The Internationalization of the Academic Library: A Systematic Review of 25 Years of Literature on International Students

ERIC Educational Resources Information Center

Click, Amanda B.; Wiley, Claire Walker; Houlihan, Meggan

2017-01-01

This study is a systematic review of the library and information science (LIS) literature related to international students and academic libraries. A systematic review involves the methodical collection and analysis of a body of literature and is growing in popularity in the LIS field. Three well-known LIS databases were systematically searched…

Building an efficient curation workflow for the Arabidopsis literature corpus

PubMed Central

Li, Donghui; Berardini, Tanya Z.; Muller, Robert J.; Huala, Eva

2012-01-01

TAIR (The Arabidopsis Information Resource) is the model organism database (MOD) for Arabidopsis thaliana, a model plant with a literature corpus of about 39 000 articles in PubMed, with over 4300 new articles added in 2011. We have developed a literature curation workflow incorporating both automated and manual elements to cope with this flood of new research articles. The current workflow can be divided into two phases: article selection and curation. Structured controlled vocabularies, such as the Gene Ontology and Plant Ontology are used to capture free text information in the literature as succinct ontology-based annotations suitable for the application of computational analysis methods. We also describe our curation platform and the use of text mining tools in our workflow. Database URL: www.arabidopsis.org PMID:23221298

The use of Research Electronic Data Capture (REDCap) software to create a database of librarian-mediated literature searches.

PubMed

Lyon, Jennifer A; Garcia-Milian, Rolando; Norton, Hannah F; Tennant, Michele R

2014-01-01

Expert-mediated literature searching, a keystone service in biomedical librarianship, would benefit significantly from regular methodical review. This article describes the novel use of Research Electronic Data Capture (REDCap) software to create a database of literature searches conducted at a large academic health sciences library. An archive of paper search requests was entered into REDCap, and librarians now prospectively enter records for current searches. Having search data readily available allows librarians to reuse search strategies and track their workload. In aggregate, this data can help guide practice and determine priorities by identifying users' needs, tracking librarian effort, and focusing librarians' continuing education.

PA01.34. Catagorical interpretation in Microsoft excel of jangam dravya database from Bruhat-Trayi & Laghu-Trayi

PubMed Central

Saraf, Abhijeet

2012-01-01

Purpose: Not a single drug in Ayurveda has been termed as non-medicinal. This means every Dravya has medicinal value in this world. Jangam dravya is an animal sourced medicine. In samhita Jangam Dravya are described first. So as per Krama Varnan Vichar, Jangam Dravyas are significant in this type. In Ayurvedic literature there is more literature on Audbhid & Parthiva Dravyas. I Total available nighantu: more than 25. Total available Rasa Grantha: about 145. There is no one Grantha on Jangam Dravya which describes their whole information. Jangam Dravyas are described in Ayurvedic literature in different views and in different branches. Gross description is available in Samhitas. But they aren’t in format. They are not compiled according to their Guna Karma, Upayogitwa, Vyadhiharatwa, and Kalpa etc. Their use in Chikitsa is minimal as their ready references are not available, though very much effective. So due to sheer need of compilation of these references this topic was selected for study. The basic need for study of Jangam Dravya is to prepare its whole DATABASE. So through this study Database of Jangam Dravya can be available like Jangam Dravya. Method: Selection of topic this is a fundamental & literary study, Selection of material, Selection of Database software & font, Collection of data & preparation of Master Chart, Preparation of Database, Interpretation & summarization of data. Result: So in this paper, we are going to focus on literature availability of jangam dravya with the help of modern technique like Microsoft Excel. And also how we can prepare and use the categorical interpretation of jangam dravya with help of database Conclusion: Jangam Dravyas are described in Ayurvedic literature in different views and in different branches. Importances of these dravyas are the main key point of this study.

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.

Consultation-Liaison Psychiatry Literature Database (2003 update). Part I: Consultation - Liaison Literature Database: 2003 update and national lists.

PubMed

Strain, James J; Strain, Jay J; Mustafa, Shawkat; Flores, Luis Ruiz Guillermo; Smith, Graeme; Mayou, Richard; Carvalho, Serafim; Chiu, Niem Mu; Zimmermann, Paulo; Fragras, Renerio; Lyons, John; Tsopolis, Nicholas; Malt, Ulrik

2003-01-01

Every day there are 10,000 scientific articles published. Since the Consultation-Liaison ("C-L") psychiatrist may be asked to consult on a patient with any medical illness, e.g., severe acute respiratory syndrome (SARS), malaria, cancer, stroke, amytrophic, lateral sclerosis, and a patient who may be on any medical drug, methods need to be developed to review the recent literature and have an awareness of key and essential current findings. At the same time, teachers need to develop a current listing of seminal papers for trainees and practitioners of this newest cross-over subspecialty of psychiatry-now called Psychosomatic Medicine. Experts selected because of their writings and acknowledged contributions to a specific clinical area or problem hope examined thousands of citations to choose those articles, chapters, books, or letters that they regard as most important to Psychosomatic Medicine. In addition, psychiatric specialists in six countries have provided their national Psychosomatic Medicine (Consultation-Liaison) lists as examples of what they regard as the most important teaching materials journals: Australia, Brazil, Greece, Mexico, Portugal, and Taiwan. It is our belief that a cogent, international, systematic review will provide the greatest success in creating a "regionally appropriate" teaching and consultation literature database with world-wide applicability. We review our current progress on this literature database and software, the technical system and data organization involved, the approach used to populate the literature system, and ongoing development plans to bring this system to the physician via mobile technologies.

Patent Databases. . .A Survey of What Is Available from DIALOG, Questel, SDC, Pergamon and INPADOC.

ERIC Educational Resources Information Center

Kulp, Carol S.

1984-01-01

Presents survey of two groups of databases covering patent literature: patent literature only and general literature that includes patents relevant to subject area of database. Description of databases and comparison tables for patent and general databases (cost, country coverage, years covered, update frequency, file size, and searchable data…

Mapping the core journals of the physical therapy literature*

PubMed Central

Fell, Dennis W; Buchanan, Melanie J; Horchen, Heidi A; Scherr, Joel A

2011-01-01

Objectives: The purpose of this study was to identify (1) core journals in the literature of physical therapy, (2) currency of references cited in that literature, and (3) online databases providing the highest coverage rate of core journals. Method: Data for each cited reference in each article of four source journals for three years were recorded, including type of literature, year of publication, and journal title. The journal titles were ranked in descending order according to the frequency of citations and divided into three zones using Bradford's Law of Scattering. Four databases were analyzed for coverage rates of articles published in the Zone 1 and Zone 2 journals in 2007. Results: Journal articles were the most frequently cited type of literature, with sixteen journals supplying one-third of the cited journal references. Physical Therapy was the most commonly cited title. There were more cited articles published from 2000 to 2007 than in any previous full decade. Of the databases analyzed, CINAHL provided the highest coverage rate for Zone 1 2007 publications. Conclusions: Results were similar to a previous study, except for changes in the order of Zone 1 journals. Results can help physical therapists and librarians determine important journals in this discipline. PMID:21753912

Building a protein name dictionary from full text: a machine learning term extraction approach.

PubMed

Shi, Lei; Campagne, Fabien

2005-04-07

The majority of information in the biological literature resides in full text articles, instead of abstracts. Yet, abstracts remain the focus of many publicly available literature data mining tools. Most literature mining tools rely on pre-existing lexicons of biological names, often extracted from curated gene or protein databases. This is a limitation, because such databases have low coverage of the many name variants which are used to refer to biological entities in the literature. We present an approach to recognize named entities in full text. The approach collects high frequency terms in an article, and uses support vector machines (SVM) to identify biological entity names. It is also computationally efficient and robust to noise commonly found in full text material. We use the method to create a protein name dictionary from a set of 80,528 full text articles. Only 8.3% of the names in this dictionary match SwissProt description lines. We assess the quality of the dictionary by studying its protein name recognition performance in full text. This dictionary term lookup method compares favourably to other published methods, supporting the significance of our direct extraction approach. The method is strong in recognizing name variants not found in SwissProt.

Building a protein name dictionary from full text: a machine learning term extraction approach

PubMed Central

Shi, Lei; Campagne, Fabien

2005-01-01

Background The majority of information in the biological literature resides in full text articles, instead of abstracts. Yet, abstracts remain the focus of many publicly available literature data mining tools. Most literature mining tools rely on pre-existing lexicons of biological names, often extracted from curated gene or protein databases. This is a limitation, because such databases have low coverage of the many name variants which are used to refer to biological entities in the literature. Results We present an approach to recognize named entities in full text. The approach collects high frequency terms in an article, and uses support vector machines (SVM) to identify biological entity names. It is also computationally efficient and robust to noise commonly found in full text material. We use the method to create a protein name dictionary from a set of 80,528 full text articles. Only 8.3% of the names in this dictionary match SwissProt description lines. We assess the quality of the dictionary by studying its protein name recognition performance in full text. Conclusion This dictionary term lookup method compares favourably to other published methods, supporting the significance of our direct extraction approach. The method is strong in recognizing name variants not found in SwissProt. PMID:15817129

Mapping the literature of athletic training

PubMed Central

Delwiche, Frances A.; Hall, Ellen F.

2007-01-01

Purpose: This paper identifies the core literature of athletic training and determines which major databases provide the most thorough intellectual access to this literature. Methods: This study collected all cited references from 2002 to 2004 of three journals widely read by those in the athletic training field. Bradford's Law of Scattering was applied to the resulting list to determine the core journal titles in the discipline. Three major databases were reviewed for extent of their coverage of these core journals. Results: Of the total 8,678 citations, one-third referenced a compact group of 6 journals; another third of the citations referenced an additional 40 titles. The remaining 2,837 citations were scattered across 1,034 additional journal titles. Conclusions: The number and scatter of citations over a three-year period identified forty-six key journals in athletic training. The study results can inform athletic trainers of the core literature in their field, encourage database producers (e.g., MEDLINE, SPORTDiscus, CINAHL) to increase coverage of titles that are not indexed or underindexed, and guide purchasing decisions for libraries serving athletic training programs. PMID:17443253

Domain fusion analysis by applying relational algebra to protein sequence and domain databases

PubMed Central

Truong, Kevin; Ikura, Mitsuhiko

2003-01-01

Background Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. Results This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at . Conclusion As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time. PMID:12734020

Population groups: indexing, coverage, and retrieval effectiveness of ethnically related health care issues in health sciences databases.

PubMed Central

Efthimiadis, E N; Afifi, M

1996-01-01

OBJECTIVES: This study examined methods of accessing (for indexing and retrieval purposes) medical research on population groups in the major abstracting and indexing services of the health sciences literature. DESIGN: The study of diseases in specific population groups is facilitated by the indexing of both diseases and populations in a database. The MEDLINE, PsycINFO, and Embase databases were selected for the study. The published thesauri for these databases were examined to establish the vocabulary in use. Indexing terms were identified and examined as to their representation in the current literature. Terms were clustered further into groups thought to reflect an end user's perspective and to facilitate subsequent analysis. The medical literature contained in the three online databases was searched with both controlled vocabulary and natural language terms. RESULTS: The three thesauri revealed shallow pre-coordinated hierarchical structures, rather difficult-to-use terms for post-coordination, and a blurring of cultural, genetic, and racial facets of populations. Post-coordination is difficult because of the system-oriented terminology, which is intended mostly for information professionals. The terminology unintentionally restricts access by the end users who lack the knowledge needed to use the thesauri effectively for information retrieval. CONCLUSIONS: Population groups are not represented adequately in the index languages of health sciences databases. Users of these databases need to be alerted to the difficulties that may be encountered in searching for information on population groups. Information and health professionals may not be able to access the literature if they are not familiar with the indexing policies on population groups. Consequently, the study points to a problem that needs to be addressed, through either the redesign of existing systems or the design of new ones to meet the goals of Healthy People 2000 and beyond. PMID:8883987

Expanding the use of administrative claims databases in conducting clinical real-world evidence studies in multiple sclerosis.

PubMed

Capkun, Gorana; Lahoz, Raquel; Verdun, Elisabetta; Song, Xue; Chen, Weston; Korn, Jonathan R; Dahlke, Frank; Freitas, Rita; Fraeman, Kathy; Simeone, Jason; Johnson, Barbara H; Nordstrom, Beth

2015-05-01

Administrative claims databases provide a wealth of data for assessing the effect of treatments in clinical practice. Our aim was to propose methodology for real-world studies in multiple sclerosis (MS) using these databases. In three large US administrative claims databases: MarketScan, PharMetrics Plus and Department of Defense (DoD), patients with MS were selected using an algorithm identified in the published literature and refined for accuracy. Algorithms for detecting newly diagnosed ('incident') MS cases were also refined and tested. Methodology based on resource and treatment use was developed to differentiate between relapses with and without hospitalization. When various patient selection criteria were applied to the MarketScan database, an algorithm requiring two MS diagnoses at least 30 days apart was identified as the preferred method of selecting patient cohorts. Attempts to detect incident MS cases were confounded by the limited continuous enrollment of patients in these databases. Relapse detection algorithms identified similar proportions of patients in the MarketScan and PharMetrics Plus databases experiencing relapses with (2% in both databases) and without (15-20%) hospitalization in the 1 year follow-up period, providing findings in the range of those in the published literature. Additional validation of the algorithms proposed here would increase their credibility. The methods suggested in this study offer a good foundation for performing real-world research in MS using administrative claims databases, potentially allowing evidence from different studies to be compared and combined more systematically than in current research practice.

BIRS – Bioterrorism Information Retrieval System

PubMed Central

Tewari, Ashish Kumar; Rashi; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Jain, Chakresh Kumar

2013-01-01

Bioterrorism is the intended use of pathogenic strains of microbes to widen terror in a population. There is a definite need to promote research for development of vaccines, therapeutics and diagnostic methods as a part of preparedness to any bioterror attack in the future. BIRS is an open-access database of collective information on the organisms related to bioterrorism. The architecture of database utilizes the current open-source technology viz PHP ver 5.3.19, MySQL and IIS server under windows platform for database designing. Database stores information on literature, generic- information and unique pathways of about 10 microorganisms involved in bioterrorism. This may serve as a collective repository to accelerate the drug discovery and vaccines designing process against such bioterrorist agents (microbes). The available data has been validated from various online resources and literature mining in order to provide the user with a comprehensive information system. Availability The database is freely available at http://www.bioterrorism.biowaves.org PMID:23390356

Predicting missing values in a home care database using an adaptive uncertainty rule method.

PubMed

Konias, S; Gogou, G; Bamidis, P D; Vlahavas, I; Maglaveras, N

2005-01-01

Contemporary literature illustrates an abundance of adaptive algorithms for mining association rules. However, most literature is unable to deal with the peculiarities, such as missing values and dynamic data creation, that are frequently encountered in fields like medicine. This paper proposes an uncertainty rule method that uses an adaptive threshold for filling missing values in newly added records. A new approach for mining uncertainty rules and filling missing values is proposed, which is in turn particularly suitable for dynamic databases, like the ones used in home care systems. In this study, a new data mining method named FiMV (Filling Missing Values) is illustrated based on the mined uncertainty rules. Uncertainty rules have quite a similar structure to association rules and are extracted by an algorithm proposed in previous work, namely AURG (Adaptive Uncertainty Rule Generation). The main target was to implement an appropriate method for recovering missing values in a dynamic database, where new records are continuously added, without needing to specify any kind of thresholds beforehand. The method was applied to a home care monitoring system database. Randomly, multiple missing values for each record's attributes (rate 5-20% by 5% increments) were introduced in the initial dataset. FiMV demonstrated 100% completion rates with over 90% success in each case, while usual approaches, where all records with missing values are ignored or thresholds are required, experienced significantly reduced completion and success rates. It is concluded that the proposed method is appropriate for the data-cleaning step of the Knowledge Discovery process in databases. The latter, containing much significance for the output efficiency of any data mining technique, can improve the quality of the mined information.

Waterpipe Smoking among College Students in the United States: A Review of the Literature

ERIC Educational Resources Information Center

Grekin, Emily R.; Ayna, Dinah

2012-01-01

Objective: To review the literature on college student waterpipe use with a focus on undergraduates in the United States. Participants: Undergraduate students. Methods: Studies were accessed using the databases PubMed, MEDLINE, PsycINFO, and Academic Search Premier. Searches included combinations of the following keywords: "waterpipe," "hookah,"…

The 21st Century Writing Program: Collaboration for the Common Good

ERIC Educational Resources Information Center

Moberg, Eric

2010-01-01

The purpose of this report is to review the literature on theoretical frameworks, best practices, and conceptual models for the 21st century collegiate writing program. Methods include electronic database searches for recent and historical peer-reviewed scholarly literature on collegiate writing programs. The author analyzed over 65 sources from…

Alternative treatment technology information center computer database system

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

Sullivan, D.

1995-10-01

The Alternative Treatment Technology Information Center (ATTIC) computer database system was developed pursuant to the 1986 Superfund law amendments. It provides up-to-date information on innovative treatment technologies to clean up hazardous waste sites. ATTIC v2.0 provides access to several independent databases as well as a mechanism for retrieving full-text documents of key literature. It can be accessed with a personal computer and modem 24 hours a day, and there are no user fees. ATTIC provides {open_quotes}one-stop shopping{close_quotes} for information on alternative treatment options by accessing several databases: (1) treatment technology database; this contains abstracts from the literature on all typesmore » of treatment technologies, including biological, chemical, physical, and thermal methods. The best literature as viewed by experts is highlighted. (2) treatability study database; this provides performance information on technologies to remove contaminants from wastewaters and soils. It is derived from treatability studies. This database is available through ATTIC or separately as a disk that can be mailed to you. (3) underground storage tank database; this presents information on underground storage tank corrective actions, surface spills, emergency response, and remedial actions. (4) oil/chemical spill database; this provides abstracts on treatment and disposal of spilled oil and chemicals. In addition to these separate databases, ATTIC allows immediate access to other disk-based systems such as the Vendor Information System for Innovative Treatment Technologies (VISITT) and the Bioremediation in the Field Search System (BFSS). The user may download these programs to their own PC via a high-speed modem. Also via modem, users are able to download entire documents through the ATTIC system. Currently, about fifty publications are available, including Superfund Innovative Technology Evaluation (SITE) program documents.« less

Lead exposure in US worksites: A literature review and development of an occupational lead exposure database from the published literature

PubMed Central

Koh, Dong-Hee; Locke, Sarah J.; Chen, Yu-Cheng; Purdue, Mark P.; Friesen, Melissa C.

2016-01-01

Background Retrospective exposure assessment of occupational lead exposure in population-based studies requires historical exposure information from many occupations and industries. Methods We reviewed published US exposure monitoring studies to identify lead exposure measurement data. We developed an occupational lead exposure database from the 175 identified papers containing 1,111 sets of lead concentration summary statistics (21% area air, 47% personal air, 32% blood). We also extracted ancillary exposure-related information, including job, industry, task/location, year collected, sampling strategy, control measures in place, and sampling and analytical methods. Results Measurements were published between 1940 and 2010 and represented 27 2-digit standardized industry classification codes. The majority of the measurements were related to lead-based paint work, joining or cutting metal using heat, primary and secondary metal manufacturing, and lead acid battery manufacturing. Conclusions This database can be used in future statistical analyses to characterize differences in lead exposure across time, jobs, and industries. PMID:25968240

[Exploration and construction of the full-text database of acupuncture literature in the Republic of China].

PubMed

Fei, Lin; Zhao, Jing; Leng, Jiahao; Zhang, Shujian

2017-10-12

The ALIPORC full-text database is targeted at a specific full-text database of acupuncture literature in the Republic of China. Starting in 2015, till now, the database has been getting completed, focusing on books relevant with acupuncture, articles and advertising documents, accomplished or published in the Republic of China. The construction of this database aims to achieve the source sharing of acupuncture medical literature in the Republic of China through the retrieval approaches to diversity and accurate content presentation, contributes to the exchange of scholars, reduces the paper damage caused by paging and simplify the retrieval of the rare literature. The writers have made the explanation of the database in light of sources, characteristics and current situation of construction; and have discussed on improving the efficiency and integrity of the database and deepening the development of acupuncture literature in the Republic of China.

Construction of the iSTAR international Study of Astronomical Reasoning Database

NASA Astrophysics Data System (ADS)

Slater, S. J.; Tatge, C. B.; Slater, T. F.; Bretones, P. S.; Schleigh, S.

2016-12-01

Perhaps more than any other science discipline-based education research field, the scholarly literature base describing and documenting astronomy education research is highly fragmented and widely dispersed across numerous journals. The resulting wide diversity of journals that publish astronomy education research presents an arduous challenge for scholars trying to best understand what work has been done and what work still needs to be done. Moreover, a vast amount of education research on the teaching and learning of astronomy exists in dissertations that were never published and even more exists in the realm of un-disseminated grey literature hosted in conference proceedings and society newsletters going back decades. With a few notable exceptions far less extensive than the current project, there has been no comprehensive repository for cataloging astronomy education research methods and results to date. In response, an international cadre of scholars coordinated by the CAPER Center for Astronomy & Physics Education Research are creating the underlying structure for an online database in order to conduct an international Study of Astronomy Reasoning, iSTAR, project. The online iSTAR database serves as an online host to bring together in one place digital copies of hard to locate journal articles, isolated dissertations and theses, and professional meeting contributions to extend the world's scholars abilities to more easily find and utilize a far broader collection of astronomy education research literature than has been previously available. Works are categorized by research method, nature of study-participants, educational learning venue studied, country and language of the study, and other fruitfully useful categories. Scholars wishing to add their own literature resources are encouraged to contribute to the online database located at istardatabase.org

Opportunities for research to improve employment for people with spinal cord injuries.

PubMed

Frieden, L; Winnegar, A J

2012-05-01

This paper reviews the literature pertaining to the employment of people who experience spinal cord injury (SCI) in the United States and recommending future research. The literature was reviewed with search terms such as SCI, employment, working from home and telework using databases in EBSCO, including Academic Search Complete and the American Psychological Association’s databases. Literature and findings on key factors related to employment illustrate the multiple dimensions of work environments, and health demands, that effect employment outcomes for people with SCI. Employment is important for people with SCI and valued in society. The literature reviewed indicates that researchers understand the work demands for people with SCI and may help to identify suitable supports, training and job opportunities. There remains a need for research focus on understanding future employment demands, necessary work skills, differing work environments and methods for increasing and preserving employment.

Solutions in radiology services management: a literature review*

PubMed Central

Pereira, Aline Garcia; Vergara, Lizandra Garcia Lupi; Merino, Eugenio Andrés Díaz; Wagner, Adriano

2015-01-01

Objective The present study was aimed at reviewing the literature to identify solutions for problems observed in radiology services. Materials and Methods Basic, qualitative, exploratory literature review at Scopus and SciELO databases, utilizing the Mendeley and Illustrator CC Adobe softwares. Results In the databases, 565 papers – 120 out of them, pdf free – were identified. Problems observed in the radiology sector are related to procedures scheduling, humanization, lack of training, poor knowledge and use of management techniques, and interaction with users. The design management provides the services with interesting solutions such as Benchmarking, CRM, Lean Approach, ServiceBlueprinting, continued education, among others. Conclusion Literature review is an important tool to identify problems and respective solutions. However, considering the small number of studies approaching management of radiology services, this is a great field of research for the development of deeper studies. PMID:26543281

How Neighborhoods Influence Child Maltreatment: A Review of the Literature and Alternative Pathways

ERIC Educational Resources Information Center

Coulton, Claudia J.; Crampton, David S.; Irwin, Molly; Spilsbury, James C.; Korbin, Jill E.

2007-01-01

Objective: To review the literature on the relationships between neighborhoods and child maltreatment and identify future directions for research in this area. Method: A search of electronic databases and a survey of experts yielded a list of 25 studies on the influence of geographically defined neighborhoods on child maltreatment. These studies…

The Identification of Children with, or at Significant Risk of, Intellectual Disabilities in Low- and Middle-Income Countries: A Review

ERIC Educational Resources Information Center

Robertson, Janet; Hatton, Chris; Emerson, Eric; Yasamy, M. Taghi

2012-01-01

Background: Developmental monitoring of children is an important strategy for the early detection and management of intellectual disabilities (ID) in high-income countries. This review summarizes the literature on identifying children with ID in low- and middle-income (LAMI) countries. Materials and methods: Electronic literature database searches…

Whistleblowing: An integrative literature review of data-based studies involving nurses.

PubMed

Jackson, Debra; Hickman, Louise D; Hutchinson, Marie; Andrew, Sharon; Smith, James; Potgieter, Ingrid; Cleary, Michelle; Peters, Kath

2014-10-27

Abstract Aim To summarise and critique the research literature about whistleblowing and nurses. Background Whistleblowing is identified as a crucial issue in maintenance of healthcare standards and nurses are frequently involved in whistleblowing events. Despite the importance of this issue, to our knowledge an evaluation of this body of the data-based literature has not been undertaken. Method An integrative literature review approach was used to summarise and critique the research literature. A comprehensive search of five databases including Medline, CINAHL, PubMed and Health Science: Nursing/Academic Edition, and Google, were searched using terms including: 'whistleblow*', 'nurs*'. In addition, relevant journals were examined, as well as reference lists of retrieved papers. Papers published during the years 2007-2013 were selected for inclusion. Findings Fifteen papers were identified, capturing data from nurses in seven countries. The findings in this review demonstrate a growing body of research for the nursing profession at large to engage and respond appropriately to issues involving suboptimal patient care or organisational wrongdoing. Conclusions Nursing plays a key role in maintaining practice standards and in reporting care that is unacceptable although the repercussions to nurses who raise concerns are insupportable. Overall, whistleblowing and how it influences the individual, their family, work colleagues, nursing practice and policy overall, requires further national and international research attention.

Domain fusion analysis by applying relational algebra to protein sequence and domain databases.

PubMed

Truong, Kevin; Ikura, Mitsuhiko

2003-05-06

Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at http://calcium.uhnres.utoronto.ca/pi. As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time.

pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature

PubMed Central

Ding, Ruoyao; Arighi, Cecilia N.; Lee, Jung-Youn; Wu, Cathy H.; Vijay-Shanker, K.

2015-01-01

Background Automatically detecting gene/protein names in the literature and connecting them to databases records, also known as gene normalization, provides a means to structure the information buried in free-text literature. Gene normalization is critical for improving the coverage of annotation in the databases, and is an essential component of many text mining systems and database curation pipelines. Methods In this manuscript, we describe a gene normalization system specifically tailored for plant species, called pGenN (pivot-based Gene Normalization). The system consists of three steps: dictionary-based gene mention detection, species assignment, and intra species normalization. We have developed new heuristics to improve each of these phases. Results We evaluated the performance of pGenN on an in-house expertly annotated corpus consisting of 104 plant relevant abstracts. Our system achieved an F-value of 88.9% (Precision 90.9% and Recall 87.2%) on this corpus, outperforming state-of-art systems presented in BioCreative III. We have processed over 440,000 plant-related Medline abstracts using pGenN. The gene normalization results are stored in a local database for direct query from the pGenN web interface (proteininformationresource.org/pgenn/). The annotated literature corpus is also publicly available through the PIR text mining portal (proteininformationresource.org/iprolink/). PMID:26258475

What is lost when searching only one literature database for articles relevant to injury prevention and safety promotion?

PubMed

Lawrence, D W

2008-12-01

To assess what is lost if only one literature database is searched for articles relevant to injury prevention and safety promotion (IPSP) topics. Serial textword (keyword, free-text) searches using multiple synonym terms for five key IPSP topics (bicycle-related brain injuries, ethanol-impaired driving, house fires, road rage, and suicidal behaviors among adolescents) were conducted in four of the bibliographic databases that are most used by IPSP professionals: EMBASE, MEDLINE, PsycINFO, and Web of Science. Through a systematic procedure, an inventory of articles on each topic in each database was conducted to identify the total unduplicated count of all articles on each topic, the number of articles unique to each database, and the articles available if only one database is searched. No single database included all of the relevant articles on any topic, and the database with the broadest coverage differed by topic. A search of only one literature database will return 16.7-81.5% (median 43.4%) of the available articles on any of five key IPSP topics. Each database contributed unique articles to the total bibliography for each topic. A literature search performed in only one database will, on average, lead to a loss of more than half of the available literature on a topic.

Tympanometry in infants: a study of the sensitivity and specificity of 226-Hz and 1,000-Hz probe tones.

PubMed

Carmo, Michele Picanço; Costa, Nayara Thais de Oliveira; Momensohn-Santos, Teresa Maria

2013-10-01

Introduction For infants under 6 months, the literature recommends 1,000-Hz tympanometry, which has a greater sensitivity for the correct identification of middle ear disorders in this population. Objective To systematically analyze national and international publications found in electronic databases that used tympanometry with 226-Hz and 1,000-Hz probe tones. Data Synthesis Initially, we identified 36 articles in the SciELO database, 11 in the Latin American and Caribbean Literature on the Health Sciences (LILACS) database, 199 in MEDLINE, 0 in the Cochrane database, 16 in ISI Web of Knowledge, and 185 in the Scopus database. We excluded 433 articles because they did not fit the selection criteria, leaving 14 publications that were analyzed in their entirety. Conclusions The 1,000-Hz tone test has greater sensitivity and specificity for the correct identification of tympanometric curve changes. However, it is necessary to clarify the doubts that still exist regarding the use of this test frequency. Improved methods for rating curves, standardization of normality criteria, and the types of curves found in infants should be addressed.

Tympanometry in Infants: A Study of the Sensitivity and Specificity of 226-Hz and 1,000-Hz Probe Tones

PubMed Central

Carmo, Michele Picanço; Costa, Nayara Thais de Oliveira; Momensohn-Santos, Teresa Maria

2013-01-01

Introduction For infants under 6 months, the literature recommends 1,000-Hz tympanometry, which has a greater sensitivity for the correct identification of middle ear disorders in this population. Objective To systematically analyze national and international publications found in electronic databases that used tympanometry with 226-Hz and 1,000-Hz probe tones. Data Synthesis Initially, we identified 36 articles in the SciELO database, 11 in the Latin American and Caribbean Literature on the Health Sciences (LILACS) database, 199 in MEDLINE, 0 in the Cochrane database, 16 in ISI Web of Knowledge, and 185 in the Scopus database. We excluded 433 articles because they did not fit the selection criteria, leaving 14 publications that were analyzed in their entirety. Conclusions The 1,000-Hz tone test has greater sensitivity and specificity for the correct identification of tympanometric curve changes. However, it is necessary to clarify the doubts that still exist regarding the use of this test frequency. Improved methods for rating curves, standardization of normality criteria, and the types of curves found in infants should be addressed. PMID:25992044

Expert searching in public health

PubMed Central

Alpi, Kristine M.

2005-01-01

Objective: The article explores the characteristics of public health information needs and the resources available to address those needs that distinguish it as an area of searching requiring particular expertise. Methods: Public health searching activities from reference questions and literature search requests at a large, urban health department library were reviewed to identify the challenges in finding relevant public health information. Results: The terminology of the information request frequently differed from the vocabularies available in the databases. Searches required the use of multiple databases and/or Web resources with diverse interfaces. Issues of the scope and features of the databases relevant to the search questions were considered. Conclusion: Expert searching in public health differs from other types of expert searching in the subject breadth and technical demands of the databases to be searched, the fluidity and lack of standardization of the vocabulary, and the relative scarcity of high-quality investigations at the appropriate level of geographic specificity. Health sciences librarians require a broad exposure to databases, gray literature, and public health terminology to perform as expert searchers in public health. PMID:15685281

A systematic review of teleophthalmological studies in Europe

PubMed Central

Labiris, Georgios; Panagiotopoulou, Eirini-Kanella; Kozobolis, Vassilios P.

2018-01-01

A systematic review of the recent literature regarding a series of ocular diseases involved in European telemedicine projects was performed based on the PubMed, Google Scholar and Springer databases in June 2017. Literature review returned 44 eligible studies; among them, emergency ophthalmology, diabetic retinopathy, glaucoma, age-related macular disease, cataract and retinopathy of prematurity. The majority of studies indicate teleophthalmology as a valid, reliable and cost-efficient method for care-provision in ophthalmology patients which delivers comparable outcomes to the traditional examination methods. PMID:29487825

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

Identifying complications of interventional procedures from UK routine healthcare databases: a systematic search for methods using clinical codes.

PubMed

Keltie, Kim; Cole, Helen; Arber, Mick; Patrick, Hannah; Powell, John; Campbell, Bruce; Sims, Andrew

2014-11-28

Several authors have developed and applied methods to routine data sets to identify the nature and rate of complications following interventional procedures. But, to date, there has been no systematic search for such methods. The objective of this article was to find, classify and appraise published methods, based on analysis of clinical codes, which used routine healthcare databases in a United Kingdom setting to identify complications resulting from interventional procedures. A literature search strategy was developed to identify published studies that referred, in the title or abstract, to the name or acronym of a known routine healthcare database and to complications from procedures or devices. The following data sources were searched in February and March 2013: Cochrane Methods Register, Conference Proceedings Citation Index - Science, Econlit, EMBASE, Health Management Information Consortium, Health Technology Assessment database, MathSciNet, MEDLINE, MEDLINE in-process, OAIster, OpenGrey, Science Citation Index Expanded and ScienceDirect. Of the eligible papers, those which reported methods using clinical coding were classified and summarised in tabular form using the following headings: routine healthcare database; medical speciality; method for identifying complications; length of follow-up; method of recording comorbidity. The benefits and limitations of each approach were assessed. From 3688 papers identified from the literature search, 44 reported the use of clinical codes to identify complications, from which four distinct methods were identified: 1) searching the index admission for specified clinical codes, 2) searching a sequence of admissions for specified clinical codes, 3) searching for specified clinical codes for complications from procedures and devices within the International Classification of Diseases 10th revision (ICD-10) coding scheme which is the methodology recommended by NHS Classification Service, and 4) conducting manual clinical review of diagnostic and procedure codes. The four distinct methods identifying complication from codified data offer great potential in generating new evidence on the quality and safety of new procedures using routine data. However the most robust method, using the methodology recommended by the NHS Classification Service, was the least frequently used, highlighting that much valuable observational data is being ignored.

Searching for Controlled Trials of Complementary and Alternative Medicine: A Comparison of 15 Databases

PubMed Central

Cogo, Elise; Sampson, Margaret; Ajiferuke, Isola; Manheimer, Eric; Campbell, Kaitryn; Daniel, Raymond; Moher, David

2011-01-01

This project aims to assess the utility of bibliographic databases beyond the three major ones (MEDLINE, EMBASE and Cochrane CENTRAL) for finding controlled trials of complementary and alternative medicine (CAM). Fifteen databases were searched to identify controlled clinical trials (CCTs) of CAM not also indexed in MEDLINE. Searches were conducted in May 2006 using the revised Cochrane highly sensitive search strategy (HSSS) and the PubMed CAM Subset. Yield of CAM trials per 100 records was determined, and databases were compared over a standardized period (2005). The Acudoc2 RCT, Acubriefs, Index to Chiropractic Literature (ICL) and Hom-Inform databases had the highest concentrations of non-MEDLINE records, with more than 100 non-MEDLINE records per 500. Other productive databases had ratios between 500 and 1500 records to 100 non-MEDLINE records—these were AMED, MANTIS, PsycINFO, CINAHL, Global Health and Alt HealthWatch. Five databases were found to be unproductive: AGRICOLA, CAIRSS, Datadiwan, Herb Research Foundation and IBIDS. Acudoc2 RCT yielded 100 CAM trials in the most recent 100 records screened. Acubriefs, AMED, Hom-Inform, MANTIS, PsycINFO and CINAHL had more than 25 CAM trials per 100 records screened. Global Health, ICL and Alt HealthWatch were below 25 in yield. There were 255 non-MEDLINE trials from eight databases in 2005, with only 10% indexed in more than one database. Yield varied greatly between databases; the most productive databases from both sampling methods were Acubriefs, Acudoc2 RCT, AMED and CINAHL. Low overlap between databases indicates comprehensive CAM literature searches will require multiple databases. PMID:19468052

Searching for controlled trials of complementary and alternative medicine: a comparison of 15 databases.

PubMed

Cogo, Elise; Sampson, Margaret; Ajiferuke, Isola; Manheimer, Eric; Campbell, Kaitryn; Daniel, Raymond; Moher, David

2011-01-01

This project aims to assess the utility of bibliographic databases beyond the three major ones (MEDLINE, EMBASE and Cochrane CENTRAL) for finding controlled trials of complementary and alternative medicine (CAM). Fifteen databases were searched to identify controlled clinical trials (CCTs) of CAM not also indexed in MEDLINE. Searches were conducted in May 2006 using the revised Cochrane highly sensitive search strategy (HSSS) and the PubMed CAM Subset. Yield of CAM trials per 100 records was determined, and databases were compared over a standardized period (2005). The Acudoc2 RCT, Acubriefs, Index to Chiropractic Literature (ICL) and Hom-Inform databases had the highest concentrations of non-MEDLINE records, with more than 100 non-MEDLINE records per 500. Other productive databases had ratios between 500 and 1500 records to 100 non-MEDLINE records-these were AMED, MANTIS, PsycINFO, CINAHL, Global Health and Alt HealthWatch. Five databases were found to be unproductive: AGRICOLA, CAIRSS, Datadiwan, Herb Research Foundation and IBIDS. Acudoc2 RCT yielded 100 CAM trials in the most recent 100 records screened. Acubriefs, AMED, Hom-Inform, MANTIS, PsycINFO and CINAHL had more than 25 CAM trials per 100 records screened. Global Health, ICL and Alt HealthWatch were below 25 in yield. There were 255 non-MEDLINE trials from eight databases in 2005, with only 10% indexed in more than one database. Yield varied greatly between databases; the most productive databases from both sampling methods were Acubriefs, Acudoc2 RCT, AMED and CINAHL. Low overlap between databases indicates comprehensive CAM literature searches will require multiple databases.

[Design and establishment of modern literature database about acupuncture Deqi].

PubMed

Guo, Zheng-rong; Qian, Gui-feng; Pan, Qiu-yin; Wang, Yang; Xin, Si-yuan; Li, Jing; Hao, Jie; Hu, Ni-juan; Zhu, Jiang; Ma, Liang-xiao

2015-02-01

A search on acupuncture Deqi was conducted using four Chinese-language biomedical databases (CNKI, Wan-Fang, VIP and CBM) and PubMed database and using keywords "Deqi" or "needle sensation" "needling feeling" "needle feel" "obtaining qi", etc. Then, a "Modern Literature Database for Acupuncture Deqi" was established by employing Microsoft SQL Server 2005 Express Edition, introducing the contents, data types, information structure and logic constraint of the system table fields. From this Database, detailed inquiries about general information of clinical trials, acupuncturists' experience, ancient medical works, comprehensive literature, etc. can be obtained. The present databank lays a foundation for subsequent evaluation of literature quality about Deqi and data mining of undetected Deqi knowledge.

(BARS) -- Bibliographic Retrieval System Sandia Shock Compression (SSC) database Shock Physics Index (SPHINX) database. Volume 1: UNIX version query guide customized application for INGRES

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

Herrmann, W.; von Laven, G.M.; Parker, T.

1993-09-01

The Bibliographic Retrieval System (BARS) is a data base management system specially designed to retrieve bibliographic references. Two databases are available, (i) the Sandia Shock Compression (SSC) database which contains over 5700 references to the literature related to stress waves in solids and their applications, and (ii) the Shock Physics Index (SPHINX) which includes over 8000 further references to stress waves in solids, material properties at intermediate and low rates, ballistic and hypervelocity impact, and explosive or shock fabrication methods. There is some overlap in the information in the two data bases.

A Survey of Bioinformatics Database and Software Usage through Mining the Literature.

PubMed

Duck, Geraint; Nenadic, Goran; Filannino, Michele; Brass, Andy; Robertson, David L; Stevens, Robert

2016-01-01

Computer-based resources are central to much, if not most, biological and medical research. However, while there is an ever expanding choice of bioinformatics resources to use, described within the biomedical literature, little work to date has provided an evaluation of the full range of availability or levels of usage of database and software resources. Here we use text mining to process the PubMed Central full-text corpus, identifying mentions of databases or software within the scientific literature. We provide an audit of the resources contained within the biomedical literature, and a comparison of their relative usage, both over time and between the sub-disciplines of bioinformatics, biology and medicine. We find that trends in resource usage differs between these domains. The bioinformatics literature emphasises novel resource development, while database and software usage within biology and medicine is more stable and conservative. Many resources are only mentioned in the bioinformatics literature, with a relatively small number making it out into general biology, and fewer still into the medical literature. In addition, many resources are seeing a steady decline in their usage (e.g., BLAST, SWISS-PROT), though some are instead seeing rapid growth (e.g., the GO, R). We find a striking imbalance in resource usage with the top 5% of resource names (133 names) accounting for 47% of total usage, and over 70% of resources extracted being only mentioned once each. While these results highlight the dynamic and creative nature of bioinformatics research they raise questions about software reuse, choice and the sharing of bioinformatics practice. Is it acceptable that so many resources are apparently never reused? Finally, our work is a step towards automated extraction of scientific method from text. We make the dataset generated by our study available under the CC0 license here: http://dx.doi.org/10.6084/m9.figshare.1281371.

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.

Methods for systematic reviews of health economic evaluations: a systematic review, comparison, and synthesis of method literature.

PubMed

Mathes, Tim; Walgenbach, Maren; Antoine, Sunya-Lee; Pieper, Dawid; Eikermann, Michaela

2014-10-01

The quality of systematic reviews of health economic evaluations (SR-HE) is often limited because of methodological shortcomings. One reason for this poor quality is that there are no established standards for the preparation of SR-HE. The objective of this study is to compare existing methods and suggest best practices for the preparation of SR-HE. To identify the relevant methodological literature on SR-HE, a systematic literature search was performed in Embase, Medline, the National Health System Economic Evaluation Database, the Health Technology Assessment Database, and the Cochrane methodology register, and webpages of international health technology assessment agencies were searched. The study selection was performed independently by 2 reviewers. Data were extracted by one reviewer and verified by a second reviewer. On the basis of the overlaps in the recommendations for the methods of SR-HE in the included papers, suggestions for best practices for the preparation of SR-HE were developed. Nineteen relevant publications were identified. The recommendations within them often differed. However, for most process steps there was some overlap between recommendations for the methods of preparation. The overlaps were taken as basis on which to develop suggestions for the following process steps of preparation: defining the research question, developing eligibility criteria, conducting a literature search, selecting studies, assessing the methodological study quality, assessing transferability, and synthesizing data. The differences in the proposed recommendations are not always explainable by the focus on certain evaluation types, target audiences, or integration in the decision process. Currently, there seem to be no standard methods for the preparation of SR-HE. The suggestions presented here can contribute to the harmonization of methods for the preparation of SR-HE. © The Author(s) 2014.

Reflective random indexing for semi-automatic indexing of the biomedical literature.

PubMed

Vasuki, Vidya; Cohen, Trevor

2010-10-01

The rapid growth of biomedical literature is evident in the increasing size of the MEDLINE research database. Medical Subject Headings (MeSH), a controlled set of keywords, are used to index all the citations contained in the database to facilitate search and retrieval. This volume of citations calls for efficient tools to assist indexers at the US National Library of Medicine (NLM). Currently, the Medical Text Indexer (MTI) system provides assistance by recommending MeSH terms based on the title and abstract of an article using a combination of distributional and vocabulary-based methods. In this paper, we evaluate a novel approach toward indexer assistance by using nearest neighbor classification in combination with Reflective Random Indexing (RRI), a scalable alternative to the established methods of distributional semantics. On a test set provided by the NLM, our approach significantly outperforms the MTI system, suggesting that the RRI approach would make a useful addition to the current methodologies.

A Comparison of Selected Bibliographic Database Subject Overlap for Agricultural Information

ERIC Educational Resources Information Center

Ritchie, Stephanie M.; Young, Lauren M.; Sigman, Jessica

2018-01-01

Agricultural researchers and science librarians must understand which research literature databases provide the most comprehensive coverage of agricultural subjects to support their inquiries. Once the domain of a few specialized databases, agricultural research literature is now covered by broad, multidisciplinary databases. The purpose of this…

Database documentation of marine mammal stranding and mortality: current status review and future prospects.

PubMed

Chan, Derek K P; Tsui, Henry C L; Kot, Brian C W

2017-11-21

Databases are systematic tools to archive and manage information related to marine mammal stranding and mortality events. Stranding response networks, governmental authorities and non-governmental organizations have established regional or national stranding networks and have developed unique standard stranding response and necropsy protocols to document and track stranded marine mammal demographics, signalment and health data. The objectives of this study were to (1) describe and review the current status of marine mammal stranding and mortality databases worldwide, including the year established, types of database and their goals; and (2) summarize the geographic range included in the database, the number of cases recorded, accessibility, filter and display methods. Peer-reviewed literature was searched, focussing on published databases of live and dead marine mammal strandings and mortality and information released from stranding response organizations (i.e. online updates, journal articles and annual stranding reports). Databases that were not published in the primary literature or recognized by government agencies were excluded. Based on these criteria, 10 marine mammal stranding and mortality databases were identified, and strandings and necropsy data found in these databases were evaluated. We discuss the results, limitations and future prospects of database development. Future prospects include the development and application of virtopsy, a new necropsy investigation tool. A centralized web-accessed database of all available postmortem multimedia from stranded marine mammals may eventually support marine conservation and policy decisions, which will allow the use of marine animals as sentinels of ecosystem health, working towards a 'One Ocean-One Health' ideal.

Fusion of Visible and Thermal Descriptors Using Genetic Algorithms for Face Recognition Systems.

PubMed

Hermosilla, Gabriel; Gallardo, Francisco; Farias, Gonzalo; San Martin, Cesar

2015-07-23

The aim of this article is to present a new face recognition system based on the fusion of visible and thermal features obtained from the most current local matching descriptors by maximizing face recognition rates through the use of genetic algorithms. The article considers a comparison of the performance of the proposed fusion methodology against five current face recognition methods and classic fusion techniques used commonly in the literature. These were selected by considering their performance in face recognition. The five local matching methods and the proposed fusion methodology are evaluated using the standard visible/thermal database, the Equinox database, along with a new database, the PUCV-VTF, designed for visible-thermal studies in face recognition and described for the first time in this work. The latter is created considering visible and thermal image sensors with different real-world conditions, such as variations in illumination, facial expression, pose, occlusion, etc. The main conclusions of this article are that two variants of the proposed fusion methodology surpass current face recognition methods and the classic fusion techniques reported in the literature, attaining recognition rates of over 97% and 99% for the Equinox and PUCV-VTF databases, respectively. The fusion methodology is very robust to illumination and expression changes, as it combines thermal and visible information efficiently by using genetic algorithms, thus allowing it to choose optimal face areas where one spectrum is more representative than the other.

