveillance using electronic databases in the Valencian Community (Spain)

PubMed Central

2013-01-01

Background Epidemiologic data of Herpes Zoster (HZ) disease in Spain are scarce. The objective of this study was to assess the epidemiology of HZ in the Valencian Community (Spain), using outpatient and hospital electronic health databases. Methods Data from 2007 to 2010 was collected from computerized health databases of a population of around 5 million inhabitants. Diagnoses were recorded by physicians using the International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM). A sample of medical records under different criteria was reviewed by a general practitioner, to assess the reliability of codification. Results The average annual incidence of HZ was 4.60 per 1000 persons-year (PY) for all ages (95% CI: 4.57-4.63), is more frequent in women [5.32/1000PY (95% CI: 5.28-5.37)] and is strongly age-related, with a peak incidence at 70-79 years. A total of 7.16/1000 cases of HZ required hospitalization. Conclusions Electronic health database used in the Valencian Community is a reliable electronic surveillance tool for HZ disease and will be useful to define trends in disease burden before and after HZ vaccine introduction. PMID:24094135

Military service member and veteran reintegration: A critical review and adapted ecological model.

PubMed

Elnitsky, Christine A; Blevins, Cara L; Fisher, Michael P; Magruder, Kathryn

2017-01-01

Returning military service members and veterans (MSMVs) experience a wide range of stress-related disorders in addition to social and occupational difficulties when reintegrating to the community. Facilitating reintegration of MSMVs following deployment is a societal priority. With an objective of identifying challenges and facilitators for reintegration of MSMVs of the current war era, we critically review and identify gaps in the literature. We searched 8 electronic databases and identified 1,764 articles. Screening of abstracts and full-text review based on our inclusion/exclusion criteria, yielded 186 articles for review. Two investigators evaluating relevant articles independently found a lack of clear definition or comprehensive theorizing about MSMV reintegration. To address these gaps, we linked the findings from the literature to provide a unified definition of reintegration and adapted the social ecological systems theory to guide research and practice aimed at MSMV reintegration. Furthermore, we identified individual, interpersonal, community, and societal challenges related to reintegration. The 186 studies published from 2001 (the start of the current war era) to 2015 included 6 experimental studies or clinical trials. Most studies do not adequately account for context or more than a narrow set of potential influences on MSMV reintegration. Little evidence was found that evaluated interventions for health conditions, rehabilitation, and employment, or effective models of integrated delivery systems. We recommend an ecological model of MSMV reintegration to advance research and practice processes and outcomes at 4 levels (individual, interpersonal, organizational, and societal). (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Is there publication bias towards brazilian articles on cancer?

PubMed Central

Loureiro, Luiz Victor Maia; Callegaro, Donato; Rocha, Altieres de Arruda; Prado, Bernard Lobato; Mutão, Taciana Sousa; Donnarumma, Carlos del Cistia; del Giglio, Auro

2013-01-01

ABSTRACT Objective: To investigate whether Brazilian articles on cancer are published in journals with an impact factor and/or repercussion (measured by the number of citations) inferior to those that come from foreign organizations. Methods: A search was carried out in PubMed for the MeSH term “neoplasm” with the limits clinical trial, affiliation of the Brazilian author(s), and interval from July 1st, 2009 to June 30, 2010. Selected for matching were non-Brazilian related articles published from three months prior to three months after the date of publication of the Brazilian study. The numbers of citations were obtained from two databases, as well as the impact factor for the journals in which the articles were published. Results: Fortythree national and 876 related international articles were identified. The Brazilian publications had a mean impact factor of 3.000 versus 3.430 of the international ones (p=0.041). There was no statistically significant difference as to the number of citations between the two groups. The affiliation of the first author with a Brazilian or foreign organization did not significantly influence the number of citations or the impact factor. Conclusion: Brazilian articles are significantly less accepted in journals with higher impact factors, although it does not compromise its repercussion on the scientific community. PMID:23579739

Literature searches on Ayurveda: An update

PubMed Central

Aggithaya, Madhur G.; Narahari, Saravu R.

2015-01-01

Introduction: The journals that publish on Ayurveda are increasingly indexed by popular medical databases in recent years. However, many Eastern journals are not indexed biomedical journal databases such as PubMed. Literature searches for Ayurveda continue to be challenging due to the nonavailability of active, unbiased dedicated databases for Ayurvedic literature. In 2010, authors identified 46 databases that can be used for systematic search of Ayurvedic papers and theses. This update reviewed our previous recommendation and identified current and relevant databases. Aims: To update on Ayurveda literature search and strategy to retrieve maximum publications. Methods: Author used psoriasis as an example to search previously listed databases and identify new. The population, intervention, control, and outcome table included keywords related to psoriasis and Ayurvedic terminologies for skin diseases. Current citation update status, search results, and search options of previous databases were assessed. Eight search strategies were developed. Hundred and five journals, both biomedical and Ayurveda, which publish on Ayurveda, were identified. Variability in databases was explored to identify bias in journal citation. Results: Five among 46 databases are now relevant – AYUSH research portal, Annotated Bibliography of Indian Medicine, Digital Helpline for Ayurveda Research Articles (DHARA), PubMed, and Directory of Open Access Journals. Search options in these databases are not uniform, and only PubMed allows complex search strategy. “The Researches in Ayurveda” and “Ayurvedic Research Database” (ARD) are important grey resources for hand searching. About 44/105 (41.5%) journals publishing Ayurvedic studies are not indexed in any database. Only 11/105 (10.4%) exclusive Ayurveda journals are indexed in PubMed. Conclusion: AYUSH research portal and DHARA are two major portals after 2010. It is mandatory to search PubMed and four other databases because all five carry citations from different groups of journals. The hand searching is important to identify Ayurveda publications that are not indexed elsewhere. Availability information of citations in Ayurveda libraries from National Union Catalogue of Scientific Serials in India if regularly updated will improve the efficacy of hand searching. A grey database (ARD) contains unpublished PG/Ph.D. theses. The AYUSH portal, DHARA (funded by Ministry of AYUSH), and ARD should be merged to form single larger database to limit Ayurveda literature searches. PMID:27313409

Let’s Get Healthy! Health Awareness Through Public Participation in an Education and Research Exhibit

PubMed Central

Marriott, Lisa K.; Cameron, William E.; Purnell, Jonathan Q.; Cetola, Stephano; Ito, Matthew K.; Williams, Craig D.; Newcomb, Kenneth C.; Randall, Joan A.; Messenger, Wyatt B.; Lipus, Adam C.; Shannon, Jackilen

2013-01-01

Background Health information technology (HIT) offers a resource for public empowerment through tailored information. Objective Use interactive community health events to improve awareness of chronic disease risk factors while collecting data to improve health. Methods Let’s Get Healthy! is an education and research program in which participants visit interactive research stations to learn about their own health (diet, body composition, blood chemistry). HIT enables computerized data collection that presents participants with immediate results and tailored educational feedback. An anonymous wristband number links collected data in a population database. Results and Lessons Learned Communities tailor events to meet community health needs with volunteers trained to conduct research. Participants experience being a research participant and contribute to an anonymous population database for both traditional research purposes and open-source community use. Conclusions By integrating HIT with community involvement, health fairs become an interactive method for engaging communities in research and raising health awareness. PMID:22982846