Fusion of Visible and Thermal Descriptors Using Genetic Algorithms for Face Recognition Systems

PubMed Central

Hermosilla, Gabriel; Gallardo, Francisco; Farias, Gonzalo; San Martin, Cesar

2015-01-01

The aim of this article is to present a new face recognition system based on the fusion of visible and thermal features obtained from the most current local matching descriptors by maximizing face recognition rates through the use of genetic algorithms. The article considers a comparison of the performance of the proposed fusion methodology against five current face recognition methods and classic fusion techniques used commonly in the literature. These were selected by considering their performance in face recognition. The five local matching methods and the proposed fusion methodology are evaluated using the standard visible/thermal database, the Equinox database, along with a new database, the PUCV-VTF, designed for visible-thermal studies in face recognition and described for the first time in this work. The latter is created considering visible and thermal image sensors with different real-world conditions, such as variations in illumination, facial expression, pose, occlusion, etc. The main conclusions of this article are that two variants of the proposed fusion methodology surpass current face recognition methods and the classic fusion techniques reported in the literature, attaining recognition rates of over 97% and 99% for the Equinox and PUCV-VTF databases, respectively. The fusion methodology is very robust to illumination and expression changes, as it combines thermal and visible information efficiently by using genetic algorithms, thus allowing it to choose optimal face areas where one spectrum is more representative than the other. PMID:26213932

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.

A Source-based Measurement Database for Occupational Exposure Assessment of Electromagnetic Fields in the INTEROCC Study: A Literature Review Approach

PubMed Central

Vila, Javier; Bowman, Joseph D.; Richardson, Lesley; Kincl, Laurel; Conover, Dave L.; McLean, Dave; Mann, Simon; Vecchia, Paolo; van Tongeren, Martie; Cardis, Elisabeth

2016-01-01

Introduction: To date, occupational exposure assessment of electromagnetic fields (EMF) has relied on occupation-based measurements and exposure estimates. However, misclassification due to between-worker variability remains an unsolved challenge. A source-based approach, supported by detailed subject data on determinants of exposure, may allow for a more individualized exposure assessment. Detailed information on the use of occupational sources of exposure to EMF was collected as part of the INTERPHONE-INTEROCC study. To support a source-based exposure assessment effort within this study, this work aimed to construct a measurement database for the occupational sources of EMF exposure identified, assembling available measurements from the scientific literature. Methods: First, a comprehensive literature search was performed for published and unpublished documents containing exposure measurements for the EMF sources identified, a priori as well as from answers of study subjects. Then, the measurements identified were assessed for quality and relevance to the study objectives. Finally, the measurements selected and complementary information were compiled into an Occupational Exposure Measurement Database (OEMD). Results: Currently, the OEMD contains 1624 sets of measurements (>3000 entries) for 285 sources of EMF exposure, organized by frequency band (0 Hz to 300 GHz) and dosimetry type. Ninety-five documents were selected from the literature (almost 35% of them are unpublished technical reports), containing measurements which were considered informative and valid for our purpose. Measurement data and complementary information collected from these documents came from 16 different countries and cover the time period between 1974 and 2013. Conclusion: We have constructed a database with measurements and complementary information for the most common sources of exposure to EMF in the workplace, based on the responses to the INTERPHONE-INTEROCC study questionnaire. This database covers the entire EMF frequency range and represents the most comprehensive resource of information on occupational EMF exposure. It is available at www.crealradiation.com/index.php/en/databases. PMID:26493616

End-of-Life and Palliative Care for People with Intellectual Disabilities Who Have Cancer or Other Life-Limiting Illness: A Review of the Literature and Available Resources

ERIC Educational Resources Information Center

Tuffrey-Wijne, Irene; Hogg, James; Curfs, Leopold

2007-01-01

Background: As patterns of morbidity and mortality are changing, more people with intellectual disabilities develop cancer or other life-limiting illness. This paper reviews the literature around the need of people with intellectual disabilities for palliative care. Methods: A range of databases and the World Wide Web were searched for relevant…

[The methods within the evaluation of disease management programmes in control-group designs using the example of diabetes mellitus - a systematic literature review].

PubMed

Drabik, A; Sawicki, P T; Müller, D; Passon, A; Stock, S

2012-08-01

Disease management programmes (DMPs) were implemented in Germany in 2002. Their evaluation is required by law. Beyond the mandatory evaluation, a growing number of published studies evaluate the DMP for diabetes mellitus type 2 in a control-group design. As patients opt into the programme on a voluntary basis it is necessary to adjust the inherent selection bias between groups. The aim of this study is to review published studies which evaluate the diabetes DMP using a control-group design with respect to the methods used. A systematic literature review of electronic databases (PUBMED, Cochrane Library, EMBASE, MEDPILOT) and a hand search of reference lists of the relevant publications was conducted to identify studies evaluating the DMP diabetes mellitus in a control-group design. 8 studies were included in the systematic literature review. 4 studies gathered retrospective claims data from sickness funds, one from physician's records, one study used prospective data from ambulatory care, and 2 studies were based on one patient survey. Methods used for adjustment of selection bias included exact matching, matching using propensity score methods, age-adjusted and sex-separated analysis, and adjustment in a regression model/analysis of covariance. One study did not apply adjustment methods. The intervention period ranged from 1 day to 4 years. Considered outcomes of studies (surrogate parameter, diabetes complications, mortality, quality of life, and claim data) depended on the database. In the evaluation of the DMP diabetes mellitus based on a control-group design neither the database nor the methods used for selection bias adjustment were consistent in the available studies. Effectiveness of DMPs cannot be judged based on this review due to heterogeneity of study designs. To allow for a comprehensive programme evaluation standardised minimum requirements for the evaluation of DMPs in the control group design are required. © Georg Thieme Verlag KG Stuttgart · New York.

Textpresso site-specific recombinases: A text-mining server for the recombinase literature including Cre mice and conditional alleles.

PubMed

Urbanski, William M; Condie, Brian G

2009-12-01

Textpresso Site Specific Recombinases (http://ssrc.genetics.uga.edu/) is a text-mining web server for searching a database of more than 9,000 full-text publications. The papers and abstracts in this database represent a wide range of topics related to site-specific recombinase (SSR) research tools. Included in the database are most of the papers that report the characterization or use of mouse strains that express Cre recombinase as well as papers that describe or analyze mouse lines that carry conditional (floxed) alleles or SSR-activated transgenes/knockins. The database also includes reports describing SSR-based cloning methods such as the Gateway or the Creator systems, papers reporting the development or use of SSR-based tools in systems such as Drosophila, bacteria, parasites, stem cells, yeast, plants, zebrafish, and Xenopus as well as publications that describe the biochemistry, genetics, or molecular structure of the SSRs themselves. Textpresso Site Specific Recombinases is the only comprehensive text-mining resource available for the literature describing the biology and technical applications of SSRs. (c) 2009 Wiley-Liss, Inc.

Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification.

PubMed

Schuemie, Martijn J; Mons, Barend; Weeber, Marc; Kors, Jan A

2007-06-01

Gene and protein name identification in text requires a dictionary approach to relate synonyms to the same gene or protein, and to link names to external databases. However, existing dictionaries are incomplete. We investigate two complementary methods for automatic generation of a comprehensive dictionary: combination of information from existing gene and protein databases and rule-based generation of spelling variations. Both methods have been reported in literature before, but have hitherto not been combined and evaluated systematically. We combined gene and protein names from several existing databases of four different organisms. The combined dictionaries showed a substantial increase in recall on three different test sets, as compared to any single database. Application of 23 spelling variation rules to the combined dictionaries further increased recall. However, many rules appeared to have no effect and some appear to have a detrimental effect on precision.

Systematic review of the literature on the effectiveness of product reformulation measures to reduce the sugar content of food and drink on the population's sugar consumption and health: a study protocol

PubMed Central

Hashem, Kawther M; He, Feng J; MacGregor, Graham A

2016-01-01

Introduction Obesity, type 2 diabetes and dental caries are all major public health problems in the UK, with significant costs to the healthcare service. We aim to conduct a systematic review to summarise the evidence on the effectiveness of product reformulation measures to reduce the sugar content of food and drink on the population's sugar consumption and health. Methods and analysis Electronic database will be systematically searched using a combination of terms, tailored to optimise sensitivity, specificity, and the syntax and functionality of each database. The databases searched will include the Cochrane Library, EMBASE, MEDLINE (Ovid) and Scopus. The bibliographies of those papers that match inclusion criteria will be searched by hand to identify any further, relevant references, which will be subject to the same screening and selection process. The database search results will be supplemented by hand searches. In addition to the peer-reviewed literature, a number of grey literature searches will be undertaken using the broad search terms ‘sugar’ and ‘food’ or ‘drink’ and ‘reduction’, these searches will include key government and organisation websites as well as general searches in Google. The selection of the studies, data collection and quality appraisal will be performed independently by 2 reviewers. Data will be initially analysed through a narrative synthesis method. If a subset of data we analyse appears comparable, we will investigate the possibility of performing a meta-analysis. Ethics and dissemination Ethics approval will not be required as this is a protocol for a systematic review. The findings will be disseminated widely through conference presentations and published in a peer-reviewed journal. PROSPERO registration number CRD42016034022. PMID:27288379

Cluster Analysis in Nursing Research: An Introduction, Historical Perspective, and Future Directions.

PubMed

Dunn, Heather; Quinn, Laurie; Corbridge, Susan J; Eldeirawi, Kamal; Kapella, Mary; Collins, Eileen G

2017-05-01

The use of cluster analysis in the nursing literature is limited to the creation of classifications of homogeneous groups and the discovery of new relationships. As such, it is important to provide clarity regarding its use and potential. The purpose of this article is to provide an introduction to distance-based, partitioning-based, and model-based cluster analysis methods commonly utilized in the nursing literature, provide a brief historical overview on the use of cluster analysis in nursing literature, and provide suggestions for future research. An electronic search included three bibliographic databases, PubMed, CINAHL and Web of Science. Key terms were cluster analysis and nursing. The use of cluster analysis in the nursing literature is increasing and expanding. The increased use of cluster analysis in the nursing literature is positioning this statistical method to result in insights that have the potential to change clinical practice.

Searching for religion and mental health studies required health, social science, and grey literature databases.

PubMed

Wright, Judy M; Cottrell, David J; Mir, Ghazala

2014-07-01

To determine the optimal databases to search for studies of faith-sensitive interventions for treating depression. We examined 23 health, social science, religious, and grey literature databases searched for an evidence synthesis. Databases were prioritized by yield of (1) search results, (2) potentially relevant references identified during screening, (3) included references contained in the synthesis, and (4) included references that were available in the database. We assessed the impact of databases beyond MEDLINE, EMBASE, and PsycINFO by their ability to supply studies identifying new themes and issues. We identified pragmatic workload factors that influence database selection. PsycINFO was the best performing database within all priority lists. ArabPsyNet, CINAHL, Dissertations and Theses, EMBASE, Global Health, Health Management Information Consortium, MEDLINE, PsycINFO, and Sociological Abstracts were essential for our searches to retrieve the included references. Citation tracking activities and the personal library of one of the research teams made significant contributions of unique, relevant references. Religion studies databases (Am Theo Lib Assoc, FRANCIS) did not provide unique, relevant references. Literature searches for reviews and evidence syntheses of religion and health studies should include social science, grey literature, non-Western databases, personal libraries, and citation tracking activities. Copyright © 2014 Elsevier Inc. All rights reserved.

Longitudinal analysis of meta-analysis literatures in the database of ISI Web of Science.

PubMed

Zhu, Changtai; Jiang, Ting; Cao, Hao; Sun, Wenguang; Chen, Zhong; Liu, Jinming

2015-01-01

The meta-analysis is regarded as an important evidence for making scientific decision. The database of ISI Web of Science collected a great number of high quality literatures including meta-analysis literatures. However, it is significant to understand the general characteristics of meta-analysis literatures to outline the perspective of meta-analysis. In this present study, we summarized and clarified some features on these literatures in the database of ISI Web of Science. We retrieved the meta-analysis literatures in the database of ISI Web of Science including SCI-E, SSCI, A&HCI, CPCI-S, CPCI-SSH, CCR-E, and IC. The annual growth rate, literature category, language, funding, index citation, agencies and countries/territories of the meta-analysis literatures were analyzed, respectively. A total of 95,719 records, which account for 0.38% (99% CI: 0.38%-0.39%) of all literatures, were found in the database. From 1997 to 2012, the annual growth rate of meta-analysis literatures was 18.18%. The literatures involved in many categories, languages, fundings, citations, publication agencies, and countries/territories. Interestingly, the index citation frequencies of the meta-analysis were significantly higher than that of other type literatures such as multi-centre study, randomize controlled trial, cohort study, case control study, and cases report (P<0.0001). The increasing numbers, intensively global influence and high citations revealed that the meta-analysis has been becoming more and more prominent in recent years. In future, in order to promote the validity of meta-analysis, the CONSORT and PRISMA standard should be continuously popularized in the field of evidence-based medicine.

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

Abbott, Jennifer; Sandberg, Tami

The Wind-Wildlife Impacts Literature Database (WILD), formerly known as the Avian Literature Database, was created in 1997. The goal of the database was to begin tracking the research that detailed the potential impact of wind energy development on birds. The Avian Literature Database was originally housed on a proprietary platform called Livelink ECM from Open- Text and maintained by in-house technical staff. The initial set of records was added by library staff. A vital part of the newly launched Drupal-based WILD database is the Bibliography module. Many of the resources included in the database have digital object identifiers (DOI). Themore » bibliographic information for any item that has a DOI can be imported into the database using this module. This greatly reduces the amount of manual data entry required to add records to the database. The content available in WILD is international in scope, which can be easily discerned by looking at the tags available in the browse menu.« less

Behavioral ecology of captive species: using behavioral adaptations to assess and enhance welfare of nonhuman zoo animals.

PubMed

Koene, Paul

2013-01-01

This project aimed to estimate a species' adaptations in nature and in captivity, assess welfare, suggest environmental changes, and find species characteristics that underlie welfare problems in nonhuman animals in the zoo. First, the current status of zoo animal welfare assessment was reviewed, and the behavioral ecology approach was outlined. In this approach, databases of species characteristics were developed using (a) literature of natural behavior and (b) captive behavior. Species characteristics were grouped in 8 functional behavioral ecological fitness-related categories: space, time, metabolic, safety, reproductive, comfort, social, and information adaptations. Assessments of the strength of behavioral adaptations in relation to environmental demands were made based on the results available from the literature. The databases with literature at the species level were coupled with databases of (c) behavioral observations and (d) welfare assessments under captive conditions. Observation and welfare assessment methods were adapted from the animal on the farm realm and applied to zoo species. It was expected that the comparison of the repertoire of behaviors in natural and captive environments would highlight welfare problems, provide solutions to welfare problems by environmental changes, and identify species characteristics underlying zoo animal welfare problems.

A method for automatically extracting infectious disease-related primers and probes from the literature

PubMed Central

2010-01-01

Background Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious diseases. The biological literature is the main information source for empirically validated primer and probe sequences. Therefore, it is becoming increasingly important for researchers to navigate this important information. In this paper, we present a four-phase method for extracting and annotating primer/probe sequences from the literature. These phases are: (1) convert each document into a tree of paper sections, (2) detect the candidate sequences using a set of finite state machine-based recognizers, (3) refine problem sequences using a rule-based expert system, and (4) annotate the extracted sequences with their related organism/gene information. Results We tested our approach using a test set composed of 297 manuscripts. The extracted sequences and their organism/gene annotations were manually evaluated by a panel of molecular biologists. The results of the evaluation show that our approach is suitable for automatically extracting DNA sequences, achieving precision/recall rates of 97.98% and 95.77%, respectively. In addition, 76.66% of the detected sequences were correctly annotated with their organism name. The system also provided correct gene-related information for 46.18% of the sequences assigned a correct organism name. Conclusions We believe that the proposed method can facilitate routine tasks for biomedical researchers using molecular methods to diagnose and prescribe different infectious diseases. In addition, the proposed method can be expanded to detect and extract other biological sequences from the literature. The extracted information can also be used to readily update available primer/probe databases or to create new databases from scratch. PMID:20682041

What do we know about sibling attended birth? An integrative literature review.

PubMed

Naber, Nora L; Miller, Suzanne; Baddock, Sally A

2018-05-08

to consolidate existing research in the field of sibling attended birth (SAB) into a body of knowledge to inform decision-making processes and guide midwifery practice throughout the sibling attended birth experience. An integrative literature review. CINAHL Complete, Cochrane Library, PubMed, Index New Zealand, Australia/New Zealand Reference Centre, grey literature databases REVIEW METHODS: An extensive search of five electronic databases as well as 17 grey literature databases was conducted. Abstracts of 2340 papers and full texts of 39 papers were scrutinised for inclusion criteria leading to 22 studies being included in this review. The Crowe Critical Appraisal Tool was used to facilitate a systematic quality appraisal process. This review included 22 studies (13 qualitative, 4 quantitative and 5 mixed methods). Studies were analysed using a narrative synthesis approach. Publications mainly focussed on families' motivations for choosing SAB, the preparation for the event, and the impact of SAB on children's behaviour and the infant/sibling relationship. This review identified that children experienced birth as a positive, exciting and important life event and parents viewed their SAB experiences as overwhelmingly positive and reported a heightened sense of family unity. Included studies did not address the long term effects of sibling attended birth, however, in the short-term, children did not show signs of trauma or severe distress, though differing levels of transient fear and anxiety were described. Families could benefit from receiving evidence based information to enable an informed decision regarding their children's involvement during pregnancy, birth and the immediate postpartum. Information shared by the midwife could focus on how families can achieve an optimal SAB experience for all family members. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Protein Disease Database of human body fluids: II. Computer methods and data issues.

PubMed

Lemkin, P F; Orr, G A; Goldstein, M P; Creed, G J; Myrick, J E; Merril, C R

1995-01-01

The Protein Disease Database (PDD) is a relational database of proteins and diseases. With this database it is possible to screen for quantitative protein abnormalities associated with disease states. These quantitative relationships use data drawn from the peer-reviewed biomedical literature. Assays may also include those observed in high-resolution electrophoretic gels that offer the potential to quantitate many proteins in a single test as well as data gathered by enzymatic or immunologic assays. We are using the Internet World Wide Web (WWW) and the Web browser paradigm as an access method for wide distribution and querying of the Protein Disease Database. The WWW hypertext transfer protocol and its Common Gateway Interface make it possible to build powerful graphical user interfaces that can support easy-to-use data retrieval using query specification forms or images. The details of these interactions are totally transparent to the users of these forms. Using a client-server SQL relational database, user query access, initial data entry and database maintenance are all performed over the Internet with a Web browser. We discuss the underlying design issues, mapping mechanisms and assumptions that we used in constructing the system, data entry, access to the database server, security, and synthesis of derived two-dimensional gel image maps and hypertext documents resulting from SQL database searches.

Ophthalmology and vision science research: part 5: surfing or sieving--using literature databases wisely.

PubMed

Sherwin, Trevor; Gilhotra, Amardeep K

2006-02-01

Literature databases are an ever-expanding resource available to the field of medical sciences. Understanding how to use such databases efficiently is critical for those involved in research. However, for the uninitiated, getting started is a major hurdle to overcome and for the occasional user, the finer points of database searching remain an unacquired skill. In the fifth and final article in this series aimed at those embarking on ophthalmology and vision science research, we look at how the beginning researcher can start to use literature databases and, by using a stepwise approach, how they can optimize their use. This instructional paper gives a hypothetical example of a researcher writing a review article and how he or she acquires the necessary scientific literature for the article. A prototype search of the Medline database is used to illustrate how even a novice might swiftly acquire the skills required for a medium-level search. It provides examples and key tips that can increase the proficiency of the occasional user. Pitfalls of database searching are discussed, as are the limitations of which the user should be aware.

Alliance Building in the Information and Online Database Industry.

ERIC Educational Resources Information Center

Alexander, Johanna Olson

2001-01-01

Presents an analysis of information industry alliance formation using environmental scanning methods. Highlights include why libraries and academic institutions should be interested; a literature review; historical context; industry and market structures; commercial and academic models; trends; and implications for information providers,…

Validated methods for identifying tuberculosis patients in health administrative databases: systematic review.

PubMed

Ronald, L A; Ling, D I; FitzGerald, J M; Schwartzman, K; Bartlett-Esquilant, G; Boivin, J-F; Benedetti, A; Menzies, D

2017-05-01

An increasing number of studies are using health administrative databases for tuberculosis (TB) research. However, there are limitations to using such databases for identifying patients with TB. To summarise validated methods for identifying TB in health administrative databases. We conducted a systematic literature search in two databases (Ovid Medline and Embase, January 1980-January 2016). We limited the search to diagnostic accuracy studies assessing algorithms derived from drug prescription, International Classification of Diseases (ICD) diagnostic code and/or laboratory data for identifying patients with TB in health administrative databases. The search identified 2413 unique citations. Of the 40 full-text articles reviewed, we included 14 in our review. Algorithms and diagnostic accuracy outcomes to identify TB varied widely across studies, with positive predictive value ranging from 1.3% to 100% and sensitivity ranging from 20% to 100%. Diagnostic accuracy measures of algorithms using out-patient, in-patient and/or laboratory data to identify patients with TB in health administrative databases vary widely across studies. Use solely of ICD diagnostic codes to identify TB, particularly when using out-patient records, is likely to lead to incorrect estimates of case numbers, given the current limitations of ICD systems in coding TB.

Complementary Value of Databases for Discovery of Scholarly Literature: A User Survey of Online Searching for Publications in Art History

ERIC Educational Resources Information Center

Nemeth, Erik

2010-01-01

Discovery of academic literature through Web search engines challenges the traditional role of specialized research databases. Creation of literature outside academic presses and peer-reviewed publications expands the content for scholarly research within a particular field. The resulting body of literature raises the question of whether scholars…

[Profile of a systematic search. Search areas, databases and reports].

PubMed

Korsbek, Lisa; Bendix, Ane Friis; Kidholm, Kristian

2006-04-03

Systematic literature search is a fundamental in evidence-based medicine. But systematic literature search is not yet a very well used way of retrieving evidence-based information. This article profiles a systematic literature search for evidence-based literature. It goes through the most central databases and gives an example of how to document the literature search. The article also sums up the literature search in all reviews in Ugeskrift for Laeger in the year 2004.

[Integrated DNA barcoding database for identifying Chinese animal medicine].

PubMed

Shi, Lin-Chun; Yao, Hui; Xie, Li-Fang; Zhu, Ying-Jie; Song, Jing-Yuan; Zhang, Hui; Chen, Shi-Lin

2014-06-01

In order to construct an integrated DNA barcoding database for identifying Chinese animal medicine, the authors and their cooperators have completed a lot of researches for identifying Chinese animal medicines using DNA barcoding technology. Sequences from GenBank have been analyzed simultaneously. Three different methods, BLAST, barcoding gap and Tree building, have been used to confirm the reliabilities of barcode records in the database. The integrated DNA barcoding database for identifying Chinese animal medicine has been constructed using three different parts: specimen, sequence and literature information. This database contained about 800 animal medicines and the adulterants and closely related species. Unknown specimens can be identified by pasting their sequence record into the window on the ID page of species identification system for traditional Chinese medicine (www. tcmbarcode. cn). The integrated DNA barcoding database for identifying Chinese animal medicine is significantly important for animal species identification, rare and endangered species conservation and sustainable utilization of animal resources.

Coverage and overlaps in bibliographic databases relevant to forensic medicine: a comparative analysis of MEDLINE.

PubMed Central

Yonker, V A; Young, K P; Beecham, S K; Horwitz, S; Cousin, K

1990-01-01

This study was designed to make a comparative evaluation of the performance of MEDLINE in covering serial literature. Forensic medicine was chosen because it is an interdisciplinary subject area that would test MEDLARS at the periphery of the system. The evaluation of database coverage was based upon articles included in the bibliographies of scholars in the field of forensic medicine. This method was considered appropriate for characterizing work used by researchers in this field. The results of comparing MEDLINE to other databases evoked some concerns about the selective indexing policy of MEDLINE in serving the interests of those working in forensic medicine. PMID:2403829

Text mining for search term development in systematic reviewing: A discussion of some methods and challenges.

PubMed

Stansfield, Claire; O'Mara-Eves, Alison; Thomas, James

2017-09-01

Using text mining to aid the development of database search strings for topics described by diverse terminology has potential benefits for systematic reviews; however, methods and tools for accomplishing this are poorly covered in the research methods literature. We briefly review the literature on applications of text mining for search term development for systematic reviewing. We found that the tools can be used in 5 overarching ways: improving the precision of searches; identifying search terms to improve search sensitivity; aiding the translation of search strategies across databases; searching and screening within an integrated system; and developing objectively derived search strategies. Using a case study and selected examples, we then reflect on the utility of certain technologies (term frequency-inverse document frequency and Termine, term frequency, and clustering) in improving the precision and sensitivity of searches. Challenges in using these tools are discussed. The utility of these tools is influenced by the different capabilities of the tools, the way the tools are used, and the text that is analysed. Increased awareness of how the tools perform facilitates the further development of methods for their use in systematic reviews. Copyright © 2017 John Wiley & Sons, Ltd.

Prediction of EST functional relationships via literature mining with user-specified parameters.

PubMed

Wang, Hei-Chia; Huang, Tian-Hsiang

2009-04-01

The massive amount of expressed sequence tags (ESTs) gathered over recent years has triggered great interest in efficient applications for genomic research. In particular, EST functional relationships can be used to determine a possible gene network for biological processes of interest. In recent years, many researchers have tried to determine EST functional relationships by analyzing the biological literature. However, it has been challenging to find efficient prediction methods. Moreover, an annotated EST is usually associated with many functions, so successful methods must be able to distinguish between relevant and irrelevant functions based on user specifications. This paper proposes a method to discover functional relationships between ESTs of interest by analyzing literature from the Medical Literature Analysis and Retrieval System Online, with user-specified parameters for selecting keywords. This method performs better than the multiple kernel documents method in setting up a specific threshold for gathering materials. The method is also able to uncover known functional relationships, as shown by a comparison with the Kyoto Encyclopedia of Genes and Genomes database. The reliable EST relationships predicted by the proposed method can help to construct gene networks for specific biological functions of interest.

Mining the literature: new methods to exploit keyword profiles.

PubMed

Andrade-Navarro, Miguel A

2012-01-01

Bibliographic records in the PubMed database of biomedical literature are annotated with Medical Subject Headings (MeSH) by curators, which summarize the content of the articles. Two recent publications explain how to generate profiles of MeSH terms for a set of bibliographic records and to use them to define any given concept by its associated literature. These concepts can then be related by their keyword profiles, and this can be used, for example, to detect new associations between genes and inherited diseases. http://www.biomedcentral.com/1471-2105/13/249/abstracthttp://genomemedicine.com/content/4/9/75/abstract.

bioNerDS: exploring bioinformatics’ database and software use through literature mining

PubMed Central

2013-01-01

Background Biology-focused databases and software define bioinformatics and their use is central to computational biology. In such a complex and dynamic field, it is of interest to understand what resources are available, which are used, how much they are used, and for what they are used. While scholarly literature surveys can provide some insights, large-scale computer-based approaches to identify mentions of bioinformatics databases and software from primary literature would automate systematic cataloguing, facilitate the monitoring of usage, and provide the foundations for the recovery of computational methods for analysing biological data, with the long-term aim of identifying best/common practice in different areas of biology. Results We have developed bioNerDS, a named entity recogniser for the recovery of bioinformatics databases and software from primary literature. We identify such entities with an F-measure ranging from 63% to 91% at the mention level and 63-78% at the document level, depending on corpus. Not attaining a higher F-measure is mostly due to high ambiguity in resource naming, which is compounded by the on-going introduction of new resources. To demonstrate the software, we applied bioNerDS to full-text articles from BMC Bioinformatics and Genome Biology. General mention patterns reflect the remit of these journals, highlighting BMC Bioinformatics’s emphasis on new tools and Genome Biology’s greater emphasis on data analysis. The data also illustrates some shifts in resource usage: for example, the past decade has seen R and the Gene Ontology join BLAST and GenBank as the main components in bioinformatics processing. Abstract Conclusions We demonstrate the feasibility of automatically identifying resource names on a large-scale from the scientific literature and show that the generated data can be used for exploration of bioinformatics database and software usage. For example, our results help to investigate the rate of change in resource usage and corroborate the suspicion that a vast majority of resources are created, but rarely (if ever) used thereafter. bioNerDS is available at http://bionerds.sourceforge.net/. PMID:23768135

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.

Health Technology Assessment in nursing: a literature review.

PubMed

Ramacciati, N

2013-03-01

The Health Technology Assessment (HTA) approach, which provides scientific support for the decisions taken within the health field, is of increasing importance worldwide. In a context of limited resources, HTA has the potential of being an efficient tool for addressing the sustainability problems and the allocation choices arising from the constant increase in demand. This study aims to investigate HTA use in nursing, both in terms of quantifying HTA evaluations of nursing phenomena which have been conducted and in terms of the extent to which nursing has used the HTA approach. The Italian context has been analysed because of the growing diffusion of the HTA in Italy along with the recent developments in the nursing profession. A narrative review of international literature was undertaken using the following databases: HTA, PubMed, CINAHL, ILISI. Seventy evaluation studies on nursing were identified from the HTA database (1.12% of all studies in the database). The areas of nursing intervention and the country of origin of the studies were identified. Two nursing studies on the HTA approach were found in the PubMed, CINAHL and HTA databases. The first focused on the evaluation of nursing technology process and analysed 126 studies in six main thematic areas; the second was a systematic review on HTA in nursing and analysed 192 studies (46 meta-analyses, 31 Finnish primary studies, 117 international primary studies). Three Italian studies were identified from the ILISI database and Italian grey literature. In the international literature, although analyses regarding the efficacy of nursing interventions have been conducted, there are to date very few research projects that focus exclusively on the HTA process as applied to nursing. The recent development of a standardized nursing language coupled with the open debate as to which research method (qualitative vs. quantitative) best serves to 'read' nursing phenomena may explain the scarce diffusion of HTA in the field of nursing. © 2012 The Author. International Nursing Review © 2012 International Council of Nurses.

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.

Ipsilateral femur and tibia fractures in pediatric patients: A systematic review

PubMed Central

Anari, Jason B; Neuwirth, Alexander L; Horn, B David; Baldwin, Keith D

2017-01-01

AIM To better understand how pediatric floating knee injuries are managed after the wide spread use of new orthopaedic technology. METHODS We searched EMBASE, COCHRANE and MEDLINE computerized literature databases from the earliest date available in the databases to February 2017 using the following search term including variants and pleural counterparts: Pediatric floating knee. All studies were thoroughly reviewed by multiple authors. Reference lists from all articles were scrutinized to identify any additional studies of interest. A final database of individual patients was assembled from the literature. Univariate and multivariate statistical tests were applied to the assembled database to assess differences in outcomes. RESULTS The English language literature contains series with a total of 97 pediatric patients who sustained floating knee injuries. Patients averaged 9.3 years of age and were mostly male (73). Approximately 25% of the fractures were open injuries, more tibia (27) than femur (10). Over 75% of the fractures of both the tibia and the femur involved the diaphysis. More than half (52) of the patients were treated non-operatively for both fractures. As a sequela of the injury 32 (33%) patients were left with a limb length discrepancy, 24 (25%) patients had lengthening of the injured limb at follow up, while 8 (8%) had shortening of the affected limb. Infection developed in 9 patients and 3 had premature physeal closure. Younger patients were more likely to be treated non-operatively (P < 0.001) and patients treated with operative intervention had statistically significant shorter hospital length of stays (P = 0.001). CONCLUSION Given the predominance of non-operative management in published studies, the available literature is not clinically relevant since the popularization of internal fixation for pediatric long-bone fractures PMID:28875130

[Current situation and developmental trend of anthelmintics by bibliometrics].

PubMed

Zheng, Qi; Chen, Ying; Tian, Li-Guang; Zhou, Xiao-Nong

2009-08-01

To understand the current situation and developmental trend of anthelmintics in English journals through a bibliometric analysis. The literature was searched in Pubmed Database (1997-2007) using the following key words: "drug therapy", "anthelmintics", "humans", "pharmacology", and "parasitology". Access Database was constructed by relative literature through proper data admission method. The relative articles in the database were sorted by different categories, such as "research categories", "publishing year" and "research drug". Data were analyzed by using SPSS software. The annual number of anthelmintics articles increased steadily from year 1997 to 2007. The average number of annual increase was about 6. The major research category was applied research. The major diseases were schistosomiasis, filariasis, ascariasis, echinococcosis and hookworm disease. The number of articles on schistosomiasis was higher than that of other four diseases (P<0.05). The major drugs involved were albendazole, praziquantel, mebendazole, ivermectin and diethylcarbamazine. Articles on the anthelmintics were published mostly in medical journals. From the total database, articles published at the top five journals occupied 5.52%, 4.39%, 3.76%, 3.26%, and 3.26%, respectively. Increasingly importance has been attached to anthelmintics in the last decade. Meanwhile, the researchers focused on a few anthelmintics, and it is inevitable to develop new drugs.

Parenting Interventions for Indigenous Child Psychosocial Functioning: A Scoping Review

ERIC Educational Resources Information Center

Macvean, Michelle; Shlonsky, Aron; Mildon, Robyn; Devine, Ben

2017-01-01

Objectives: To scope evaluations of Indigenous parenting programs designed to improve child psychosocial outcomes. Methods: Electronic databases, gray literature, Indigenous websites and journals, and reference lists were searched. The search was restricted to high-income countries with a history of colonialism. Results: Sixteen studies describing…

The economic impact of Clostridium difficile infection: a systematic review.

PubMed

Nanwa, Natasha; Kendzerska, Tetyana; Krahn, Murray; Kwong, Jeffrey C; Daneman, Nick; Witteman, William; Mittmann, Nicole; Cadarette, Suzanne M; Rosella, Laura; Sander, Beate

2015-04-01

With Clostridium difficile infection (CDI) on the rise, knowledge of the current economic burden of CDI can inform decisions on interventions related to CDI. We systematically reviewed CDI cost-of-illness (COI) studies. We performed literature searches in six databases: MEDLINE, Embase, the Health Technology Assessment Database, the National Health Service Economic Evaluation Database, the Cost-Effectiveness Analysis Registry, and EconLit. We also searched gray literature and conducted reference list searches. Two reviewers screened articles independently. One reviewer abstracted data and assessed quality using a modified guideline for economic evaluations. The second reviewer validated the abstraction and assessment. We identified 45 COI studies between 1988 and June 2014. Most (84%) of the studies were from the United States, calculating costs of hospital stays (87%), and focusing on direct costs (100%). Attributable mean CDI costs ranged from $8,911 to $30,049 for hospitalized patients. Few studies stated resource quantification methods (0%), an epidemiological approach (0%), or a justified study perspective (16%) in their cost analyses. In addition, few studies conducted sensitivity analyses (7%). Forty-five COI studies quantified and confirmed the economic impact of CDI. Costing methods across studies were heterogeneous. Future studies should follow standard COI methodology, expand study perspectives (e.g., patient), and explore populations least studied (e.g., community-acquired CDI).

Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification.

PubMed

Mehryary, Farrokh; Kaewphan, Suwisa; Hakala, Kai; Ginter, Filip

2016-01-01

Biomedical event extraction is one of the key tasks in biomedical text mining, supporting various applications such as database curation and hypothesis generation. Several systems, some of which have been applied at a large scale, have been introduced to solve this task. Past studies have shown that the identification of the phrases describing biological processes, also known as trigger detection, is a crucial part of event extraction, and notable overall performance gains can be obtained by solely focusing on this sub-task. In this paper we propose a novel approach for filtering falsely identified triggers from large-scale event databases, thus improving the quality of knowledge extraction. Our method relies on state-of-the-art word embeddings, event statistics gathered from the whole biomedical literature, and both supervised and unsupervised machine learning techniques. We focus on EVEX, an event database covering the whole PubMed and PubMed Central Open Access literature containing more than 40 million extracted events. The top most frequent EVEX trigger words are hierarchically clustered, and the resulting cluster tree is pruned to identify words that can never act as triggers regardless of their context. For rarely occurring trigger words we introduce a supervised approach trained on the combination of trigger word classification produced by the unsupervised clustering method and manual annotation. The method is evaluated on the official test set of BioNLP Shared Task on Event Extraction. The evaluation shows that the method can be used to improve the performance of the state-of-the-art event extraction systems. This successful effort also translates into removing 1,338,075 of potentially incorrect events from EVEX, thus greatly improving the quality of the data. The method is not solely bound to the EVEX resource and can be thus used to improve the quality of any event extraction system or database. The data and source code for this work are available at: http://bionlp-www.utu.fi/trigger-clustering/.

[Establishement for regional pelvic trauma database in Hunan Province].

PubMed

Cheng, Liang; Zhu, Yong; Long, Haitao; Yang, Junxiao; Sun, Buhua; Li, Kanghua

2017-04-28

To establish a database for pelvic trauma in Hunan Province, and to start the work of multicenter pelvic trauma registry.
 Methods: To establish the database, literatures relevant to pelvic trauma were screened, the experiences from the established trauma database in China and abroad were learned, and the actual situations for pelvic trauma rescue in Hunan Province were considered. The database for pelvic trauma was established based on the PostgreSQL and the advanced programming language Java 1.6.
 Results: The complex procedure for pelvic trauma rescue was described structurally. The contents for the database included general patient information, injurious condition, prehospital rescue, conditions in admission, treatment in hospital, status on discharge, diagnosis, classification, complication, trauma scoring and therapeutic effect. The database can be accessed through the internet by browser/servicer. The functions for the database include patient information management, data export, history query, progress report, video-image management and personal information management.
 Conclusion: The database with whole life cycle pelvic trauma is successfully established for the first time in China. It is scientific, functional, practical, and user-friendly.

Text mining in livestock animal science: introducing the potential of text mining to animal sciences.

PubMed

Sahadevan, S; Hofmann-Apitius, M; Schellander, K; Tesfaye, D; Fluck, J; Friedrich, C M

2012-10-01

In biological research, establishing the prior art by searching and collecting information already present in the domain has equal importance as the experiments done. To obtain a complete overview about the relevant knowledge, researchers mainly rely on 2 major information sources: i) various biological databases and ii) scientific publications in the field. The major difference between the 2 information sources is that information from databases is available, typically well structured and condensed. The information content in scientific literature is vastly unstructured; that is, dispersed among the many different sections of scientific text. The traditional method of information extraction from scientific literature occurs by generating a list of relevant publications in the field of interest and manually scanning these texts for relevant information, which is very time consuming. It is more than likely that in using this "classical" approach the researcher misses some relevant information mentioned in the literature or has to go through biological databases to extract further information. Text mining and named entity recognition methods have already been used in human genomics and related fields as a solution to this problem. These methods can process and extract information from large volumes of scientific text. Text mining is defined as the automatic extraction of previously unknown and potentially useful information from text. Named entity recognition (NER) is defined as the method of identifying named entities (names of real world objects; for example, gene/protein names, drugs, enzymes) in text. In animal sciences, text mining and related methods have been briefly used in murine genomics and associated fields, leaving behind other fields of animal sciences, such as livestock genomics. The aim of this work was to develop an information retrieval platform in the livestock domain focusing on livestock publications and the recognition of relevant data from cattle and pigs. For this purpose, the rather noncomprehensive resources of pig and cattle gene and protein terminologies were enriched with orthologue synonyms, integrated in the NER platform, ProMiner, which is successfully used in human genomics domain. Based on the performance tests done, the present system achieved a fair performance with precision 0.64, recall 0.74, and F(1) measure of 0.69 in a test scenario based on cattle literature.

Inclusion of children with developmental disabilities in Arab countries: A review of the research literature from 1990 to 2014.

PubMed

Alkhateeb, Jamal M; Hadidi, Muna S; Alkhateeb, Amal J

2016-01-01

In this study, a literature review was conducted to analyze studies published from 1990 to 2014 in English-written literature on inclusion of children with developmental disabilities in Arab countries. This study sought to review and analyze research conducted on Inclusive Education (IE) in Arab countries. The following electronic databases were used in searching the relevant literature: ScienceDirect, SpringerLink, PsychINFO, EBSCOhost Databases, ProQuest Dissertations and Theses Database, ERIC, and Google Scholar. After the publications to be included in this study were retrieved, each study was reviewed and analyzed. Each study was examined for details such as authors, title of research, publication year, country, purpose, methods, and key findings. The results showed that a total of 42 empirical studies related to inclusion of children with developmental disabilities in Arab countries have been published. More than two-thirds of these studies came from United Arab Emirates (UAE), Jordan, and Saudi Arabia. The majority of the studies were published in the last 6 years. The main parameters in these studies were: attitudes toward inclusion, barriers to inclusion, and evaluating inclusion. The results of the current study revealed that relatively little IE research has been conducted in Arab countries. More research is warranted to test the generalizability of the results of the current study. Further research is also needed to analyze IE practices and demonstrate strategies for the effective implementation of IE in these countries. Copyright © 2015 Elsevier Ltd. All rights reserved.

Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy.

PubMed

Bekhuis, Tanja

2006-04-03

Innovative biomedical librarians and information specialists who want to expand their roles as expert searchers need to know about profound changes in biology and parallel trends in text mining. In recent years, conceptual biology has emerged as a complement to empirical biology. This is partly in response to the availability of massive digital resources such as the network of databases for molecular biologists at the National Center for Biotechnology Information. Developments in text mining and hypothesis discovery systems based on the early work of Swanson, a mathematician and information scientist, are coincident with the emergence of conceptual biology. Very little has been written to introduce biomedical digital librarians to these new trends. In this paper, background for data and text mining, as well as for knowledge discovery in databases (KDD) and in text (KDT) is presented, then a brief review of Swanson's ideas, followed by a discussion of recent approaches to hypothesis discovery and testing. 'Testing' in the context of text mining involves partially automated methods for finding evidence in the literature to support hypothetical relationships. Concluding remarks follow regarding (a) the limits of current strategies for evaluation of hypothesis discovery systems and (b) the role of literature-based discovery in concert with empirical research. Report of an informatics-driven literature review for biomarkers of systemic lupus erythematosus is mentioned. Swanson's vision of the hidden value in the literature of science and, by extension, in biomedical digital databases, is still remarkably generative for information scientists, biologists, and physicians.

Shorter Versus Longer Shift Durations to Mitigate Fatigue and Fatigue-Related Risks in Emergency Medical Services Personnel and Related Shift Workers: A Systematic Review

DOT National Transportation Integrated Search

2018-01-11

Background: This study comprehensively reviewed the literature on the impact of shorter versus longer shifts on critical and important outcomes for Emergency Medical Services (EMS) personnel and related shift worker groups. Methods: Six databases (e....

School-Based Obesity Interventions: A Literature Review

ERIC Educational Resources Information Center

Shaya, Fadia T.; Flores, David; Gbarayor, Confidence M.; Wang, Jingshu

2008-01-01

Background: Childhood obesity is an impending epidemic. This article is an overview of different interventions conducted in school settings so as to guide efforts for an effective management of obesity in children, thus minimizing the risk of adult obesity and related cardiovascular risk. Methods: PubMed and OVID Medline databases were searched…

Methods and Software for Building Bibliographic Data Bases.

ERIC Educational Resources Information Center

Daehn, Ralph M.

1985-01-01

This in-depth look at database management systems (DBMS) for microcomputers covers data entry, information retrieval, security, DBMS software and design, and downloading of literature search results. The advantages of in-house systems versus online search vendors are discussed, and specifications of three software packages and 14 sources are…

Curricular initiatives that enhance student knowledge and perceptions of sexual and gender minority groups: a critical interpretive synthesis

PubMed Central

Desrosiers, Jennifer; Wilkinson, Tim; Abel, Gillian; Pitama, Suzanne

2016-01-01

Background There is no accepted best practice for optimizing tertiary student knowledge, perceptions, and skills to care for sexual and gender diverse groups. The objective of this research was to synthesize the relevant literature regarding effective curricular initiatives designed to enhance tertiary level student knowledge, perceptions, and skills to care for sexual and gender diverse populations. Methods A modified Critical Interpretive Synthesis using a systematic search strategy was conducted in 2015. This method was chosen to synthesize the relevant qualitative and quantitative literature as it allows for the depth and breadth of information to be captured and new constructs to be illuminated. Databases searched include AMED, CINAHL EBM Reviews, ERIC, Ovid MEDLINE, Ovid Nursing Database, PsychInfo, and Google Scholar. Results Thirty-one articles were included in this review. Curricular initiatives ranging from discrete to multimodal approaches have been implemented. Successful initiatives included discrete sessions with time for processing, and multi-modal strategies. Multi-modal approaches that encouraged awareness of one’s lens and privilege in conjunction with facilitated communication seemed the most effective. Conclusions The literature is limited to the evaluation of explicit curricula. The wider cultural competence literature offers further insight by highlighting the importance of broad and embedded forces including social influences, the institutional climate, and the implicit, or hidden, curriculum. A combined interpretation of the complementary cultural competence and sexual and gender diversity literature provides a novel understanding of the optimal content and context for the delivery of a successful curricular initiative. PMID:28344699

Complications after craniosynostosis surgery: comparison of the 2012 Kids' Inpatient Database and Pediatric NSQIP Database.

PubMed

Lin, Yimo; Pan, I-Wen; Mayer, Rory R; Lam, Sandi

2015-12-01

OBJECT Research conducted using large administrative data sets has increased in recent decades, but reports on the fidelity and reliability of such data have been mixed. The goal of this project was to compare data from a large, administrative claims data set with a quality improvement registry in order to ascertain similarities and differences in content. METHODS Data on children younger than 12 months with nonsyndromic craniosynostosis who underwent surgery in 2012 were queried in both the Kids' Inpatient Database (KID) and the American College of Surgeons Pediatric National Surgical Quality Improvement Program (Peds NSQIP). Data from published clinical craniosynostosis surgery series are reported for comparison. RESULTS Among patients younger than 12 months of age, a total of 1765 admissions were identified in KID and 391 in Peds NSQIP in 2012. Only nonsyndromic patients were included. The mean length of stay was 3.2 days in KID and 4 days in Peds NSQIP. The rates of cardiac events (0.5% in KID, 0.3% in Peds NSQIP, and 0.4%-2.2% in the literature), stroke/intracranial bleeds (0.4% in KID, 0.5% in Peds NSQIP, and 0.3%-1.2% in the literature), infection (0.2% in KID, 0.8% in Peds NSQIP, and 0%-8% in the literature), wound disruption (0.2% in KID, 0.5% in Peds NSQIP, 0%-4% in the literature), and seizures (0.7% in KID, 0.8% in Peds NSQIP, 0%-0.8% in the literature) were low and similar between the 2 data sets. The reported rates of blood transfusion (36% in KID, 64% in Peds NSQIP, and 1.7%-100% in the literature) varied between the 2 data sets. CONCLUSIONS Both the KID and Peds NSQIP databases provide large samples of surgical patients, with more cases reported in KID. The rates of complications studied were similar between the 2 data sets, with the exception of blood transfusion events where the retrospective chart review process of Peds NSQIP captured almost double the rate reported in KID.

Statistical modeling of occupational chlorinated solvent exposures for case–control studies using a literature-based database

PubMed Central

Hein, Misty J.; Waters, Martha A.; Ruder, Avima M.; Stenzel, Mark R.; Blair, Aaron; Stewart, Patricia A.

2010-01-01

Objectives: Occupational exposure assessment for population-based case–control studies is challenging due to the wide variety of industries and occupations encountered by study participants. We developed and evaluated statistical models to estimate the intensity of exposure to three chlorinated solvents—methylene chloride, 1,1,1-trichloroethane, and trichloroethylene—using a database of air measurement data and associated exposure determinants. Methods: A measurement database was developed after an extensive review of the published industrial hygiene literature. The database of nearly 3000 measurements or summary measurements included sample size, measurement characteristics (year, duration, and type), and several potential exposure determinants associated with the measurements: mechanism of release (e.g. evaporation), process condition, temperature, usage rate, type of ventilation, location, presence of a confined space, and proximity to the source. The natural log-transformed measurement levels in the exposure database were modeled as a function of the measurement characteristics and exposure determinants using maximum likelihood methods. Assuming a single lognormal distribution of the measurements, an arithmetic mean exposure intensity level was estimated for each unique combination of exposure determinants and decade. Results: The proportions of variability in the measurement data explained by the modeled measurement characteristics and exposure determinants were 36, 38, and 54% for methylene chloride, 1,1,1-trichloroethane, and trichloroethylene, respectively. Model parameter estimates for the exposure determinants were in the anticipated direction. Exposure intensity estimates were plausible and exhibited internal consistency, but the ability to evaluate validity was limited. Conclusions: These prediction models can be used to estimate chlorinated solvent exposure intensity for jobs reported by population-based case–control study participants that have sufficiently detailed information regarding the exposure determinants. PMID:20418277

Reference point detection for camera-based fingerprint image based on wavelet transformation.

PubMed

Khalil, Mohammed S

2015-04-30

Fingerprint recognition systems essentially require core-point detection prior to fingerprint matching. The core-point is used as a reference point to align the fingerprint with a template database. When processing a larger fingerprint database, it is necessary to consider the core-point during feature extraction. Numerous core-point detection methods are available and have been reported in the literature. However, these methods are generally applied to scanner-based images. Hence, this paper attempts to explore the feasibility of applying a core-point detection method to a fingerprint image obtained using a camera phone. The proposed method utilizes a discrete wavelet transform to extract the ridge information from a color image. The performance of proposed method is evaluated in terms of accuracy and consistency. These two indicators are calculated automatically by comparing the method's output with the defined core points. The proposed method is tested on two data sets, controlled and uncontrolled environment, collected from 13 different subjects. In the controlled environment, the proposed method achieved a detection rate 82.98%. In uncontrolled environment, the proposed method yield a detection rate of 78.21%. The proposed method yields promising results in a collected-image database. Moreover, the proposed method outperformed compare to existing method.

Evidence-based librarianship: searching for the needed EBL evidence.

PubMed

Eldredge, J D

2000-01-01

This paper discusses the challenges of finding evidence needed to implement Evidence-Based Librarianship (EBL). Focusing first on database coverage for three health sciences librarianship journals, the article examines the information contents of different databases. Strategies are needed to search for relevant evidence in the library literature via these databases, and the problems associated with searching the grey literature of librarianship. Database coverage, plausible search strategies, and the grey literature of library science all pose challenges to finding the needed research evidence for practicing EBL. Health sciences librarians need to ensure that systems are designed that can track and provide access to needed research evidence to support Evidence-Based Librarianship (EBL).

Mapping the literature of nursing: 1996–2000

PubMed Central

Allen, Margaret (Peg); Jacobs, Susan Kaplan; Levy, June R.

2006-01-01

Introduction: This project is a collaborative effort of the Task Force on Mapping the Nursing Literature of the Nursing and Allied Health Resources Section of the Medical Library Association. This overview summarizes eighteen studies covering general nursing and sixteen specialties. Method: Following a common protocol, citations from source journals were analyzed for a three-year period within the years 1996 to 2000. Analysis included cited formats, age, and ranking of the frequency of cited journal titles. Highly cited journals were analyzed for coverage in twelve health sciences and academic databases. Results: Journals were the most frequently cited format, followed by books. More than 60% of the cited resources were published in the previous seven years. Bradford's law was validated, with a small core of cited journals accounting for a third of the citations. Medical and science databases provided the most comprehensive access for biomedical titles, while CINAHL and PubMed provided the best access for nursing journals. Discussion: Beyond a heavily cited core, nursing journal citations are widely dispersed among a variety of sources and disciplines, with corresponding access via a variety of bibliographic tools. Results underscore the interdisciplinary nature of the nursing profession. Conclusion: For comprehensive searches, nurses need to search multiple databases. Libraries need to provide access to databases beyond PubMed, including CINAHL and academic databases. Database vendors should improve their coverage of nursing, biomedical, and psychosocial titles identified in these studies. Additional research is needed to update these studies and analyze nursing specialties not covered. PMID:16636714

A computational platform to maintain and migrate manual functional annotations for BioCyc databases.

PubMed

Walsh, Jesse R; Sen, Taner Z; Dickerson, Julie A

2014-10-12

BioCyc databases are an important resource for information on biological pathways and genomic data. Such databases represent the accumulation of biological data, some of which has been manually curated from literature. An essential feature of these databases is the continuing data integration as new knowledge is discovered. As functional annotations are improved, scalable methods are needed for curators to manage annotations without detailed knowledge of the specific design of the BioCyc database. We have developed CycTools, a software tool which allows curators to maintain functional annotations in a model organism database. This tool builds on existing software to improve and simplify annotation data imports of user provided data into BioCyc databases. Additionally, CycTools automatically resolves synonyms and alternate identifiers contained within the database into the appropriate internal identifiers. Automating steps in the manual data entry process can improve curation efforts for major biological databases. The functionality of CycTools is demonstrated by transferring GO term annotations from MaizeCyc to matching proteins in CornCyc, both maize metabolic pathway databases available at MaizeGDB, and by creating strain specific databases for metabolic engineering.

Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments.

PubMed

Linder, Suzanne K; Kamath, Geetanjali R; Pratt, Gregory F; Saraykar, Smita S; Volk, Robert J

2015-04-01

To compare the effectiveness of two search methods in identifying studies that used the Control Preferences Scale (CPS), a health care decision-making instrument commonly used in clinical settings. We searched the literature using two methods: (1) keyword searching using variations of "Control Preferences Scale" and (2) cited reference searching using two seminal CPS publications. We searched three bibliographic databases [PubMed, Scopus, and Web of Science (WOS)] and one full-text database (Google Scholar). We report precision and sensitivity as measures of effectiveness. Keyword searches in bibliographic databases yielded high average precision (90%) but low average sensitivity (16%). PubMed was the most precise, followed closely by Scopus and WOS. The Google Scholar keyword search had low precision (54%) but provided the highest sensitivity (70%). Cited reference searches in all databases yielded moderate sensitivity (45-54%), but precision ranged from 35% to 75% with Scopus being the most precise. Cited reference searches were more sensitive than keyword searches, making it a more comprehensive strategy to identify all studies that use a particular instrument. Keyword searches provide a quick way of finding some but not all relevant articles. Goals, time, and resources should dictate the combination of which methods and databases are used. Copyright © 2015 Elsevier Inc. All rights reserved.

Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments

PubMed Central

Linder, Suzanne K.; Kamath, Geetanjali R.; Pratt, Gregory F.; Saraykar, Smita S.; Volk, Robert J.

2015-01-01

Objective To compare the effectiveness of two search methods in identifying studies that used the Control Preferences Scale (CPS), a healthcare decision-making instrument commonly used in clinical settings. Study Design & Setting We searched the literature using two methods: 1) keyword searching using variations of “control preferences scale” and 2) cited reference searching using two seminal CPS publications. We searched three bibliographic databases [PubMed, Scopus, Web of Science (WOS)] and one full-text database (Google Scholar). We report precision and sensitivity as measures of effectiveness. Results Keyword searches in bibliographic databases yielded high average precision (90%), but low average sensitivity (16%). PubMed was the most precise, followed closely by Scopus and WOS. The Google Scholar keyword search had low precision (54%) but provided the highest sensitivity (70%). Cited reference searches in all databases yielded moderate sensitivity (45–54%), but precision ranged from 35–75% with Scopus being the most precise. Conclusion Cited reference searches were more sensitive than keyword searches, making it a more comprehensive strategy to identify all studies that use a particular instrument. Keyword searches provide a quick way of finding some but not all relevant articles. Goals, time and resources should dictate the combination of which methods and databases are used. PMID:25554521

Plantar fasciitis in athletes: diagnostic and treatment strategies. A systematic review

PubMed Central

Petraglia, Federica; Ramazzina, Ileana; Costantino, Cosimo

2017-01-01

Summary Background: Plantar fasciitis (PF) is reported in different sports mainly in running and soccer athletes. Purpose of this study is to conduct a systematic review of published literature concerning the diagnosis and treatment of PF in both recreational and élite athletes. The review was conducted and reported in accordance with the PRISMA statement. Methods: The following electronic databases were searched: PubMed, Cochrane Library and Scopus. As far as PF diagnosis, we investigated the electronic databases from January 2006 to June 2016, whereas in considering treatments all data in literature were investigated. Results: For both diagnosis and treatment, 17 studies matched inclusion criteria. The results have highlighted that the most frequently used diagnostic techniques were Ultrasonography and Magnetic Resonance Imaging. Conventional, complementary, and alternative treatment approaches were assessed. Conclusions: In reviewing literature, we were unable to find any specific diagnostic algorithm for PF in athletes, due to the fact that no different diagnostic strategies were used for athletes and non-athletes. As for treatment, a few literature data are available and it makes difficult to suggest practice guidelines. Specific studies are necessary to define the best treatment algorithm for both recreational and élite athletes. Level of evidence: Ib. PMID:28717618

Semi-automating the manual literature search for systematic reviews increases efficiency.

PubMed

Chapman, Andrea L; Morgan, Laura C; Gartlehner, Gerald

2010-03-01

To minimise retrieval bias, manual literature searches are a key part of the search process of any systematic review. Considering the need to have accurate information, valid results of the manual literature search are essential to ensure scientific standards; likewise efficient approaches that minimise the amount of personnel time required to conduct a manual literature search are of great interest. The objective of this project was to determine the validity and efficiency of a new manual search method that utilises the scopus database. We used the traditional manual search approach as the gold standard to determine the validity and efficiency of the proposed scopus method. Outcome measures included completeness of article detection and personnel time involved. Using both methods independently, we compared the results based on accuracy of the results, validity and time spent conducting the search, efficiency. Regarding accuracy, the scopus method identified the same studies as the traditional approach indicating its validity. In terms of efficiency, using scopus led to a time saving of 62.5% compared with the traditional approach (3 h versus 8 h). The scopus method can significantly improve the efficiency of manual searches and thus of systematic reviews.

Unconstrained and contactless hand geometry biometrics.

PubMed

de-Santos-Sierra, Alberto; Sánchez-Ávila, Carmen; Del Pozo, Gonzalo Bailador; Guerra-Casanova, Javier

2011-01-01

This paper presents a hand biometric system for contact-less, platform-free scenarios, proposing innovative methods in feature extraction, template creation and template matching. The evaluation of the proposed method considers both the use of three contact-less publicly available hand databases, and the comparison of the performance to two competitive pattern recognition techniques existing in literature: namely support vector machines (SVM) and k-nearest neighbour (k-NN). Results highlight the fact that the proposed method outcomes existing approaches in literature in terms of computational cost, accuracy in human identification, number of extracted features and number of samples for template creation. The proposed method is a suitable solution for human identification in contact-less scenarios based on hand biometrics, providing a feasible solution to devices with limited hardware requirements like mobile devices.

Unconstrained and Contactless Hand Geometry Biometrics

PubMed Central

de-Santos-Sierra, Alberto; Sánchez-Ávila, Carmen; del Pozo, Gonzalo Bailador; Guerra-Casanova, Javier

2011-01-01

This paper presents a hand biometric system for contact-less, platform-free scenarios, proposing innovative methods in feature extraction, template creation and template matching. The evaluation of the proposed method considers both the use of three contact-less publicly available hand databases, and the comparison of the performance to two competitive pattern recognition techniques existing in literature: namely Support Vector Machines (SVM) and k-Nearest Neighbour (k-NN). Results highlight the fact that the proposed method outcomes existing approaches in literature in terms of computational cost, accuracy in human identification, number of extracted features and number of samples for template creation. The proposed method is a suitable solution for human identification in contact-less scenarios based on hand biometrics, providing a feasible solution to devices with limited hardware requirements like mobile devices. PMID:22346634

[Analysis of relation between the development of study and literatures about benign positional paroxysmal vertigo published international and domestic].

PubMed

Jia, Jianping; Sun, Xiaohui; Dai, Song; Sang, Yuehong

2016-01-01

Benign paroxysmal positional vertigo (BPPV) is a common vestibular disorder that causes vertigo. Study of BPPV has dramatically rapid progress in recent years. We analyze the BPPV growth We searched the international data quantity year by year in database of PubMed, ScienceDirect and WILEY before 2014 respectively, then we searched the domestic data quantity year by year in database of CNKI, VIP and Wanfang Data before 2015 by selecting "Benign paroxysmal positional vertigo" as the keywords. Then we carried out regression analysis with the gathered results in above databases to determine data growth regularity and main factors that affect future development of BPPV. Also, we analyzes published BPPV papers in domestic and international journals. PubMed database contains 808 literatures, ScienceDirect contains 177 database and WILEY contains 46 literatures, All together we collected 1 038 international articles. CNKI contains 440 literatures, VIP contains 580 literatures and WanFang data contains 449 literatures. All together we collected 1 469 domestic literatures. It shows the rising trend of the literature accumulation amount of BPPV. The scattered point diagram of BPPV shows an exponential growing trend, which was growing slowly in the early time but rapidly in recent years. It shows that the development of BPPV has three stages from international arical: exploration period (before 1985), breakthrough period (1986-1998). The deepening stage (after 1998), Chinese literature also has three stages from domestic BPPV precess. Blank period (before the year of 1982), the enlightenment period (1982-2004), the deepening stage (after the year of 2004). In the pregress of BPPV, many outsantding sccholars played an important role in domestic scitifction of researching, which has produced a certain influence in the worldwide.

Procedures of assessment on the quantification of thoracic kyphosis and lumbar lordosis by radiography and photogrammetry: A literature review.

PubMed

Porto, Alessandra Beggiato; Okazaki, Victor Hugo Alves

2017-10-01

The quantification of thoracic kyphosis and lumbar lordosis can be assessed in different ways; among them radiography and photogrammetry. However, the assessment procedures are not consistent in the literature for either method. The objective of this study was to conduct a literature review about postural assessment through radiography and photogrammetry, for delineating the procedures for both methods. In total 38 studies were selected by an online search in the MEDLINE and LILACS databases with the keywords: radiograph and posture, postural alignment, photogrammetry or photometry or biophotogrammetry. For the radiographic method, the results showed divergences in arm positioning and in the calculation of thoracic and lumbar angles. The photogrammetry demonstrated differences in relation to the camera, tripod, plumb line and feet positioning, angle calculation, software utilization, and the use of footwear. Standardization is proposed for both methods to help establish normative values and comparisons between diagnoses. Copyright © 2017 Elsevier Ltd. All rights reserved.

Using "Reader's Guide to Periodical Literature" on CD-Rom To Teach Database Searching to High School Students.

ERIC Educational Resources Information Center

Kern, Joanne F.

The lack of opportunity for high school sophomores to learn database searching was addressed by the implementation of a computerized magazine article search program. "Reader's Guide to Periodical Literature" on CD-ROM was used to train students in database searching during the time they were assigned to the library to do research papers…

Representations of African Americans in the Grief and Mourning Literature from 1998 to 2014: A Systematic Review.

PubMed

Granek, Leeat; Peleg-Sagy, Tal

2015-01-01

The authors examined representations of African Americans in the grief literature to assess (a) frequencies; (b) content; and (c) use of universalist or a contextualized framework. They conducted searches in 3 databases that target the grief literature published in the last 15 years. Fifty-nine articles met the criteria. There are a small number of studies published on African Americans and these tend to focus on homicide. Many studies had incomplete methods. Comparison studies were common and pathological grief outcomes that were validated on White populations were used as outcome variables with African American participants.

Mining the literature: new methods to exploit keyword profiles

PubMed Central

2012-01-01

Bibliographic records in the PubMed database of biomedical literature are annotated with Medical Subject Headings (MeSH) by curators, which summarize the content of the articles. Two recent publications explain how to generate profiles of MeSH terms for a set of bibliographic records and to use them to define any given concept by its associated literature. These concepts can then be related by their keyword profiles, and this can be used, for example, to detect new associations between genes and inherited diseases. See related research articles: http://www.biomedcentral.com/1471-2105/13/249/abstracthttp://genomemedicine.com/content/4/9/75/abstract PMID:23114100

Multiple approaches to fine-grained indexing of the biomedical literature.

PubMed

Neveol, Aurelie; Shooshan, Sonya E; Humphrey, Susanne M; Rindflesh, Thomas C; Aronson, Alan R

2007-01-01

The number of articles in the MEDLINE database is expected to increase tremendously in the coming years. To ensure that all these documents are indexed with continuing high quality, it is necessary to develop tools and methods that help the indexers in their daily task. We present three methods addressing a novel aspect of automatic indexing of the biomedical literature, namely producing MeSH main heading/subheading pair recommendations. The methods, (dictionary-based, post- processing rules and Natural Language Processing rules) are described and evaluated on a genetics-related corpus. The best overall performance is obtained for the subheading genetics (70% precision and 17% recall with post-processing rules, 48% precision and 37% recall with the dictionary-based method). Future work will address extending this work to all MeSH subheadings and a more thorough study of method combination.

Variation in population levels of physical activity in European adults according to cross-European studies: a systematic literature review within DEDIPAC.

PubMed

Loyen, Anne; Van Hecke, Linde; Verloigne, Maïté; Hendriksen, Ingrid; Lakerveld, Jeroen; Steene-Johannessen, Jostein; Vuillemin, Anne; Koster, Annemarie; Donnelly, Alan; Ekelund, Ulf; Deforche, Benedicte; De Bourdeaudhuij, Ilse; Brug, Johannes; van der Ploeg, Hidde P

2016-06-28

Physical inactivity is a well-known public health risk that should be monitored at the population level. Physical activity levels are often surveyed across Europe. This systematic literature review aims to provide an overview of all existing cross-European studies that assess physical activity in European adults, describe the variation in population levels according to these studies, and discuss the impact of the assessment methods. Six literature databases (PubMed, EMBASE, CINAHL, PsycINFO, SportDiscus and OpenGrey) were searched, supplemented with backward- and forward tracking and searching authors' and experts' literature databases. Articles were included if they reported on observational studies measuring total physical activity and/or physical activity in leisure time in the general population in two or more European countries. Each record was reviewed, extracted and assessed by two independent researchers and disagreements were resolved by a third researcher. The review protocol of this review is registered in the PROSPERO database under registration number CRD42014010334. Of the 9,756 unique identified articles, twenty-five were included in this review, reporting on sixteen different studies, including 2 to 35 countries and 321 to 274,740 participants. All but two of the studies used questionnaires to assess physical activity, with the majority of studies using the IPAQ-short questionnaire. The remaining studies used accelerometers. The percentage of participants who either were or were not meeting the physical activity recommendations was the most commonly reported outcome variable, with the percentage of participants meeting the recommendations ranging from 7% to 96% across studies and countries. The included studies showed substantial variation in the assessment methods, reported outcome variables and, consequently, the presented physical activity levels. Because of this, absolute population levels of physical activity in European adults are currently unknown. However, when ranking countries, Ireland, Italy, Malta, Portugal, and Spain generally appear to be among the less active countries. Objective data of adults across Europe is currently limited. These findings highlight the need for standardisation of the measurement methods, as well as cross-European monitoring of physical activity levels.

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.

Ponseti method in the management of clubfoot under 2 years of age: A systematic review

PubMed Central

Luximon, Ameersing; Al-Jumaily, Adel; Balasankar, Suchita Kothe; Naik, Ganesh R.

2017-01-01

Background Congenital talipes equinovarus (CTEV), also known as clubfoot, is common congenital orthopedic foot deformity in children characterized by four components of foot deformities: hindfoot equinus, hindfoot varus, midfoot cavus, and forefoot adduction. Although a number of conservative and surgical methods have been proposed to correct the clubfoot deformity, the relapses of the clubfoot are not uncommon. Several previous literatures discussed about the technical details of Ponseti method, adherence of Ponseti protocol among walking age or older children. However there is a necessity to investigate the relapse pattern, compliance of bracing, number of casts used in treatment and the percentages of surgical referral under two years of age for clear understanding and better practice to achieve successful outcome without or reduce relapse. Therefore this study aims to review the current evidence of Ponseti method (manipulation, casting, percutaneous Achilles tenotomy, and bracing) in the management of clubfoot under two years of age. Materials and methods Articles were searched from 2000 to 2015, in the following databases to identify the effectiveness of Ponseti method treatment for clubfoot: Medline, Cumulative Index to Nursing and Allied Health Literature (CINHAL), PubMed, and Scopus. The database searches were limited to articles published in English, and articles were focused on the effectiveness of Ponseti method on children with less than 2 years of age. Results Of the outcome of 1095 articles from four electronic databases, twelve articles were included in the review. Pirani scoring system, Dimeglio scoring system, measuring the range of motion and rate of relapses were used as outcome measures. Conclusions In conclusion, all reviewed, 12 articles reported that Ponseti method is a very effective method to correct the clubfoot deformities. However, we noticed that relapses occur in nine studies, which is due to the non-adherence of bracing regime and other factors such as low income and social economic status. PMID:28632733

PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literature.

PubMed

Yoo, Danny; Xu, Iris; Berardini, Tanya Z; Rhee, Seung Yon; Narayanasamy, Vijay; Twigger, Simon

2006-03-01

For most systems in biology, a large body of literature exists that describes the complexity of the system based on experimental results. Manual review of this literature to extract targeted information into biological databases is difficult and time consuming. To address this problem, we developed PubSearch and PubFetch, which store literature, keyword, and gene information in a relational database, index the literature with keywords and gene names, and provide a Web user interface for annotating the genes from experimental data found in the associated literature. A set of protocols is provided in this unit for installing, populating, running, and using PubSearch and PubFetch. In addition, we provide support protocols for performing controlled vocabulary annotations. Intended users of PubSearch and PubFetch are database curators and biology researchers interested in tracking the literature and capturing information about genes of interest in a more effective way than with conventional spreadsheets and lab notebooks.

Database Access Systems.

ERIC Educational Resources Information Center

Dalrymple, Prudence W.; Roderer, Nancy K.

1994-01-01

Highlights the changes that have occurred from 1987-93 in database access systems. Topics addressed include types of databases, including CD-ROMs; enduser interface; database selection; database access management, including library instruction and use of primary literature; economic issues; database users; the search process; and improving…

The search for reliable aqueous solubility (Sw) and octanol-water partition coefficient (Kow) data for hydrophobic organic compounds; DDT and DDE as a case study

USGS Publications Warehouse

Pontolillo, James; Eganhouse, R.P.

2001-01-01

The accurate determination of an organic contaminant?s physico-chemical properties is essential for predicting its environmental impact and fate. Approximately 700 publications (1944?2001) were reviewed and all known aqueous solubilities (Sw) and octanol-water partition coefficients (Kow) for the organochlorine pesticide, DDT, and its persistent metabolite, DDE were compiled and examined. Two problems are evident with the available database: 1) egregious errors in reporting data and references, and 2) poor data quality and/or inadequate documentation of procedures. The published literature (particularly the collative literature such as compilation articles and handbooks) is characterized by a preponderance of unnecessary data duplication. Numerous data and citation errors are also present in the literature. The percentage of original Sw and Kow data in compilations has decreased with time, and in the most recent publications (1994?97) it composes only 6?26 percent of the reported data. The variability of original DDT/DDE Sw and Kow data spans 2?4 orders of magnitude, and there is little indication that the uncertainty in these properties has declined over the last 5 decades. A criteria-based evaluation of DDT/DDE Sw and Kow data sources shows that 95?100 percent of the database literature is of poor or unevaluatable quality. The accuracy and reliability of the vast majority of the data are unknown due to inadequate documentation of the methods of determination used by the authors. [For example, estimates of precision have been reported for only 20 percent of experimental Sw data and 10 percent of experimental Kow data.] Computational methods for estimating these parameters have been increasingly substituted for direct or indirect experimental determination despite the fact that the data used for model development and validation may be of unknown reliability. Because of the prevalence of errors, the lack of methodological documentation, and unsatisfactory data quality, the reliability of the DDT/ DDE Sw and Kow database is questionable. The nature and extent of the errors documented in this study are probably indicative of a more general problem in the literature of hydrophobic organic compounds. Under these circumstances, estimation of critical environmental parameters on the basis of Sw and Kow (for example, bioconcentration factors, equilibrium partition coefficients) is inadvisable because it will likely lead to incorrect environmental risk assessments. The current state of the database indicates that much greater efforts are needed to: 1) halt the proliferation of erroneous data and references, 2) initiate a coordinated program to develop improved methods of property determination, 3) establish and maintain consistent reporting requirements for physico-chemical property data, and 4) create a mechanism for archiving reliable data for widespread use in the scientific/regulatory community.

An Evidence-Based Systematic Review on Cognitive Interventions for Individuals with Dementia

ERIC Educational Resources Information Center

Hopper, Tammy; Bourgeois, Michelle; Pimentel, Jane; Qualls, Constance Dean; Hickey, Ellen; Frymark, Tobi; Schooling, Tracy

2013-01-01

Purpose: To evaluate the current state of research evidence related to cognitive interventions for individuals with Alzheimer's disease or related dementias. Method: A systematic search of the literature was conducted across 27 electronic databases based on a set of a priori questions, inclusion/exclusion criteria, and search parameters. Studies…

Prevalence of purulent vaginal discharge in dairy herds depends on timing but not method of detection

USDA-ARS?s Scientific Manuscript database

A review of existing literature was conducted to determine the prevalence of purulent vaginal discharge (PVD) in dairy herds around the world and detection methodologies that influence prevalence estimates. Four databases (PubMed, Google Scholar, Web of Science, and Scopus) were queried with the sea...

Teaching Students with Intellectual or Developmental Disabilities to Write: A Review of the Literature

ERIC Educational Resources Information Center

Joseph, Laurice M.; Konrad, Moira

2009-01-01

The purpose of this review was to identify effective methods for teaching writing to students with intellectual disabilities. After criteria were established, database searches and hand searches of selected peer-reviewed journals were conducted. Findings revealed a relatively small number of studies that met the criteria for inclusion.…

Is the Party Over? Cannabis and Juvenile Psychiatric Disorder: The Past 10 Years

ERIC Educational Resources Information Center

Rey, Joseph M.; Martin, Andres; Krabman, Peter

2004-01-01

Objective: To critically review cannabis research during the past 10 years in relation to rates of use, behavioral problems, and mental disorders in young people. Method: Studies published in English between 1994 and 2004 were identified through systematic searches of literature databases. The material was selectively reviewed focusing on child…

A Replication of Failure, Not a Failure to Replicate

ERIC Educational Resources Information Center

Holden, Gary; Barker, Kathleen; Kuppens, Sofie; Rosenberg, Gary; LeBreton, Jonathan

2015-01-01

Purpose: The increasing role of systematic reviews in knowledge production demands greater rigor in the literature search process. The performance of the Social Work Abstracts (SWA) database has been examined multiple times over the past three decades. The current study is a replication within this line of research. Method: Issue-level coverage…

Auditory Processing Disorder and Auditory/Language Interventions: An Evidence-Based Systematic Review

ERIC Educational Resources Information Center

Fey, Marc E.; Richard, Gail J.; Geffner, Donna; Kamhi, Alan G.; Medwetsky, Larry; Paul, Diane; Ross-Swain, Deborah; Wallach, Geraldine P.; Frymark, Tobi; Schooling, Tracy

2011-01-01

Purpose: In this systematic review, the peer-reviewed literature on the efficacy of interventions for school-age children with auditory processing disorder (APD) is critically evaluated. Method: Searches of 28 electronic databases yielded 25 studies for analysis. These studies were categorized by research phase (e.g., exploratory, efficacy) and…

Toward Improved Collections in Medical Humanities: Fiction in Academic Health Sciences Libraries

ERIC Educational Resources Information Center

Dali, Keren; Dilevko, Juris

2006-01-01

Although fiction plays a prominent role in the interdisciplinary field of medical humanities (MH), it is physically and intellectually isolated from non-fiction in academic health sciences libraries. Using the Literature, Arts, and Medicine Database (LAMD) as a tool for selection and subject analysis, we suggest a method of integrating fiction…

Standardized Tests of Handwriting Readiness: A Systematic Review of the Literature

ERIC Educational Resources Information Center

van Hartingsveldt, Margo J.; de Groot, Imelda J. M.; Aarts, Pauline B. M.; Nijhuis-van der Sanden, Maria W. G.

2011-01-01

Aim: To establish if there are psychometrically sound standardized tests or test items to assess handwriting readiness in 5- and 6-year-old children on the levels of occupations activities/tasks and performance. Method: Electronic databases were searched to identify measurement instruments. Tests were included in a systematic review if: (1)…

Obesity and Intellectual Disability in New Zealand

ERIC Educational Resources Information Center

Stedman, Kurstyn V.; Leland, Louis S., Jr.

2010-01-01

Background: The international literature suggests that obesity is likely to be more pronounced in the population of people with intellectual disability (ID). However, there are no published New Zealand data for this population. Method: We accessed a database containing anonymous data for a New Zealand ID population. Ninety-eight people of 141 had…

Literature Review: Update on Amphetamine Neurotoxicity and Its Relevance to the Treatment of ADHD

ERIC Educational Resources Information Center

Advokat, Claire

2007-01-01

Objective: A review of amphetamine treatment for attention-deficit/hyperactivity disorder (ADHD) was conducted, to obtain information on the long-term neurological consequences of this therapy. Method: Several databases were accessed for research articles on the effects of amphetamine in the brain of laboratory animals and ADHD diagnosed…

77 FR 72858 - Toxicological Review of Inorganic Arsenic (Cancer and Noncancer Effects): In Support of Summary...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-06

... public stakeholder workshop to inform the development of a state of the science toxicological review of... database. Workshop participants will be asked to highlight significant new and emerging research, discuss methods for evaluating literature, identify critical research issues (including mode of action) that may...

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information

PubMed Central

Wilbur, W. John

2012-01-01

The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical–gene interactions, chemical–disease relationships and gene–disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein–protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team. PMID:23160415

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.

PubMed

Kim, Sun; Kim, Won; Wei, Chih-Hsuan; Lu, Zhiyong; Wilbur, W John

2012-01-01

The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical-gene interactions, chemical-disease relationships and gene-disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein-protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team.

Data collection and assessment of commonly consumed foods and recipes in six geo-political zones in Nigeria: important for the development of a National Food Composition Database and Dietary Assessment.

PubMed

Ene-Obong, Henrietta N; Sanusi, Rasaki A; Udenta, Elizabeth A; Williams, Ima O; Anigo, Kola M; Chibuzo, Elizabeth C; Aliyu, Hassan M; Ekpe, Onot O; Davidson, Gloria I

2013-10-01

A cross-sectional study was undertaken to collect and assess commonly consumed foods/recipes from the six geopolitical zones in Nigeria for the production of food composition database (FCDB) for dietary assessment. Communities used were selected using a multi-stage sampling plan. Focus group discussions, interviews, recipe documentation, food preparations and literature reviews were employed. Qualitative methods were used to analyse and present data. SWOT (strengths, weaknesses, opportunities, and threats) analysis was used to evaluate the project. A total of 322 recipes were collected out of which 110 were soups. Food consumption patterns across the geographical zones were found to be changing. Variations in recipes and methods of preparation of similar foods were observed. Factors to be considered in the development of a country-specific FCDB were identified. There were challenges with the use of values reported in literature for Nigerian foods. The study justifies the need for a country-specific FCDB that will include traditional recipes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Database citation in full text biomedical articles.

PubMed

Kafkas, Şenay; Kim, Jee-Hyub; McEntyre, Johanna R

2013-01-01

Molecular biology and literature databases represent essential infrastructure for life science research. Effective integration of these data resources requires that there are structured cross-references at the level of individual articles and biological records. Here, we describe the current patterns of how database entries are cited in research articles, based on analysis of the full text Open Access articles available from Europe PMC. Focusing on citation of entries in the European Nucleotide Archive (ENA), UniProt and Protein Data Bank, Europe (PDBe), we demonstrate that text mining doubles the number of structured annotations of database record citations supplied in journal articles by publishers. Many thousands of new literature-database relationships are found by text mining, since these relationships are also not present in the set of articles cited by database records. We recommend that structured annotation of database records in articles is extended to other databases, such as ArrayExpress and Pfam, entries from which are also cited widely in the literature. The very high precision and high-throughput of this text-mining pipeline makes this activity possible both accurately and at low cost, which will allow the development of new integrated data services.

Database Citation in Full Text Biomedical Articles

PubMed Central

Kafkas, Şenay; Kim, Jee-Hyub; McEntyre, Johanna R.

2013-01-01

Molecular biology and literature databases represent essential infrastructure for life science research. Effective integration of these data resources requires that there are structured cross-references at the level of individual articles and biological records. Here, we describe the current patterns of how database entries are cited in research articles, based on analysis of the full text Open Access articles available from Europe PMC. Focusing on citation of entries in the European Nucleotide Archive (ENA), UniProt and Protein Data Bank, Europe (PDBe), we demonstrate that text mining doubles the number of structured annotations of database record citations supplied in journal articles by publishers. Many thousands of new literature-database relationships are found by text mining, since these relationships are also not present in the set of articles cited by database records. We recommend that structured annotation of database records in articles is extended to other databases, such as ArrayExpress and Pfam, entries from which are also cited widely in the literature. The very high precision and high-throughput of this text-mining pipeline makes this activity possible both accurately and at low cost, which will allow the development of new integrated data services. PMID:23734176

Google Scholar versus PubMed in locating primary literature to answer drug-related questions.

PubMed

Freeman, Maisha Kelly; Lauderdale, Stacy A; Kendrach, Michael G; Woolley, Thomas W

2009-03-01

Google Scholar linked more visitors to biomedical journal Web sites than did PubMed after the database's initial release; however, its usefulness in locating primary literature articles is unknown. To assess in both databases the availability of primary literature target articles; total number of citations; availability of free, full-text journal articles; and number of primary literature target articles retrieved by year within the first 100 citations of the search results. Drug information question reviews published in The Annals of Pharmacotherapy Drug Information Rounds column served as targets to determine the retrieval ability of Google Scholar and PubMed searches. Reviews printed in this column from January 2006 to June 2007 were eligible for study inclusion. Articles were chosen if at least 2 key words of the printed article were included in the PubMed Medical Subject Heading (MeSH) database, and these terms were searched in both databases. Twenty-two of 33 (67%) eligible Drug Information Rounds articles met the inclusion criteria. The median number of primary literature articles used in each of these articles was 6.5 (IQR 4.8, 8.3; mean +/- SD 8 +/- 5.4). No significant differences were found for the mean number of target primary literature articles located within the first 100 citations in Google Scholar and PubMed searches (5.1 +/- 3.9 vs 5.3 +/- 3.3; p = 0.868). Google Scholar searches located more total results than PubMed (2211.6 +/- 3999.5 vs 44.2 +/- 47.4; p = 0.019). The availability of free, full-text journal articles per Drug Information Rounds article was similar between the databases (1.8 +/- 1.7 vs 2.3 +/- 1.7; p = 0.325). More primary literature articles published prior to 2000 were located with Google Scholar searches compared with PubMed (62.8% vs 34.9%; p = 0.017); however, no statistically significant differences between the databases were observed for articles published after 2000 (66.4 vs 77.1; p = 0.074). No significant differences were identified in the number of target primary literature articles located between databases. PubMed searches yielded fewer total citations than Google Scholar results; however, PubMed appears to be more specific than Google Scholar for locating relevant primary literature articles.

Presence and Accuracy of Drug Dosage Recommendations for Continuous Renal Replacement Therapy in Tertiary Drug Information References

PubMed Central

Gorman, Sean K; Slavik, Richard S; Lam, Stefanie

2012-01-01

Background: Clinicians commonly rely on tertiary drug information references to guide drug dosages for patients who are receiving continuous renal replacement therapy (CRRT). It is unknown whether the dosage recommendations in these frequently used references reflect the most current evidence. Objective: To determine the presence and accuracy of drug dosage recommendations for patients undergoing CRRT in 4 drug information references. Methods: Medications commonly prescribed during CRRT were identified from an institutional medication inventory database, and evidence-based dosage recommendations for this setting were developed from the primary and secondary literature. The American Hospital Formulary System—Drug Information (AHFS–DI), Micromedex 2.0 (specifically the DRUGDEX and Martindale databases), and the 5th edition of Drug Prescribing in Renal Failure (DPRF5) were assessed for the presence of drug dosage recommendations in the CRRT setting. The dosage recommendations in these tertiary references were compared with the recommendations derived from the primary and secondary literature to determine concordance. Results: Evidence-based drug dosage recommendations were developed for 33 medications administered in patients undergoing CRRT. The AHFS–DI provided no dosage recommendations specific to CRRT, whereas the DPRF5 provided recommendations for 27 (82%) of the medications and the Micromedex 2.0 application for 20 (61%) (13 [39%] in the DRUGDEX database and 16 [48%] in the Martindale database, with 9 medications covered by both). The dosage recommendations were in concordance with evidence-based recommendations for 12 (92%) of the 13 medications in the DRUGDEX database, 26 (96%) of the 27 in the DPRF5, and all 16 (100%) of those in the Martindale database. Conclusions: One prominent tertiary drug information resource provided no drug dosage recommendations for patients undergoing CRRT. However, 2 of the databases in an Internet-based medical information application and the latest edition of a renal specialty drug information resource provided recommendations for a majority of the medications investigated. Most dosage recommendations were similar to those derived from the primary and secondary literature. The most recent edition of the DPRF is the preferred source of information when prescribing dosage regimens for patients receiving CRRT. PMID:22783029

Leadership Curricula in Nursing Education: A Critical Literature Review and Gap Analysis.

PubMed

Morrow, Kelly J

2015-07-01

The Institute of Medicine's Future of Nursing report advises nursing education programs to integrate and embed leadership content within all areas of prelicensure nursing curriculum. This critical literature review synthesizes the state of the science of leadership curricula in prelicensure baccalaureate nursing education programs from 2008 to 2013. Gaps are identified and discussed. The Academic Search Premier and Health Source databases were searched, using the keywords baccalaureate nursing education and leadership. The CINAHL database was searched, using the keywords leadership, education, nursing, and baccalaureate. The 13 peer-reviewed articles identified for inclusion comprised descriptive articles (n = 8), mixed-methods studies (n = 2), quantitative studies (n = 2), and a qualitative study (n = 1). The underlying theme identified is the study and use of active learning strategies. Subthemes within this context were the use of reflection, peer learning, interdisciplinary teams, organizational partnerships, and curricular reform. Copyright 2015, SLACK Incorporated.

A Diagram Editor for Efficient Biomedical Knowledge Capture and Integration

PubMed Central

Yu, Bohua; Jakupovic, Elvis; Wilson, Justin; Dai, Manhong; Xuan, Weijian; Mirel, Barbara; Athey, Brian; Watson, Stanley; Meng, Fan

2008-01-01

Understanding the molecular mechanisms underlying complex disorders requires the integration of data and knowledge from different sources including free text literature and various biomedical databases. To facilitate this process, we created the Biomedical Concept Diagram Editor (BCDE) to help researchers distill knowledge from data and literature and aid the process of hypothesis development. A key feature of BCDE is the ability to capture information with a simple drag-and-drop. This is a vast improvement over manual methods of knowledge and data recording and greatly increases the efficiency of the biomedical researcher. BCDE also provides a unique concept matching function to enforce consistent terminology, which enables conceptual relationships deposited by different researchers in the BCDE database to be mined and integrated for intelligible and useful results. We hope BCDE will promote the sharing and integration of knowledge from different researchers for effective hypothesis development. PMID:21347131

Supported Decision-Making: Implications from Positive Psychology for Assessment and Intervention in Rehabilitation and Employment.

PubMed

Uyanik, Hatice; Shogren, Karrie A; Blanck, Peter

2017-12-01

Purpose This article reviews existing literature on positive psychology, supported decision-making (SDM), employment, and disability. It examines interventions and assessments that have been empirically evaluated for the enhancement of decision-making and overall well-being of people with disabilities. Additionally, conceptual themes present in the literature were explored. Methods A systematic review was conducted across two databases (ERIC and PsychINFO) using various combination of keywords of 'disabilit*', work rehabilitation and employment terms, positive psychology terms, and SDM components. Seven database searches were conducted with diverse combinations of keywords, which identified 1425 results in total to be screened for relevance using their titles and abstracts. Database search was supplemented with hand searches of oft-cited journals, ancestral search, and supplemental search from grey literature. Results Only four studies were identified in the literature targeting SDM and positive psychology related constructs in the employment and job development context. Results across the studies indicated small to moderate impacts of the assessment and interventions on decision-making and engagement outcomes. Conceptually there are thematic areas of potential overlap, although they are limited in the explicit integration of theory in supported decision-making, positive psychology, disability, and employment. Conclusion Results suggest a need for additional scholarship in this area that focuses on theory development and integration as well as empirical work. Such work should examine the potential utility of considering positive psychological interventions when planning for SDM in the context of career development activities to enhance positive outcomes related to decision-making, self-determination, and other positive psychological constructs.

Homeless youth: a concept analysis.

PubMed

Washington, Philisie Starling

2011-07-01

INTRODUCTION. A variety of terms have been used to describe the homeless youth population. PURPOSE. The purpose of this article is to analyze the conceptual meanings of the term homeless youths by examining the evolution of the concept and its related terms in the current literature. Method. Online databases from 1990-2010 were analyzed using the Rodgers evolutionary approach. RESULTS. The 6 attributes relating to homeless youth were physical location, age, health, behavior, choice, and survival. CONCLUSION. The analysis provided insight and clarification of homeless youth from a variety of related terms in the literature.

Users’ guide to the surgical literature: how to perform a high-quality literature search

PubMed Central

Waltho, Daniel; Kaur, Manraj Nirmal; Haynes, R. Brian; Farrokhyar, Forough; Thoma, Achilleas

2015-01-01

Summary The article “Users’ guide to the surgical literature: how to perform a literature search” was published in 2003, but the continuing technological developments in databases and search filters have rendered that guide out of date. The present guide fills an existing gap in this area; it provides the reader with strategies for developing a searchable clinical question, creating an efficient search strategy, accessing appropriate databases, and skillfully retrieving the best evidence to address the research question. PMID:26384150

Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications

PubMed Central

Hegedűs, Tamás; Chaubey, Pururawa Mayank; Várady, György; Szabó, Edit; Sarankó, Hajnalka; Hofstetter, Lia; Roschitzki, Bernd; Sarkadi, Balázs

2015-01-01

Based on recent results, the determination of the easily accessible red blood cell (RBC) membrane proteins may provide new diagnostic possibilities for assessing mutations, polymorphisms or regulatory alterations in diseases. However, the analysis of the current mass spectrometry-based proteomics datasets and other major databases indicates inconsistencies—the results show large scattering and only a limited overlap for the identified RBC membrane proteins. Here, we applied membrane-specific proteomics studies in human RBC, compared these results with the data in the literature, and generated a comprehensive and expandable database using all available data sources. The integrated web database now refers to proteomic, genetic and medical databases as well, and contains an unexpected large number of validated membrane proteins previously thought to be specific for other tissues and/or related to major human diseases. Since the determination of protein expression in RBC provides a method to indicate pathological alterations, our database should facilitate the development of RBC membrane biomarker platforms and provide a unique resource to aid related further research and diagnostics. Database URL: http://rbcc.hegelab.org PMID:26078478

Classics Online.

ERIC Educational Resources Information Center

Clayman, Dee L.

1995-01-01

Appraises several databases devoted to classical literature. Thesaurus Linguae Graecae (TLG) contains the entire extant corpus of ancient Greek literature, including works on lexicography and historiography, extending into the 15th century. Other works awaiting completion are the Database of Classical Bibliography and a CD-ROM pictorial dictionary…

Radiography Students' Learning: A Literature Review.

PubMed

Holmström, Anneli; Ahonen, Sanna-Mari

2016-01-01

To describe research methodology and findings concerning radiography students' learning. Health sciences databases were searched to perform a traditional narrative literature review. Thirty-five peer-reviewed articles published between 2000 and 2014 were analyzed using thematic analysis. Specific methods of learning were found to be of the most interest. The studies focused primarily on the use and usability of a method or the students' general experiences of it. The most commonly studied methods were e-learning and interprofessional learning, which students perceived as positive methods for theoretical studies and clinical training. Students' learning regarding research was the focus of only one article reporting a wide variety of students' research interests. Most studies reported quantitative research gathered from questionnaires and surveys. Additional research, especially from a qualitative point of view, is needed to deepen the evidence-based knowledge of radiography student learning.

Vision science literature of Nepal in the database "Web of Science".

PubMed

Risal, S; Prasad, H N

2012-01-01

Vision Science is considered to be a quite developed discipline in Nepal, with much research currently in progress. Though the results of these endeavors are published in scientific journals, formal citation analyses have not been performed on works contributed by Nepalese vision scientists. To study Nepal's contribution to vision science literature in the database "Web of Science". The primary data source of this paper was Web of Science, a citation database of Thomas Reuters. All bibliometric analyses were performed with the help of Web of Science analysis service. In the current database of vision science literature, Nepalese authors contributed 112 publications to Web of Science, 95 of which were original articles. Pokharel GP had the highest number of citations among contributing authors of Nepal. Hennig A contributed the highest number of article as a first author. The Nepal Eye Hospital contributed the highest number of articles as an institution to the field of Vision Science. Currently, only two journals from Nepal including Journal of Nepal Medical Association (JAMA) are indexed in the Web of Science database (Sieving, 2012). To evaluate the total productivity of vision science literature from Nepal, total publication counts from national journals and articles indexed in other databases such as PubMed and Scopus must also be considered. © NEPjOPH.

Monitoring the Sodium Content of Restaurant Foods: Public Health Challenges and Opportunities

PubMed Central

Cogswell, Mary E.; Gunn, Janelle P.; Curtis, Christine J.; Rhodes, Donna; Hoy, Kathy; Pehrsson, Pamela; Nickle, Melissa; Merritt, Robert

2013-01-01

We reviewed methods of studies assessing restaurant foods’ sodium content and nutrition databases. We systematically searched the 1964–2012 literature and manually examined references in selected articles and studies. Twenty-six (5.2%) of the 499 articles we found met the inclusion criteria and were abstracted. Five were conducted nationally. Sodium content determination methods included laboratory analysis (n = 15), point-of-purchase nutrition information or restaurants’ Web sites (n = 8), and menu analysis with a nutrient database (n = 3). There is no comprehensive data system that provides all information needed to monitor changes in sodium or other nutrients among restaurant foods. Combining information from different sources and methods may help inform a comprehensive system to monitor sodium content reduction efforts in the US food supply and to develop future strategies. PMID:23865701

MimoSA: a system for minimotif annotation

PubMed Central

2010-01-01

Background Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature. Results We have built the MimoSA application for minimotif annotation. The application supports management of the Minimotif Miner database, literature tracking, and annotation of new minimotifs. MimoSA enables the visualization, organization, selection and editing functions of minimotifs and their attributes in the MnM database. For the literature components, Mimosa provides paper status tracking and scoring of papers for annotation through a freely available machine learning approach, which is based on word correlation. The paper scoring algorithm is also available as a separate program, TextMine. Form-driven annotation of minimotif attributes enables entry of new minimotifs into the MnM database. Several supporting features increase the efficiency of annotation. The layered architecture of MimoSA allows for extensibility by separating the functions of paper scoring, minimotif visualization, and database management. MimoSA is readily adaptable to other annotation efforts that manually curate literature into a MySQL database. Conclusions MimoSA is an extensible application that facilitates minimotif annotation and integrates with the Minimotif Miner database. We have built MimoSA as an application that integrates dynamic abstract scoring with a high performance relational model of minimotif syntax. MimoSA's TextMine, an efficient paper-scoring algorithm, can be used to dynamically rank papers with respect to context. PMID:20565705

Systematic literature review of methodologies and data sources of existing economic models across the full spectrum of Alzheimer’s disease and dementia from apparently healthy through disease progression to end of life care: a systematic review protocol

PubMed Central

Karagiannidou, Maria; Wittenberg, Raphael; Landeiro, Filipa Isabel Trigo; Park, A-La; Fry, Andra; Knapp, Martin; Tockhorn-Heidenreich, Antje; Castro Sanchez, Amparo Yovanna; Ghinai, Isaac; Handels, Ron; Lecomte, Pascal; Wolstenholme, Jane

2018-01-01

Introduction Dementia is one of the greatest health challenges the world will face in the coming decades, as it is one of the principal causes of disability and dependency among older people. Economic modelling is used widely across many health conditions to inform decisions on health and social care policy and practice. The aim of this literature review is to systematically identify, review and critically evaluate existing health economics models in dementia. We included the full spectrum of dementia, including Alzheimer’s disease (AD), from preclinical stages through to severe dementia and end of life. This review forms part of the Real world Outcomes across the Alzheimer’s Disease spectrum for better care: multimodal data Access Platform (ROADMAP) project. Methods and analysis Electronic searches were conducted in Medical Literature Analysis and Retrieval System Online, Excerpta Medica dataBASE, Economic Literature Database, NHS Economic Evaluation Database, Cochrane Central Register of Controlled Trials, Cost-Effectiveness Analysis Registry, Research Papers in Economics, Database of Abstracts of Reviews of Effectiveness, Science Citation Index, Turning Research Into Practice and Open Grey for studies published between January 2000 and the end of June 2017. Two reviewers will independently assess each study against predefined eligibility criteria. A third reviewer will resolve any disagreement. Data will be extracted using a predefined data extraction form following best practice. Study quality will be assessed using the Phillips checklist for decision analytic modelling. A narrative synthesis will be used. Ethics and dissemination The results will be made available in a scientific peer-reviewed journal paper, will be presented at relevant conferences and will also be made available through the ROADMAP project. PROSPERO registration number CRD42017073874. PMID:29884696

Mixing it but not mixed-up: mixed methods research in medical education (a critical narrative review).

PubMed

Maudsley, Gillian

2011-01-01

Some important research questions in medical education and health services research need 'mixed methods research' (particularly synthesizing quantitative and qualitative findings). The approach is not new, but should be more explicitly reported. The broad search question here, of a disjointed literature, was thus: What is mixed methods research - how should it relate to medical education research?, focused on explicit acknowledgement of 'mixing'. Literature searching focused on Web of Knowledge supplemented by other databases across disciplines. Five main messages emerged: - Thinking quantitative and qualitative, not quantitative versus qualitative - Appreciating that mixed methods research blends different knowledge claims, enquiry strategies, and methods - Using a 'horses for courses' [whatever works] approach to the question, and clarifying the mix - Appreciating how medical education research competes with the 'evidence-based' movement, health services research, and the 'RCT' - Being more explicit about the role of mixed methods in medical education research, and the required expertise Mixed methods research is valuable, yet the literature relevant to medical education is fragmented and poorly indexed. The required time, effort, expertise, and techniques deserve better recognition. More write-ups should explicitly discuss the 'mixing' (particularly of findings), rather than report separate components.

An incremental database access method for autonomous interoperable databases

NASA Technical Reports Server (NTRS)

Roussopoulos, Nicholas; Sellis, Timos

1994-01-01

We investigated a number of design and performance issues of interoperable database management systems (DBMS's). The major results of our investigation were obtained in the areas of client-server database architectures for heterogeneous DBMS's, incremental computation models, buffer management techniques, and query optimization. We finished a prototype of an advanced client-server workstation-based DBMS which allows access to multiple heterogeneous commercial DBMS's. Experiments and simulations were then run to compare its performance with the standard client-server architectures. The focus of this research was on adaptive optimization methods of heterogeneous database systems. Adaptive buffer management accounts for the random and object-oriented access methods for which no known characterization of the access patterns exists. Adaptive query optimization means that value distributions and selectives, which play the most significant role in query plan evaluation, are continuously refined to reflect the actual values as opposed to static ones that are computed off-line. Query feedback is a concept that was first introduced to the literature by our group. We employed query feedback for both adaptive buffer management and for computing value distributions and selectivities. For adaptive buffer management, we use the page faults of prior executions to achieve more 'informed' management decisions. For the estimation of the distributions of the selectivities, we use curve-fitting techniques, such as least squares and splines, for regressing on these values.

Increasing access to Latin American social medicine resources: a preliminary report*

PubMed Central

Buchanan, Holly Shipp; Waitzkin, Howard; Eldredge, Jonathan; Davidson, Russ; Iriart, Celia; Teal, Janis

2003-01-01

Purpose: This preliminary report describes the development and implementation of a project to improve access to literature in Latin American social medicine (LASM). Methods: The University of New Mexico project team collaborated with participants from Argentina, Brazil, Chile, and Ecuador to identify approximately 400 articles and books in Latin American social medicine. Structured abstracts were prepared, translated into English, Spanish, and Portuguese, assigned Medical Subject Headings (MeSH), and loaded into a Web-based database for public searching. The project has initiated Web-based publication for two LASM journals. Evaluation included measures of use and content. Results: The LASM Website (http://hsc.unm.edu/lasm) and database create access to formerly little-known literature that addresses problems relevant to current medicine and public health. This Website offers a unique resource for researchers, practitioners, and teachers who seek to understand the links between socioeconomic conditions and health. The project provides a model for collaboration between librarians and health care providers. Challenges included procurement of primary material; preparation of concise abstracts; working with trilingual translations of abstracts, metadata, and indexing; and the work processes of the multidisciplinary team. Conclusions: The literature of Latin American social medicine has become more readily available to researchers worldwide. The LASM project serves as a collaborative model for the creation of sustainable solutions for disseminating information that is difficult to access through traditional methods. PMID:14566372

Analysing patent landscapes in plant biotechnology and new plant breeding techniques.

PubMed

Parisi, Claudia; Rodríguez-Cerezo, Emilio; Thangaraj, Harry

2013-02-01

This article aims to inform the reader of the importance of searching patent landscapes in plant biotechnology and the use of basic tools to perform a patent search. The recommendations for a patent search strategy are illustrated with the specific example of zinc finger nuclease technology for genetic engineering in plants. Within this scope, we provide a general introduction to searching using two online and free-access patent databases esp@cenet and PatentScope. The essential features of the two databases, and their functionality is described, together with short descriptions to enable the reader to understand patents, searching, their content, patent families, and their territorial scope. We mostly stress the value of patent searching for mining scientific, rather than legal information. Search methods through the use of keywords and patent codes are elucidated together with suggestions about how to search with or combine codes with keywords and we also comment on limitations of each method. We stress the importance of patent literature to complement more mainstream scientific literature, and the relative complexities and difficulties in searching patents compared to the latter. A parallel online resource where we describe detailed search exercises is available through reference for those intending further exploration. In essence this is aimed at a novice patent searcher who may want to examine accessory patent literature to complement knowledge gained from mainstream journal resources.

Preferences and Attitudes toward Progress Reporting Methods of Parents from Diverse Backgrounds

ERIC Educational Resources Information Center

Sousa, Darlene Anastacia; Luze, Gayle; Hughes-Belding, Kere

2014-01-01

There is a growing movement in education toward data-based decision-making requiring frequent monitoring of student progress. However, the literature fails to provide direction as to the best means of communicating information about a child's progress with his or her parents. Given the increasing number of immigrant families being served, it…

Children of Parents with Intellectual Disability: Facing Poor Outcomes or Faring Okay?

ERIC Educational Resources Information Center

Collings, Susan; Llewellyn, Gwynnyth

2012-01-01

Background: Children of parents with intellectual disability are assumed to be at risk of poor outcomes but a comprehensive review of the literature has not previously been undertaken. Method: A database and reference search from March 2010 to March 2011 resulted in 26 studies for review. Results: Two groups of studies were identified. The first…

An Evidence-Based Systematic Review on Communication Treatments for Individuals with Right Hemisphere Brain Damage

ERIC Educational Resources Information Center

Blake, Margaret Lehman; Frymark, Tobi; Venedictov, Rebecca

2013-01-01

Purpose: The purpose of this review is to evaluate and summarize the research evidence related to the treatment of individuals with right hemisphere communication disorders. Method: A comprehensive search of the literature using key words related to right hemisphere brain damage and communication treatment was conducted in 27 databases (e.g.,…

Comparing the Effects of Working Memory-Based Interventions for Children with Language Impairment. EBP Briefs. Volume 9, Issue 1

ERIC Educational Resources Information Center

Farquharson, Kelly; Franzluebbers, Chelsea E.

2014-01-01

Clinical Question: Do working memory-based interventions improve language, reading, and/or working memory skills in school-aged children with language impairment? Method: Literature review of evidence-based practice (EBP) intervention comparisons. Sources: Google Scholar, ASHA journals database, Academic OneFile, Academic Search Complete, and…

[A Terahertz Spectral Database Based on Browser/Server Technique].

PubMed

Zhang, Zhuo-yong; Song, Yue

2015-09-01

With the solution of key scientific and technical problems and development of instrumentation, the application of terahertz technology in various fields has been paid more and more attention. Owing to the unique characteristic advantages, terahertz technology has been showing a broad future in the fields of fast, non-damaging detections, as well as many other fields. Terahertz technology combined with other complementary methods can be used to cope with many difficult practical problems which could not be solved before. One of the critical points for further development of practical terahertz detection methods depends on a good and reliable terahertz spectral database. We developed a BS (browser/server) -based terahertz spectral database recently. We designed the main structure and main functions to fulfill practical requirements. The terahertz spectral database now includes more than 240 items, and the spectral information was collected based on three sources: (1) collection and citation from some other abroad terahertz spectral databases; (2) collected from published literatures; and (3) spectral data measured in our laboratory. The present paper introduced the basic structure and fundament functions of the terahertz spectral database developed in our laboratory. One of the key functions of this THz database is calculation of optical parameters. Some optical parameters including absorption coefficient, refractive index, etc. can be calculated based on the input THz time domain spectra. The other main functions and searching methods of the browser/server-based terahertz spectral database have been discussed. The database search system can provide users convenient functions including user registration, inquiry, displaying spectral figures and molecular structures, spectral matching, etc. The THz database system provides an on-line searching function for registered users. Registered users can compare the input THz spectrum with the spectra of database, according to the obtained correlation coefficient one can perform the searching task very fast and conveniently. Our terahertz spectral database can be accessed at http://www.teralibrary.com. The proposed terahertz spectral database is based on spectral information so far, and will be improved in the future. We hope this terahertz spectral database can provide users powerful, convenient, and high efficient functions, and could promote the broader applications of terahertz technology.

CardioTF, a database of deconstructing transcriptional circuits in the heart system

PubMed Central

2016-01-01

Background: Information on cardiovascular gene transcription is fragmented and far behind the present requirements of the systems biology field. To create a comprehensive source of data for cardiovascular gene regulation and to facilitate a deeper understanding of genomic data, the CardioTF database was constructed. The purpose of this database is to collate information on cardiovascular transcription factors (TFs), position weight matrices (PWMs), and enhancer sequences discovered using the ChIP-seq method. Methods: The Naïve-Bayes algorithm was used to classify literature and identify all PubMed abstracts on cardiovascular development. The natural language learning tool GNAT was then used to identify corresponding gene names embedded within these abstracts. Local Perl scripts were used to integrate and dump data from public databases into the MariaDB management system (MySQL). In-house R scripts were written to analyze and visualize the results. Results: Known cardiovascular TFs from humans and human homologs from fly, Ciona, zebrafish, frog, chicken, and mouse were identified and deposited in the database. PWMs from Jaspar, hPDI, and UniPROBE databases were deposited in the database and can be retrieved using their corresponding TF names. Gene enhancer regions from various sources of ChIP-seq data were deposited into the database and were able to be visualized by graphical output. Besides biocuration, mouse homologs of the 81 core cardiac TFs were selected using a Naïve-Bayes approach and then by intersecting four independent data sources: RNA profiling, expert annotation, PubMed abstracts and phenotype. Discussion: The CardioTF database can be used as a portal to construct transcriptional network of cardiac development. Availability and Implementation: Database URL: http://www.cardiosignal.org/database/cardiotf.html. PMID:27635320

The global compendium of Aedes aegypti and Ae. albopictus occurrence

NASA Astrophysics Data System (ADS)

Kraemer, Moritz U. G.; Sinka, Marianne E.; Duda, Kirsten A.; Mylne, Adrian; Shearer, Freya M.; Brady, Oliver J.; Messina, Jane P.; Barker, Christopher M.; Moore, Chester G.; Carvalho, Roberta G.; Coelho, Giovanini E.; van Bortel, Wim; Hendrickx, Guy; Schaffner, Francis; Wint, G. R. William; Elyazar, Iqbal R. F.; Teng, Hwa-Jen; Hay, Simon I.

2015-07-01

Aedes aegypti and Ae. albopictus are the main vectors transmitting dengue and chikungunya viruses. Despite being pathogens of global public health importance, knowledge of their vectors’ global distribution remains patchy and sparse. A global geographic database of known occurrences of Ae. aegypti and Ae. albopictus between 1960 and 2014 was compiled. Herein we present the database, which comprises occurrence data linked to point or polygon locations, derived from peer-reviewed literature and unpublished studies including national entomological surveys and expert networks. We describe all data collection processes, as well as geo-positioning methods, database management and quality-control procedures. This is the first comprehensive global database of Ae. aegypti and Ae. albopictus occurrence, consisting of 19,930 and 22,137 geo-positioned occurrence records respectively. Both datasets can be used for a variety of mapping and spatial analyses of the vectors and, by inference, the diseases they transmit.

The global compendium of Aedes aegypti and Ae. albopictus occurrence

PubMed Central

Kraemer, Moritz U. G.; Sinka, Marianne E.; Duda, Kirsten A.; Mylne, Adrian; Shearer, Freya M.; Brady, Oliver J.; Messina, Jane P.; Barker, Christopher M.; Moore, Chester G.; Carvalho, Roberta G.; Coelho, Giovanini E.; Van Bortel, Wim; Hendrickx, Guy; Schaffner, Francis; Wint, G. R. William; Elyazar, Iqbal R. F.; Teng, Hwa-Jen; Hay, Simon I.

2015-01-01

Aedes aegypti and Ae. albopictus are the main vectors transmitting dengue and chikungunya viruses. Despite being pathogens of global public health importance, knowledge of their vectors’ global distribution remains patchy and sparse. A global geographic database of known occurrences of Ae. aegypti and Ae. albopictus between 1960 and 2014 was compiled. Herein we present the database, which comprises occurrence data linked to point or polygon locations, derived from peer-reviewed literature and unpublished studies including national entomological surveys and expert networks. We describe all data collection processes, as well as geo-positioning methods, database management and quality-control procedures. This is the first comprehensive global database of Ae. aegypti and Ae. albopictus occurrence, consisting of 19,930 and 22,137 geo-positioned occurrence records respectively. Both datasets can be used for a variety of mapping and spatial analyses of the vectors and, by inference, the diseases they transmit. PMID:26175912

MEDLINE: the options for health professionals.

PubMed

Wood, E H

1994-01-01

The bibliographic database MEDLINE, produced by the National Library of Medicine (NLM), is a computerized index to the world's biomedical literature. The database can be searched back to 1966 and contains 6.8 million records. The various means of access are divided, for the purposes of this article, into three categories: logging onto a remote host computer by telephone and modem or by the Internet; subscribing to part or all of the database on compact disc (CD-ROM); and leasing the data on a transport medium such as magnetic tape or CDs for loading on a local host computer. Decisions about which method is preferable in a given situation depend on cost, availability of hardware and software, local expertise, and the size of the intended user population. Trends include increased access to the Internet by health professionals, increased network speed, links from MEDLINE records to full-text databases or online journals, and integration of MEDLINE into wider health information systems.

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

PubMed Central

Reguly, Teresa; Breitkreutz, Ashton; Boucher, Lorrie; Breitkreutz, Bobby-Joe; Hon, Gary C; Myers, Chad L; Parsons, Ainslie; Friesen, Helena; Oughtred, Rose; Tong, Amy; Stark, Chris; Ho, Yuen; Botstein, David; Andrews, Brenda; Boone, Charles; Troyanskya, Olga G; Ideker, Trey; Dolinski, Kara; Batada, Nizar N; Tyers, Mike

2006-01-01

Background The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference. Results We describe here a comprehensive database of genetic and protein interactions, and associated experimental evidence, for the budding yeast Saccharomyces cerevisiae, as manually curated from over 31,793 abstracts and online publications. This literature-curated (LC) dataset contains 33,311 interactions, on the order of all extant HTP datasets combined. Surprisingly, HTP protein-interaction datasets currently achieve only around 14% coverage of the interactions in the literature. The LC network nevertheless shares attributes with HTP networks, including scale-free connectivity and correlations between interactions, abundance, localization, and expression. We find that essential genes or proteins are enriched for interactions with other essential genes or proteins, suggesting that the global network may be functionally unified. This interconnectivity is supported by a substantial overlap of protein and genetic interactions in the LC dataset. We show that the LC dataset considerably improves the predictive power of network-analysis approaches. The full LC dataset is available at the BioGRID () and SGD () databases. Conclusion Comprehensive datasets of biological interactions derived from the primary literature provide critical benchmarks for HTP methods, augment functional prediction, and reveal system-level attributes of biological networks. PMID:16762047

Information prescriptions, 1930–2013: an international history and comprehensive review*

PubMed Central

McKnight, Michelynn

2014-01-01

Objectives: Recently, government agencies in several countries have promoted information prescription programs to increase patients' understanding of their conditions. The practice has a long history and many publications, but no comprehensive literature reviews such as this. Methods: Using a variety of high-precision and high-recall strategies, the researcher searched two dozen online bibliographic databases, citation databases, and repositories, as well as many print sources, to identify and retrieve documents for review. Of these documents, ninety relevant English-language case reports, research reports, and reviews published from 1930–2013 met the study criteria. Results: Early to mid-twentieth century reports covered long-standing practices and used no rigorous research methods. The literature since the mid-1990s reports on short-term trial projects, especially of government-sponsored programs in the United States and United Kingdom. Although the concept of information prescription has been in the literature and practiced for decades, no long-term research studies were found. Conclusions: Most of the literature is anecdotal concerning small pilot projects. The reports investigate physician, patient, and librarian satisfaction but not changes in patient knowledge or behavior. Many twenty-first century projects emphasize materials and projects from specific government agencies and commercial enterprises. Implications: While the practice is commonly believed to be a good idea and there are many publications on the subject, few studies provide any evidence of the efficacy of information prescriptions for increased patient knowledge. Well-designed and executed large or long-term studies might produce needed evidence for professional practice. PMID:25349545

A kinetics database and scripts for PHREEQC

NASA Astrophysics Data System (ADS)

Hu, B.; Zhang, Y.; Teng, Y.; Zhu, C.

2017-12-01

Kinetics of geochemical reactions has been increasingly used in numerical models to simulate coupled flow, mass transport, and chemical reactions. However, the kinetic data are scattered in the literature. To assemble a kinetic dataset for a modeling project is an intimidating task for most. In order to facilitate the application of kinetics in geochemical modeling, we assembled kinetics parameters into a database for the geochemical simulation program, PHREEQC (version 3.0). Kinetics data were collected from the literature. Our database includes kinetic data for over 70 minerals. The rate equations are also programmed into scripts with the Basic language. Using the new kinetic database, we simulated reaction path during the albite dissolution process using various rate equations in the literature. The simulation results with three different rate equations gave difference reaction paths at different time scale. Another application involves a coupled reactive transport model simulating the advancement of an acid plume in an acid mine drainage site associated with Bear Creek Uranium tailings pond. Geochemical reactions including calcite, gypsum, and illite were simulated with PHREEQC using the new kinetic database. The simulation results successfully demonstrated the utility of new kinetic database.

Acupuncture for treating sciatica: a systematic review protocol

PubMed Central

Qin, Zongshi; Liu, Xiaoxu; Yao, Qin; Zhai, Yanbing; Liu, Zhishun

2015-01-01

Introduction This systematic review aims to assess the effectiveness and safety of acupuncture for treating sciatica. Methods The following nine databases will be searched from their inception to 30 October 2014: MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials (CENTRAL), the Chinese Biomedical Literature Database (CBM), the Chinese Medical Current Content (CMCC), the Chinese Scientific Journal Database (VIP database), the Wan-Fang Database, the China National Knowledge Infrastructure (CNKI) and Citation Information by National Institute of Informatics (CiNii). Randomised controlled trials (RCTs) of acupuncture for sciatica in English, Chinese or Japanese without restriction of publication status will be included. Two researchers will independently undertake study selection, extraction of data and assessment of study quality. Meta-analysis will be conducted after screening of studies. Data will be analysed using risk ratio for dichotomous data, and standardised mean difference or weighted mean difference for continuous data. Dissemination This systematic review will be disseminated electronically through a peer-reviewed publication or conference presentations. Trial registration number PROSPERO CRD42014015001. PMID:25922105

RDIS: The Rabies Disease Information System.

PubMed

Dharmalingam, Baskeran; Jothi, Lydia

2015-01-01

Rabies is a deadly viral disease causing acute inflammation or encephalitis of the brain in human beings and other mammals. Therefore, it is of interest to collect information related to the disease from several sources including known literature databases for further analysis and interpretation. Hence, we describe the development of a database called the Rabies Disease Information System (RDIS) for this purpose. The online database describes the etiology, epidemiology, pathogenesis and pathology of the disease using diagrammatic representations. It provides information on several carriers of the rabies viruses like dog, bat, fox and civet, and their distributions around the world. Information related to the urban and sylvatic cycles of transmission of the virus is also made available. The database also contains information related to available diagnostic methods and vaccines for human and other animals. This information is of use to medical, veterinary and paramedical practitioners, students, researchers, pet owners, animal lovers, livestock handlers, travelers and many others. The database is available for free http://rabies.mscwbif.org/home.html.

Deep learning of mutation-gene-drug relations from the literature.

PubMed

Lee, Kyubum; Kim, Byounggun; Choi, Yonghwa; Kim, Sunkyu; Shin, Wonho; Lee, Sunwon; Park, Sungjoon; Kim, Seongsoon; Tan, Aik Choon; Kang, Jaewoo

2018-01-25

Molecular biomarkers that can predict drug efficacy in cancer patients are crucial components for the advancement of precision medicine. However, identifying these molecular biomarkers remains a laborious and challenging task. Next-generation sequencing of patients and preclinical models have increasingly led to the identification of novel gene-mutation-drug relations, and these results have been reported and published in the scientific literature. Here, we present two new computational methods that utilize all the PubMed articles as domain specific background knowledge to assist in the extraction and curation of gene-mutation-drug relations from the literature. The first method uses the Biomedical Entity Search Tool (BEST) scoring results as some of the features to train the machine learning classifiers. The second method uses not only the BEST scoring results, but also word vectors in a deep convolutional neural network model that are constructed from and trained on numerous documents such as PubMed abstracts and Google News articles. Using the features obtained from both the BEST search engine scores and word vectors, we extract mutation-gene and mutation-drug relations from the literature using machine learning classifiers such as random forest and deep convolutional neural networks. Our methods achieved better results compared with the state-of-the-art methods. We used our proposed features in a simple machine learning model, and obtained F1-scores of 0.96 and 0.82 for mutation-gene and mutation-drug relation classification, respectively. We also developed a deep learning classification model using convolutional neural networks, BEST scores, and the word embeddings that are pre-trained on PubMed or Google News data. Using deep learning, the classification accuracy improved, and F1-scores of 0.96 and 0.86 were obtained for the mutation-gene and mutation-drug relations, respectively. We believe that our computational methods described in this research could be used as an important tool in identifying molecular biomarkers that predict drug responses in cancer patients. We also built a database of these mutation-gene-drug relations that were extracted from all the PubMed abstracts. We believe that our database can prove to be a valuable resource for precision medicine researchers.

A Mixed Methods Analysis of a Library Based Handheld Intervention with Rural Clinicians

PubMed Central

Wallace, Richard L.; Woodward, Nakia J.; Wolf, Katherine M.

2014-01-01

Background The East Tennessee State University Quillen College of Medicine Library has participated for several years in projects to provide rural clinicians with health information resources. Objectives To determine if a strategy of handheld devices with a best-evidence point-of-care disease tool and a drug database paired with access to a medical library for full-text articles and training to use the tools would be an affordable way to meet the information needs of rural underserved clinicians. Methods This study is a mixed methods methodology. The first project was evaluated using a randomized controlled trial (RCT) methodology. The second was evaluated qualitatively using interviews and focus groups. Results The quantitative findings discovered that clinicians equipped with a handheld device with evidence-based software more frequently found answers to clinical questions, found answers more quickly, were more satisfied with information they found, and use expensive resources such as continuing medical education, online databases, and textbooks less than the group that did not have access to online technology. Qualitative results supported the quantitative findings. Conclusion Librarians can implement a three-pronged strategy of the secondary literature via a handheld, the primary literature via LoansomeDoc, and quality training to meet basic information needs of rural clinicians. PMID:25155980

Constructing a Graph Database for Semantic Literature-Based Discovery.

PubMed

Hristovski, Dimitar; Kastrin, Andrej; Dinevski, Dejan; Rindflesch, Thomas C

2015-01-01

Literature-based discovery (LBD) generates discoveries, or hypotheses, by combining what is already known in the literature. Potential discoveries have the form of relations between biomedical concepts; for example, a drug may be determined to treat a disease other than the one for which it was intended. LBD views the knowledge in a domain as a network; a set of concepts along with the relations between them. As a starting point, we used SemMedDB, a database of semantic relations between biomedical concepts extracted with SemRep from Medline. SemMedDB is distributed as a MySQL relational database, which has some problems when dealing with network data. We transformed and uploaded SemMedDB into the Neo4j graph database, and implemented the basic LBD discovery algorithms with the Cypher query language. We conclude that storing the data needed for semantic LBD is more natural in a graph database. Also, implementing LBD discovery algorithms is conceptually simpler with a graph query language when compared with standard SQL.

Existing Approaches to Chemical, Biological, Radiological, and Nuclear (CBRN) Education and Training for Health Professionals: Findings from an Integrative Literature Review.

PubMed

Kako, Mayumi; Hammad, Karen; Mitani, Satoko; Arbon, Paul

2018-04-01

This review was conducted to explore the literature to determine the availability, content, and evaluation of existing chemical, biological, radiological, and nuclear (CBRN) education programs for health professionals. An integrative review of the international literature describing disaster education for CBRN (2004-2016) was conducted. The following relevant databases were searched: Proquest, Pubmed, Science Direct, Scopus, Journals @ OVID, Google Scholar, Medline, and Ichuschi ver. 5 (Japanese database for health professionals). The search terms used were: "disaster," "chemical," "biological," "radiological," "nuclear," "CBRN," "health professional education," and "method." The following Medical Subject Headings (MeSH) terms, "education," "nursing," "continuing," "disasters," "disaster planning," and "bioterrorism," were used wherever possible and appropriate. The retrieved articles were narratively analyzed according to availability, content, and method. The content was thematically analyzed to provide an overview of the core content of the training. The literature search identified 619 potentially relevant articles for this study. Duplicates (n=104) were removed and 87 articles were identified for title review. In total, 67 articles were discarded, yielding 20 articles for all-text review, following 11 studies were retained for analysis, including one Japanese study. All articles published in English were from the USA, apart from the two studies located in Japan and Sweden. The most typical content in the selected literature was CBRN theory (n=11), followed by studies based on incident command (n=8), decontamination (n=7), disaster management (n=7), triage (n=7), personal protective equipment (PPE) use (n = 5), and post-training briefing (n=3). While the CBRN training course requires the participants to gain specific skills and knowledge, proposed training courses should be effectively constructed to include approaches such as scenario-based simulations, depending on the participants' needs. Kako M , Hammad K , Mitani S , Arbon P . Existing approaches to chemical, biological, radiological, and nuclear (CBRN) education and training for health professionals: findings from an integrative literature review. Prehosp Disaster Med. 2018;33(2):182-190.

Databases: Beyond the Basics.

ERIC Educational Resources Information Center

Whittaker, Robert

This presented paper offers an elementary description of database characteristics and then provides a survey of databases that may be useful to the teacher and researcher in Slavic and East European languages and literatures. The survey focuses on commercial databases that are available, usable, and needed. Individual databases discussed include:…

Economic evaluation of diagnostic methods used in dentistry. A systematic review.

PubMed

Christell, Helena; Birch, Stephen; Horner, Keith; Lindh, Christina; Rohlin, Madeleine

2014-11-01

To review the literature of economic evaluations regarding diagnostic methods used in dentistry. Four databases (MEDLINE, Web of Science, The Cochrane library, the NHS Economic Evaluation Database) were searched for studies, complemented by hand search, until February 2013. Two authors independently screened all titles or abstracts and then applied inclusion and exclusion criteria to select full-text publications published in English, which reported an economic evaluation comparing at least two alternative methods. Studies of diagnostic methods were assessed by four reviewers using a protocol based on the QUADAS tool regarding diagnostic methods and a check-list for economic evaluations. The results of the data extraction were summarized in a structured table and as a narrative description. From 476 identified full-text publications, 160 were considered to be economic evaluations. Only 12 studies (7%) were on diagnostic methods, whilst 78 studies (49%) were on prevention and 70 (40%) on treatment. Among studies on diagnostic methods, there was between-study heterogeneity methodologically, regarding the diagnostic method analysed and type of economic evaluation addressed. Generally, the choice of economic evaluation method was not justified and the perspective of the study not stated. Costing of diagnostic methods varied. A small body of literature addresses economic evaluation of diagnostic methods in dentistry. Thus, there is a need for studies from various perspectives with well defined research questions and measures of the cost and effectiveness. Economic resources in healthcare are finite. For diagnostic methods, an understanding of efficacy provides only part of the information needed for evidence-based practice. This study highlighted a paucity of economic evaluations of diagnostic methods used in dentistry, indicating that much of what we practise lacks sufficient evidence.

Applications of Protein Thermodynamic Database for Understanding Protein Mutant Stability and Designing Stable Mutants.

PubMed

Gromiha, M Michael; Anoosha, P; Huang, Liang-Tsung

2016-01-01

Protein stability is the free energy difference between unfolded and folded states of a protein, which lies in the range of 5-25 kcal/mol. Experimentally, protein stability is measured with circular dichroism, differential scanning calorimetry, and fluorescence spectroscopy using thermal and denaturant denaturation methods. These experimental data have been accumulated in the form of a database, ProTherm, thermodynamic database for proteins and mutants. It also contains sequence and structure information of a protein, experimental methods and conditions, and literature information. Different features such as search, display, and sorting options and visualization tools have been incorporated in the database. ProTherm is a valuable resource for understanding/predicting the stability of proteins and it can be accessed at http://www.abren.net/protherm/ . ProTherm has been effectively used to examine the relationship among thermodynamics, structure, and function of proteins. We describe the recent progress on the development of methods for understanding/predicting protein stability, such as (1) general trends on mutational effects on stability, (2) relationship between the stability of protein mutants and amino acid properties, (3) applications of protein three-dimensional structures for predicting their stability upon point mutations, (4) prediction of protein stability upon single mutations from amino acid sequence, and (5) prediction methods for addressing double mutants. A list of online resources for predicting has also been provided.

A nearest neighbor approach for automated transporter prediction and categorization from protein sequences.

PubMed

Li, Haiquan; Dai, Xinbin; Zhao, Xuechun

2008-05-01

Membrane transport proteins play a crucial role in the import and export of ions, small molecules or macromolecules across biological membranes. Currently, there are a limited number of published computational tools which enable the systematic discovery and categorization of transporters prior to costly experimental validation. To approach this problem, we utilized a nearest neighbor method which seamlessly integrates homologous search and topological analysis into a machine-learning framework. Our approach satisfactorily distinguished 484 transporter families in the Transporter Classification Database, a curated and representative database for transporters. A five-fold cross-validation on the database achieved a positive classification rate of 72.3% on average. Furthermore, this method successfully detected transporters in seven model and four non-model organisms, ranging from archaean to mammalian species. A preliminary literature-based validation has cross-validated 65.8% of our predictions on the 11 organisms, including 55.9% of our predictions overlapping with 83.6% of the predicted transporters in TransportDB.

UROTRAUMA: AUA GUIDELINE

PubMed Central

Morey, Allen F.; Brandes, Steve; Dugi, Daniel David; Armstrong, John H.; Breyer, Benjamin N.; Broghammer, Joshua A.; Erickson, Bradley A.; Holzbeierlein, Jeff; Hudak, Steven J.; Mirvis, Stuart; Pruitt, Jeffrey H.; Reston, James T.; Santucci, Richard A.; Smith, Thomas G.; Wessells, Hunter

2014-01-01

Purpose The authors of this guideline reviewed the urologic trauma literature to guide clinicians in the appropriate methods of evaluation and management of genitourinary injuries. Methods A systematic review of the literature using the MEDLINE® and EMBASE databases (search dates 1/1/90-9/19/12) was conducted to identify peer-reviewed publications relevant to urotrauma. The review yielded an evidence base of 372 studies after application of inclusion/exclusion criteria. These publications were used to inform the statements presented in the guideline as Standards, Recommendations or Options. When sufficient evidence existed, the body of evidence for a particular treatment was assigned a strength rating of A (high), B (moderate) or C (low). In the absence of sufficient evidence, additional information is provided as Clinical Principles and Expert Opinions. PMID:24857651

Methods for the guideline-based development of quality indicators--a systematic review

PubMed Central

2012-01-01

Background Quality indicators (QIs) are used in many healthcare settings to measure, compare, and improve quality of care. For the efficient development of high-quality QIs, rigorous, approved, and evidence-based development methods are needed. Clinical practice guidelines are a suitable source to derive QIs from, but no gold standard for guideline-based QI development exists. This review aims to identify, describe, and compare methodological approaches to guideline-based QI development. Methods We systematically searched medical literature databases (Medline, EMBASE, and CINAHL) and grey literature. Two researchers selected publications reporting methodological approaches to guideline-based QI development. In order to describe and compare methodological approaches used in these publications, we extracted detailed information on common steps of guideline-based QI development (topic selection, guideline selection, extraction of recommendations, QI selection, practice test, and implementation) to predesigned extraction tables. Results From 8,697 hits in the database search and several grey literature documents, we selected 48 relevant references. The studies were of heterogeneous type and quality. We found no randomized controlled trial or other studies comparing the ability of different methodological approaches to guideline-based development to generate high-quality QIs. The relevant publications featured a wide variety of methodological approaches to guideline-based QI development, especially regarding guideline selection and extraction of recommendations. Only a few studies reported patient involvement. Conclusions Further research is needed to determine which elements of the methodological approaches identified, described, and compared in this review are best suited to constitute a gold standard for guideline-based QI development. For this research, we provide a comprehensive groundwork. PMID:22436067

Aggression and Violence among Iranian Adolescents and Youth: A 10-year Systematic Review

PubMed Central

Sadeghi, Saeid; Farajzadegan, Ziba; Kelishadi, Roya; Heidari, Kamal

2014-01-01

Background: Although the overwhelming majority of Iranian adolescents are well-adjusted, a substantial group exhibits high levels of maladjustment and deficient functioning. Escalation of criminal violence among the youth population has become a major public policy issue and a serious public health problem. In reviewing a 10-year literature, this article aimed to describe and propose primary assumptions regarding the correlates of aggressive and violent behaviors in Iranian adolescents and youth. Methods: Bibliographic databases such as PubMed and Google Scholar along with Iranian databases including PubMed, IranMedex, Magiran, Irandoc, Psychoinfo, and Emrofor Scientific Information Database, and Magiran constituted the databases which we searched for the relevant literature. Overall 98 articles met the inclusion criteria, allowing us to initiate the discussion. Results: Reportedly, prevalence of violence and aggression among the Iranian adolescents and youth ranged from 30% to 65.5% while males being 2½ times more affected than females. The role of gender, family environment, family size, socioeconomic status, and victimization in perpetuating the circumstances was apparent. Conclusions: Relatively high prevalence of violence and aggression among Iranian youth and adolescents is a warning sign and a great challenge to the social system. Reviewed studies suffer from certain methodological and conceptual limitations. Undertaking community-based studies to estimate the actual extent of the problem is warranted. PMID:26157572

Mapping the literature of maternal-child/gynecologic nursing

PubMed Central

Jacobs, Susan Kaplan

2006-01-01

Objectives: As part of a project to map the literature of nursing, sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association, this study identifies core journals cited in maternal-child/gynecologic nursing and the indexing services that access the cited journals. Methods: Three source journals were selected and subjected to a citation analysis of articles from 1996 to 1998. Results: Journals were the most frequently cited format (74.1%), followed by books (19.7%), miscellaneous (4.2%), and government documents (1.9%). Bradford's Law of Scattering was applied to the results, ranking cited journal references in descending order. One-third of the citations were found in a core of 14 journal titles; one-third were dispersed among a middle zone of 100 titles; and the remaining third were scattered in a larger zone of 1,194 titles. Indexing coverage for the core titles was most comprehensive in PubMed/MEDLINE, followed by Science Citation Index and CINAHL. Conclusion: The core of journals cited in this nursing specialty revealed a large number of medical titles, thus, the biomedical databases provide the best access. The interdisciplinary nature of maternal-child/ gynecologic nursing topics dictates that social sciences databases are an important adjunct. The study results will assist librarians in collection development, provide end users with guidelines for selecting databases, and influence database producers to consider extending coverage to identified titles. PMID:16710464

BrainMap VBM: An environment for structural meta-analysis.

PubMed

Vanasse, Thomas J; Fox, P Mickle; Barron, Daniel S; Robertson, Michaela; Eickhoff, Simon B; Lancaster, Jack L; Fox, Peter T

2018-05-02

The BrainMap database is a community resource that curates peer-reviewed, coordinate-based human neuroimaging literature. By pairing the results of neuroimaging studies with their relevant meta-data, BrainMap facilitates coordinate-based meta-analysis (CBMA) of the neuroimaging literature en masse or at the level of experimental paradigm, clinical disease, or anatomic location. Initially dedicated to the functional, task-activation literature, BrainMap is now expanding to include voxel-based morphometry (VBM) studies in a separate sector, titled: BrainMap VBM. VBM is a whole-brain, voxel-wise method that measures significant structural differences between or within groups which are reported as standardized, peak x-y-z coordinates. Here we describe BrainMap VBM, including the meta-data structure, current data volume, and automated reverse inference functions (region-to-disease profile) of this new community resource. CBMA offers a robust methodology for retaining true-positive and excluding false-positive findings across studies in the VBM literature. As with BrainMap's functional database, BrainMap VBM may be synthesized en masse or at the level of clinical disease or anatomic location. As a use-case scenario for BrainMap VBM, we illustrate a trans-diagnostic data-mining procedure wherein we explore the underlying network structure of 2,002 experiments representing over 53,000 subjects through independent components analysis (ICA). To reduce data-redundancy effects inherent to any database, we demonstrate two data-filtering approaches that proved helpful to ICA. Finally, we apply hierarchical clustering analysis (HCA) to measure network- and disease-specificity. This procedure distinguished psychiatric from neurological diseases. We invite the neuroscientific community to further exploit BrainMap VBM with other modeling approaches. © 2018 Wiley Periodicals, Inc.

Effective use of latent semantic indexing and computational linguistics in biological and biomedical applications.

PubMed

Chen, Hongyu; Martin, Bronwen; Daimon, Caitlin M; Maudsley, Stuart

2013-01-01

Text mining is rapidly becoming an essential technique for the annotation and analysis of large biological data sets. Biomedical literature currently increases at a rate of several thousand papers per week, making automated information retrieval methods the only feasible method of managing this expanding corpus. With the increasing prevalence of open-access journals and constant growth of publicly-available repositories of biomedical literature, literature mining has become much more effective with respect to the extraction of biomedically-relevant data. In recent years, text mining of popular databases such as MEDLINE has evolved from basic term-searches to more sophisticated natural language processing techniques, indexing and retrieval methods, structural analysis and integration of literature with associated metadata. In this review, we will focus on Latent Semantic Indexing (LSI), a computational linguistics technique increasingly used for a variety of biological purposes. It is noted for its ability to consistently outperform benchmark Boolean text searches and co-occurrence models at information retrieval and its power to extract indirect relationships within a data set. LSI has been used successfully to formulate new hypotheses, generate novel connections from existing data, and validate empirical data.

Quantifying Data Quality for Clinical Trials Using Electronic Data Capture

PubMed Central

Nahm, Meredith L.; Pieper, Carl F.; Cunningham, Maureen M.

2008-01-01

Background Historically, only partial assessments of data quality have been performed in clinical trials, for which the most common method of measuring database error rates has been to compare the case report form (CRF) to database entries and count discrepancies. Importantly, errors arising from medical record abstraction and transcription are rarely evaluated as part of such quality assessments. Electronic Data Capture (EDC) technology has had a further impact, as paper CRFs typically leveraged for quality measurement are not used in EDC processes. Methods and Principal Findings The National Institute on Drug Abuse Treatment Clinical Trials Network has developed, implemented, and evaluated methodology for holistically assessing data quality on EDC trials. We characterize the average source-to-database error rate (14.3 errors per 10,000 fields) for the first year of use of the new evaluation method. This error rate was significantly lower than the average of published error rates for source-to-database audits, and was similar to CRF-to-database error rates reported in the published literature. We attribute this largely to an absence of medical record abstraction on the trials we examined, and to an outpatient setting characterized by less acute patient conditions. Conclusions Historically, medical record abstraction is the most significant source of error by an order of magnitude, and should be measured and managed during the course of clinical trials. Source-to-database error rates are highly dependent on the amount of structured data collection in the clinical setting and on the complexity of the medical record, dependencies that should be considered when developing data quality benchmarks. PMID:18725958

Difficulties and challenges associated with literature searches in operating room management, complete with recommendations.

PubMed

Wachtel, Ruth E; Dexter, Franklin

2013-12-01

The purpose of this article is to teach operating room managers, financial analysts, and those with a limited knowledge of search engines, including PubMed, how to locate articles they need in the areas of operating room and anesthesia group management. Many physicians are unaware of current literature in their field and evidence-based practices. The most common source of information is colleagues. Many people making management decisions do not read published scientific articles. Databases such as PubMed are available to search for such articles. Other databases, such as citation indices and Google Scholar, can be used to uncover additional articles. Nevertheless, most people who do not know how to use these databases are reluctant to utilize help resources when they do not know how to accomplish a task. Most people are especially reluctant to use on-line help files. Help files and search databases are often difficult to use because they have been designed for users already familiar with the field. The help files and databases have specialized vocabularies unique to the application. MeSH terms in PubMed are not useful alternatives for operating room management, an important limitation, because MeSH is the default when search terms are entered in PubMed. Librarians or those trained in informatics can be valuable assets for searching unusual databases, but they must possess the domain knowledge relative to the subject they are searching. The search methods we review are especially important when the subject area (e.g., anesthesia group management) is so specific that only 1 or 2 articles address the topic of interest. The materials are presented broadly enough that the reader can extrapolate the findings to other areas of clinical and management issues in anesthesiology.

Initial Teacher Training to Promote Health and Well-Being in Schools--A Systematic Review of Effectiveness, Barriers and Facilitators

ERIC Educational Resources Information Center

Shepherd, Jonathan; Pickett, Karen; Dewhirst, Sue; Byrne, Jenny; Speller, Viv; Grace, Marcus; Almond, Palo; Roderick, Paul

2016-01-01

Objectives: To conduct a systematic review of effectiveness, and barriers and facilitators, of initial teacher training to promote health and well-being in schools. Design: Systematic review of the literature. Method: A total of 20 bibliographic databases were searched, including MEDLINE, EMBASE and the Social Science Citation Index. Studies were…

Evidence-Based Systematic Review: Effects of Intensity of Treatment and Constraint-Induced Language Therapy for Individuals with Stroke-Induced Aphasia

ERIC Educational Resources Information Center

Cherney, Leora R.; Patterson, Janet P.; Raymer, Anastasia; Frymark, Tobi; Schooling, Tracy

2008-01-01

Purpose: This systematic review summarizes evidence for intensity of treatment and constraint-induced language therapy (CILT) on measures of language impairment and communication activity/participation in individuals with stroke-induced aphasia. Method: A systematic search of the aphasia literature using 15 electronic databases (e.g., PubMed,…

Wind-Wildlife Impacts Literature Database (WILD)(Fact Sheet)

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

Not Available

The Wind-Wildlife Impacts Literature Database (WILD), developed and maintained by the National Wind Technology Center (NWTC) at the National Renewable Energy Laboratory (NREL), is comprised of over 1,000 citations pertaining to the effects of land-based wind, offshore wind, marine and hydrokinetic, power lines, and communication and television towers on wildlife.

Sensory overload: A concept analysis.

PubMed

Scheydt, Stefan; Müller Staub, Maria; Frauenfelder, Fritz; Nielsen, Gunnar H; Behrens, Johann; Needham, Ian

2017-04-01

In the context of mental disorders sensory overload is a widely described phenomenon used in conjunction with psychiatric interventions such as removal from stimuli. However, the theoretical foundation of sensory overload as addressed in the literature can be described as insufficient and fragmentary. To date, the concept of sensory overload has not yet been sufficiently specified or analyzed. The aim of the study was to analyze the concept of sensory overload in mental health care. A literature search was undertaken using specific electronic databases, specific journals and websites, hand searches, specific library catalogues, and electronic publishing databases. Walker and Avant's method of concept analysis was used to analyze the sources included in the analysis. All aspects of the method of Walker and Avant were covered in this concept analysis. The conceptual understanding has become more focused, the defining attributes, influencing factors and consequences are described and empirical referents identified. The concept analysis is a first step in the development of a middle-range descriptive theory of sensory overload based on social scientific and stress-theoretical approaches. This specification may serve as a fundament for further research, for the development of a nursing diagnosis or for guidelines. © 2017 Australian College of Mental Health Nurses Inc.

Mapping the literature of perfusion.

PubMed Central

Hall, E F

1999-01-01

Perfusionists select and operate the equipment necessary for monitoring, supporting, or temporarily replacing the patient's circulatory or respiratory function. There are over 3,000 perfusionists working in U.S. hospitals, medical and perfusionist groups, and as independent contractors. The purpose of this study was to identify the core literature of perfusion and to determine which major databases provide the most thorough access to this literature. This paper is part of the Medical Library Association Nursing and Allied Health Resource Section's project to map the literature of the allied health professions. It uses a bibliometric methodology to identify core journals. A group of forty-three journals was determined to make up the core journal literature of perfusion. MEDLINE provided the best overall indexing coverage for these journals, but librarians and perfusionists will wish to supplement its use with the Cumulative Index to Nursing and Allied Health Literature in order to access the journals written primarily for perfusionists. The study results can guide purchasing and database searching decisions of collection development and reference librarians, encourage the database producer to increase coverage of titles that are unindexed or underindexed, and advise perfusionists of the best access to their core literature. PMID:10427432

Development of an electronic database for Acute Pain Service outcomes

PubMed Central

Love, Brandy L; Jensen, Louise A; Schopflocher, Donald; Tsui, Ban CH

2012-01-01

BACKGROUND: Quality assurance is increasingly important in the current health care climate. An electronic database can be used for tracking patient information and as a research tool to provide quality assurance for patient care. OBJECTIVE: An electronic database was developed for the Acute Pain Service, University of Alberta Hospital (Edmonton, Alberta) to record patient characteristics, identify at-risk populations, compare treatment efficacies and guide practice decisions. METHOD: Steps in the database development involved identifying the goals for use, relevant variables to include, and a plan for data collection, entry and analysis. Protocols were also created for data cleaning quality control. The database was evaluated with a pilot test using existing data to assess data collection burden, accuracy and functionality of the database. RESULTS: A literature review resulted in an evidence-based list of demographic, clinical and pain management outcome variables to include. Time to assess patients and collect the data was 20 min to 30 min per patient. Limitations were primarily software related, although initial data collection completion was only 65% and accuracy of data entry was 96%. CONCLUSIONS: The electronic database was found to be relevant and functional for the identified goals of data storage and research. PMID:22518364

Impact of comorbidity and healthcare utilization on colorectal cancer stage at diagnosis: literature review

PubMed Central

Corkum, Mark; Urquhart, Robin; Burge, Fred; Porter, Geoffrey; Johnston, Grace

2013-01-01

Purpose Individuals diagnosed with cancer close to death have low access to enrollment in palliative care programs. The purpose of this literature review was to assess the usefulness of pre-diagnostic comorbidity and healthcare utilization as indicators of late-stage colorectal cancer (CRC) diagnosis, to help with early identification of individuals who may benefit from palliative care. Methods A literature search was conducted in relevant databases using title/abstract terms which included “cancer,” “stage,” “diagnosis,” “determinants,” “predictors,” and “associated.” Included studies examined whether comorbidity and/or healthcare utilization had an impact on the stage at which CRC was diagnosed. A standardized data abstraction form was used to assess the eligibility of each study. Thirteen articles were included in the literature review. These studies were assessed and synthesized using qualitative methodology. Results We found much heterogeneity among study variables. The findings of this literature review point to the presence of comorbidity and non-emergent healthcare utilization as having no association with late-stage diagnosis. Conversely, emergency room presentation (ERP) was associated with late-stage diagnosis. Conclusions The results of this literature review did not find strong evidence to suggest that comorbidity and healthcare utilization are potential indicators of late-stage diagnosis. However, ERP may be useful as a flag for consideration of prompt referral to palliative care. Additional research is required to identify potential indicators of late-stage diagnosis that may be available in administrative databases, particularly in the area of healthcare utilization. PMID:22101505

Cervical Spine Involvement in Mild Traumatic Brain Injury: A Review

PubMed Central

Morin, Michael; Langevin, Pierre

2016-01-01

Background. There is a lack of scientific evidence in the literature on the involvement of the cervical spine in mTBI; however, its involvement is clinically accepted. Objective. This paper reviews evidence for the involvement of the cervical spine in mTBI symptoms, the mechanisms of injury, and the efficacy of therapy for cervical spine with concussion-related symptoms. Methods. A keyword search was conducted on PubMed, ICL, SportDiscus, PEDro, CINAHL, and Cochrane Library databases for articles published since 1990. The reference lists of articles meeting the criteria (original data articles, literature reviews, and clinical guidelines) were also searched in the same databases. Results. 4,854 records were screened and 43 articles were retained. Those articles were used to describe different subjects such as mTBI's signs and symptoms, mechanisms of injury, and treatments of the cervical spine. Conclusions. The hypothesis of cervical spine involvement in post-mTBI symptoms and in PCS (postconcussion syndrome) is supported by increasing evidence and is widely accepted clinically. For the management and treatment of mTBIs, few articles were available in the literature, and relevant studies showed interesting results about manual therapy and exercises as efficient tools for health care practitioners. PMID:27529079

Electroacupuncture for women with stress urinary incontinence: Protocol for a systematic review and meta-analysis.

PubMed

Huang, Weixin; Li, Xiaohui; Wang, Yuanping; Yan, Xia; Wu, Siping

2017-12-01

Stress urinary incontinence (SUI) is a widespread complaint in the adult women. Electroacupuncture has been widely applied in the treatment of SUI. But its efficacy has not been evaluated scientifically and systematically. Therefore, we provide a protocol of systematic evaluation to assess the effectiveness and safety of electroacupuncture treatment on women with SUI. The retrieved databases include 3 English literature databases, namely PubMed, Embase, and Cochrane Library, and 3 Chinese literature databases, namely Chinese Biomedical Literature Database (CBM), China National Knowledge Infrastructure (CNKI), and Wanfang Database. The randomized controlled trials (RCTs) of the electroacupuncture treatment on women with SUI will be searched in the above-mentioned databases from the time when the respective databases were established to December 2017. The change from baseline in the amount of urine leakage measured by the 1-hour pad test will be accepted as the primary outcomes. We will use RevMan V.5.3 software as well to compute the data synthesis carefully when a meta-analysis is allowed. This study will provide a high-quality synthesis to assess the effectiveness and safety of electroacupuncture treatment on women with SUI. The conclusion of our systematic review will provide evidence to judge whether electroacupuncture is an effective intervention for women with SUI. PROSPERO CRD42017070947.

Curricular initiatives that enhance student knowledge and perceptions of sexual and gender minority groups: a critical interpretive synthesis.

PubMed

Desrosiers, Jennifer; Wilkinson, Tim; Abel, Gillian; Pitama, Suzanne

2016-10-01

There is no accepted best practice for optimizing tertiary student knowledge, perceptions, and skills to care for sexual and gender diverse groups. The objective of this research was to synthesize the relevant literature regarding effective curricular initiatives designed to enhance tertiary level student knowledge, perceptions, and skills to care for sexual and gender diverse populations. A modified Critical Interpretive Synthesis using a systematic search strategy was conducted in 2015. This method was chosen to synthesize the relevant qualitative and quantitative literature as it allows for the depth and breadth of information to be captured and new constructs to be illuminated. Databases searched include AMED, CINAHL EBM Reviews, ERIC, Ovid MEDLINE, Ovid Nursing Database, PsychInfo, and Google Scholar. Thirty-one articles were included in this review. Curricular initiatives ranging from discrete to multimodal approaches have been implemented. Successful initiatives included discrete sessions with time for processing, and multi-modal strategies. Multi-modal approaches that encouraged awareness of one's lens and privilege in conjunction with facilitated communication seemed the most effective. The literature is limited to the evaluation of explicit curricula. The wider cultural competence literature offers further insight by highlighting the importance of broad and embedded forces including social influences, the institutional climate, and the implicit, or hidden, curriculum. A combined interpretation of the complementary cultural competence and sexual and gender diversity literature provides a novel understanding of the optimal content and context for the delivery of a successful curricular initiative.

DEXTER: Disease-Expression Relation Extraction from Text.

PubMed

Gupta, Samir; Dingerdissen, Hayley; Ross, Karen E; Hu, Yu; Wu, Cathy H; Mazumder, Raja; Vijay-Shanker, K

2018-01-01

Gene expression levels affect biological processes and play a key role in many diseases. Characterizing expression profiles is useful for clinical research, and diagnostics and prognostics of diseases. There are currently several high-quality databases that capture gene expression information, obtained mostly from large-scale studies, such as microarray and next-generation sequencing technologies, in the context of disease. The scientific literature is another rich source of information on gene expression-disease relationships that not only have been captured from large-scale studies but have also been observed in thousands of small-scale studies. Expression information obtained from literature through manual curation can extend expression databases. While many of the existing databases include information from literature, they are limited by the time-consuming nature of manual curation and have difficulty keeping up with the explosion of publications in the biomedical field. In this work, we describe an automated text-mining tool, Disease-Expression Relation Extraction from Text (DEXTER) to extract information from literature on gene and microRNA expression in the context of disease. One of the motivations in developing DEXTER was to extend the BioXpress database, a cancer-focused gene expression database that includes data derived from large-scale experiments and manual curation of publications. The literature-based portion of BioXpress lags behind significantly compared to expression information obtained from large-scale studies and can benefit from our text-mined results. We have conducted two different evaluations to measure the accuracy of our text-mining tool and achieved average F-scores of 88.51 and 81.81% for the two evaluations, respectively. Also, to demonstrate the ability to extract rich expression information in different disease-related scenarios, we used DEXTER to extract information on differential expression information for 2024 genes in lung cancer, 115 glycosyltransferases in 62 cancers and 826 microRNA in 171 cancers. All extractions using DEXTER are integrated in the literature-based portion of BioXpress.Database URL: http://biotm.cis.udel.edu/DEXTER.

GAPscreener: an automatic tool for screening human genetic association literature in PubMed using the support vector machine technique.

PubMed

Yu, Wei; Clyne, Melinda; Dolan, Siobhan M; Yesupriya, Ajay; Wulf, Anja; Liu, Tiebin; Khoury, Muin J; Gwinn, Marta

2008-04-22

Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a substantial proportion of the abstracts in PubMed, identifying them with standard queries is not always accurate or efficient. Further automating the literature-screening process can reduce the burden of a labor-intensive and time-consuming traditional literature search. The Support Vector Machine (SVM), a well-established machine learning technique, has been successful in classifying text, including biomedical literature. The GAPscreener, a free SVM-based software tool, can be used to assist in screening PubMed abstracts for human genetic association studies. The data source for this research was the HuGE Navigator, formerly known as the HuGE Pub Lit database. Weighted SVM feature selection based on a keyword list obtained by the two-way z score method demonstrated the best screening performance, achieving 97.5% recall, 98.3% specificity and 31.9% precision in performance testing. Compared with the traditional screening process based on a complex PubMed query, the SVM tool reduced by about 90% the number of abstracts requiring individual review by the database curator. The tool also ascertained 47 articles that were missed by the traditional literature screening process during the 4-week test period. We examined the literature on genetic associations with preterm birth as an example. Compared with the traditional, manual process, the GAPscreener both reduced effort and improved accuracy. GAPscreener is the first free SVM-based application available for screening the human genetic association literature in PubMed with high recall and specificity. The user-friendly graphical user interface makes this a practical, stand-alone application. The software can be downloaded at no charge.

NASA STI Database, Aerospace Database and ARIN coverage of 'space law'

NASA Technical Reports Server (NTRS)

Buchan, Ronald L.

1992-01-01

The space-law coverage provided by the NASA STI Database, the Aerospace Database, and ARIN is briefly described. Particular attention is given to the space law content of the two Databases and of ARIN, the NASA Thesauras space law terminology, space law publication forms, and the availability of the space law literature.

Wenxin Keli for atrial fibrillation

PubMed Central

He, Zhuogen; Zheng, Minan; Xie, Pingchang; Wang, Yuanping; Yan, Xia; Deng, Dingwei

2018-01-01

Abstract Background: Atrial fibrillation (AF) is a most common cardiac arrhythmia in clinical practice. In China, Wenxin Keli (WXKL) therapy is a common treatment for AF, but its effects and safety remain uncertain. This protocol is to provide the methods used to assess the effectiveness and safety of WXKL for the treatment of patients with AF. Methods: We will search comprehensively the 4 English databases EMBASE, the Cochrane Central Register of Controlled Trials (Cochrane Library), PubMed, and Medline and 3 Chinese databases China National Knowledge Infrastructure (CNKI), Chinese Biomedical Literature Database (CBM), and Chinese Science and Technology Periodical database (VIP) on computer on March 2018 for the randomized controlled trials (RCTs) regarding WXKL for AF. The therapeutic effects according to the sinus rhythm and p-wave dispersion (Pwd) will be accepted as the primary outcomes. We will use RevMan V.5.3 software as well to compute the data synthesis carefully when a meta-analysis is allowed. Results: This study will provide a high-quality synthesis of current evidence of WXKL for AF. Conclusion: The conclusion of our systematic review will provide evidence to judge whether WXKL is an effective intervention for patient with AF. PROSPERO registration number: PROSPERO CRD 42018082045. PMID:29702984

A systematic review of pseudophakic monovision for presbyopia correction

PubMed Central

Labiris, Georgios; Toli, Aspa; Perente, Aslin; Ntonti, Panagiota; Kozobolis, Vassilios P.

2017-01-01

A systematic review of the recent literature regarding pseudophakic monovision as a reliable methods for presbyopia correction was performed based on the PubMed, MEDLINE, Nature and the American Academy of Ophthalmology databases in July 2015 and data from 18 descriptive and 12 comparative studies were included in this narrative review. Pseudophakic monosvision seems to be an effective method for presbyopia with high rates of spectacles independence and minimal dysphotopsia side-effects, that should be considered by the modern cataract surgeons. PMID:28730093

Multiple kernels learning-based biological entity relationship extraction method.

PubMed

Dongliang, Xu; Jingchang, Pan; Bailing, Wang

2017-09-20

Automatic extracting protein entity interaction information from biomedical literature can help to build protein relation network and design new drugs. There are more than 20 million literature abstracts included in MEDLINE, which is the most authoritative textual database in the field of biomedicine, and follow an exponential growth over time. This frantic expansion of the biomedical literature can often be difficult to absorb or manually analyze. Thus efficient and automated search engines are necessary to efficiently explore the biomedical literature using text mining techniques. The P, R, and F value of tag graph method in Aimed corpus are 50.82, 69.76, and 58.61%, respectively. The P, R, and F value of tag graph kernel method in other four evaluation corpuses are 2-5% higher than that of all-paths graph kernel. And The P, R and F value of feature kernel and tag graph kernel fuse methods is 53.43, 71.62 and 61.30%, respectively. The P, R and F value of feature kernel and tag graph kernel fuse methods is 55.47, 70.29 and 60.37%, respectively. It indicated that the performance of the two kinds of kernel fusion methods is better than that of simple kernel. In comparison with the all-paths graph kernel method, the tag graph kernel method is superior in terms of overall performance. Experiments show that the performance of the multi-kernels method is better than that of the three separate single-kernel method and the dual-mutually fused kernel method used hereof in five corpus sets.

Variation in population levels of sedentary time in European adults according to cross-European studies: a systematic literature review within DEDIPAC.

PubMed

Loyen, Anne; Verloigne, Maïté; Van Hecke, Linde; Hendriksen, Ingrid; Lakerveld, Jeroen; Steene-Johannessen, Jostein; Koster, Annemarie; Donnelly, Alan; Ekelund, Ulf; Deforche, Benedicte; De Bourdeaudhuij, Ilse; Brug, Johannes; van der Ploeg, Hidde P

2016-06-28

Sedentary behaviour is increasingly recognized as a public health risk that needs to be monitored at the population level. Across Europe, there is increasing interest in assessing population levels of sedentary time. This systematic literature review aims to provide an overview of all existing cross-European studies that measure sedentary time in adults, to describe the variation in population levels across these studies and to discuss the impact of assessment methods. Six literature databases (PubMed, EMBASE, CINAHL, PsycINFO, SportDiscus and OpenGrey) were searched, supplemented with backward- and forward tracking and searching authors' and experts' literature databases. Articles were included if they reported on observational studies measuring any form of sedentary time in the general population in two or more European countries. Each record was reviewed, extracted and assessed by two independent researchers, and disagreements were resolved by a third researcher. The review protocol of this review is registered in the PROSPERO database under registration number CRD42014010335. Of the 9,756 unique articles that were identified in the search, twelve articles were eligible for inclusion in this review, reporting on six individual studies and three Eurobarometer surveys. These studies represented 2 to 29 countries, and 321 to 65,790 participants. Eleven studies focused on total sedentary time, while one studied screen time. The majority of studies used questionnaires to assess sedentary time, while two studies used accelerometers. Total sedentary time was reported most frequently and varied from 150 (median) to 620 (mean) minutes per day across studies and countries. One third of European countries were not included in any of the studies. Objective measures of European adults are currently limited, and most studies used single-item self-reported questions without assessing sedentary behaviour types or domains. Findings varied substantially between studies, meaning that population levels of sedentary time in European adults are currently unknown. In general, people living in northern Europe countries appear to report more sedentary time than southern Europeans. The findings of this review highlight the need for standardisation of the measurement methods and the added value of cross-European surveillance of sedentary behaviour.

Automated detection of records in biological sequence databases that are inconsistent with the literature.

PubMed

Bouadjenek, Mohamed Reda; Verspoor, Karin; Zobel, Justin

2017-07-01

We investigate and analyse the data quality of nucleotide sequence databases with the objective of automatic detection of data anomalies and suspicious records. Specifically, we demonstrate that the published literature associated with each data record can be used to automatically evaluate its quality, by cross-checking the consistency of the key content of the database record with the referenced publications. Focusing on GenBank, we describe a set of quality indicators based on the relevance paradigm of information retrieval (IR). Then, we use these quality indicators to train an anomaly detection algorithm to classify records as "confident" or "suspicious". Our experiments on the PubMed Central collection show assessing the coherence between the literature and database records, through our algorithms, is an effective mechanism for assisting curators to perform data cleansing. Although fewer than 0.25% of the records in our data set are known to be faulty, we would expect that there are many more in GenBank that have not yet been identified. By automated comparison with literature they can be identified with a precision of up to 10% and a recall of up to 30%, while strongly outperforming several baselines. While these results leave substantial room for improvement, they reflect both the very imbalanced nature of the data, and the limited explicitly labelled data that is available. Overall, the obtained results show promise for the development of a new kind of approach to detecting low-quality and suspicious sequence records based on literature analysis and consistency. From a practical point of view, this will greatly help curators in identifying inconsistent records in large-scale sequence databases by highlighting records that are likely to be inconsistent with the literature. Copyright © 2017 Elsevier Inc. All rights reserved.

The Impact of Online Bibliographic Databases on Teaching and Research in Political Science.

ERIC Educational Resources Information Center

Reichel, Mary

The availability of online bibliographic databases greatly facilitates literature searching in political science. The advantages to searching databases online include combination of concepts, comprehensiveness, multiple database searching, free-text searching, currency, current awareness services, document delivery service, and convenience.…

Online drug databases: a new method to assess and compare inclusion of clinically relevant information.

PubMed

Silva, Cristina; Fresco, Paula; Monteiro, Joaquim; Rama, Ana Cristina Ribeiro

2013-08-01

Evidence-Based Practice requires health care decisions to be based on the best available evidence. The model "Information Mastery" proposes that clinicians should use sources of information that have previously evaluated relevance and validity, provided at the point of care. Drug databases (DB) allow easy and fast access to information and have the benefit of more frequent content updates. Relevant information, in the context of drug therapy, is that which supports safe and effective use of medicines. Accordingly, the European Guideline on the Summary of Product Characteristics (EG-SmPC) was used as a standard to evaluate the inclusion of relevant information contents in DB. To develop and test a method to evaluate relevancy of DB contents, by assessing the inclusion of information items deemed relevant for effective and safe drug use. Hierarchical organisation and selection of the principles defined in the EGSmPC; definition of criteria to assess inclusion of selected information items; creation of a categorisation and quantification system that allows score calculation; calculation of relative differences (RD) of scores for comparison with an "ideal" database, defined as the one that achieves the best quantification possible for each of the information items; pilot test on a sample of 9 drug databases, using 10 drugs frequently associated in literature with morbidity-mortality and also being widely consumed in Portugal. Main outcome measure Calculate individual and global scores for clinically relevant information items of drug monographs in databases, using the categorisation and quantification system created. A--Method development: selection of sections, subsections, relevant information items and corresponding requisites; system to categorise and quantify their inclusion; score and RD calculation procedure. B--Pilot test: calculated scores for the 9 databases; globally, all databases evaluated significantly differed from the "ideal" database; some DB performed better but performance was inconsistent at subsections level, within the same DB. The method developed allows quantification of the inclusion of relevant information items in DB and comparison with an "ideal database". It is necessary to consult diverse DB in order to find all the relevant information needed to support clinical drug use.

Needs assessment for next generation computer-aided mammography reference image databases and evaluation studies.

PubMed

Horsch, Alexander; Hapfelmeier, Alexander; Elter, Matthias

2011-11-01

Breast cancer is globally a major threat for women's health. Screening and adequate follow-up can significantly reduce the mortality from breast cancer. Human second reading of screening mammograms can increase breast cancer detection rates, whereas this has not been proven for current computer-aided detection systems as "second reader". Critical factors include the detection accuracy of the systems and the screening experience and training of the radiologist with the system. When assessing the performance of systems and system components, the choice of evaluation methods is particularly critical. Core assets herein are reference image databases and statistical methods. We have analyzed characteristics and usage of the currently largest publicly available mammography database, the Digital Database for Screening Mammography (DDSM) from the University of South Florida, in literature indexed in Medline, IEEE Xplore, SpringerLink, and SPIE, with respect to type of computer-aided diagnosis (CAD) (detection, CADe, or diagnostics, CADx), selection of database subsets, choice of evaluation method, and quality of descriptions. 59 publications presenting 106 evaluation studies met our selection criteria. In 54 studies (50.9%), the selection of test items (cases, images, regions of interest) extracted from the DDSM was not reproducible. Only 2 CADx studies, not any CADe studies, used the entire DDSM. The number of test items varies from 100 to 6000. Different statistical evaluation methods are chosen. Most common are train/test (34.9% of the studies), leave-one-out (23.6%), and N-fold cross-validation (18.9%). Database-related terminology tends to be imprecise or ambiguous, especially regarding the term "case". Overall, both the use of the DDSM as data source for evaluation of mammography CAD systems, and the application of statistical evaluation methods were found highly diverse. Results reported from different studies are therefore hardly comparable. Drawbacks of the DDSM (e.g. varying quality of lesion annotations) may contribute to the reasons. But larger bias seems to be caused by authors' own decisions upon study design. RECOMMENDATIONS/CONCLUSION: For future evaluation studies, we derive a set of 13 recommendations concerning the construction and usage of a test database, as well as the application of statistical evaluation methods.

Implementation of customized health information technology in diabetes self management programs.

PubMed

Alexander, Susan; Frith, Karen H; O'Keefe, Louise; Hennigan, Michael A

2011-01-01

The project was a nurse-led implementation of a software application, designed to combine clinical and demographic records for a diabetes education program, which would result in secure, long-term record storage. Clinical information systems may be prohibitively expensive for small practices and require extensive training for implementation. A review of the literature suggests that the use of simple, practice-based registries offer an economical method of monitoring the outcomes of diabetic patients. The database was designed using a common software application, Microsoft Access. The theory used to guide implementation and staff training was Rogers' Diffusion of Innovations theory (1995). Outcomes after a 3-month period included incorporation of 100% of new clinical and demographic patient records into the database and positive changes in staff attitudes regarding software applications used in diabetes self-management training. These objectives were met while keeping project costs under budgeted amounts. As a function of the clinical nurse specialist (CNS) researcher role, there is a need for CNSs to identify innovative and economical methods of data collection. The success of this nurse-led project reinforces suggestions in the literature for less costly methods of data maintenance in small practice settings. Ongoing utilization and enhancement have resulted in the creation of a robust database that could aid in the research of multiple clinical issues. Clinical nurse specialists can use existing evidence to guide and improve both their own practice and outcomes for patients and organizations. Further research regarding specific factors that predict efficient transition of informatics applications, how these factors vary according to practice settings, and the role of the CNS in implementation of such applications is needed.

[A brief review of research on chronic disease management based on collaborative care model in China].

PubMed

Li, Huayan; Fuller, Jeffrey; Sun, Mei; Wang, Yong; Xu, Shuang; Feng, Hui

2014-11-01

To evaluate the situation for chronic disease management in China, and to seek the method for improving the collaborative management for chronic diseases in community. We searched literature between January 2008 and November 2013 from the Database, such as China Academic Journal Full-Text Database, and PubMed. The screening was strictly in accordance with the inclusion and exclusion criteria and a summary was made among the selected literature based on a collaboration model. We got 698 articles after rough screen and finally selected 33. All studies were involved in patient's self-management support, but only 9 studies mentioned the communication within the team, and 11 showed a clear team division of labor. Chronic disease community management in China displays some disadvantages. It really needs a general service team with clear roles and responsibilities for team members to improve the service ability of team members and provide patients with various forms of self management services.

Oral oncoprevention by phytochemicals - a systematic review disclosing the therapeutic dilemma.

PubMed

Bhavana, Sujana Mulk; Lakshmi, Chintamaneni Raja

2014-10-01

The aim of this article is to emphasize and focus on the preclinical and clinical update on phytochemicals and their role in prevention of oral carcinogenesis. Accordingly, the literature search was made following database: Embase, Medline, Science Citation index, NIH public access, pubmed and Cochrane Database of systematic reviews. Several internet websites were also searched to access publications from major phytochemical research sites and relevant information was obtained with regards to each plant chemical. The authors also spotted different list servers through wignet.com, Stanford cancer research etc: The data base search was made from the inception to 1988 and updated till 2013. A systematic method was obtained for literature search and data collection was critiqued. 60 articles were searched, among which there were only 6 systematic reviews on phytochemicals regarding oral carcinogenesis. Additional articles were obtained on phytochemicals and their mechanism of action in other cancers, which were regarded as background material. The studies done by various authors on each phytochemical has been briefly emphasized.

The curation of genetic variants: difficulties and possible solutions.

PubMed

Pandey, Kapil Raj; Maden, Narendra; Poudel, Barsha; Pradhananga, Sailendra; Sharma, Amit Kumar

2012-12-01

The curation of genetic variants from biomedical articles is required for various clinical and research purposes. Nowadays, establishment of variant databases that include overall information about variants is becoming quite popular. These databases have immense utility, serving as a user-friendly information storehouse of variants for information seekers. While manual curation is the gold standard method for curation of variants, it can turn out to be time-consuming on a large scale thus necessitating the need for automation. Curation of variants described in biomedical literature may not be straightforward mainly due to various nomenclature and expression issues. Though current trends in paper writing on variants is inclined to the standard nomenclature such that variants can easily be retrieved, we have a massive store of variants in the literature that are present as non-standard names and the online search engines that are predominantly used may not be capable of finding them. For effective curation of variants, knowledge about the overall process of curation, nature and types of difficulties in curation, and ways to tackle the difficulties during the task are crucial. Only by effective curation, can variants be correctly interpreted. This paper presents the process and difficulties of curation of genetic variants with possible solutions and suggestions from our work experience in the field including literature support. The paper also highlights aspects of interpretation of genetic variants and the importance of writing papers on variants following standard and retrievable methods. Copyright © 2012. Published by Elsevier Ltd.

The Curation of Genetic Variants: Difficulties and Possible Solutions

PubMed Central

Pandey, Kapil Raj; Maden, Narendra; Poudel, Barsha; Pradhananga, Sailendra; Sharma, Amit Kumar

2012-01-01

The curation of genetic variants from biomedical articles is required for various clinical and research purposes. Nowadays, establishment of variant databases that include overall information about variants is becoming quite popular. These databases have immense utility, serving as a user-friendly information storehouse of variants for information seekers. While manual curation is the gold standard method for curation of variants, it can turn out to be time-consuming on a large scale thus necessitating the need for automation. Curation of variants described in biomedical literature may not be straightforward mainly due to various nomenclature and expression issues. Though current trends in paper writing on variants is inclined to the standard nomenclature such that variants can easily be retrieved, we have a massive store of variants in the literature that are present as non-standard names and the online search engines that are predominantly used may not be capable of finding them. For effective curation of variants, knowledge about the overall process of curation, nature and types of difficulties in curation, and ways to tackle the difficulties during the task are crucial. Only by effective curation, can variants be correctly interpreted. This paper presents the process and difficulties of curation of genetic variants with possible solutions and suggestions from our work experience in the field including literature support. The paper also highlights aspects of interpretation of genetic variants and the importance of writing papers on variants following standard and retrievable methods. PMID:23317699

Three Library and Information Science Databases Revisited: Currency, Coverage and Overlap, Interindexing Consistency.

ERIC Educational Resources Information Center

Blackwell, Michael Lind

This study evaluates the "Education Resources Information Center" (ERIC), "Library and Information Science Abstracts" (LISA), and "Library Literature" (LL) databases, determining how long the databases take to enter records (indexing delay), how much duplication of effort exists among the three databases (indexing…

How to Define Family Meals in "Shokuiku" (Food and Nutrition Education).

PubMed

Takimoto, Hidemi; Sarukura, Nobuko; Ishikawa-Takata, Kazuko

2015-01-01

The Japanese government has set 11 targets to promote "Shokuiku." However, among the 11 targets, only two targets (frequency of shared family meals and the proportion of breakfast skipping in children and young men) are quantitative goals. The increase in children eating alone is often lamented in the popular media, but the methodology for identifying the status of family meals ("Kyoshoku"), or how the responses should be validated, is rarely discussed. In the current review, we attempt to clarify how a family meal and survey responses are defined, by searching literature published after 2009, using the following keywords: "family meals" or "shared meals," in the PubMed database for English. For literature published in Japanese, we searched the Igakuchuo-Zassi Database and Google Scholar for relevant studies. In the English literature, questions were likely to focus on whether a dinner or any meal was eaten together with family members living together, while Japanese literature was more focused on "breakfast or dinner" eaten together with family members. The response options varied across different studies, such as the number of family meals a week, or the number of days (per week) these family meals were eaten. We found it quite difficult to compare across the studies, as there is no standardized definition or response options for "family meals." Further studies are needed in order to develop a standardized method to assess the current status of "family meals."

Learning spinal manipulation: A best-evidence synthesis of teaching methods.

PubMed

Stainsby, Brynne E; Clarke, Michelle C S; Egonia, Jade R

2016-10-01

The purpose of this study was to evaluate the effectiveness of different reported methods used to teach spinal manipulative therapy to chiropractic students. For this best-evidence literature synthesis, 5 electronic databases were searched from 1900 to 2015. Eligible studies were critically appraised using the criteria of the Scottish Intercollegiate Guidelines Network. Scientifically admissible studies were synthesized following best-evidence synthesis principles. Twenty articles were critically appraised, including 9 randomized clinical trials, 9 cohort studies, and 2 systematic reviews/meta-analyses. Eleven articles were accepted as scientifically admissible. The type of teaching method aids included a Thrust in Motion cervical manikin, instrumented cardiopulmonary reanimation manikin, padded contact with a load cell, instrumented treatment table with force sensor/transducer, and Dynadjust instrument. Several different methods exist in the literature for teaching spinal manipulative therapy techniques; however, future research in this developing area of chiropractic education is proposed. It is suggested that various teaching methods be included in the regular curricula of chiropractic colleges to aid in developing manipulation skills, efficiency, and knowledge of performance.

Subject searching of monographs online in the medical literature.

PubMed

Brahmi, F A

1988-01-01

Searching by subject for monographic information online in the medical literature is a challenging task. The NLM database of choice is CATLINE. Other NLM databases of interest are BIOTHICSLINE, CANCERLIT, HEALTH, POPLINE, and TOXLINE. Ten BRS databases are also discussed. Of these, Books in Print, Bookinfo, and OCLC are explored further. The databases are compared as to number of total records and number and percentage of monographs. Three topics were searched on CROSS to compare hits on BBIP, BOOK, and OCLC. The same searches were run on CATLINE. The parameters of time coverage and language were equalized and the resulting citations were compared and analyzed for duplication and uniqueness. With the input of CATLINE tapes into OCLC, OCLC has become the database of choice for searching by subject for medical monographs.

Applying systematic review search methods to the grey literature: a case study examining guidelines for school-based breakfast programs in Canada.

PubMed

Godin, Katelyn; Stapleton, Jackie; Kirkpatrick, Sharon I; Hanning, Rhona M; Leatherdale, Scott T

2015-10-22

Grey literature is an important source of information for large-scale review syntheses. However, there are many characteristics of grey literature that make it difficult to search systematically. Further, there is no 'gold standard' for rigorous systematic grey literature search methods and few resources on how to conduct this type of search. This paper describes systematic review search methods that were developed and applied to complete a case study systematic review of grey literature that examined guidelines for school-based breakfast programs in Canada. A grey literature search plan was developed to incorporate four different searching strategies: (1) grey literature databases, (2) customized Google search engines, (3) targeted websites, and (4) consultation with contact experts. These complementary strategies were used to minimize the risk of omitting relevant sources. Since abstracts are often unavailable in grey literature documents, items' abstracts, executive summaries, or table of contents (whichever was available) were screened. Screening of publications' full-text followed. Data were extracted on the organization, year published, who they were developed by, intended audience, goal/objectives of document, sources of evidence/resources cited, meals mentioned in the guidelines, and recommendations for program delivery. The search strategies for identifying and screening publications for inclusion in the case study review was found to be manageable, comprehensive, and intuitive when applied in practice. The four search strategies of the grey literature search plan yielded 302 potentially relevant items for screening. Following the screening process, 15 publications that met all eligibility criteria remained and were included in the case study systematic review. The high-level findings of the case study systematic review are briefly described. This article demonstrated a feasible and seemingly robust method for applying systematic search strategies to identify web-based resources in the grey literature. The search strategy we developed and tested is amenable to adaptation to identify other types of grey literature from other disciplines and answering a wide range of research questions. This method should be further adapted and tested in future research syntheses.

Revisiting the National Physical Education Content Standards: What Do We Really Know about Our Achievement of the Physically Educated/Literate Person?

ERIC Educational Resources Information Center

Hastie, Peter A.

2017-01-01

Purpose: The purpose of this paper was to review the research literature in physical education to establish what is currently known about the extent to which the national outcome goals have been achieved. Method: Papers were selected through an initial search of the EBSCO database, with main identifiers included being physical education, physical…

GRATEFUL MED

EPA Science Inventory

Since the early 1970s, the National Library of Medicine (NLM) has made searching the biomedical literature faster and easier by providing online information on NLMs family of databases -- (currently 40 online databases). MEDLINE?, NLMs premier database, has over 8.5 million citat...

Hypersonic and Supersonic Flow Roadmaps Using Bibliometrics and Database Tomography.

ERIC Educational Resources Information Center

Kostoff, R. N.; Eberhart, Henry J.; Toothman, Darrell Ray

1999-01-01

Database Tomography (DT) is a textual database-analysis system consisting of algorithms for extracting multiword phrase frequencies and proximities from a large textual database, to augment interpretative capabilities of the expert human analyst. Describes use of the DT process, supplemented by literature bibliometric analyses, to derive technical…

Protein-protein interaction predictions using text mining methods.

PubMed

Papanikolaou, Nikolas; Pavlopoulos, Georgios A; Theodosiou, Theodosios; Iliopoulos, Ioannis

2015-03-01

It is beyond any doubt that proteins and their interactions play an essential role in most complex biological processes. The understanding of their function individually, but also in the form of protein complexes is of a great importance. Nowadays, despite the plethora of various high-throughput experimental approaches for detecting protein-protein interactions, many computational methods aiming to predict new interactions have appeared and gained interest. In this review, we focus on text-mining based computational methodologies, aiming to extract information for proteins and their interactions from public repositories such as literature and various biological databases. We discuss their strengths, their weaknesses and how they complement existing experimental techniques by simultaneously commenting on the biological databases which hold such information and the benchmark datasets that can be used for evaluating new tools. Copyright © 2014 Elsevier Inc. All rights reserved.

Automated Literature Searches for Longitudinal Tracking of Cancer Research Training Program Graduates.

PubMed

Padilla, Luz A; Desmond, Renee A; Brooks, C Michael; Waterbor, John W

2018-06-01

A key outcome measure of cancer research training programs is the number of cancer-related peer-reviewed publications after training. Because program graduates do not routinely report their publications, staff must periodically conduct electronic literature searches on each graduate. The purpose of this study is to compare findings of an innovative computer-based automated search program versus repeated manual literature searches to identify post-training peer-reviewed publications. In late 2014, manual searches for publications by former R25 students identified 232 cancer-related articles published by 112 of 543 program graduates. In 2016, a research assistant was instructed in performing Scopus literature searches for comparison with individual PubMed searches on our 543 program graduates. Through 2014, Scopus found 304 cancer publications, 220 of that had been retrieved manually plus an additional 84 papers. However, Scopus missed 12 publications found manually. Together, both methods found 316 publications. The automated method found 96.2 % of the 316 publications while individual searches found only 73.4 %. An automated search method such as using the Scopus database is a key tool for conducting comprehensive literature searches, but it must be supplemented with periodic manual searches to find the initial publications of program graduates. A time-saving feature of Scopus is the periodic automatic alerts of new publications. Although a training period is needed and initial costs can be high, an automated search method is worthwhile due to its high sensitivity and efficiency in the long term.

A Bibliometric Assessment of Global Ice Bucket Challenge (Amyotrophic Lateral Sclerosis) Research.

PubMed

Ram, Shri

2016-10-01

This study is a quantitative and qualitative assessment of the global research trends on amyotrophic lateral sclerosis (ALS) (popularly known as Ice Bucket Challenge), through related literatures retrieved from SCOPUS multidisciplinary database for the period 1974-2013. This study is aimed at analyzing the literature on ALS in terms of document type, language, annual growth, productive country, journal, authors, subject, and most cited articles. The bibliographic data for this study was retrieved from the SCOPUS database using keywords 'amyotrophic lateral sclerosis', 'motor neurone disease', 'Charcot disease', 'Lou Gehrig's disease', 'Ice Bucket Challenge' available in title, abstract, and keyword fields of Scopus database from 1974 to 2013. The literature analysis included 21,750 articles during the period from 1974 to 2013 in different areas of ALS. USA was the most productive country in terms of literature produced, while Neurology was the most productive journal. An intensive awareness created by 'Ice Bucket Challenge' has attracted masses, and an intensive growth of literature is pertinent on ALS. The results of this study are expressed in terms of growth of literature, output of individual countries, and authors, and will be helpful in collaborative research in future.

Cheerleading injuries: A narrative review of the literature

PubMed Central

Bagnulo, Angela

2012-01-01

Background: With its increase in participation rate and complex stunts and gymnastic-like maneuvers, cheerleading injuries are on the rise. Objective: A structured narrative review of the literature was performed to discover the status of the literature on a growing yet under recognized sport. Cheerleading injuries are described in terms of distribution, etiology, and prevention. Methods: A literature search was conducted. The articles were then reviewed and included based on broad criteria set out by the author. Results: The search produced 87 articles related to cheerleading injuries or articles with a mention of cheerleading. A total of 26 articles were included in this review based on the inclusion criteria. The most common injury experienced by a cheerleader is an ankle ligament sprain. Summary: The recognition of cheerleading as a sport and a mandatory reporting database are needed along with further research for injury prevention strategies to be implemented. PMID:23204573

Enabling medication management through health information technology (Health IT).

PubMed

McKibbon, K Ann; Lokker, Cynthia; Handler, Steve M; Dolovich, Lisa R; Holbrook, Anne M; O'Reilly, Daria; Tamblyn, Robyn; J Hemens, Brian; Basu, Runki; Troyan, Sue; Roshanov, Pavel S; Archer, Norman P; Raina, Parminder

2011-04-01

The objective of the report was to review the evidence on the impact of health information technology (IT) on all phases of the medication management process (prescribing and ordering, order communication, dispensing, administration and monitoring as well as education and reconciliation), to identify the gaps in the literature and to make recommendations for future research. We searched peer-reviewed electronic databases, grey literature, and performed hand searches. Databases searched included MEDLINE®, Embase, CINAHL (Cumulated Index to Nursing and Allied Health Literature), Cochrane Database of Systematic Reviews, International Pharmaceutical Abstracts, Compendex, Inspec (which includes IEEE Xplore), Library and Information Science Abstracts, E-Prints in Library and Information Science, PsycINFO, Sociological Abstracts, and Business Source Complete. Grey literature searching involved Internet searching, reviewing relevant Web sites, and searching electronic databases of grey literatures. AHRQ also provided all references in their e-Prescribing, bar coding, and CPOE knowledge libraries. Paired reviewers looked at citations to identify studies on a range of health IT used to assist in the medication management process (MMIT) during multiple levels of screening (titles and abstracts, full text and final review for assignment of questions and data abstrction). Randomized controlled trials and cohort, case-control, and case series studies were independently assessed for quality. All data were abstracted by one reviewer and examined by one of two different reviewers with content and methods expertise. 40,582 articles were retrieved. After duplicates were removed, 32,785 articles were screened at the title and abstract phase. 4,578 full text articles were assessed and 789 articles were included in the final report. Of these, 361 met only content criteria and were listed without further abstraction. The final report included data from 428 articles across the seven key questions. Study quality varied according to phase of medication management. Substantially more studies, and studies with stronger comparative methods, evaluated prescribing and monitoring. Clinical decision support systems (CDSS) and computerized provider order entry (CPOE) systems were studied more than any other application of MMIT. Physicians were more often the subject of evaluation than other participants. Other health care professionals, patients, and families are important but not studied as thoroughly as physicians. These nonphysicians groups often value different aspects of MMIT, have diverse needs, and use systems differently. Hospitals and ambulatory clinics were well-represented in the literature with less emphasis placed on long-term care facilities, communities, homes, and nonhospital pharmacies. Most studies evaluated changes in process and outcomes of use, usability, and knowledge, skills, and attitudes. Most showed moderate to substantial improvement with implementation of MMIT. Economics studies and those with clinical outcomes were less frequently studied. Those articles that did address economics and clinical outcomes often showed equivocal findings on the effectiveness and cost-effectiveness of MMIT systems. Qualitative studies provided evidence of strong perceptions, both positive and negative, of the effects of MMIT and unintended consequences. We found little data on the effects of forms of medications, conformity, standards, and open source status. Much descriptive literature discusses implementation issues but little strong evidence exists. Interest is strong in MMIT and more groups and institutions will implement systems in the next decades, especially with the Federal Government's push toward more health IT to support better and more cost-effective health care. MMIT is well-studied, although on closer examination of the literature the evidence is not uniform across phases of medication management, groups of people involved, or types of MMIT. MMIT holds the promise of improved processes; clinical and economics studies and the understanding of sustainability issues are lacking.

The methodological quality of systematic reviews published in high-impact nursing journals: a review of the literature.

PubMed

Pölkki, Tarja; Kanste, Outi; Kääriäinen, Maria; Elo, Satu; Kyngäs, Helvi

2014-02-01

To analyse systematic review articles published in the top 10 nursing journals to determine the quality of the methods employed within them. Systematic review is defined as a scientific research method that synthesises high-quality scientific knowledge on a given topic. The number of such reviews in nursing science has increased dramatically during recent years, but their methodological quality has not previously been assessed. A review of the literature using a narrative approach. Ranked impact factor scores for nursing journals were obtained from the Journal Citation Report database of the Institute of Scientific Information (ISI Web of Knowledge). All issues from the years 2009 and 2010 of the top 10 ranked journals were included. CINAHL and MEDLINE databases were searched to locate studies using the search terms 'systematic review' and 'systematic literature review'. A total of 39 eligible studies were identified. Their methodological quality was evaluated through the specific criteria of quality assessment, description of synthesis and strengths and weaknesses reported in the included studies. Most of the eligible systematic reviews included several different designs or types of quantitative study. The majority included a quality assessment, and a total of 17 different criteria were identified. The method of synthesis was mentioned in about half of the reviews, the most common being narrative synthesis. The weaknesses of reviews were discussed, while strengths were rarely highlighted. The methodological quality of the systematic reviews examined varied considerably, although they were all published in nursing journals with a high-impact factor. Despite the fact that systematic reviews are considered the most robust source of research evidence, they vary in methodological quality. This point is important to consider in clinical practice when applying the results to patient care. © 2013 Blackwell Publishing Ltd.

Participatory methods in pediatric participatory research: a systematic review.

PubMed

Haijes, Hanneke A; van Thiel, Ghislaine J M W

2016-05-01

Meaningful child participation in medical research is seen as important. In order to facilitate further development of participatory research, we performed a systematic literature study to describe and assess the available knowledge on participatory methods in pediatric research. A search was executed in five databases: PubMed, CINAHL, PsycINFO, Scopus, and Cochrane. After careful screening of relevant papers, finally 24 documents were included in our analysis. Literature on participatory methods in pediatric research appears generally to be descriptive, whereby high-quality evidence is lacking. Overall, five groups of participatory methods for children could be distinguished: observational, verbal, written, visual, and active methods. The choice for one of these methods should be based on the child's age, on social and demographic characteristics, and on the research objectives. To date, these methods are still solely used for obtaining data, yet they are suitable for conducting meaningful participation. This may result in a successful partnership between children and researchers. Researchers conducting participatory research with children can use this systematic review in order to weigh the current knowledge about the participatory methods presented.

Trends in the Scholarship on Teachers of Color for Diverse Populations: Implications for Multicultural Education.

ERIC Educational Resources Information Center

Sheets, Rosa Hernandez

This paper reviews patterns in the literature on minority teachers and teacher preparation. The study involved an extensive literature search using the following database selections: Books in Print A-Z; ERIC Database 1966-2000; Education Abstracts FTX 6/83-12/99; PsycINFO 1984-2000/02; Sociological Abstracts 1963-1999/12; and Social Sciences Abst…

[The relevance between obstructive sleep apnea hypopnea syndrome andchronic obstructive pulmonary disease in China: A Meta-analysis].

PubMed

Du, G D; Ma, L; Lv, Y H; Huang, L H; Fan, C Y; Xiang, Y; Lei, Q; Hu, R

2016-10-20

Objective: To assess the correlation between obstructive sleep apnea hypopnea syndrome(OSAHS) and chronic obstructive pulmonary disease(COPD). Method: Databases such as Chinese Biomedical Literature Database, PubMed, Chinese Academic Journals full-text database, Wanfang Resource Database and Chongqing VIP have been searched to collect literatures about the relationship between OSAHS and COPD. The literature in conference proceedings and certain unpublished articles were also manually retrieved. RCT conformed to the condition was evaluated according to the standards of literature assessment, and the data has been extracted. The RevMan5.3 software was applied to carry out the same Metaanalysis. Result: Totally 19 articles were included, and Metaanalysis reveal that overlap syndrome(OS) patient's apnea hypopnea index is significantly higher than those of OSAHS patients［WMD=7.56, 95% CI （4.19,10.94）, P <0.01］; The LSaO₂ of OS patients is significantly lower than OSAHS patients［WMD=-10.50, 95% CI (-11.58, -6.08), P <0.01］; OS patients' FEV₁/FVC is significantly lower than COPD patients［WMD=4.65,95% CI （1.15,8.15）, P <0.01］.The results revealed that subgroup analysis according to the sample volume, age, body mass index(BMI) and FEV₁/FVC between OS patients and OSAHS patients has heterogeneity, but when analysis with the score of ESS the heterogeneity does not exist. Further, the subgroup analysis according to the sample volume, BMI, AHI,LSaO₂ and the time of Oxygen is lower than 90%(T90) those index between OS patients and COPD patients has heterogeneity, and the heterogeneity does not exist when subgroup is analyses with neck circumference. The funnel schema was nearly symmetry with little bias. Conclusion: The experimental results indicate that OSAHS is significantly related with COPD, and they may be the mutual risk factor for each other.. Copyright© by the Editorial Department of Journal of Clinical Otorhinolaryngology Head and Neck Surgery.

The Significance of Scalp Involvement in Pemphigus: A Literature Review

PubMed Central

Sar-Pomian, Marta; Rudnicka, Lidia

2018-01-01

Scalp is a unique location for pemphigus because of the abundance of desmogleins localized in hair follicles. Scalp involvement is observed in up to 60% of patients in the course of pemphigus. The lesions may occasionally lead to alopecia. Unforced removal of anagen hairs in a pull test is a sign of high disease activity. Direct immunofluorescence of plucked hair bulbs is considered a reliable diagnostic method in patients with pemphigus. Follicular acantholysis is a characteristic histopathological feature of pemphigus lesions localized on the scalp. Trichoscopy may serve as a supplementary method in the diagnosis of pemphigus. This review summarizes the most recent data concerning scalp involvement in pemphigus vulgaris and pemphigus foliaceus. A systematic literature search was conducted in three medical databases: PubMed, Embase, and Web of Science. The analysis included literature data about desmoglein distribution in hair follicles, as well as information about clinical manifestations, histopathology, immunopathology, and trichoscopy of scalp lesions in pemphigus and their response to treatment. PMID:29770335

Effects of therapy for dysphagia in Parkinson's disease: systematic review.

PubMed

Baijens, Laura W J; Speyer, Renée

2009-03-01

This systematic review explores the effects of dysphagia treatment for Parkinson's disease. The review includes rehabilitative, surgical, pharmacologic, and other treatments. Only oropharyngeal dysphagia is selected for this literature search, excluding dysphagia due to esophageal or gastric disorders. The effects of deep brain stimulation on dysphagia are not included. In general, the literature concerning dysphagia treatment in Parkinson's disease is rather limited. Most effect studies show diverse methodologic problems. Multiple case studies and trials are identified by searching biomedical literature databases PubMed and Embase, and by hand-searching reference lists. The conclusions of most studies cannot be compared with one another because of heterogeneous therapy methods and outcome measures. Further research based on randomized controlled trials to determine the effectiveness of different therapies for dysphagia in Parkinson's disease is required.

JANE, A new information retrieval system for the Radiation Shielding Information Center

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

Trubey, D.K.

A new information storage and retrieval system has been developed for the Radiation Shielding Information Center (RSIC) at Oak Ridge National Laboratory to replace mainframe systems that have become obsolete. The database contains citations and abstracts of literature which were selected by RSIC analysts and indexed with terms from a controlled vocabulary. The database, begun in 1963, has been maintained continuously since that time. The new system, called JANE, incorporates automatic indexing techniques and on-line retrieval using the RSIC Data General Eclipse MV/4000 minicomputer, Automatic indexing and retrieval techniques based on fuzzy-set theory allow the presentation of results in ordermore » of Retrieval Status Value. The fuzzy-set membership function depends on term frequency in the titles and abstracts and on Term Discrimination Values which indicate the resolving power of the individual terms. These values are determined by the Cover Coefficient method. The use of a commercial database base to store and retrieve the indexing information permits rapid retrieval of the stored documents. Comparisons of the new and presently-used systems for actual searches of the literature indicate that it is practical to replace the mainframe systems with a minicomputer system similar to the present version of JANE. 18 refs., 10 figs.« less

Complementary and Alternative Medicines Use during Pregnancy: A Systematic Review of Pregnant Women and Healthcare Professional Views and Experiences

PubMed Central

Pallivalappila, Abdul Rouf; Stewart, Derek; Shetty, Ashalatha; Pande, Binita; McLay, James S.

2013-01-01

Aims. To undertake a systematic review of the recent (2008–2013) primary literature, describing views and experiences of CAM use during pregnancy by women and healthcare professionals. Method. Medline, Cumulative Index to Nursing and Allied Health Literature, Cochrane Database of Systematic Review Library and Allied, and Complementary Medicine Database were searched. Studies reporting systemic CAM products (homeopathic preparations, herbal medicines, Vitamins and minerals, homeopathy, and special diets) alone or in combination with other nonsystemic CAM modalities (e.g., acupuncture) were included. Results. Database searches retrieved 2,549 citations. Removal of duplicates followed by review of titles and abstracts yielded 32 relevant studies. Twenty-two reported the perspectives of women and their CAM use during pregnancy, while 10 focused on healthcare professionals. The majority of studies had significant flaws in study design and reporting, including a lack of appropriate definitions of CAM and associated modalities, absence of detailed checklists provided to participants, the use of convenience sampling, and a general lack of scientific robustness in terms of data validity and reliability. Conclusion. To permit generalisability of study findings, there is an urgent need to expand the evidence base assessing CAMs use during pregnancy using appropriately designed studies. PMID:24194778

Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II.

PubMed

Lu, Zhiyong; Hirschman, Lynette

2012-01-01

Manual curation of data from the biomedical literature is a rate-limiting factor for many expert curated databases. Despite the continuing advances in biomedical text mining and the pressing needs of biocurators for better tools, few existing text-mining tools have been successfully integrated into production literature curation systems such as those used by the expert curated databases. To close this gap and better understand all aspects of literature curation, we invited submissions of written descriptions of curation workflows from expert curated databases for the BioCreative 2012 Workshop Track II. We received seven qualified contributions, primarily from model organism databases. Based on these descriptions, we identified commonalities and differences across the workflows, the common ontologies and controlled vocabularies used and the current and desired uses of text mining for biocuration. Compared to a survey done in 2009, our 2012 results show that many more databases are now using text mining in parts of their curation workflows. In addition, the workshop participants identified text-mining aids for finding gene names and symbols (gene indexing), prioritization of documents for curation (document triage) and ontology concept assignment as those most desired by the biocurators. DATABASE URL: http://www.biocreative.org/tasks/bc-workshop-2012/workflow/.

Recent progress in automatically extracting information from the pharmacogenomic literature

PubMed Central

Garten, Yael; Coulet, Adrien; Altman, Russ B

2011-01-01

The biomedical literature holds our understanding of pharmacogenomics, but it is dispersed across many journals. In order to integrate our knowledge, connect important facts across publications and generate new hypotheses we must organize and encode the contents of the literature. By creating databases of structured pharmocogenomic knowledge, we can make the value of the literature much greater than the sum of the individual reports. We can, for example, generate candidate gene lists or interpret surprising hits in genome-wide association studies. Text mining automatically adds structure to the unstructured knowledge embedded in millions of publications, and recent years have seen a surge in work on biomedical text mining, some specific to pharmacogenomics literature. These methods enable extraction of specific types of information and can also provide answers to general, systemic queries. In this article, we describe the main tasks of text mining in the context of pharmacogenomics, summarize recent applications and anticipate the next phase of text mining applications. PMID:21047206

Documentation of ethnomedicinal information and antimicrobial validation of Thespesia populnea used by Yanadi tribe of Ganugapenta village, Chittoor district, Andhra Pradesh, India

PubMed Central

Savithramma, Nataru; Yugandhar, Pulicherla; Devi, Pallipati Suvarnalatha; Ankanna, Sade; Suhrulatha, Damai; Prasad, Koya Siva; Ranjani, Ramakrishanan; Nagaraju, Nagoji; Chetty, Kummara Madhava

2017-01-01

Aim: This study aimed to document the traditional knowledge of medicinal plants and antimicrobial validation of Thespesia populnea used by Yanadi tribe of Chittoor district, Andhra Pradesh, India. Materials and Methods: The study was mainly focused on documentation of medicinal plants used by Yanadi tribe to treat different diseases with a standard questionnaire. These plants were cross-checked in Dr. Dukes Database and available literature to know the significance of this tribe on medicinal knowledge. Among the documented plants, T. populnea was selected for antimicrobial activity with disc diffusion assay. Results: Among the documented medicinal plants, herbs were the most utilized plants, followed by leaf part of the plants; paste form of medicinal preparation was the dominant one among the mode of preparations and oral administration was generally followed by this tribe. When checked these plants in Dr. Duke’s Phytochemical and Ethnobotanical Database most of the medicinal plants were matched at least one medicinal use and most of them were correlated with existing literature. In antimicrobial activity, the microbial pathogens Klebsiella pneumonia among bacteria and Rhizopus arrhizus among fungi were most susceptible to methanol extract of T. populnea. Conclusion: From this study, we conclude that the preparation and dosage of the medicines by Yanadi tribe of this area is unique and the correlation of medicinal data with Duke’s Database and existing literature reveals high medicinal significance of claimed data of this tribe and potential inhibitory activity of T. populnea could be studied further to isolate effective antimicrobial agents. PMID:28512597

PrimateLit Database: Submit Literature for Indexing

Science.gov Websites

Access PrimateLit Using this Site About the Project Submit Literature for Indexing Copyright Info Center WI Regional Primate Resource Center Submit Literature for Indexing PrimateLit has not been

The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents

PubMed Central

Ecker, David J; Sampath, Rangarajan; Willett, Paul; Wyatt, Jacqueline R; Samant, Vivek; Massire, Christian; Hall, Thomas A; Hari, Kumar; McNeil, John A; Büchen-Osmond, Cornelia; Budowle, Bruce

2005-01-01

Background Thousands of different microorganisms affect the health, safety, and economic stability of populations. Many different medical and governmental organizations have created lists of the pathogenic microorganisms relevant to their missions; however, the nomenclature for biological agents on these lists and pathogens described in the literature is inexact. This ambiguity can be a significant block to effective communication among the diverse communities that must deal with epidemics or bioterrorist attacks. Results We have developed a database known as the Microbial Rosetta Stone. The database relates microorganism names, taxonomic classifications, diseases, specific detection and treatment protocols, and relevant literature. The database structure facilitates linkage to public genomic databases. This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. Conclusion The Microbial Rosetta Stone is available at . The database provides public access to up-to-date taxonomic classifications of organisms that cause human diseases, improves the consistency of nomenclature in disease reporting, and provides useful links between different public genomic and public health databases. PMID:15850481

The Era of the Large Databases: Outcomes After Gastroesophageal Surgery According to NSQIP, NIS, and NCDB Databases. Systematic Literature Review.

PubMed

Batista Rodríguez, Gabriela; Balla, Andrea; Fernández-Ananín, Sonia; Balagué, Carmen; Targarona, Eduard M

2018-05-01

The term big data refers to databases that include large amounts of information used in various areas of knowledge. Currently, there are large databases that allow the evaluation of postoperative evolution, such as the American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP), the Healthcare Cost and Utilization Project (HCUP) National Inpatient Sample (NIS), and the National Cancer Database (NCDB). The aim of this review was to evaluate the clinical impact of information obtained from these registries regarding gastroesophageal surgery. A systematic review using the Meta-analysis of Observational Studies in Epidemiology guidelines was performed. The research was carried out using the PubMed database identifying 251 articles. All outcomes related to gastroesophageal surgery were analyzed. A total of 34 articles published between January 2007 and July 2017 were included, for a total of 345 697 patients. Studies were analyzed and divided according to the type of surgery and main theme in (1) esophageal surgery and (2) gastric surgery. The information provided by these databases is an effective way to obtain levels of evidence not obtainable by conventional methods. Furthermore, this information is useful for the external validation of previous studies, to establish benchmarks that allow comparisons between centers and have a positive impact on the quality of care.

Drinking Water Treatability Database (Database)

EPA Science Inventory

The drinking Water Treatability Database (TDB) will provide data taken from the literature on the control of contaminants in drinking water, and will be housed on an interactive, publicly-available USEPA web site. It can be used for identifying effective treatment processes, rec...

[Characteristics of acupoint application for the sub-healthy condition treated with ancient and modern acupuncture based on data mining exploration].

PubMed

Cai, Liyan; Wu, Jie; Ma, Tingting; Yang, Lijie

2015-10-01

The acupoint selection was retrieved from the ancient and modern literature on the treatment of sub-healthy condition with acupuncture. The law of acupoint application was analyzed so as to provide a certain reference to the determination of acupoint prescription in clinical acupuncture. The ancient literature was retrieved from Chinese basic ancient literature database. The modern literature was retrieved from Cochrane Library, Medline, PubMed, Ovid evidence-based medicine database, Chinese biomedical literature database, China journal full-text database, VIP journal full-text database and Wanfang database. The database mining software was adopted to explore the law of acupoint application in treatment of sub-healthy conditions with ancient and modern acupuncture. The acupoint use frequency, compatibility association rule, law for meridian use and the use regularity of specific points were analyzed. In the ancient treatment for sub-healthy condition, the top five commonly used acupoints are Shenmen (HT 7), Zhaohai (KI 6), Taibai (SP 3), Daling (PC 7) and Taixi (KI 3). The most commonly combined points are Zhangmen (LR 13), Taibai (SP 3) and Zhaohai (KI 6). The most commonly used meridians are the bladder meridian of foot-taiyang, kidney meridian of foot-shaoyin and liver meridian of foot-jueyin. The most commonly used specific points are the five-shu points. The most commonly used acupoints are located in the lower limbs. In the modern treatment, the top five commonly used acupoints are Zusanli (ST 36), Sanyinjiao (SP 6), Baihui (GV 20), Shenshu (BL 23) and Guanyuan (CV 4). The most commonly supplemented points are Hegu (LI 4) and Taichong (LR 3). The most commonly used meridians are the bladder meridian of foot-taiyang, the conception vessel and the governor vessel. The most commonly used specific points are the back-shu points. The most commonly used acupoints are located in the lower limbs. After the systematic comprehension of the relevant ancient and modern literature, the most commonly used acupoints are selected along the bladder meridian of foot-taiyang, and the most commonly used specific points are the back-shu points, the five-shu points and the front-mu-points. the acupoints are mostly located in the lower limbs.

Unbiased Protein Association Study on the Public Human Proteome Reveals Biological Connections between Co-Occurring Protein Pairs

PubMed Central

2017-01-01

Mass-spectrometry-based, high-throughput proteomics experiments produce large amounts of data. While typically acquired to answer specific biological questions, these data can also be reused in orthogonal ways to reveal new biological knowledge. We here present a novel method for such orthogonal data reuse of public proteomics data. Our method elucidates biological relationships between proteins based on the co-occurrence of these proteins across human experiments in the PRIDE database. The majority of the significantly co-occurring protein pairs that were detected by our method have been successfully mapped to existing biological knowledge. The validity of our novel method is substantiated by the extremely few pairs that can be mapped to existing knowledge based on random associations between the same set of proteins. Moreover, using literature searches and the STRING database, we were able to derive meaningful biological associations for unannotated protein pairs that were detected using our method, further illustrating that as-yet unknown associations present highly interesting targets for follow-up analysis. PMID:28480704

An overview of biomedical literature search on the World Wide Web in the third millennium.

PubMed

Kumar, Prince; Goel, Roshni; Jain, Chandni; Kumar, Ashish; Parashar, Abhishek; Gond, Ajay Ratan

2012-06-01

Complete access to the existing pool of biomedical literature and the ability to "hit" upon the exact information of the relevant specialty are becoming essential elements of academic and clinical expertise. With the rapid expansion of the literature database, it is almost impossible to keep up to date with every innovation. Using the Internet, however, most people can freely access this literature at any time, from almost anywhere. This paper highlights the use of the Internet in obtaining valuable biomedical research information, which is mostly available from journals, databases, textbooks and e-journals in the form of web pages, text materials, images, and so on. The authors present an overview of web-based resources for biomedical researchers, providing information about Internet search engines (e.g., Google), web-based bibliographic databases (e.g., PubMed, IndMed) and how to use them, and other online biomedical resources that can assist clinicians in reaching well-informed clinical decisions.

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

PubMed Central

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

2008-01-01

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

What methods do reviews of normative ethics literature use for search, selection, analysis, and synthesis? In-depth results from a systematic review of reviews.

PubMed

Mertz, Marcel; Strech, Daniel; Kahrass, Hannes

2017-12-19

(Semi-)systematic approaches to finding, analysing, and synthesising ethics literature on medical topics are still in their infancy. However, our recent systematic review showed that the rate of publication of such (semi-)systematic reviews has increased in the last two decades. This is not only true for reviews of empirical ethics literature, but also for reviews of normative ethics literature. In the latter case, there is currently little in the way of standards and guidance available. Therefore, the methods and reporting strategies of such reviews vary greatly. The purpose of the follow-up study we present was to obtain deeper methodological insight into the ways reviews of normative literature are actually conducted and to analyse the methods used. Our search in the PubMed, PhilPapers, and Google Scholar databases led to the identification of 183 reviews of ethics literature published between 1997 and 2015, of which 84 were identified as reviews of normative and mixed literature. Qualitative content analysis was used to extract and synthesise descriptions of search, selection, quality appraisal, analysis, and synthesis methods. We further assessed quantitatively how often certain methods (e.g. search strategies, data analysis procedures) were used by the reviews. The overall reporting quality varies among the analysed reviews and was generally poor even for major criteria regarding the search and selection of literature. For example, only 24 (29%) used a PRISMA flowchart. Also, only 55 (66%) reviews mentioned the information unit they sought to extract, and 12 (14%) stated an ethical approach as the theoretical basis for the analysis. Interpretable information on the synthesis method was given by 47 (60%); the most common methods applied were qualitative methods commonly used in social science research (83%). Reviews which fail to provide sufficient relevant information to readers have reduced methodological transparency regardless of actual methodological quality. In order to increase the internal validity (i.e. reproducibility) as well as the external validity (i.e. utility for the intended audience) of future reviews of normative literature, we suggest more accurate reporting regarding the goal of the review, the definition of the information unit, the ethical approach used, and technical aspects.

Comparability of methods assigning monetary costs to diets: derivation from household till receipts versus cost database estimation using 4-day food diaries.

PubMed

Timmins, K A; Morris, M A; Hulme, C; Edwards, K L; Clarke, G P; Cade, J E

2013-10-01

Diet cost could influence dietary patterns, with potential health consequences. Assigning a monetary cost to diet is challenging, and there are contrasting methods in the literature. This study compares two methods-a food cost database linked to 4-day diet diaries and an individual cost calculated from household till receipts. The Diet and Nutrition Tool for Evaluation (DANTE) had supermarket prices (cost per 100 g) added to its food composition table. Agreement between diet costs calculated using DANTE from food diaries and expenditure recorded using food purchase till receipts for 325 individuals was assessed using correlation and Bland Altman (BA) plots. The mean difference between the methods' estimates was £0.10. The BA showed 95% limits of agreement of £2.88 and -£3.08. Excluding the highest 5% of diet cost values from each collection method reduced the mean difference to £0.02, with limits of agreement ranging from £2.31 to -£2.35. Agreement between the methods was stronger for males and for adults. Diet cost estimates using a food price database with 4-day food diaries are comparable to recorded expenditure from household till receipts at the population or group level. At the individual level, however, estimates differed by as much as £3.00 per day. The methods agreed less when estimating diet costs of children, females or those with more expensive diets.

Limb length inequality: clinical implications for assessment and intervention.

PubMed

Brady, Rebecca J; Dean, John B; Skinner, T Marc; Gross, Michael T

2003-05-01

The purpose of this paper is to review relevant literature concerning limb length inequalities in adults and to make recommendations for assessment and intervention based on the literature and our own clinical experience. Literature searches were conducted in the MEDLINE, PubMed, and CINAHL databases. Limb length inequality and common classification criteria are defined and etiological factors are presented. Common methods of detecting limb length inequality include direct (tape measure methods), indirect (pelvic leveling), and radiological techniques. Interventions include shoe inserts or external shoe lift therapy for mild cases. Surgery may be appropriate in severe cases. Little agreement exists regarding the prevalence of limb length inequality, the degree of limb length inequality that is considered clinically significant, and the reliability and validity of assessment methods. Based on correlational studies, the relationship between limb length inequality and orthopaedic pathologies is questionable. Stronger support for the link between low back pain (LBP) and limb length inequality is provided by intervention studies. Methods involving palpation of pelvic landmarks with block correction have the most support for clinical assessment of limb length inequality. Standing radiographs are suggested when clinical assessment methods are unsatisfactory. Clinicians should exercise caution when undertaking intervention strategies for limb length inequality of less than 5 mm when limb length inequality has been identified with clinical techniques. Recommendations are provided regarding intervention strategies.

Response rate differences between web and alternative data collection methods for public health research: a systematic review of the literature.

PubMed

Blumenberg, Cauane; Barros, Aluísio J D

2018-07-01

To systematically review the literature and compare response rates (RRs) of web surveys to alternative data collection methods in the context of epidemiologic and public health studies. We reviewed the literature using PubMed, LILACS, SciELO, WebSM, and Google Scholar databases. We selected epidemiologic and public health studies that considered the general population and used two parallel data collection methods, being one web-based. RR differences were analyzed using two-sample test of proportions, and pooled using random effects. We investigated agreement using Bland-and-Altman, and correlation using Pearson's coefficient. We selected 19 studies (nine randomized trials). The RR of the web-based data collection was 12.9 percentage points (p.p.) lower (95% CI = - 19.0, - 6.8) than the alternative methods, and 15.7 p.p. lower (95% CI = - 24.2, - 7.3) considering only randomized trials. Monetary incentives did not reduce the RR differences. A strong positive correlation (r = 0.83) between the RRs was observed. Web-based data collection present lower RRs compared to alternative methods. However, it is not recommended to interpret this as a meta-analytical evidence due to the high heterogeneity of the studies.

Rigorous, robust and systematic: Qualitative research and its contribution to burn care. An integrative review.

PubMed

Kornhaber, Rachel Anne; de Jong, A E E; McLean, L

2015-12-01

Qualitative methods are progressively being implemented by researchers for exploration within healthcare. However, there has been a longstanding and wide-ranging debate concerning the relative merits of qualitative research within the health care literature. This integrative review aimed to exam the contribution of qualitative research in burns care and subsequent rehabilitation. Studies were identified using an electronic search strategy using the databases PubMed, Cumulative Index of Nursing and Allied Health Literature (CINAHL), Excerpta Medica database (EMBASE) and Scopus of peer reviewed primary research in English between 2009 to April 2014 using Whittemore and Knafl's integrative review method as a guide for analysis. From the 298 papers identified, 26 research papers met the inclusion criteria. Across all studies there was an average of 22 participants involved in each study with a range of 6-53 participants conducted across 12 nations that focussed on burns prevention, paediatric burns, appropriate acquisition and delivery of burns care, pain and psychosocial implications of burns trauma. Careful and rigorous application of qualitative methodologies promotes and enriches the development of burns knowledge. In particular, the key elements in qualitative methodological process and its publication are critical in disseminating credible and methodologically sound qualitative research. Copyright © 2015 Elsevier Ltd and ISBI. All rights reserved.

Health state utility values in locally advanced and metastatic breast cancer by treatment line: a systematic review.

PubMed

Paracha, Noman; Thuresson, Per-Olof; Moreno, Santiago G; MacGilchrist, Katherine S

2016-10-01

For patients with late-stage (metastatic) breast cancer, the impact of treatment on health-related quality of life is a key factor in decision-making. A systematic review was conducted to identify health state utility values (HSUVs) for late-stage breast cancer, derived using methods preferred by health technology assessment (HTA) agencies, by treatment line. The aim was to generate a list of HSUVs, that could help to justify the values used to populate cost-utility models. Areas covered: Ten electronic databases, international congress websites and online HSUV databases were searched (January 1995-May 2014) for HSUVs for adults with late-stage breast cancer that had been derived from methods favoured by HTA agencies. Publications were included only if they reported studies that originated HSUVs. Expert commentary: Large numbers of HSUVs are available for late-stage breast cancer in the published literature. Contrary to expectations, the HSUVs reported in the literature vary greatly for some health states. As a result, the choice of HSUV can have considerable implications for the outcomes of economic evaluations. Standardization of HSUV methodology is expected to reduce variability; however, further research is recommended for assessing the sensitivity of generic preference-based measures in late-stage (metastatic) breast cancer.

Tone as a health concept: An analysis.

PubMed

McDowall, Donald; Emmanuel, Elizabeth; Grace, Sandra; Chaseling, Marilyn

2017-11-01

Concept analysis. This paper is a report on the analysis of the concept of tone in chiropractic. The purpose of this paper is to clarify the concept of tone as originally understood by Daniel David Palmer from 1895 to 1914 and to monitor its evolution over time. Data was sourced from Palmer's original work, published between 1895 and 1914. A literature search from 1980 to 2016 was also performed on the online databases CINHAL, PubMed and Scopus with key terms including 'tone', 'chiropractic', 'Palmer', 'vitalism', 'health', 'homeostasis', 'holism' and 'wellness'. Finally hand-searches were conducted through chiropractic books and professional literature from 1906 to 1980 for any references to 'tone'. Rodgers' evolutionary method of analysis was used to categorise the data in relation to the surrogates, attributes, references, antecedents and consequences of tone. A total of 49 references were found: five from publications by Palmer; three from the database searches, and; the remaining 41 from professional books, trade journals and websites. There is no clear interpretation of tone in the contemporary chiropractic literature. Tone is closely aligned with functional neurology and can be understood as an interface between the metaphysical and the biomedical. Using the concept of tone as a foundation for practice could strengthen the identity of the chiropractic profession. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bladder Cancer Recovery Pathways: A Systematic Review

PubMed Central

Maloney, Ian; Parker, Daniel C.; Cookson, Michael S.; Patel, Sanjay

2017-01-01

Background: Enhanced recovery pathways, also known as fast-track protocols, have been adopted since the early 2000s by various surgical specialties with the goal of improving patient outcomes and reducing the cost burden of major surgery on the health care system. Objective: To review the scientific literature on the origin of enhanced recovery pathways, track the contemporary utilization of such practices for patients undergoing radical cystectomy, and analyze the available data regarding their effect on morbidity, mortality, and treatment cost. Methods: A literature search of multiple electronic databases was undertaken. Manuscripts including patients undergoing radical cystectomy were chosen based on predefined criteria with an emphasis on randomized controlled trials and cohort studies. Strength of evidence for each study that met inclusion criteria was assessed based on the risk of bias, consistency, directness, and precision. Results: Database searches resulted in 1,236 potentially relevant articles. A total of 485 articles were selected for full-text dual review and 106 studies in 52 publications met the inclusion criteria. Conclusion: The utilization of enhanced recovery pathways with the goal of improving overall patient morbidity and mortality is well supported in the literature, however standardization of implementation and adherence across institutions is lacking, and their direct efficacy on reducing preventable treatment related expenditures is unconfirmed. PMID:29152551

Use of patient safety culture instruments in operating rooms: A systematic literature review.

PubMed

Zhao, Pujng; Li, Yaqin; Li, Zhi; Jia, Pengli; Zhang, Longhao; Zhang, Mingming

2017-05-01

To identify and qualitatively describe, in a literature review, how the instruments were used to evaluate patient safety culture in the operating rooms of published studies. Systematic searches of the literature were conducted using the major database including MEDLINE, EMbase, The Cochrane Library, and four Chinese databases including Chinese Biomedical Literature Database (CBM), Wanfang Data, Chinese Scientific Journal Database (VIP), and Chinese Journals Full-text Database (CNKI) for studies published up to March 2016. We summarized and analyzed the country scope, the instrument utilized in the study, the year when the instrument was used, and fields of operating rooms. Study populations, study settings, and the time span between baseline and follow-up phase were evaluated according to the study design. We identified 1025 references, of which 99 were obtained for full-text assessment; 47 of these studies were deemed relevant and included in the literature review. Most of the studies were from the USA. The most commonly used patient safety culture instrument was Safety Attitude Questionnaire. All identified instruments were used after 2002 and across many fields. Most included studies on patient safety culture were conducted in teaching hospitals or university hospitals. The study population in the cross-sectional studies was much more than that in the before-after studies. The time span between baseline and follow-up phase of before-after studies were almost over three months. Although patient safety culture is considered important in health care and patient safety, the number of studies in which patient safety culture has been estimated using the instruments in operating rooms, is fairly small. © 2017 Chinese Cochrane Center, West China Hospital of Sichuan University and John Wiley & Sons Australia, Ltd.

Terminated Trials in the ClinicalTrials.gov Results Database: Evaluation of Availability of Primary Outcome Data and Reasons for Termination

PubMed Central

Williams, Rebecca J.; Tse, Tony; DiPiazza, Katelyn; Zarin, Deborah A.

2015-01-01

Background Clinical trials that end prematurely (or “terminate”) raise financial, ethical, and scientific concerns. The extent to which the results of such trials are disseminated and the reasons for termination have not been well characterized. Methods and Findings A cross-sectional, descriptive study of terminated clinical trials posted on the ClinicalTrials.gov results database as of February 2013 was conducted. The main outcomes were to characterize the availability of primary outcome data on ClinicalTrials.gov and in the published literature and to identify the reasons for trial termination. Approximately 12% of trials with results posted on the ClinicalTrials.gov results database (905/7,646) were terminated. Most trials were terminated for reasons other than accumulated data from the trial (68%; 619/905), with an insufficient rate of accrual being the lead reason for termination among these trials (57%; 350/619). Of the remaining trials, 21% (193/905) were terminated based on data from the trial (findings of efficacy or toxicity) and 10% (93/905) did not specify a reason. Overall, data for a primary outcome measure were available on ClinicalTrials.gov and in the published literature for 72% (648/905) and 22% (198/905) of trials, respectively. Primary outcome data were reported on the ClinicalTrials.gov results database and in the published literature more frequently (91% and 46%, respectively) when the decision to terminate was based on data from the trial. Conclusions Trials terminate for a variety of reasons, not all of which reflect failures in the process or an inability to achieve the intended goals. Primary outcome data were reported most often when termination was based on data from the trial. Further research is needed to identify best practices for disseminating the experience and data resulting from terminated trials in order to help ensure maximal societal benefit from the investments of trial participants and others involved with the study. PMID:26011295

Systematic review of the literature on the effectiveness of product reformulation measures to reduce the sugar content of food and drink on the population's sugar consumption and health: a study protocol.

PubMed

Hashem, Kawther M; He, Feng J; MacGregor, Graham A

2016-06-09

Obesity, type 2 diabetes and dental caries are all major public health problems in the UK, with significant costs to the healthcare service. We aim to conduct a systematic review to summarise the evidence on the effectiveness of product reformulation measures to reduce the sugar content of food and drink on the population's sugar consumption and health. Electronic database will be systematically searched using a combination of terms, tailored to optimise sensitivity, specificity, and the syntax and functionality of each database. The databases searched will include the Cochrane Library, EMBASE, MEDLINE (Ovid) and Scopus. The bibliographies of those papers that match inclusion criteria will be searched by hand to identify any further, relevant references, which will be subject to the same screening and selection process. The database search results will be supplemented by hand searches. In addition to the peer-reviewed literature, a number of grey literature searches will be undertaken using the broad search terms 'sugar' and 'food' or 'drink' and 'reduction', these searches will include key government and organisation websites as well as general searches in Google. The selection of the studies, data collection and quality appraisal will be performed independently by 2 reviewers. Data will be initially analysed through a narrative synthesis method. If a subset of data we analyse appears comparable, we will investigate the possibility of performing a meta-analysis. Ethics approval will not be required as this is a protocol for a systematic review. The findings will be disseminated widely through conference presentations and published in a peer-reviewed journal. CRD42016034022. 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/

Empirical cost models for estimating power and energy consumption in database servers

NASA Astrophysics Data System (ADS)

Valdivia Garcia, Harold Dwight

The explosive growth in the size of data centers, coupled with the widespread use of virtualization technology has brought power and energy consumption as major concerns for data center administrators. Provisioning decisions must take into consideration not only target application performance but also the power demands and total energy consumption incurred by the hardware and software to be deployed at the data center. Failure to do so will result in damaged equipment, power outages, and inefficient operation. Since database servers comprise one of the most popular and important server applications deployed in such facilities, it becomes necessary to have accurate cost models that can predict the power and energy demands that each database workloads will impose in the system. In this work we present an empirical methodology to estimate the power and energy cost of database operations. Our methodology uses multiple-linear regression to derive accurate cost models that depend only on readily available statistics such as selectivity factors, tuple size, numbers columns and relational cardinality. Moreover, our method does not need measurement of individual hardware components, but rather total power and energy consumption measured at a server. We have implemented our methodology, and ran experiments with several server configurations. Our experiments indicate that we can predict power and energy more accurately than alternative methods found in the literature.

Learning spinal manipulation: A best-evidence synthesis of teaching methods*

PubMed Central

Stainsby, Brynne E.; Clarke, Michelle C.S.; Egonia, Jade R.

2016-01-01

Objective: The purpose of this study was to evaluate the effectiveness of different reported methods used to teach spinal manipulative therapy to chiropractic students. Methods: For this best-evidence literature synthesis, 5 electronic databases were searched from 1900 to 2015. Eligible studies were critically appraised using the criteria of the Scottish Intercollegiate Guidelines Network. Scientifically admissible studies were synthesized following best-evidence synthesis principles. Results: Twenty articles were critically appraised, including 9 randomized clinical trials, 9 cohort studies, and 2 systematic reviews/meta-analyses. Eleven articles were accepted as scientifically admissible. The type of teaching method aids included a Thrust in Motion cervical manikin, instrumented cardiopulmonary reanimation manikin, padded contact with a load cell, instrumented treatment table with force sensor/transducer, and Dynadjust instrument. Conclusions: Several different methods exist in the literature for teaching spinal manipulative therapy techniques; however, future research in this developing area of chiropractic education is proposed. It is suggested that various teaching methods be included in the regular curricula of chiropractic colleges to aid in developing manipulation skills, efficiency, and knowledge of performance. PMID:26998630

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.

Use of keyword hierarchies to interpret gene expression patterns.

PubMed

Masys, D R; Welsh, J B; Lynn Fink, J; Gribskov, M; Klacansky, I; Corbeil, J

2001-04-01

High-density microarray technology permits the quantitative and simultaneous monitoring of thousands of genes. The interpretation challenge is to extract relevant information from this large amount of data. A growing variety of statistical analysis approaches are available to identify clusters of genes that share common expression characteristics, but provide no information regarding the biological similarities of genes within clusters. The published literature provides a potential source of information to assist in interpretation of clustering results. We describe a data mining method that uses indexing terms ('keywords') from the published literature linked to specific genes to present a view of the conceptual similarity of genes within a cluster or group of interest. The method takes advantage of the hierarchical nature of Medical Subject Headings used to index citations in the MEDLINE database, and the registry numbers applied to enzymes.

Use of MALDI-TOF Mass Spectrometry and a Custom Database to Characterize Bacteria Indigenous to a Unique Cave Environment (Kartchner Caverns, AZ, USA)

PubMed Central

Zhang, Lin; Vranckx, Katleen; Janssens, Koen; Sandrin, Todd R.

2015-01-01

MALDI-TOF mass spectrometry has been shown to be a rapid and reliable tool for identification of bacteria at the genus and species, and in some cases, strain levels. Commercially available and open source software tools have been developed to facilitate identification; however, no universal/standardized data analysis pipeline has been described in the literature. Here, we provide a comprehensive and detailed demonstration of bacterial identification procedures using a MALDI-TOF mass spectrometer. Mass spectra were collected from 15 diverse bacteria isolated from Kartchner Caverns, AZ, USA, and identified by 16S rDNA sequencing. Databases were constructed in BioNumerics 7.1. Follow-up analyses of mass spectra were performed, including cluster analyses, peak matching, and statistical analyses. Identification was performed using blind-coded samples randomly selected from these 15 bacteria. Two identification methods are presented: similarity coefficient-based and biomarker-based methods. Results show that both identification methods can identify the bacteria to the species level. PMID:25590854

Use of MALDI-TOF mass spectrometry and a custom database to characterize bacteria indigenous to a unique cave environment (Kartchner Caverns, AZ, USA).

PubMed

Zhang, Lin; Vranckx, Katleen; Janssens, Koen; Sandrin, Todd R

2015-01-02

MALDI-TOF mass spectrometry has been shown to be a rapid and reliable tool for identification of bacteria at the genus and species, and in some cases, strain levels. Commercially available and open source software tools have been developed to facilitate identification; however, no universal/standardized data analysis pipeline has been described in the literature. Here, we provide a comprehensive and detailed demonstration of bacterial identification procedures using a MALDI-TOF mass spectrometer. Mass spectra were collected from 15 diverse bacteria isolated from Kartchner Caverns, AZ, USA, and identified by 16S rDNA sequencing. Databases were constructed in BioNumerics 7.1. Follow-up analyses of mass spectra were performed, including cluster analyses, peak matching, and statistical analyses. Identification was performed using blind-coded samples randomly selected from these 15 bacteria. Two identification methods are presented: similarity coefficient-based and biomarker-based methods. Results show that both identification methods can identify the bacteria to the species level.

Thermodynamic database for proteins: features and applications.

PubMed

Gromiha, M Michael; Sarai, Akinori

2010-01-01

We have developed a thermodynamic database for proteins and mutants, ProTherm, which is a collection of a large number of thermodynamic data on protein stability along with the sequence and structure information, experimental methods and conditions, and literature information. This is a valuable resource for understanding/predicting the stability of proteins, and it can be accessible at http://www.gibk26.bse.kyutech.ac.jp/jouhou/Protherm/protherm.html . ProTherm has several features including various search, display, and sorting options and visualization tools. We have analyzed the data in ProTherm to examine the relationship among thermodynamics, structure, and function of proteins. We describe the progress on the development of methods for understanding/predicting protein stability, such as (i) relationship between the stability of protein mutants and amino acid properties, (ii) average assignment method, (iii) empirical energy functions, (iv) torsion, distance, and contact potentials, and (v) machine learning techniques. The list of online resources for predicting protein stability has also been provided.

Comparison of CINAHL, EMBASE, and MEDLINE databases for the nurse researcher.

PubMed

Burnham, J; Shearer, B

1993-01-01

The purpose of this research was to determine which of three databases, CINAHL, EMBASE or MEDLINE, should be accessed when researching nursing topics. The three databases were searched for citations on topics selected by three nurse researchers and the results were compared. For the search of nursing care literature on a medical condition, it was helpful to search both CINAHL and MEDLINE. CINAHL provided the majority of relevant articles for the second search, on computers and privacy, but inclusion of MEDLINE and EMBASE enhanced retrieval somewhat. The search on substance abuse in pregnancy, not restricted to nursing literature, retrieved better results when searching both MEDLINE and EMBASE. Due to the nature and distribution of the nursing literature, it is especially important for the searcher to understand and respond to the focus of the researcher.

Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE.

PubMed

Névéol, Aurélie; Wilbur, W John; Lu, Zhiyong

2012-01-01

High-throughput experiments and bioinformatics techniques are creating an exploding volume of data that are becoming overwhelming to keep track of for biologists and researchers who need to access, analyze and process existing data. Much of the available data are being deposited in specialized databases, such as the Gene Expression Omnibus (GEO) for microarrays or the Protein Data Bank (PDB) for protein structures and coordinates. Data sets are also being described by their authors in publications archived in literature databases such as MEDLINE and PubMed Central. Currently, the curation of links between biological databases and the literature mainly relies on manual labour, which makes it a time-consuming and daunting task. Herein, we analysed the current state of link curation between GEO, PDB and MEDLINE. We found that the link curation is heterogeneous depending on the sources and databases involved, and that overlap between sources is low, <50% for PDB and GEO. Furthermore, we showed that text-mining tools can automatically provide valuable evidence to help curators broaden the scope of articles and database entries that they review. As a result, we made recommendations to improve the coverage of curated links, as well as the consistency of information available from different databases while maintaining high-quality curation. Database URLs: http://www.ncbi.nlm.nih.gov/PubMed, http://www.ncbi.nlm.nih.gov/geo/, http://www.rcsb.org/pdb/

Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE

PubMed Central

Névéol, Aurélie; Wilbur, W. John; Lu, Zhiyong

2012-01-01

High-throughput experiments and bioinformatics techniques are creating an exploding volume of data that are becoming overwhelming to keep track of for biologists and researchers who need to access, analyze and process existing data. Much of the available data are being deposited in specialized databases, such as the Gene Expression Omnibus (GEO) for microarrays or the Protein Data Bank (PDB) for protein structures and coordinates. Data sets are also being described by their authors in publications archived in literature databases such as MEDLINE and PubMed Central. Currently, the curation of links between biological databases and the literature mainly relies on manual labour, which makes it a time-consuming and daunting task. Herein, we analysed the current state of link curation between GEO, PDB and MEDLINE. We found that the link curation is heterogeneous depending on the sources and databases involved, and that overlap between sources is low, <50% for PDB and GEO. Furthermore, we showed that text-mining tools can automatically provide valuable evidence to help curators broaden the scope of articles and database entries that they review. As a result, we made recommendations to improve the coverage of curated links, as well as the consistency of information available from different databases while maintaining high-quality curation. Database URLs: http://www.ncbi.nlm.nih.gov/PubMed, http://www.ncbi.nlm.nih.gov/geo/, http://www.rcsb.org/pdb/ PMID:22685160

Assessing research productivity in an oncology research institute: the role of the documentation center.

PubMed Central

Ugolini, D; Bogliolo, A; Parodi, S; Casilli, C; Santi, L

1997-01-01

An evaluation method used to assess the quality of research productivity and to provide priorities for budget allocation purposes is presented. This method, developed by a working group of the National Institute for Research on Cancer (IST), Genoa, Italy, is based on the partitioning of categories of the Science Citation Index and Journal Citation Reports (SCI-JCR) into deciles, which normalizes journal impact factors in order to gauge the quality of the productivity. A second parameter related to the number of staff of each institute department co-authoring a given paper has been introduced in order to guide departmental budget allocations. The information scientists of the IST Documentation Center who participated in the working group played a pivotal role in developing the computerized database of publications, providing and analyzing data, supplying and evaluating literature on the topic, and placing international bibliographic databases at the working group's disposal. PMID:9028569

Acupuncture for patients with Alzheimer's disease: a systematic review protocol

PubMed Central

Zhou, Jing; Peng, Weina; Li, Wang; Liu, Zhishun

2014-01-01

Introduction The aim of this protocol is to provide the methods used to assess the effectiveness and safety of acupuncture for the treatment of patients with Alzheimer's disease. Methods and analysis We will search the following electronic databases: The Cochrane Library, PubMed, Medline, Embase, PsycINFO, Chinese Biomedical Literature Database, Chinese Medical Current Contents and China National Knowledge Infrastructure without restriction of language and publication status. Other sources such as Chinese acupuncture journals and the reference list of selected studies will also be searched. After screening the studies, a meta-analysis of randomised controlled trials will be conducted, if possible. Results expressed as risk ratios for dichotomous data and standardised or weighted mean differences for continuous data, will be used for data synthesis. Dissemination The protocol of this systematic review will be disseminated in a peer-reviewed journal and presented at a relevant conference. Trial registration number PROSPERO CRD42014009619 PMID:25142265

Rural Medical Education: Review of the Literature

ERIC Educational Resources Information Center

Curran, Vernon R.; Bornstein, Stephen; Jong, Michael; Fleet, Lisa

2004-01-01

(Purpose) This report summarizes a synthesis of the literature related to the evidence, initiatives and approaches to rural/northern medical education, particularly its role in strengthening the medical workforce in rural areas. (Methodology) A literature review was conducted involving the literature databases MEDLINE (January 1990-March 2003),…

Manual hyperinflation in airway clearance in pediatric patients: a systematic review

PubMed Central

de Godoy, Vanessa Cristina Waetge Pires; Zanetti, Nathalia Mendonça; Johnston, Cíntia

2013-01-01

Objective To perform an assessment of the available literature on manual hyperinflation as a respiratory physical therapy technique used in pediatric patients, with the main outcome of achieving airway clearance. Methods We reviewed articles included in the Lilacs (Latin American and Caribbean Literature on Health Sciences/Literatura Latino Americana e do Caribe em Ciências da Saúde), Cochrane Library, Medline (via Virtual Health Library and PubMed), SciELO (Scientific Electronic Library), and PEDro (Physiotherapy Evidence Database) databases from 2002 to 2013 using the following search terms: "physiotherapy (techniques)", "respiratory therapy", "intensive care", and "airway clearance". The selected studies were classified according to the level of evidence and grades of recommendation (method of the Oxford Centre for Evidence-Based Medicine) by two examiners, while a third examiner repeated the search and analysis and checked the classification of the articles. Results Three articles were included for analysis, comprising 250 children (aged 0 to 16 years). The main diagnoses were acute respiratory failure, recovery following heart congenital disease and upper abdominal surgery, bone marrow transplantation, asthma, tracheal reconstruction, brain injury, airway injury, and heterogeneous lung diseases. The studies were classified as having a level of evidence 2C and grade of recommendation C. Conclusions Manual hyperinflation appeared useful for airway clearance in the investigated population, although the evidence available in the literature remains insufficient. Therefore, controlled randomized studies are needed to establish the safety and efficacy of manual hyperinflation in pediatric patients. However, manual hyperinflation must be performed by trained physical therapists only. PMID:24213091

Adaptive Fourier decomposition based R-peak detection for noisy ECG Signals.

PubMed

Ze Wang; Chi Man Wong; Feng Wan

2017-07-01

An adaptive Fourier decomposition (AFD) based R-peak detection method is proposed for noisy ECG signals. Although lots of QRS detection methods have been proposed in literature, most detection methods require high signal quality. The proposed method extracts the R waves from the energy domain using the AFD and determines the R-peak locations based on the key decomposition parameters, achieving the denoising and the R-peak detection at the same time. Validated by clinical ECG signals in the MIT-BIH Arrhythmia Database, the proposed method shows better performance than the Pan-Tompkin (PT) algorithm in both situations of a native PT and the PT with a denoising process.

Information prescriptions, 1930-2013: an international history and comprehensive review.

PubMed

McKnight, Michelynn

2014-10-01

Recently, government agencies in several countries have promoted information prescription programs to increase patients' understanding of their conditions. The practice has a long history and many publications, but no comprehensive literature reviews such as this. Using a variety of high-precision and high-recall strategies, the researcher searched two dozen online bibliographic databases, citation databases, and repositories, as well as many print sources, to identify and retrieve documents for review. Of these documents, ninety relevant English-language case reports, research reports, and reviews published from 1930-2013 met the study criteria. Early to mid-twentieth century reports covered long-standing practices and used no rigorous research methods. The literature since the mid-1990s reports on short-term trial projects, especially of government-sponsored programs in the United States and United Kingdom. Although the concept of information prescription has been in the literature and practiced for decades, no long-term research studies were found. Most of the literature is anecdotal concerning small pilot projects. The reports investigate physician, patient, and librarian satisfaction but not changes in patient knowledge or behavior. Many twenty-first century projects emphasize materials and projects from specific government agencies and commercial enterprises. While the practice is commonly believed to be a good idea and there are many publications on the subject, few studies provide any evidence of the efficacy of information prescriptions for increased patient knowledge. Well-designed and executed large or long-term studies might produce needed evidence for professional practice.

Warm-ups for military fitness testing: rapid evidence assessment of the literature.

PubMed

Zeno, Stacey A; Purvis, Dianna; Crawford, Cindy; Lee, Courtney; Lisman, Peter; Deuster, Patricia A

2013-07-01

Warm-up exercises are commonly used before exercise as a method to physiologically prepare for strenuous physical activity. Various warm-up exercises are often implemented but without scientific merit and, at times, may be detrimental to performance. To date, no systematic reviews have examined the effectiveness of warm-up exercises for military physical fitness test (PFT) or combat fitness test (CFT). The purpose of this rapid evidence assessment of the literature was to examine the quantity, quality, and effectiveness of warm-up exercises for PFT and identify those that might increase PFT and/or CFT scores, as reported in the literature. Literature searches of randomized controlled trials were performed across various databases from database inception to May 2011. Methodological quality of included studies was assessed using the Scottish Intercollegiate Guidelines Network (SIGN) 50 criteria for randomized controlled trial designs, and studies were individually described. Subject matter experts summarized the results applicable or generalizable to military testing. The search yielded a total of 1177 citations, with 37 fitting our inclusion criteria. Cardiovascular warm-ups increased sprint/running time, but dynamic stretching and dynamic warm-ups had the most positive outcome for the various exercise tests examined. Systematically, static stretching had no beneficial or detrimental effect on exercise performance but did improve range of movement exercises. Selected warm-up exercise may increase PFT and possibly CFT scores. Further research is needed to investigate the efficacy of dynamic stretching and dynamic warm-ups.

pGenN, a gene normalization tool for plant genes and proteins in scientific literature.

PubMed

Ding, Ruoyao; Arighi, Cecilia N; Lee, Jung-Youn; Wu, Cathy H; Vijay-Shanker, K

2015-01-01

Automatically detecting gene/protein names in the literature and connecting them to databases records, also known as gene normalization, provides a means to structure the information buried in free-text literature. Gene normalization is critical for improving the coverage of annotation in the databases, and is an essential component of many text mining systems and database curation pipelines. In this manuscript, we describe a gene normalization system specifically tailored for plant species, called pGenN (pivot-based Gene Normalization). The system consists of three steps: dictionary-based gene mention detection, species assignment, and intra species normalization. We have developed new heuristics to improve each of these phases. We evaluated the performance of pGenN on an in-house expertly annotated corpus consisting of 104 plant relevant abstracts. Our system achieved an F-value of 88.9% (Precision 90.9% and Recall 87.2%) on this corpus, outperforming state-of-art systems presented in BioCreative III. We have processed over 440,000 plant-related Medline abstracts using pGenN. The gene normalization results are stored in a local database for direct query from the pGenN web interface (proteininformationresource.org/pgenn/). The annotated literature corpus is also publicly available through the PIR text mining portal (proteininformationresource.org/iprolink/).

A narrative review of undergraduate peer-based healthcare ethics teaching

PubMed Central

Allikmets, Silvia; Knights, Felicity

2015-01-01

Objectives This study explores the literature in establishing the value of undergraduate peer-based healthcare ethics teaching as an educational methodology. Methods A narrative review of the literature concerning peer-based ethics teaching was conducted. MEDLINE, EMBASE, CINAHL, SCOPUS databases, and the Cochrane Library, were systematically searched for studies of peer-based ethics or professionalism teaching. Selected studies related peer-based teaching to ethics education outcomes. Results Ten publications were identified. Selected studies were varied in their chosen intervention methodology and analysis. Collectively, the identified studies suggest peer-based ethics education is an effective and valued educational methodology in training healthcare professionals. One paper suggests peer-based ethics teaching has advantages over traditional didactic methods. Peer-based ethics teaching also receives positive feedback from student participants. However, the limited literature base demonstrates a clear need for more evaluation of this pedagogy. Conclusions The current literature base suggests that undergraduate peer based healthcare ethics teaching is valuable in terms of efficacy and student satisfaction. We conclude that the medical community should invest in further study in order to capitalise upon the potential of peer-based ethics teaching in undergraduate healthcare education. PMID:26668050

Use of Action Research in Nursing Education

PubMed Central

Pehler, Shelley-Rae; Stombaugh, Angela

2016-01-01

Purpose. The purpose of this article is to describe action research in nursing education and to propose a definition of action research for providing guidelines for research proposals and criteria for assessing potential publications for nursing higher education. Methods. The first part of this project involved a search of the literature on action research in nursing higher education from 1994 to 2013. Searches were conducted in the CINAHL and MEDLINE databases. Applying the criteria identified, 80 publications were reviewed. The second part of the project involved a literature review of action research methodology from several disciplines to assist in assessing articles in this review. Results. This article summarizes the nursing higher education literature reviewed and provides processes and content related to four topic areas in nursing higher education. The descriptions assist researchers in learning more about the complexity of both the action research process and the varied outcomes. The literature review of action research in many disciplines along with the review of action research in higher education provided a framework for developing a nursing-education-centric definition of action research. Conclusions. Although guidelines for developing action research and criteria for publication are suggested, continued development of methods for synthesizing action research is recommended. PMID:28078138

CHERNOLITTM. Chernobyl Bibliographic Search System

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

Caff, F., Jr.; Kennedy, R.A.; Mahaffey, J.A.

1992-03-02

The Chernobyl Bibliographic Search System (Chernolit TM) provides bibliographic data in a usable format for research studies relating to the Chernobyl nuclear accident that occurred in the former Ukrainian Republic of the USSR in 1986. Chernolit TM is a portable and easy to use product. The bibliographic data is provided under the control of a graphical user interface so that the user may quickly and easily retrieve pertinent information from the large database. The user may search the database for occurrences of words, names, or phrases; view bibliographic references on screen; and obtain reports of selected references. Reports may bemore » viewed on the screen, printed, or accumulated in a folder that is written to a disk file when the user exits the software. Chernolit TM provides a cost-effective alternative to multiple, independent literature searches. Forty-five hundred references concerning the accident, including abstracts, are distributed with Chernolit TM. The data contained in the database were obtained from electronic literature searches and from requested donations from individuals and organizations. These literature searches interrogated the Energy Science and Technology database (formerly DOE ENERGY) of the DIALOG Information Retrieval Service. Energy Science and Technology, provided by the U.S. DOE, Washington, D.C., is a multi-disciplinary database containing references to the world`s scientific and technical literature on energy. All unclassified information processed at the Office of Scientific and Technical Information (OSTI) of the U.S. DOE is included in the database. In addition, information on many documents has been manually added to Chernolit TM. Most of this information was obtained in response to requests for data sent to people and/or organizations throughout the world.« less

Chernobyl Bibliographic Search System

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

Carr, Jr, F.; Kennedy, R. A.; Mahaffey, J. A.

1992-05-11

The Chernobyl Bibliographic Search System (Chernolit TM) provides bibliographic data in a usable format for research studies relating to the Chernobyl nuclear accident that occurred in the former Ukrainian Republic of the USSR in 1986. Chernolit TM is a portable and easy to use product. The bibliographic data is provided under the control of a graphical user interface so that the user may quickly and easily retrieve pertinent information from the large database. The user may search the database for occurrences of words, names, or phrases; view bibliographic references on screen; and obtain reports of selected references. Reports may bemore » viewed on the screen, printed, or accumulated in a folder that is written to a disk file when the user exits the software. Chernolit TM provides a cost-effective alternative to multiple, independent literature searches. Forty-five hundred references concerning the accident, including abstracts, are distributed with Chernolit TM. The data contained in the database were obtained from electronic literature searches and from requested donations from individuals and organizations. These literature searches interrogated the Energy Science and Technology database (formerly DOE ENERGY) of the DIALOG Information Retrieval Service. Energy Science and Technology, provided by the U.S. DOE, Washington, D.C., is a multi-disciplinary database containing references to the world''s scientific and technical literature on energy. All unclassified information processed at the Office of Scientific and Technical Information (OSTI) of the U.S. DOE is included in the database. In addition, information on many documents has been manually added to Chernolit TM. Most of this information was obtained in response to requests for data sent to people and/or organizations throughout the world.« less

Workshop Report on a Future Information Infrastructure for the Physical Sciences. The Facts of the Matter: Finding, Understanding, and Using Information about out Physical World Held at the National Academy of Sciences on May 30-31, 2000

DTIC Science & Technology

2000-05-31

Grey Literature Network Service ( Farace , Dominic,1997) as, “that which is produced on all levels of government, academics, business and industry in... literature is available, on-line, to scientific workers throughout the world, for a world scientific database.” These reports served as the base to begin...all the world’s formal scientific literature is available, on-line, to scientific workers throughout the world, for a world scientific database

Literature classification for semi-automated updating of biological knowledgebases

PubMed Central

2013-01-01

Background As the output of biological assays increase in resolution and volume, the body of specialized biological data, such as functional annotations of gene and protein sequences, enables extraction of higher-level knowledge needed for practical application in bioinformatics. Whereas common types of biological data, such as sequence data, are extensively stored in biological databases, functional annotations, such as immunological epitopes, are found primarily in semi-structured formats or free text embedded in primary scientific literature. Results We defined and applied a machine learning approach for literature classification to support updating of TANTIGEN, a knowledgebase of tumor T-cell antigens. Abstracts from PubMed were downloaded and classified as either "relevant" or "irrelevant" for database update. Training and five-fold cross-validation of a k-NN classifier on 310 abstracts yielded classification accuracy of 0.95, thus showing significant value in support of data extraction from the literature. Conclusion We here propose a conceptual framework for semi-automated extraction of epitope data embedded in scientific literature using principles from text mining and machine learning. The addition of such data will aid in the transition of biological databases to knowledgebases. PMID:24564403

HPIminer: A text mining system for building and visualizing human protein interaction networks and pathways.

PubMed

Subramani, Suresh; Kalpana, Raja; Monickaraj, Pankaj Moses; Natarajan, Jeyakumar

2015-04-01

The knowledge on protein-protein interactions (PPI) and their related pathways are equally important to understand the biological functions of the living cell. Such information on human proteins is highly desirable to understand the mechanism of several diseases such as cancer, diabetes, and Alzheimer's disease. Because much of that information is buried in biomedical literature, an automated text mining system for visualizing human PPI and pathways is highly desirable. In this paper, we present HPIminer, a text mining system for visualizing human protein interactions and pathways from biomedical literature. HPIminer extracts human PPI information and PPI pairs from biomedical literature, and visualize their associated interactions, networks and pathways using two curated databases HPRD and KEGG. To our knowledge, HPIminer is the first system to build interaction networks from literature as well as curated databases. Further, the new interactions mined only from literature and not reported earlier in databases are highlighted as new. A comparative study with other similar tools shows that the resultant network is more informative and provides additional information on interacting proteins and their associated networks. Copyright © 2015 Elsevier Inc. All rights reserved.

Examining the relationship between infectious diseases and flooding in Europe: A systematic literature review and summary of possible public health interventions.

PubMed

Brown, Lisa; Murray, Virginia

2013-01-01

Introduction Many infectious diseases are sensitive to climatic changes; specifically, flooding. This systematic literature review aimed to strengthen the quality and completeness of evidence on infectious diseases following flooding, relevant to Europe. Methods A systematic literature review from 2004-2012 was performed. Focused searches of the following databases were conducted: Medline, Scopus, PubMed, Cochrane Library, and Evidence Aid. Personal communications with key informants were also reviewed. Results Thirty-eight studies met the inclusion criteria. Evidence suggested that water-borne, rodent-borne, and vector-borne diseases have been associated with flooding in Europe, although at a lower incidence than developing countries. Conclusion Disease surveillance and early warning systems, coupled with effective prevention and response capabilities, can reduce current and future vulnerability to infectious diseases following flooding.

Review of Maxillary Expansion Appliance Activation Methods: Engineering and Clinical Perspectives

PubMed Central

Romanyk, D. L.; Lagravere, M. O.; Toogood, R. W.; Major, P. W.; Carey, J. P.

2010-01-01

Objective. Review the reported activation methods of maxillary expansion devices for midpalatal suture separation from an engineering perspective and suggest areas of improvement. Materials and Methods. A literature search of Scopus and PubMed was used to determine current expansion methods. A U.S. and Canadian patent database search was also conducted using patent classification and keywords. Any paper presenting a new method of expansion was included. Results. Expansion methods in use, or patented, can be classified as either a screw- or spring-type, magnetic, or shape memory alloy expansion appliance. Conclusions. Each activation method presented unique advantages and disadvantages from both clinical and engineering perspectives. Areas for improvement still remain and are identified in the paper. PMID:20948570

Applying a "Big Data" Literature System to Recommend Antihypertensive Drugs for Hypertension Patients with Diabetes Mellitus.

PubMed

Shu, Jing-Xian; Li, Ying; He, Ting; Chen, Ling; Li, Xue; Zou, Lin-Lin; Yin, Lu; Li, Xiao-Hui; Wang, An-Li; Liu, Xing; Yuan, Hong

2018-01-07

BACKGROUND The explosive increase in medical literature has changed therapeutic strategies, but it is challenging for physicians to keep up-to-date on the medical literature. Scientific literature data mining on a large-scale of can be used to refresh physician knowledge and better improve the quality of disease treatment. MATERIAL AND METHODS This paper reports on a reformulated version of a data mining method called MedRank, which is a network-based algorithm that ranks therapy for a target disease based on the MEDLINE literature database. MedRank algorithm input for this study was a clear definition of the disease model; the algorithm output was the accurate recommendation of antihypertensive drugs. Hypertension with diabetes mellitus was chosen as the input disease model. The ranking output of antihypertensive drugs are based on the Joint National Committee (JNC) guidelines, one through eight, and the publication dates, ≤1977, ≤1980, ≤1984, ≤1988, ≤1993, ≤1997, ≤2003, and ≤2013. The McNemar's test was used to evaluate the efficacy of MedRank based on specific JNC guidelines. RESULTS The ranking order of antihypertensive drugs changed with the date of the published literature, and the MedRank algorithm drug recommendations had excellent consistency with the JNC guidelines in 2013 (P=1.00 from McNemar's test, Kappa=0.78, P=1.00). Moreover, the Kappa index increased over time. Sensitivity was better than specificity for MedRank; in addition, sensitivity was maintained at a high level, and specificity increased from 1997 to 2013. CONCLUSIONS The use of MedRank in ranking medical literature on hypertension with diabetes mellitus in our study suggests possible application in clinical practice; it is a potential method for supporting antihypertensive drug-prescription decisions.

Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets

PubMed Central

Aubry, Marc; Monnier, Annabelle; Chicault, Celine; de Tayrac, Marie; Galibert, Marie-Dominique; Burgun, Anita; Mosser, Jean

2006-01-01

Background Large-scale genomic studies based on transcriptome technologies provide clusters of genes that need to be functionally annotated. The Gene Ontology (GO) implements a controlled vocabulary organised into three hierarchies: cellular components, molecular functions and biological processes. This terminology allows a coherent and consistent description of the knowledge about gene functions. The GO terms related to genes come primarily from semi-automatic annotations made by trained biologists (annotation based on evidence) or text-mining of the published scientific literature (literature profiling). Results We report an original functional annotation method based on a combination of evidence and literature that overcomes the weaknesses and the limitations of each approach. It relies on the Gene Ontology Annotation database (GOA Human) and the PubGene biomedical literature index. We support these annotations with statistically associated GO terms and retrieve associative relations across the three GO hierarchies to emphasise the major pathways involved by a gene cluster. Both annotation methods and associative relations were quantitatively evaluated with a reference set of 7397 genes and a multi-cluster study of 14 clusters. We also validated the biological appropriateness of our hybrid method with the annotation of a single gene (cdc2) and that of a down-regulated cluster of 37 genes identified by a transcriptome study of an in vitro enterocyte differentiation model (CaCo-2 cells). Conclusion The combination of both approaches is more informative than either separate approach: literature mining can enrich an annotation based only on evidence. Text-mining of the literature can also find valuable associated MEDLINE references that confirm the relevance of the annotation. Eventually, GO terms networks can be built with associative relations in order to highlight cooperative and competitive pathways and their connected molecular functions. PMID:16674810

CASMI 2013: Identification of Small Molecules by Tandem Mass Spectrometry Combined with Database and Literature Mining

PubMed Central

Newsome, Andrew G.; Nikolic, Dejan

2014-01-01

The Critical Assessment of Small Molecule Identification (CASMI) contest was initiated in 2012 to evaluate manual and automated strategies for the identification of small molecules from raw mass spectrometric data. The authors participated in both category 1 (molecular formula determination) and category 2 (molecular structure determination) of the second annual CASMI contest (CASMI 2013) using slow but effective manual methods. The provided high resolution mass spectrometric data were interpreted manually using a combination of molecular formula calculators, fragment and neutral loss analysis, literature consultation, manual database searches, deductive logic, and experience. The authors submitted correct formulas as lead candidates for 16 of 16 challenges and submitted correct structure solutions as lead candidates for 14 of 16 challenges. One structure submission (Challenge 3) was very close but not exact (N2-acetylglutaminylisoleucinamide instead of the correct N2-acetylglutaminylleucinamide). A solution for one (Challenge 13) was not submitted due to an inability to reconcile the provided fragmentation pattern with any known structures with the provided molecular composition. PMID:26819877

The Role of Free/Libre and Open Source Software in Learning Health Systems.

PubMed

Paton, C; Karopka, T

2017-08-01

Objective: To give an overview of the role of Free/Libre and Open Source Software (FLOSS) in the context of secondary use of patient data to enable Learning Health Systems (LHSs). Methods: We conducted an environmental scan of the academic and grey literature utilising the MedFLOSS database of open source systems in healthcare to inform a discussion of the role of open source in developing LHSs that reuse patient data for research and quality improvement. Results: A wide range of FLOSS is identified that contributes to the information technology (IT) infrastructure of LHSs including operating systems, databases, frameworks, interoperability software, and mobile and web apps. The recent literature around the development and use of key clinical data management tools is also reviewed. Conclusions: FLOSS already plays a critical role in modern health IT infrastructure for the collection, storage, and analysis of patient data. The nature of FLOSS systems to be collaborative, modular, and modifiable may make open source approaches appropriate for building the digital infrastructure for a LHS. Georg Thieme Verlag KG Stuttgart.

Inorganic Crystal Structure Database (ICSD)

National Institute of Standards and Technology Data Gateway

SRD 84 FIZ/NIST Inorganic Crystal Structure Database (ICSD) (PC database for purchase)   The Inorganic Crystal Structure Database (ICSD) is produced cooperatively by the Fachinformationszentrum Karlsruhe(FIZ) and the National Institute of Standards and Technology (NIST). The ICSD is a comprehensive collection of crystal structure data of inorganic compounds containing more than 140,000 entries and covering the literature from 1915 to the present.

Canto: an online tool for community literature curation.

PubMed

Rutherford, Kim M; Harris, Midori A; Lock, Antonia; Oliver, Stephen G; Wood, Valerie

2014-06-15

Detailed curation of published molecular data is essential for any model organism database. Community curation enables researchers to contribute data from their papers directly to databases, supplementing the activity of professional curators and improving coverage of a growing body of literature. We have developed Canto, a web-based tool that provides an intuitive curation interface for both curators and researchers, to support community curation in the fission yeast database, PomBase. Canto supports curation using OBO ontologies, and can be easily configured for use with any species. Canto code and documentation are available under an Open Source license from http://curation.pombase.org/. Canto is a component of the Generic Model Organism Database (GMOD) project (http://www.gmod.org/). © The Author 2014. Published by Oxford University Press.

Selecting CD-ROM databases for nursing students: a comparison of MEDLINE and the Cumulative Index to Nursing and Allied Health Literature (CINAHL).

PubMed

Okuma, E

1994-01-01

With the introduction of the Cumulative Index to Nursing and Allied Health Literature (CINAHL) on CD-ROM, research was initiated to compare coverage of nursing journals by CINAHL and MEDLINE in this format, expanding on previous comparison of these databases in print and online. The study assessed search results for eight topics in 1989 and 1990 citations in both databases, each produced by SilverPlatter. Results were tallied and analyzed for number of records retrieved, unique and overlapping records, relevance, and appropriateness. An overall precision score was developed. The goal of the research was to develop quantifiable tools to help determine which database to purchase for an academic library serving an undergraduate nursing program.

Selecting CD-ROM databases for nursing students: a comparison of MEDLINE and the Cumulative Index to Nursing and Allied Health Literature (CINAHL).

PubMed Central

Okuma, E

1994-01-01

With the introduction of the Cumulative Index to Nursing and Allied Health Literature (CINAHL) on CD-ROM, research was initiated to compare coverage of nursing journals by CINAHL and MEDLINE in this format, expanding on previous comparison of these databases in print and online. The study assessed search results for eight topics in 1989 and 1990 citations in both databases, each produced by SilverPlatter. Results were tallied and analyzed for number of records retrieved, unique and overlapping records, relevance, and appropriateness. An overall precision score was developed. The goal of the research was to develop quantifiable tools to help determine which database to purchase for an academic library serving an undergraduate nursing program. PMID:8136757

Examining database persistence of ISO/EN 13606 standardized electronic health record extracts: relational vs. NoSQL approaches.

PubMed

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Lozano-Rubí, Raimundo; Serrano-Balazote, Pablo; Castro, Antonio L; Moreno, Oscar; Pascual, Mario

2017-08-18

The objective of this research is to compare the relational and non-relational (NoSQL) database systems approaches in order to store, recover, query and persist standardized medical information in the form of ISO/EN 13606 normalized Electronic Health Record XML extracts, both in isolation and concurrently. NoSQL database systems have recently attracted much attention, but few studies in the literature address their direct comparison with relational databases when applied to build the persistence layer of a standardized medical information system. One relational and two NoSQL databases (one document-based and one native XML database) of three different sizes have been created in order to evaluate and compare the response times (algorithmic complexity) of six different complexity growing queries, which have been performed on them. Similar appropriate results available in the literature have also been considered. Relational and non-relational NoSQL database systems show almost linear algorithmic complexity query execution. However, they show very different linear slopes, the former being much steeper than the two latter. Document-based NoSQL databases perform better in concurrency than in isolation, and also better than relational databases in concurrency. Non-relational NoSQL databases seem to be more appropriate than standard relational SQL databases when database size is extremely high (secondary use, research applications). Document-based NoSQL databases perform in general better than native XML NoSQL databases. EHR extracts visualization and edition are also document-based tasks more appropriate to NoSQL database systems. However, the appropriate database solution much depends on each particular situation and specific problem.

GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique

PubMed Central

Yu, Wei; Clyne, Melinda; Dolan, Siobhan M; Yesupriya, Ajay; Wulf, Anja; Liu, Tiebin; Khoury, Muin J; Gwinn, Marta

2008-01-01

Background Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a substantial proportion of the abstracts in PubMed, identifying them with standard queries is not always accurate or efficient. Further automating the literature-screening process can reduce the burden of a labor-intensive and time-consuming traditional literature search. The Support Vector Machine (SVM), a well-established machine learning technique, has been successful in classifying text, including biomedical literature. The GAPscreener, a free SVM-based software tool, can be used to assist in screening PubMed abstracts for human genetic association studies. Results The data source for this research was the HuGE Navigator, formerly known as the HuGE Pub Lit database. Weighted SVM feature selection based on a keyword list obtained by the two-way z score method demonstrated the best screening performance, achieving 97.5% recall, 98.3% specificity and 31.9% precision in performance testing. Compared with the traditional screening process based on a complex PubMed query, the SVM tool reduced by about 90% the number of abstracts requiring individual review by the database curator. The tool also ascertained 47 articles that were missed by the traditional literature screening process during the 4-week test period. We examined the literature on genetic associations with preterm birth as an example. Compared with the traditional, manual process, the GAPscreener both reduced effort and improved accuracy. Conclusion GAPscreener is the first free SVM-based application available for screening the human genetic association literature in PubMed with high recall and specificity. The user-friendly graphical user interface makes this a practical, stand-alone application. The software can be downloaded at no charge. PMID:18430222

Transgenic Wheat, Barley and Oats: Future Prospects

NASA Astrophysics Data System (ADS)

Dunwell, Jim M.

Following the success of transgenic maize and rice, methods have now been developed for the efficient introduction of genes into wheat, barley and oats. This review summarizes the present position in relation to these three species, and also uses information from field trial databases and the patent literature to assess the future trends in the exploitation of transgenic material. This analysis includes agronomic traits and also discusses opportunities in expanding areas such as biofuels and biopharming.

Agency, Social and Healthcare Supports for Adults with Intellectual Disability at the End of Life in Out-of-Home, Non-Institutional Community Residences in Western Nations: A Literature Review

ERIC Educational Resources Information Center

Moro, Teresa T.; Savage, Teresa A.; Gehlert, Sarah

2017-01-01

Background: The nature and quality of end-of-life care received by adults with intellectual disabilities in out-of-home, non-institutional community agency residences in Western nations is not well understood. Method: A range of databases and search engines were used to locate conceptual, clinical and research articles from relevant peer-reviewed…

CamMedNP: building the Cameroonian 3D structural natural products database for virtual screening.

PubMed

Ntie-Kang, Fidele; Mbah, James A; Mbaze, Luc Meva'a; Lifongo, Lydia L; Scharfe, Michael; Hanna, Joelle Ngo; Cho-Ngwa, Fidelis; Onguéné, Pascal Amoa; Owono Owono, Luc C; Megnassan, Eugene; Sippl, Wolfgang; Efange, Simon M N

2013-04-16

Computer-aided drug design (CADD) often involves virtual screening (VS) of large compound datasets and the availability of such is vital for drug discovery protocols. We present CamMedNP - a new database beginning with more than 2,500 compounds of natural origin, along with some of their derivatives which were obtained through hemisynthesis. These are pure compounds which have been previously isolated and characterized using modern spectroscopic methods and published by several research teams spread across Cameroon. In the present study, 224 distinct medicinal plant species belonging to 55 plant families from the Cameroonian flora have been considered. About 80 % of these have been previously published and/or referenced in internationally recognized journals. For each compound, the optimized 3D structure, drug-like properties, plant source, collection site and currently known biological activities are given, as well as literature references. We have evaluated the "drug-likeness" of this database using Lipinski's "Rule of Five". A diversity analysis has been carried out in comparison with the ChemBridge diverse database. CamMedNP could be highly useful for database screening and natural product lead generation programs.

The U.S. Dairy Forage Research Center (USDFRC) Condensed Tannin NMR Database.

PubMed

Zeller, Wayne E; Schatz, Paul F

2017-06-28

This Perspective describes a solution-state NMR database for flavan-3-ol monomers and condensed tannin dimers through tetramers obtained from the literature to 2015, containing data searchable by structure, molecular formula, degrees of polymerization, and 1 H and 13 C chemical shifts of the condensed tannins. Citations for all literature references are provided and should serve as valuable resource for scientists working in the field of condensed tannin research. The database will be periodically updated as additional information becomes available, typically on a yearly basis and is available for use, free of charge, from the U.S. Dairy Forage Research Center (USDFRC) Website.

OrganismTagger: detection, normalization and grounding of organism entities in biomedical documents.

PubMed

Naderi, Nona; Kappler, Thomas; Baker, Christopher J O; Witte, René

2011-10-01

Semantic tagging of organism mentions in full-text articles is an important part of literature mining and semantic enrichment solutions. Tagged organism mentions also play a pivotal role in disambiguating other entities in a text, such as proteins. A high-precision organism tagging system must be able to detect the numerous forms of organism mentions, including common names as well as the traditional taxonomic groups: genus, species and strains. In addition, such a system must resolve abbreviations and acronyms, assign the scientific name and if possible link the detected mention to the NCBI Taxonomy database for further semantic queries and literature navigation. We present the OrganismTagger, a hybrid rule-based/machine learning system to extract organism mentions from the literature. It includes tools for automatically generating lexical and ontological resources from a copy of the NCBI Taxonomy database, thereby facilitating system updates by end users. Its novel ontology-based resources can also be reused in other semantic mining and linked data tasks. Each detected organism mention is normalized to a canonical name through the resolution of acronyms and abbreviations and subsequently grounded with an NCBI Taxonomy database ID. In particular, our system combines a novel machine-learning approach with rule-based and lexical methods for detecting strain mentions in documents. On our manually annotated OT corpus, the OrganismTagger achieves a precision of 95%, a recall of 94% and a grounding accuracy of 97.5%. On the manually annotated corpus of Linnaeus-100, the results show a precision of 99%, recall of 97% and grounding accuracy of 97.4%. The OrganismTagger, including supporting tools, resources, training data and manual annotations, as well as end user and developer documentation, is freely available under an open-source license at http://www.semanticsoftware.info/organism-tagger. witte@semanticsoftware.info.

Tracing the scientific outputs in the field of Ebola research based on publications in the Web of Science.

PubMed

Yi, Fengyun; Yang, Pin; Sheng, Huifeng

2016-04-15

Ebola virus disease (hereafter EVD or Ebola) has a high fatality rate. The devastating effects of the current epidemic of Ebola in West Africa have put the global health response in acute focus. In response, the World Health Organization (WHO) has declared the Ebola outbreak in West Africa as a "Public Health Emergency of International Concern". A small proportion of scientific literature is dedicated to Ebola research. To identify global research trends in Ebola research, the Institute for Scientific Information (ISI) Web of Science™ database was used to search for data, which encompassed original articles published from 1900 to 2013. The keyword "Ebola" was used to identify articles for the purposes of this review. In order to include all published items, the database was searched using the Basic Search method. The earliest record of literature about Ebola indexed in the Web of Science is from 1977. A total of 2477 publications on Ebola, published between 1977 and 2014 (with the number of publications increasing annually), were retrieved from the database. Original research articles (n = 1623, 65.5%) were the most common type of publication. Almost all (96.5%) of the literature in this field was in English. The USA had the highest scientific output and greatest number of funding agencies. Journal of Virology published 239 papers on Ebola, followed by Journal of Infectious Diseases and Virology, which published 113 and 99 papers, respectively. A total of 1911 papers on Ebola were cited 61,477 times. This analysis identified the current state of research and trends in studies about Ebola between 1977 and 2014. Our bibliometric analysis provides a historical perspective on the progress in Ebola research.

LITERATURE REVIEW AND REPORT: SURFACE-SEDIMENT SAMPLER DATABASE

EPA Science Inventory

A literature review was conducted to identify available surface sediment sampling technologies with an ability to collect undisturbed sediments to depths of up to 1 meter below the water sediment interface. This survey was conducted using published literature and references, Envi...

Multi-Database Searching in the Behavioral Sciences--Part I: Basic Techniques and Core Databases.

ERIC Educational Resources Information Center

Angier, Jennifer J.; Epstein, Barbara A.

1980-01-01

Outlines practical searching techniques in seven core behavioral science databases accessing psychological literature: Psychological Abstracts, Social Science Citation Index, Biosis, Medline, Excerpta Medica, Sociological Abstracts, ERIC. Use of individual files is discussed and their relative strengths/weaknesses are compared. Appended is a list…

Designing Corporate Databases to Support Technology Innovation

ERIC Educational Resources Information Center

Gultz, Michael Jarett

2012-01-01

Based on a review of the existing literature on database design, this study proposed a unified database model to support corporate technology innovation. This study assessed potential support for the model based on the opinions of 200 technology industry executives, including Chief Information Officers, Chief Knowledge Officers and Chief Learning…

Effect of microstructure on the elasto-viscoplastic deformation of dual phase titanium structures

NASA Astrophysics Data System (ADS)

Ozturk, Tugce; Rollett, Anthony D.

2018-02-01

The present study is devoted to the creation of a process-structure-property database for dual phase titanium alloys, through a synthetic microstructure generation method and a mesh-free fast Fourier transform based micromechanical model that operates on a discretized image of the microstructure. A sensitivity analysis is performed as a precursor to determine the statistically representative volume element size for creating 3D synthetic microstructures based on additively manufactured Ti-6Al-4V characteristics, which are further modified to expand the database for features of interest, e.g., lath thickness. Sets of titanium hardening parameters are extracted from literature, and The relative effect of the chosen microstructural features is quantified through comparisons of average and local field distributions.

Economic Evaluation in Global Perspective: A Bibliometric Analysis of the Recent Literature.

PubMed

Pitt, Catherine; Goodman, Catherine; Hanson, Kara

2016-02-01

We present a bibliometric analysis of recently published full economic evaluations of health interventions and reflect critically on the implications of our findings for this growing field. We created a database drawing on 14 health, economic, and/or general literature databases for articles published between 1 January 2012 and 3 May 2014 and identified 2844 economic evaluations meeting our criteria. We present findings regarding the sensitivity, specificity, and added value of searches in the different databases. We examine the distribution of publications between countries, regions, and health areas studied and compare the relative volume of research with disease burden. We analyse authors' country and institutional affiliations, journals and journal type, language, and type of economic evaluation conducted. More than 1200 economic evaluations were published annually, of which 4% addressed low-income countries, 4% lower-middle-income countries, 14% upper-middle-income countries, and 83% high-income countries. Across country income levels, 53, 54, 86, and 100% of articles, respectively, included an author based in a country within the income level studied. Biomedical journals published 74% of economic evaluations. The volume of research across health areas correlates more closely with disease burden in high-income than in low-income and middle-income countries. Our findings provide an empirical basis for further study on methods, research prioritization, and capacity development in health economic evaluation. © 2016 The Authors. Health Economics published by John Wiley & Sons Ltd.

Gaussian Multiscale Aggregation Applied to Segmentation in Hand Biometrics

PubMed Central

de Santos Sierra, Alberto; Ávila, Carmen Sánchez; Casanova, Javier Guerra; del Pozo, Gonzalo Bailador

2011-01-01

This paper presents an image segmentation algorithm based on Gaussian multiscale aggregation oriented to hand biometric applications. The method is able to isolate the hand from a wide variety of background textures such as carpets, fabric, glass, grass, soil or stones. The evaluation was carried out by using a publicly available synthetic database with 408,000 hand images in different backgrounds, comparing the performance in terms of accuracy and computational cost to two competitive segmentation methods existing in literature, namely Lossy Data Compression (LDC) and Normalized Cuts (NCuts). The results highlight that the proposed method outperforms current competitive segmentation methods with regard to computational cost, time performance, accuracy and memory usage. PMID:22247658

Gaussian multiscale aggregation applied to segmentation in hand biometrics.

PubMed

de Santos Sierra, Alberto; Avila, Carmen Sánchez; Casanova, Javier Guerra; del Pozo, Gonzalo Bailador

2011-01-01

This paper presents an image segmentation algorithm based on Gaussian multiscale aggregation oriented to hand biometric applications. The method is able to isolate the hand from a wide variety of background textures such as carpets, fabric, glass, grass, soil or stones. The evaluation was carried out by using a publicly available synthetic database with 408,000 hand images in different backgrounds, comparing the performance in terms of accuracy and computational cost to two competitive segmentation methods existing in literature, namely Lossy Data Compression (LDC) and Normalized Cuts (NCuts). The results highlight that the proposed method outperforms current competitive segmentation methods with regard to computational cost, time performance, accuracy and memory usage.

Inclusion of individuals with special needs in regular education: a literature review.

PubMed

Silva, Fabiana Trevisani; Gonçalves, Eduardo Augusto Vella; Alvarenga, Kátia de Freitas

2012-01-01

To critically analyze the inclusion of individuals with special needs in regular education in Brazil, considering social and legal aspects, through literature review. The literature search was conducted in open access databases: LILACS, SciELO, Portal Cochrane and IUSDATA, the latter belonging to the Library of the Law School of the University of São Paulo, considering all articles published until December 2010. The search strategy used the following keywords: inclusive education; special education; inclusive proposal; individuals with special needs. In the search, only studies in which the summary or the body of the article were related to the purpose of the study were evaluated and selected. The potentially relevant articles for review were presented in a protocol form containing the eligibility criteria of the study, methods used, characteristics of the analyzed group or manuscripts, type of intervention used in the study, and results obtained. Articles classified as expert opinions, despite their low level of scientific evidence, were considered in this work, since they are often found in the literature on the issue. A total of 1,399 articles was found and 120 potentially relevant articles were selected after reading their abstracts. From these, 67 articles were cited in more than one database, which resulted in 53 articles to be fully read. Fifteen of these articles were excluded after reading because they did not meet the inclusion criteria. Thus, 38 studies were included and analyzed. Following a critical analysis of the literature in the field, it was concluded that, so far, in general, the school receives individuals with special needs; however, there is a long way to go to actually include these individuals, although Brazil has the scope of inclusion. Therefore, it is necessary to establish public policies and guidelines aimed at effective inclusion.

CADDIS Volume 5. Causal Databases: Interactive Conceptual Diagrams (ICDs)

EPA Pesticide Factsheets

In Interactive Conceptual Diagram (ICD) section of CADDIS allows users to create conceptual model diagrams, search a literature-based evidence database, and then attach that evidence to their diagrams.

Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles.

PubMed

Kafkas, Şenay; Kim, Jee-Hyub; Pi, Xingjun; McEntyre, Johanna R

2015-01-01

In this study, we present an analysis of data citation practices in full text research articles and their corresponding supplementary data files, made available in the Open Access set of articles from Europe PubMed Central. Our aim is to investigate whether supplementary data files should be considered as a source of information for integrating the literature with biomolecular databases. Using text-mining methods to identify and extract a variety of core biological database accession numbers, we found that the supplemental data files contain many more database citations than the body of the article, and that those citations often take the form of a relatively small number of articles citing large collections of accession numbers in text-based files. Moreover, citation of value-added databases derived from submission databases (such as Pfam, UniProt or Ensembl) is common, demonstrating the reuse of these resources as datasets in themselves. All the database accession numbers extracted from the supplementary data are publicly accessible from http://dx.doi.org/10.5281/zenodo.11771. Our study suggests that supplementary data should be considered when linking articles with data, in curation pipelines, and in information retrieval tasks in order to make full use of the entire research article. These observations highlight the need to improve the management of supplemental data in general, in order to make this information more discoverable and useful.

Cost and cost-effectiveness studies in urologic oncology using large administrative databases.

PubMed

Wang, Ye; Mossanen, Matthew; Chang, Steven L

2018-04-01

Urologic cancers are not only among the most common types of cancers, but also among the most expensive cancers to treat in the United States. This study aimed to review the use of CEAs and other cost analyses in urologic oncology using large databases to better understand the value of management strategies of these cancers. A literature review on CEAs and other cost analyses in urologic oncology using large databases. The options for and costs of diagnosing, treating, and following patients with urologic cancers can be expected to rise in the coming years. There are numerous opportunities in each urologic cancer to use CEAs to both lower costs and provide high-quality services. Improved cancer care must balance the integration of novelty with ensuring reasonable costs to patients and the health care system. With the increasing focus cost containment, appreciating the value of competing strategies in caring for our patients is pivotal. Leveraging methods such as CEAs and harnessing large databases may help evaluate the merit of established or emerging strategies. Copyright © 2018 Elsevier Inc. All rights reserved.

Text mining for metabolic pathways, signaling cascades, and protein networks.

PubMed

Hoffmann, Robert; Krallinger, Martin; Andres, Eduardo; Tamames, Javier; Blaschke, Christian; Valencia, Alfonso

2005-05-10

The complexity of the information stored in databases and publications on metabolic and signaling pathways, the high throughput of experimental data, and the growing number of publications make it imperative to provide systems to help the researcher navigate through these interrelated information resources. Text-mining methods have started to play a key role in the creation and maintenance of links between the information stored in biological databases and its original sources in the literature. These links will be extremely useful for database updating and curation, especially if a number of technical problems can be solved satisfactorily, including the identification of protein and gene names (entities in general) and the characterization of their types of interactions. The first generation of openly accessible text-mining systems, such as iHOP (Information Hyperlinked over Proteins), provides additional functions to facilitate the reconstruction of protein interaction networks, combine database and text information, and support the scientist in the formulation of novel hypotheses. The next challenge is the generation of comprehensive information regarding the general function of signaling pathways and protein interaction networks.

Creating a literature database of low-calorie sweeteners and health studies: evidence mapping.

PubMed

Wang, Ding Ding; Shams-White, Marissa; Bright, Oliver John M; Parrott, J Scott; Chung, Mei

2016-01-05

Evidence mapping is an emerging tool used to systematically identify, organize and summarize the quantity and focus of scientific evidence on a broad topic, but there are currently no methodological standards. Using the topic of low-calorie sweeteners (LCS) and selected health outcomes, we describe the process of creating an evidence-map database and demonstrate several example descriptive analyses using this database. The process of creating an evidence-map database is described in detail. The steps include: developing a comprehensive literature search strategy, establishing study eligibility criteria and a systematic study selection process, extracting data, developing outcome groups with input from expert stakeholders and tabulating data using descriptive analyses. The database was uploaded onto SRDR™ (Systematic Review Data Repository), an open public data repository. Our final LCS evidence-map database included 225 studies, of which 208 were interventional studies and 17 were cohort studies. An example bubble plot was produced to display the evidence-map data and visualize research gaps according to four parameters: comparison types, population baseline health status, outcome groups, and study sample size. This plot indicated a lack of studies assessing appetite and dietary intake related outcomes using LCS with a sugar intake comparison in people with diabetes. Evidence mapping is an important tool for the contextualization of in-depth systematic reviews within broader literature and identifies gaps in the evidence base, which can be used to inform future research. An open evidence-map database has the potential to promote knowledge translation from nutrition science to policy.

A narrative literature review to direct spinal cord injury patient education programming.

PubMed

van Wyk, Kim; Backwell, Amber; Townson, Andrea

2015-01-01

To summarize the evidence on SCI-related education literature, while looking at potential barriers, solutions, benefits, and patient preferences regarding SCI patient education. A literature review was conducted using 5 electronic databases. Quality appraisal instruments were designed to determine the methodological rigor of the quantitative and qualitative studies found. Selected articles were read in their entirety and themes were abstracted. Fourteen articles met the inclusion criteria for this narrative literature review, all of which were based on research studies. Seven of these 14 were quantitative studies, 3 were qualitative studies, and 4 were mixed-methods studies. To improve SCI education during rehabilitation, programs should maximize the receptiveness of newly injured patients to SCI-related information, optimize the delivery of SCI education, increase the number of opportunities for learning, promote and support lifelong learning, and include patient and program evaluation. How these strategies are specifically implemented needs to be determined by program management in consultation with various stakeholders, whilst considering the unique characteristics of the rehabilitation facility.

Effective pedagogies for teaching math to nursing students: a literature review.

PubMed

Hunter Revell, Susan M; McCurry, Mary K

2013-11-01

Improving mathematical competency and problem-solving skills in undergraduate nursing students has been an enduring challenge for nurse educators. A number of teaching strategies have been used to address this problem with varying degrees of success. This paper discusses a literature review which examined undergraduate nursing student challenges to learning math, methods used to teach math and problem-solving skills, and the use of innovative pedagogies for teaching. The literature was searched using the Cumulative Index of Nursing and Allied Health Literature and Education Resource Information Center databases. Key search terms included: math*, nurs*, nursing student, calculation, technology, medication administration, challenges, problem-solving, personal response system, clickers, computer and multi-media. Studies included in the review were published in English from 1990 to 2011. Results support four major themes which include: student challenges to learning, traditional pedagogies, curriculum strategies, and technology and integrative methods as pedagogy. The review concludes that there is a need for more innovative pedagogical strategies for teaching math to student nurses. Nurse educators in particular play a central role in helping students learn the conceptual basis, as well as practical hands-on methods, to problem solving and math competency. It is recommended that an integrated approach inclusive of technology will benefit students through better performance, increased understanding, and improved student satisfaction. Copyright © 2012 Elsevier Ltd. All rights reserved.

Best practices in ranking communicable disease threats: a literature review, 2015.

PubMed

O'Brien, Eleanor Charlotte; Taft, Rachel; Geary, Katie; Ciotti, Massimo; Suk, Jonathan E

2016-04-28

The threat of serious, cross-border communicable disease outbreaks in Europe poses a significant challenge to public health and emergency preparedness because the relative likelihood of these threats and the pathogens involved are constantly shifting in response to a range of changing disease drivers. To inform strategic planning by enabling effective resource allocation to manage the consequences of communicable disease outbreaks, it is useful to be able to rank and prioritise pathogens. This paper reports on a literature review which identifies and evaluates the range of methods used for risk ranking. Searches were performed across biomedical and grey literature databases, supplemented by reference harvesting and citation tracking. Studies were selected using transparent inclusion criteria and underwent quality appraisal using a bespoke checklist based on the AGREE II criteria. Seventeen studies were included in the review, covering five methodologies. A narrative analysis of the selected studies suggests that no single methodology was superior. However, many of the methods shared common components, around which a 'best-practice' framework was formulated. This approach is intended to help inform decision makers' choice of an appropriate risk-ranking study design.

Using high-throughput literature mining to support read-across predictions of skin sensitization (WC)

EPA Science Inventory

Read-across predictions require high quality measured data for source analogues. These data are typically retrieved from structured databases, but biomedical literature data are often untapped because current literature mining approaches are resource intensive. Our high-throughpu...

A recent advance in the automatic indexing of the biomedical literature.

PubMed

Névéol, Aurélie; Shooshan, Sonya E; Humphrey, Susanne M; Mork, James G; Aronson, Alan R

2009-10-01

The volume of biomedical literature has experienced explosive growth in recent years. This is reflected in the corresponding increase in the size of MEDLINE, the largest bibliographic database of biomedical citations. Indexers at the US National Library of Medicine (NLM) need efficient tools to help them accommodate the ensuing workload. After reviewing issues in the automatic assignment of Medical Subject Headings (MeSH terms) to biomedical text, we focus more specifically on the new subheading attachment feature for NLM's Medical Text Indexer (MTI). Natural Language Processing, statistical, and machine learning methods of producing automatic MeSH main heading/subheading pair recommendations were assessed independently and combined. The best combination achieves 48% precision and 30% recall. After validation by NLM indexers, a suitable combination of the methods presented in this paper was integrated into MTI as a subheading attachment feature producing MeSH indexing recommendations compliant with current state-of-the-art indexing practice.

Theory-based interventions in physical activity: a systematic review of literature in Iran.

PubMed

Abdi, Jalal; Eftekhar, Hassan; Estebsari, Fatemeh; Sadeghi, Roya

2014-11-30

Lack of physical activity is ranked fourth among the causes of human death and chronic diseases. Using models and theories to design, implement, and evaluate the health education and health promotion interventions has many advantages. Using models and theories of physical activity, we decided to systematically study the educational and promotional interventions carried out in Iran from 2003 to 2013.Three information databases were used to systematically select papers using key words including Iranian Magazine Database (MAGIRAN), Iran Medical Library (MEDLIB), and Scientific Information Database (SID). Twenty papers were selected and studied .Having been applied in 9 studies, The Trans Theoretical Model (TTM) was the most widespread model in Iran (PENDER in 3 studies, BASNEF in 2, and the Theory of Planned Behavior in 2 studies). With regards to the educational methods, almost all studies used a combination of methods. The most widely used Integrative educational method was group discussion. Only one integrated study was done. Behavior maintenance was not addressed in 75% of the studies. Almost all studies used self-reporting instruments. The effectiveness of educational methods was assessed in none of the studies. Most of the included studies had several methodological weaknesses, which hinder the validity and applicability of their results. According to the findings, the necessity of need assessment in using models, epidemiology and methodology consultation, addressing maintenance of physical activity, using other theories and models such as social marketing and social-cognitive theory, and other educational methods like empirical and complementary are suggested.

Structured methodology review identified seven (RETREAT) criteria for selecting qualitative evidence synthesis approaches.

PubMed

Booth, Andrew; Noyes, Jane; Flemming, Kate; Gerhardus, Ansgar; Wahlster, Philip; van der Wilt, Gert Jan; Mozygemba, Kati; Refolo, Pietro; Sacchini, Dario; Tummers, Marcia; Rehfuess, Eva

2018-07-01

To compare and contrast different methods of qualitative evidence synthesis (QES) against criteria identified from the literature and to map their attributes to inform selection of the most appropriate QES method to answer research questions addressed by qualitative research. Electronic databases, citation searching, and a study register were used to identify studies reporting QES methods. Attributes compiled from 26 methodological papers (2001-2014) were used as a framework for data extraction. Data were extracted into summary tables by one reviewer and then considered within the author team. We identified seven considerations determining choice of methods from the methodological literature, encapsulated within the mnemonic Review question-Epistemology-Time/Timescale-Resources-Expertise-Audience and purpose-Type of data. We mapped 15 different published QES methods against these seven criteria. The final framework focuses on stand-alone QES methods but may also hold potential when integrating quantitative and qualitative data. These findings offer a contemporary perspective as a conceptual basis for future empirical investigation of the advantages and disadvantages of different methods of QES. It is hoped that this will inform appropriate selection of QES approaches. Copyright © 2018 Elsevier Inc. All rights reserved.

National Databases for Neurosurgical Outcomes Research: Options, Strengths, and Limitations.

PubMed

Karhade, Aditya V; Larsen, Alexandra M G; Cote, David J; Dubois, Heloise M; Smith, Timothy R

2017-08-05

Quality improvement, value-based care delivery, and personalized patient care depend on robust clinical, financial, and demographic data streams of neurosurgical outcomes. The neurosurgical literature lacks a comprehensive review of large national databases. To assess the strengths and limitations of various resources for outcomes research in neurosurgery. A review of the literature was conducted to identify surgical outcomes studies using national data sets. The databases were assessed for the availability of patient demographics and clinical variables, longitudinal follow-up of patients, strengths, and limitations. The number of unique patients contained within each data set ranged from thousands (Quality Outcomes Database [QOD]) to hundreds of millions (MarketScan). Databases with both clinical and financial data included PearlDiver, Premier Healthcare Database, Vizient Clinical Data Base and Resource Manager, and the National Inpatient Sample. Outcomes collected by databases included patient-reported outcomes (QOD); 30-day morbidity, readmissions, and reoperations (National Surgical Quality Improvement Program); and disease incidence and disease-specific survival (Surveillance, Epidemiology, and End Results-Medicare). The strengths of large databases included large numbers of rare pathologies and multi-institutional nationally representative sampling; the limitations of these databases included variable data veracity, variable data completeness, and missing disease-specific variables. The improvement of existing large national databases and the establishment of new registries will be crucial to the future of neurosurgical outcomes research. Copyright © 2017 by the Congress of Neurological Surgeons

Tips and tricks for using the internet for professional purposes.

PubMed

Ceylan, Hasan Huseyin; Güngören, Nurdan; Küçükdurmaz, Fatih

2017-05-01

Online resources provide access to large amounts of information which is expanding every day. Using search engines for reaching the relevant, updated and complete literature that is indexed in various bibliographical databases has already become part of the medical professionals' everyday life.However, most researchers often fail to conduct a efficient literature search on the internet. The right techniques in literature search save time and improve the quality of the retrieved data.Efficient literature search is not a talent but a learnable skill, which should be a formal part of medical education.This review briefly outlines the commonly used bibliographic databases, namely Pubmed, Cochrane Library, Web of Science, Scopus, EMBASE, CINAHL and Google Scholar. Also the definition of grey literature and its features are summarised. Cite this article: EFORT Open Rev 2017;2. DOI: 10.1302/2058-5241.2.160066. Originally published online at www.efortopenreviews.org.

Tips and tricks for using the internet for professional purposes

PubMed Central

Ceylan, Hasan Huseyin; Güngören, Nurdan; Küçükdurmaz, Fatih

2017-01-01

Online resources provide access to large amounts of information which is expanding every day. Using search engines for reaching the relevant, updated and complete literature that is indexed in various bibliographical databases has already become part of the medical professionals’ everyday life. However, most researchers often fail to conduct a efficient literature search on the internet. The right techniques in literature search save time and improve the quality of the retrieved data. Efficient literature search is not a talent but a learnable skill, which should be a formal part of medical education. This review briefly outlines the commonly used bibliographic databases, namely Pubmed, Cochrane Library, Web of Science, Scopus, EMBASE, CINAHL and Google Scholar. Also the definition of grey literature and its features are summarised. Cite this article: EFORT Open Rev 2017;2. DOI: 10.1302/2058-5241.2.160066. Originally published online at www.efortopenreviews.org PMID:28630750

[Meta-analysis of relationship between extranodal tumor deposits and prognosis in patients with colorectal cancer].

PubMed

Zhang, Xianxiang; Shao, Shihong; Gao, Yuan; Zhang, Maoshen; Lu, Yun

2016-03-01

To investigate the relationship between extranodal tumor deposits and prognosis in patients with colorectal cancer. The literatures on extranodal tumor deposits and postoperative survival rate in patients with colorectal cancer published at home and abroad from 1990 to 2014 were retrieved in 15 English literature databases such as MEDLINE/PubMed, Web of Science, Directory of Open Access Journals(DOAJ), SpringerLink and Chinese literature databases such as Chinese Biomedical Literature Database CD-ROM, China National Knowledge Infrastructure (CNKI) Database with the internet platform of Yonsei University Library. After screening for inclusion, data extraction and quality assessment, meta-analysis was conducted by the Review Manager 5.3 software. There were 10 studies meeting the inclusion criteria for meta-analysis. The total sample size of the studies was 4 068 cases with ENTD(+) 727 cases, while ENTD(-) 3 341 cases. Meta analysis showed that 5-year overall survival rate and 5-year relapse-free survival rate were significantly lower in ENTD(+) group than those in ENTD(-) group (OR 0.27, 0.23; 95% CI:0.18 to 0.43, 0.16 to 0.34 respectively, both P=0.000); the 5-year overall survival rates were both significantly lower in ENTD(+) group as compared to ENTD(-) group for patients with N0 and N(+) colorectal cancer (both P<0.05). Extranodal tumor deposits is a poor prognostic factor of patients with colorectal cancer.

OntoMate: a text-mining tool aiding curation at the Rat Genome Database

PubMed Central

Liu, Weisong; Laulederkind, Stanley J. F.; Hayman, G. Thomas; Wang, Shur-Jen; Nigam, Rajni; Smith, Jennifer R.; De Pons, Jeff; Dwinell, Melinda R.; Shimoyama, Mary

2015-01-01

The Rat Genome Database (RGD) is the premier repository of rat genomic, genetic and physiologic data. Converting data from free text in the scientific literature to a structured format is one of the main tasks of all model organism databases. RGD spends considerable effort manually curating gene, Quantitative Trait Locus (QTL) and strain information. The rapidly growing volume of biomedical literature and the active research in the biological natural language processing (bioNLP) community have given RGD the impetus to adopt text-mining tools to improve curation efficiency. Recently, RGD has initiated a project to use OntoMate, an ontology-driven, concept-based literature search engine developed at RGD, as a replacement for the PubMed (http://www.ncbi.nlm.nih.gov/pubmed) search engine in the gene curation workflow. OntoMate tags abstracts with gene names, gene mutations, organism name and most of the 16 ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. All listed terms are linked both to data entry boxes and a term browser in the curation tool. OntoMate also provides user-activated filters for species, date and other parameters relevant to the literature search. Using the system for literature search and import has streamlined the process compared to using PubMed. The system was built with a scalable and open architecture, including features specifically designed to accelerate the RGD gene curation process. With the use of bioNLP tools, RGD has added more automation to its curation workflow. Database URL: http://rgd.mcw.edu PMID:25619558

Nuclear science abstracts (NSA) database 1948--1974 (on the Internet)

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

NONE

Nuclear Science Abstracts (NSA) is a comprehensive abstract and index collection of the International Nuclear Science and Technology literature for the period 1948 through 1976. Included are scientific and technical reports of the US Atomic Energy Commission, US Energy Research and Development Administration and its contractors, other agencies, universities, and industrial and research organizations. Coverage of the literature since 1976 is provided by Energy Science and Technology Database. Approximately 25% of the records in the file contain abstracts. These are from the following volumes of the print Nuclear Science Abstracts: Volumes 12--18, Volume 29, and Volume 33. The database containsmore » over 900,000 bibliographic records. All aspects of nuclear science and technology are covered, including: Biomedical Sciences; Metals, Ceramics, and Other Materials; Chemistry; Nuclear Materials and Waste Management; Environmental and Earth Sciences; Particle Accelerators; Engineering; Physics; Fusion Energy; Radiation Effects; Instrumentation; Reactor Technology; Isotope and Radiation Source Technology. The database includes all records contained in Volume 1 (1948) through Volume 33 (1976) of the printed version of Nuclear Science Abstracts (NSA). This worldwide coverage includes books, conference proceedings, papers, patents, dissertations, engineering drawings, and journal literature. This database is now available for searching through the GOV. Research Center (GRC) service. GRC is a single online web-based search service to well known Government databases. Featuring powerful search and retrieval software, GRC is an important research tool. The GRC web site is at http://grc.ntis.gov.« less

Data Mining Applied to Analysis of Contraceptive Methods Among College Students.

PubMed

Simões, Priscyla Waleska; Cesconetto, Samuel; Dalló, Eduardo Daminelli; de Souza Pires, Maria Marlene; Comunello, Eros; Borges Tomaz, Felipe; Xavier, Eduardo Pícolo; da Rosa Brunel Alves, Pedro Antonio; Ceretta, Luciane Bisognin; Manenti, Sandra Aparecida

2017-01-01

The aim of this study was to use the Data Mining to analyze the profile of the use of contraceptive methods in a university population. We used a database about sexuality performed on a university population in southern Brazil. The results obtained by the generated rules are largely in line with the literature and epidemiology worldwide, showing significant points of vulnerability in the university population. Validation measures of the study, as such, accuracy, sensitivity, specificity, and area under the ROC curve were higher or at least similar as compared to recent studies using the same methodology.

Comparative study of minutiae selection algorithms for ISO fingerprint templates

NASA Astrophysics Data System (ADS)

Vibert, B.; Charrier, C.; Le Bars, J.-M.; Rosenberger, C.

2015-03-01

We address the selection of fingerprint minutiae given a fingerprint ISO template. Minutiae selection plays a very important role when a secure element (i.e. a smart-card) is used. Because of the limited capability of computation and memory, the number of minutiae of a stored reference in the secure element is limited. We propose in this paper a comparative study of 6 minutiae selection methods including 2 methods from the literature and 1 like reference (No Selection). Experimental results on 3 fingerprint databases from the Fingerprint Verification Competition show their relative efficiency in terms of performance and computation time.

CADDIS Volume 5. Causal Databases: CADLink

EPA Pesticide Factsheets

CADLink, an improved tool for searching and organizing literature-based evidence, will be released in Fall 2016. The original CADDIS literature resource, CADLit, is unavailable as we make these improvements.

Solutions in radiology services management: a literature review.

PubMed

Pereira, Aline Garcia; Vergara, Lizandra Garcia Lupi; Merino, Eugenio Andrés Díaz; Wagner, Adriano

2015-01-01

The present study was aimed at reviewing the literature to identify solutions for problems observed in radiology services. Basic, qualitative, exploratory literature review at Scopus and SciELO databases, utilizing the Mendeley and Illustrator CC Adobe softwares. In the databases, 565 papers - 120 out of them, pdf free - were identified. Problems observed in the radiology sector are related to procedures scheduling, humanization, lack of training, poor knowledge and use of management techniques, and interaction with users. The design management provides the services with interesting solutions such as Benchmarking, CRM, Lean Approach, ServiceBlueprinting, continued education, among others. Literature review is an important tool to identify problems and respective solutions. However, considering the small number of studies approaching management of radiology services, this is a great field of research for the development of deeper studies.

A systematic review and appraisal of methods of developing and validating lifestyle cardiovascular disease risk factors questionnaires.

PubMed

Nse, Odunaiya; Quinette, Louw; Okechukwu, Ogah

2015-09-01

Well developed and validated lifestyle cardiovascular disease (CVD) risk factors questionnaires is the key to obtaining accurate information to enable planning of CVD prevention program which is a necessity in developing countries. We conducted this review to assess methods and processes used for development and content validation of lifestyle CVD risk factors questionnaires and possibly develop an evidence based guideline for development and content validation of lifestyle CVD risk factors questionnaires. Relevant databases at the Stellenbosch University library were searched for studies conducted between 2008 and 2012, in English language and among humans. Using the following databases; pubmed, cinahl, psyc info and proquest. Search terms used were CVD risk factors, questionnaires, smoking, alcohol, physical activity and diet. Methods identified for development of lifestyle CVD risk factors were; review of literature either systematic or traditional, involvement of expert and /or target population using focus group discussion/interview, clinical experience of authors and deductive reasoning of authors. For validation, methods used were; the involvement of expert panel, the use of target population and factor analysis. Combination of methods produces questionnaires with good content validity and other psychometric properties which we consider good.

How Many People Search the ERIC Database Each Day?

ERIC Educational Resources Information Center

Rudner, Lawrence

This study estimated the number of people searching the ERIC database each day. The Educational Resources Information Center (ERIC) is a national information system designed to provide ready access to an extensive body of education-related literature. Federal funds traditionally have paid for the development of the database, but not the…

Literature Review and Database of Relations Between Salinity and Aquatic Biota: Applications to Bowdoin National Wildlife Refuge, Montana

USGS Publications Warehouse

Gleason, Robert A.; Tangen, Brian A.; Laubhan, Murray K.; Finocchiaro, Raymond G.; Stamm, John F.

2009-01-01

Long-term accumulation of salts in wetlands at Bowdoin National Wildlife Refuge (NWR), Mont., has raised concern among wetland managers that increasing salinity may threaten plant and invertebrate communities that provide important habitat and food resources for migratory waterfowl. Currently, the U.S. Fish and Wildlife Service (USFWS) is evaluating various water management strategies to help maintain suitable ranges of salinity to sustain plant and invertebrate resources of importance to wildlife. To support this evaluation, the USFWS requested that the U.S. Geological Survey (USGS) provide information on salinity ranges of water and soil for common plants and invertebrates on Bowdoin NWR lands. To address this need, we conducted a search of the literature on occurrences of plants and invertebrates in relation to salinity and pH of the water and soil. The compiled literature was used to (1) provide a general overview of salinity concepts, (2) document published tolerances and adaptations of biota to salinity, (3) develop databases that the USFWS can use to summarize the range of reported salinity values associated with plant and invertebrate taxa, and (4) perform database summaries that describe reported salinity ranges associated with plants and invertebrates at Bowdoin NWR. The purpose of this report is to synthesize information to facilitate a better understanding of the ecological relations between salinity and flora and fauna when developing wetland management strategies. A primary focus of this report is to provide information to help evaluate and address salinity issues at Bowdoin NWR; however, the accompanying databases, as well as concepts and information discussed, are applicable to other areas or refuges. The accompanying databases include salinity values reported for 411 plant taxa and 330 invertebrate taxa. The databases are available in Microsoft Excel version 2007 (http://pubs.usgs.gov/sir/2009/5098/downloads/databases_21april2009.xls) and contain 27 data fields that include variables such as taxonomic identification, values for salinity and pH, wetland classification, location of study, and source of data. The databases are not exhaustive of the literature and are biased toward wetland habitats located in the glaciated North-Central United States; however, the databases do encompass a diversity of biota commonly found in brackish and freshwater inland wetland habitats.

Gender discrimination and nursing: α literature review.

PubMed

Kouta, Christiana; Kaite, Charis P

2011-01-01

This article aims to examine gender stereotypes in relation to men in nursing, discuss gender discrimination cases in nursing, and explore methods used for promoting equal educational opportunities during nursing studies. The literature review was based on related databases, such as CINAHL, Science Direct, MEDLINE, and EBSCO. Legal case studies are included in order to provide a more practical example of those barriers existing for men pursuing nursing, as well as statistical data concerning gender discrimination and male attrition to nursing schools in relation to those barriers. These strengthen the validity of the manuscript. Literature review showed that gender discrimination is still prevalent within nursing profession. Nursing faculty should prepare male nursing students to interact effectively with female clients as well. Role modeling the therapeutic relationship with clients is one strategy that may help male students. In general, the faculty should provide equal learning opportunities to nursing students. Copyright © 2011 Elsevier Inc. All rights reserved.

Whistleblowing: An integrative literature review of data-based studies involving nurses.

PubMed

Jackson, Debra; Hickman, Louise D; Hutchinson, Marie; Andrew, Sharon; Smith, James; Potgieter, Ingrid; Cleary, Michelle; Peters, Kath

2014-01-01

Abstract Aim: To summarise and critique the research literature about whistleblowing and nurses. Whistleblowing is identified as a crucial issue in maintenance of healthcare standards and nurses are frequently involved in whistleblowing events. Despite the importance of this issue, to our knowledge an evaluation of this body of the data-based literature has not been undertaken. An integrative literature review approach was used to summarise and critique the research literature. A comprehensive search of five databases including Medline, CINAHL, PubMed and Health Science: Nursing/Academic Edition, and Google, were searched using terms including: 'Whistleblow*,' 'nurs*.' In addition, relevant journals were examined, as well as reference lists of retrieved papers. Papers published during the years 2007-2013 were selected for inclusion. Fifteen papers were identified, capturing data from nurses in seven countries. The findings in this review demonstrate a growing body of research for the nursing profession at large to engage and respond appropriately to issues involving suboptimal patient care or organisational wrongdoing. Nursing plays a key role in maintaining practice standards and in reporting care that is unacceptable although the repercussions to nurses who raise concerns are insupportable. Overall, whistleblowing and how it influences the individual, their family, work colleagues, nursing practice and policy overall, requires further national and international research attention.

Increasing access to Latin American social medicine resources: a preliminary report.

PubMed

Buchanan, Holly Shipp; Waitzkin, Howard; Eldredge, Jonathan; Davidson, Russ; Iriart, Celia; Teal, Janis

2003-10-01

This preliminary report describes the development and implementation of a project to improve access to literature in Latin American social medicine (LASM). The University of New Mexico project team collaborated with participants from Argentina, Brazil, Chile, and Ecuador to identify approximately 400 articles and books in Latin American social medicine. Structured abstracts were prepared, translated into English, Spanish, and Portuguese, assigned Medical Subject Headings (MeSH), and loaded into a Web-based database for public searching. The project has initiated Web-based publication for two LASM journals. Evaluation included measures of use and content. The LASM Website (http://hsc.unm.edu/lasm) and database create access to formerly little-known literature that addresses problems relevant to current medicine and public health. This Website offers a unique resource for researchers, practitioners, and teachers who seek to understand the links between socioeconomic conditions and health. The project provides a model for collaboration between librarians and health care providers. Challenges included procurement of primary material; preparation of concise abstracts; working with trilingual translations of abstracts, metadata, and indexing; and the work processes of the multidisciplinary team. The literature of Latin American social medicine has become more readily available to researchers worldwide. The LASM project serves as a collaborative model for the creation of sustainable solutions for disseminating information that is difficult to access through traditional methods.

Free/Libre Open Source Software in Health Care: A Review

PubMed Central

Schmuhl, Holger; Demski, Hans

2014-01-01

Objectives To assess the current state of the art and the contribution of Free/Libre Open Source Software in health care (FLOSS-HC). Methods The review is based on a narrative review of the scientific literature as well as sources in the context of FLOSS-HC available through the Internet. All relevant available sources have been integrated into the MedFLOSS database and are freely available to the community. Results The literature review reveals that publications about FLOSS-HC are scarce. The largest part of information about FLOSS-HC is available on dedicated websites and not in the academic literature. There are currently FLOSS alternatives available for nearly every specialty in health care. Maturity and quality varies considerably and there is little information available on the percentage of systems that are actually used in health care delivery. Conclusions The global impact of FLOSS-HC is still very limited and no figures on the penetration and usage of FLOSS-HC are available. However, there has been a considerable growth in the last 5 to 10 years. While there where only few systems available a decade ago, in the meantime many systems got available (e.g., more than 300 in the MedFLOSS database). While FLOSS concepts play an important role in most IT related sectors (e.g., telecommunications, embedded devices) the healthcare industry is lagging behind this trend. PMID:24627814

Primary prevention of dental erosion by calcium and fluoride: a systematic review.

PubMed

Zini, A; Krivoroutski, Y; Vered, Y

2014-02-01

Overviews of the current literature only provide summaries of existing relevant preventive strategies for dental erosion. To perform a systematic review according to the quantitative meta-analysis method of the scientific literature on prevention of dental erosion. The focused question will address primary prevention of dental erosion by calcium and fluoride. Randomized clinical trials (RCTs) regarding dental erosion prevention. The search included five databases: Embase, Cochrane database of systematic reviews, PubMed (MEDLINE), FDA publication and Berman medical library of the Hebrew University. The search included data in the English language, with effect on preventing dental erosion always presented as mean enamel loss and measured by profilometer. Statistical meta-analysis was performed by StatsDirect program and PEPI statistical software. Fixed- and random-effect models were used to analyse the data. Heterogeneity tests were employed to validate the fixed-effect model assumption. A total of 475 articles on dental erosion prevention were located. A four-stage selection process was employed, and 10 RCT articles were found to be suitable for meta-analysis. The number of studies on prevention of dental erosion maintaining standards of evidence-based dentistry remains insufficient to reach any definite conclusions. The focused questions of this review cannot be addressed according to the existing literature. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Zirconia in dental implantology: A review

PubMed Central

Apratim, Abhishek; Eachempati, Prashanti; Krishnappa Salian, Kiran Kumar; Singh, Vijendra; Chhabra, Saurabh; Shah, Sanket

2015-01-01

Background: Titanium has been the most popular material of choice for dental implantology over the past few decades. Its properties have been found to be most suitable for the success of implant treatment. But recently, zirconia is slowly emerging as one of the materials which might replace the gold standard of dental implant, i.e., titanium. Materials and Methods: Literature was searched to retrieve information about zirconia dental implant and studies were critically analyzed. PubMed database was searched for information about zirconia dental implant regarding mechanical properties, osseointegration, surface roughness, biocompatibility, and soft tissue health around it. The literature search was limited to English language articles published from 1975 to 2015. Results: A total of 45 papers met the inclusion criteria for this review, among the relevant search in the database. Conclusion: Literature search showed that some of the properties of zirconia seem to be suitable for making it an ideal dental implant, such as biocompatibility, osseointegration, favourable soft tissue response and aesthetics due to light transmission and its color. At the same time, some studies also point out its drawbacks. It was also found that most of the studies on zirconia dental implants are short-term studies and there is a need for more long-term clinical trials to prove that zirconia is worth enough to replace titanium as a biomaterial in dental implantology. PMID:26236672

Influence of gender in the recognition of basic facial expressions: A critical literature review

PubMed Central

Forni-Santos, Larissa; Osório, Flávia L

2015-01-01

AIM: To conduct a systematic literature review about the influence of gender on the recognition of facial expressions of six basic emotions. METHODS: We made a systematic search with the search terms (face OR facial) AND (processing OR recognition OR perception) AND (emotional OR emotion) AND (gender or sex) in PubMed, PsycINFO, LILACS, and SciELO electronic databases for articles assessing outcomes related to response accuracy and latency and emotional intensity. The articles selection was performed according to parameters set by COCHRANE. The reference lists of the articles found through the database search were checked for additional references of interest. RESULTS: In respect to accuracy, women tend to perform better than men when all emotions are considered as a set. Regarding specific emotions, there seems to be no gender-related differences in the recognition of happiness, whereas results are quite heterogeneous in respect to the remaining emotions, especially sadness, anger, and disgust. Fewer articles dealt with the parameters of response latency and emotional intensity, which hinders the generalization of their findings, especially in the face of their methodological differences. CONCLUSION: The analysis of the studies conducted to date do not allow for definite conclusions concerning the role of the observer’s gender in the recognition of facial emotion, mostly because of the absence of standardized methods of investigation. PMID:26425447

A retrospective analysis of in vivo eye irritation, skin irritation and skin sensitisation studies with agrochemical formulations: Setting the scene for development of alternative strategies.

PubMed

Corvaro, M; Gehen, S; Andrews, K; Chatfield, R; Macleod, F; Mehta, J

2017-10-01

Analysis of the prevalence of health effects in large scale databases is key in defining testing strategies within the context of Integrated Approaches on Testing and Assessment (IATA), and is relevant to drive policy changes in existing regulatory toxicology frameworks towards non-animal approaches. A retrospective analysis of existing results from in vivo skin irritation, eye irritation, and skin sensitisation studies on a database of 223 agrochemical formulations is herein published. For skin or eye effects, high prevalence of mild to non-irritant formulations (i.e. per GHS, CLP or EPA classification) would generally suggest a bottom-up approach. Severity of erythema or corneal opacity, for skinor eye effects respectively, were the key drivers for classification, consistent with existing literature. The reciprocal predictivity of skin versus eye irritation and the good negative predictivity of the GHS additivity calculation approach (>85%) provided valuable non-testing evidence for irritation endpoints. For dermal sensitisation, concordance on data from three different methods confirmed the high false negative rate for the Buehler method in this product class. These results have been reviewed together with existing literature on the use of in vitro alternatives for agrochemical formulations, to propose improvements to current regulatory strategies and to identify further research needs. Copyright © 2017 Elsevier Inc. All rights reserved.

Mapping the literature of emergency nursing

PubMed Central

Alpi, Kristine M.

2006-01-01

Purpose: Emergency nursing covers a broad spectrum of health care from trauma surgery support to preventive health care. The purpose of this study is to identify the core literature of emergency nursing and to determine which databases provide the most thorough indexing access to the literature cited in emergency nursing journals. This study is part of the Medical Library Association's Nursing and Allied Health Resources Section's project to map the nursing literature. Methods: Four key emergency nursing journals were selected and subjected to citation analysis based on Bradford's Law of Scattering. Results: A group of 12 journals made up 33.3% of the 7,119 citations, another 33.3% of the citations appeared in 92 journals, with the remaining 33.3% scattered across 822 journals. Three of the core 12 journals were emergency medicine titles, and 2 were emergency nursing titles from the selected source journals. Government publications constituted 7.5% of the literature cited. Conclusions: PubMed/MEDLINE provided the best overall indexing coverage for the journals, followed by CINAHL. However, CINAHL provided the most complete coverage for the source journals and the majority of the nursing and emergency medical technology publications and should be consulted by librarians and nurses seeking emergency nursing literature. PMID:16710456

Chinese journals: a guide for epidemiologists

PubMed Central

Fung, Isaac CH

2008-01-01

Chinese journals in epidemiology, preventive medicine and public health contain much that is of potential international interest. However, few non-Chinese speakers are acquainted with this literature. This article therefore provides an overview of the contemporary scene in Chinese biomedical journal publication, Chinese bibliographic databases and Chinese journals in epidemiology, preventive medicine and public health. The challenge of switching to English as the medium of publication, the development of publishing bibliometric data from Chinese databases, the prospect of an Open Access publication model in China, the issue of language bias in literature reviews and the quality of Chinese journals are discussed. Epidemiologists are encouraged to search the Chinese bibliographic databases for Chinese journal articles. PMID:18826604

A multidisciplinary database for global distribution

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

Wolfe, P.J.

The issue of selenium toxicity in the environment has been documented in the scientific literature for over 50 years. Recent studies reveal a complex connection between selenium and human and animal populations. This article introduces a bibliographic citation database on selenium in the environment developed for global distribution via the Internet by the University of Wyoming Libraries. The database incorporates material from commercial sources, print abstracts, indexes, and U.S. government literature, resulting in a multidisciplinary resource. Relevant disciplines include, biology, medicine, veterinary science, botany, chemistry, geology, pollution, aquatic sciences, ecology, and others. It covers the years 1985-1996 for most subjectmore » material, with additional years being added as resources permit.« less

The Experiences of Students without Disabilities in Inclusive Physical Education Classrooms: A Review of Literature

ERIC Educational Resources Information Center

Ruscitti, Robert Joseph; Thomas, Scott Gordon; Bentley, Danielle Christine

2017-01-01

The purpose of this literature review was to analyse studies of the experiences of students without disabilities (SWOD) in inclusive physical education (PE) classes. The literature published from 1975 to 2015 was compiled from three online databases (PsycInfo, Physical Education Index and ERIC). Included literature met inclusion criteria focussed…

Analyzing Library Literature on Academic Library Automation: Authorship and Subject Coverage.

ERIC Educational Resources Information Center

Lin, Pei-Yu

The purpose of this study is to identify and determine the extent of technological change in the development of automation as it is reflected in the professional literature and the rates at which males and females contribute to this literature. A database search of Library Literature on WILSONDISC was undertaken to identify publications written in…

Pedagogical Approaches to Diagnostic Imaging Education: A Narrative Review of the Literature

PubMed Central

Linaker, Kathleen L.

2015-01-01

Objective The purpose of this study was to examine literature on how radiology is taught and learned by both radiology residents and undergraduates in the health professions. Methods A review of the literature was performed using relevant key words. Articles were retrieved through December 2012 using PubMed, ScienceDirect, ERIC, Proquest, and ICL databases along with a manual review of references. Results Of the 4716 unique abstracts reviewed by the author, 91 were found to be relevant to the purpose of this study. The literature retrieved reported pedagogical approaches to teaching radiology including the following: problem solving, technology as teacher, independent learning tools, visiting lectureships, case based teaching, and conferences. There was some exploration of the relative effectiveness of educational formats. Suggestions for future research identify 7 areas of relative consistency. Conclusion Radiology is a clinical skill that requires integration science, clinical information, clinical experiences, and information recorded on diagnostic imaging studies. The research in this area focuses on problem solving, the use of algorithm/scripts, introducing uncertainty in clinical scenarios, incorporating technology in learning environments, active learning techniques, and methods of independent learning. Although the literature in this area is still in its infancy, the research examining the relative effectiveness of these various educational formats is often contradictory, suggesting that this is a complex area of study with numerous factors influencing student learning. PMID:26770173

The Effect of Calcium Sodium Phosphosilicate on Dentin Hypersensitivity: A Systematic Review and Meta-Analysis

PubMed Central

Chen, Bin; Mei, Li; Yao, Liang; Tian, Jinhui; Li, Huang

2015-01-01

Objective To investigate the effect of calcium sodium phosphosilicate (CSPS) in treating dentin hypersensitivity (DH) and to compare this effect to that of a negative (placebo) control. Materials and Methods Several databases, including Medline, EMBASE, Web of Science, The Cochrane Library, and the Chinese Biomedical Literature Database, were searched to identify relevant articles published through January 2015; grey literature (i.e., academic literature that is not formally published) was also searched. Two authors performed data extraction independently and jointly using data collection forms. The primary outcome was the DH pain response to routine activities or to thermal, tactile, evaporative, or electrical stimuli, and the secondary outcome was the side effects of CSPS use. Each study was evaluated using the Cochrane Collaboration tool for assessing risk bias. Meta-analysis of studies with the same participant demographics, interventions, controls, assessment methods and follow-up periods was performed. The Grading of Recommendations Assessment Development and Evaluation System was used to assess the quality of the evidence and the risk of bias across studies. Results Meta-analysis demonstrated that toothpaste containing 5% CSPS was more effective than the negative control at relieving dentin sensitivity, with the level of evidence classified as “moderate”. In addition, prophylaxis paste containing 15% calcium sodium phosphosilicate was favored over the negative control at reducing post-periodontal therapy hypersensitivity, with the level of evidence categorized as “low”. Only two studies reported side effects of CSPS use. Conclusions The majority of studies found that calcium sodium phosphosilicate was more effective than the negative control at alleviating DH. Because strong evidence is scarce, high-quality, well-designed clinical trials are required in the future before definitive recommendations can be made. PMID:26544035

Climate change and human health: what are the research trends? A scoping review protocol

PubMed Central

Herlihy, Niamh; Bar-Hen, Avner; Verner, Glenn; Fischer, Helen; Sauerborn, Rainer; Depoux, Anneliese; Flahault, Antoine; Schütte, Stefanie

2016-01-01

Introduction For 28 years, the Intergovernmental Panel on Climate Change (IPCC) has been assessing the potential risks associated with anthropogenic climate change. Although interest in climate change and health is growing, the implications arising from their interaction remain understudied. Generating a greater understanding of the health impacts of climate change could be key step in inciting some of the changes necessary to decelerate global warming. A long-term and broad overview of the existing scientific literature in the field of climate change and health is currently missing in order to ensure that all priority areas are being adequately addressed. In this paper we outline our methods to conduct a scoping review of the published peer-reviewed literature on climate change and health between 1990 and 2015. Methods and analysis A detailed search strategy will be used to search the PubMed and Web of Science databases. Specific inclusion and exclusion criteria will be applied in order to capture the most relevant literature in the time frame chosen. Data will be extracted, categorised and coded to allow for statistical analysis of the results. Ethics and dissemination No ethical approval was required for this study. A searchable database of climate change and health publications will be developed and a manuscript will be complied for publication and dissemination of the findings. We anticipate that this study will allow us to map the trends observed in publications over the 25-year time period in climate change and health research. It will also identify the research areas with the highest volume of publications as well as highlight the research trends in climate change and health. PMID:28011805

CardioTF, a database of deconstructing transcriptional circuits in the heart system.

PubMed

Zhen, Yisong

2016-01-01

Information on cardiovascular gene transcription is fragmented and far behind the present requirements of the systems biology field. To create a comprehensive source of data for cardiovascular gene regulation and to facilitate a deeper understanding of genomic data, the CardioTF database was constructed. The purpose of this database is to collate information on cardiovascular transcription factors (TFs), position weight matrices (PWMs), and enhancer sequences discovered using the ChIP-seq method. The Naïve-Bayes algorithm was used to classify literature and identify all PubMed abstracts on cardiovascular development. The natural language learning tool GNAT was then used to identify corresponding gene names embedded within these abstracts. Local Perl scripts were used to integrate and dump data from public databases into the MariaDB management system (MySQL). In-house R scripts were written to analyze and visualize the results. Known cardiovascular TFs from humans and human homologs from fly, Ciona, zebrafish, frog, chicken, and mouse were identified and deposited in the database. PWMs from Jaspar, hPDI, and UniPROBE databases were deposited in the database and can be retrieved using their corresponding TF names. Gene enhancer regions from various sources of ChIP-seq data were deposited into the database and were able to be visualized by graphical output. Besides biocuration, mouse homologs of the 81 core cardiac TFs were selected using a Naïve-Bayes approach and then by intersecting four independent data sources: RNA profiling, expert annotation, PubMed abstracts and phenotype. The CardioTF database can be used as a portal to construct transcriptional network of cardiac development. Database URL: http://www.cardiosignal.org/database/cardiotf.html.

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.

OSTMED.DR®, an Osteopathic Medicine Digital Library.

PubMed

Fitterling, Lori; Powers, Elaine; Vardell, Emily

2018-01-01

The OSTMED.DR® database provides access to both citation and full-text osteopathic literature, including the Journal of the American Osteopathic Association. Currently, it is a free database searchable using basic and advanced search features.

BiKEGG: a COBRA toolbox extension for bridging the BiGG and KEGG databases.

PubMed

Jamialahmadi, Oveis; Motamedian, Ehsan; Hashemi-Najafabadi, Sameereh

2016-10-18

Development of an interface tool between the Biochemical, Genetic and Genomic (BiGG) and KEGG databases is necessary for simultaneous access to the features of both databases. For this purpose, we present the BiKEGG toolbox, an open source COBRA toolbox extension providing a set of functions to infer the reaction correspondences between the KEGG reaction identifiers and those in the BiGG knowledgebase using a combination of manual verification and computational methods. Inferred reaction correspondences using this approach are supported by evidence from the literature, which provides a higher number of reconciled reactions between these two databases compared to the MetaNetX and MetRxn databases. This set of equivalent reactions is then used to automatically superimpose the predicted fluxes using COBRA methods on classical KEGG pathway maps or to create a customized metabolic map based on the KEGG global metabolic pathway, and to find the corresponding reactions in BiGG based on the genome annotation of an organism in the KEGG database. Customized metabolic maps can be created for a set of pathways of interest, for the whole KEGG global map or exclusively for all pathways for which there exists at least one flux carrying reaction. This flexibility in visualization enables BiKEGG to indicate reaction directionality as well as to visualize the reaction fluxes for different static or dynamic conditions in an animated manner. BiKEGG allows the user to export (1) the output visualized metabolic maps to various standard image formats or save them as a video or animated GIF file, and (2) the equivalent reactions for an organism as an Excel spreadsheet.

A Systematic Review of Mixed Methods Research on Human Factors and Ergonomics in Health Care

PubMed Central

Carayon, Pascale; Kianfar, Sarah; Li, Yaqiong; Xie, Anping; Alyousef, Bashar; Wooldridge, Abigail

2016-01-01

This systematic literature review provides information on the use of mixed methods research in human factors and ergonomics (HFE) research in health care. Using the PRISMA methodology, we searched four databases (PubMed, PsycInfo, Web of Science, and Engineering Village) for studies that met the following inclusion criteria: (1) field study in health care, (2) mixing of qualitative and quantitative data, (3) HFE issues, and (4) empirical evidence. Using an iterative and collaborative process supported by a structured data collection form, the six authors identified a total of 58 studies that primarily address HFE issues in health information technology (e.g., usability) and in the work of healthcare workers. About two-thirds of the mixed methods studies used the convergent parallel study design where quantitative and qualitative data were collected simultaneously. A variety of methods were used for collecting data, including interview, survey and observation. The most frequent combination involved interview for qualitative data and survey for quantitative data. The use of mixed methods in healthcare HFE research has increased over time. However, increasing attention should be paid to the formal literature on mixed methods research to enhance the depth and breadth of this research. PMID:26154228

All Information Is Not Equal: Using the Literature Databases PubMed and The Cochrane Library for Identifying the Evidence on Granulocyte Transfusion Therapy.

PubMed

Metzendorf, Maria-Inti; Schulz, Manuela; Braun, Volker

2014-10-01

To be able to take well-informed decisions or carry out sound research, clinicians and researchers alike require specific information seeking skills matching their respective information needs. Biomedical information is traditionally available via different literature databases. This article gives an introduction to two diverging sources, PubMed (23 million references) and The Cochrane Library (800,000 references), both of which offer sophisticated instruments for searching an increasing amount of medical publications of varied quality and ambition. Whereas PubMed as an unfiltered source of primary literature comprises all different kinds of publication types occurring in academic journals, The Cochrane Library is a pre-filtered source which offers access to either synthesized publication types or critically appraised and carefully selected references. A search approach has to be carried out deliberately and requires a good knowledge on the scope and features of the databases as well as on the ability to build a search strategy in a structured way. We present a specific and a sensitive search approach, making use of both databases within two application case scenarios in order to identify the evidence on granulocyte transfusions for infections in adult patients with neutropenia.

Generating PubMed Chemical Queries for Consumer Health Literature

PubMed Central

Loo, Jeffery; Chang, Hua Florence; Hochstein, Colette; Sun, Ying

2005-01-01

Two popular NLM resources that provide information for consumers about chemicals and their safety are the Household Products Database and Haz-Map. Search queries to PubMed via web links were generated from these databases. The query retrieves consumer health-oriented literature about adverse effects of chemicals. The retrieval was limited to a manageable set of 20 to 60 citations, achieved by successively applying increasing limits to the search until the desired number of references was reached. PMID:16779322

Mass Casualty Incident Primary Triage Methods in China.

PubMed

Chen, Jin-Hong; Yang, Jun; Yang, Yu; Zheng, Jing-Chen

2015-10-05

To evaluate the technical characteristics and application of mass casualty incident (MCI) primary triage (PT) methods applied in China. Chinese literature was searched by Chinese Academic Journal Network Publishing Database (founded in June 2014). The English literature was searched by PubMed (MEDLINE) (1950 to June 2014). We also searched Official Websites of Chinese Central Government's (http://www.gov.cn/), National Health and Family Planning Commission of China (http://www.nhfpc.gov.cn/), and China Earthquake Information (http://www.csi.ac.cn/). We included studies associated with mass casualty events related to China, the PT applied in China, guidelines and standards, and application and development of the carding PT method in China. From 3976 potentially relevant articles, 22 met the inclusion criteria, 20 Chinese, and 2 English. These articles included 13 case reports, 3 retrospective analyses of MCI, two methods introductions, three national or sectoral criteria, and one simulated field testing and validation. There were a total of 19 kinds of MCI PT methods that have been reported in China from 1950 to 2014. In addition, there were 15 kinds of PT methods reported in the literature from the instance of the application. The national and sectoral current triage criteria are developed mainly for earthquake relief. Classification is not clear. Vague criteria (especially between moderate and severe injuries) operability are not practical. There are no triage methods and research for children and special populations. There is no data and evidence supported triage method. We should revise our existing classification and criteria so it is clearer and easier to be grasped in order to build a real, practical, and efficient PT method.

Healthy Settings in Hospital - How to Prevent Burnout Syndrome in Nurses: Literature Review.

PubMed

Friganović, Adriano; Kovačević, Irena; Ilić, Boris; Žulec, Mirna; Krikšić, Valentina; Grgas Bile, Cecilija

2017-06-01

Healthy settings involve a holistic and multidisciplinary method that integrates actions towards risk factors. In hospital settings, a high level of stress can lead to depression, anxiety, decreased job satisfaction and lower loyalty to the organization. Burnout syndrome can be defined as physical, psychological and emotional exhaustion, depersonalization, and low sense of personal accomplishment. The aim of this literature review was to make systematic literature analysis to provide scientific evidence for the consequences of constant exposure to high levels of stress and for the methods to be used to prevent burnout syndrome among health care workers. The Medline database was searched to identify relevant studies and articles published during the last 15 years. The key words used in this survey were burnout syndrome, prevention, nurses, and healthy settings. The 6 eligible studies were included in literature review. Evidence showed nurses to be exposed to stress and to have symptoms of burnout syndrome. As a result of burnout syndrome, chronic fatigue and reduced working capacity occur, thus raising the risk of adverse events. In conclusion, the occurrence of burnout syndrome is a major problem for hospitals and healthcare system. Action plan for hospital burnout syndrome prevention would greatly reduce the incidence and improve the quality of health care.

Diagnosis and management of primary hepatic pregnancy: literature review of 31 cases.

PubMed

Wang, Jicai; Su, Zhilei; Lu, Shounan; Fu, Wen; Liu, Zhifa; Jiang, Xingming; Tai, Sheng

2018-05-21

To summarize the appropriate diagnostic methods and therapeutic options for primary hepatic pregnancy (PHP). Literature searches were performed in Pubmed, Web of Science, Cochrane Library and Embase databases (1956-2017), using the following search terms: primary hepatic pregnancy, hepatic pregnancy, liver pregnancy, hepatic ectopic pregnancy and intrahepatic pregnancy. Further literature was confirmed through cross-referencing. Thirty-one cases were reviewed and collected. The site mostly described in literatures is the right lobe of liver (93.5%). Main symptoms of PHP included abdominal pain (77.4%), amenorrhea (45.2%), acuteperitonism (32.3%), shock (25.8%) and vomit (16.1%). Majority of patients (83.9%) were treated by laparotomy. Less-invasive approaches (16.1%) such as laparoscopy or combination of postoperative injection of methotrexate were used less frequently. The outcome was acceptable at the end of the follow-up period in ten cases (1-72 months) and the recovery rate was 96.7%. One patient died and other complications were noted in three patients during the postoperative period. The clinical diagnosis of PHP can be settled up by comprehensive analysis of serum HCG levels, ultrasound and imaging. The analysis should be assessed carefully before therapeutic procedure. Invasive methods should be preferential. Less-invasive approaches can be selected when the patients have stable hemodynamics and non-acute abdomen.

HNdb: an integrated database of gene and protein information on head and neck squamous cell carcinoma

PubMed Central

Henrique, Tiago; José Freitas da Silveira, Nelson; Henrique Cunha Volpato, Arthur; Mioto, Mayra Mataruco; Carolina Buzzo Stefanini, Ana; Bachir Fares, Adil; Gustavo da Silva Castro Andrade, João; Masson, Carolina; Verónica Mendoza López, Rossana; Daumas Nunes, Fabio; Paulo Kowalski, Luis; Severino, Patricia; Tajara, Eloiza Helena

2016-01-01

The total amount of scientific literature has grown rapidly in recent years. Specifically, there are several million citations in the field of cancer. This makes it difficult, if not impossible, to manually retrieve relevant information on the mechanisms that govern tumor behavior or the neoplastic process. Furthermore, cancer is a complex disease or, more accurately, a set of diseases. The heterogeneity that permeates many tumors is particularly evident in head and neck (HN) cancer, one of the most common types of cancer worldwide. In this study, we present HNdb, a free database that aims to provide a unified and comprehensive resource of information on genes and proteins involved in HN squamous cell carcinoma, covering data on genomics, transcriptomics, proteomics, literature citations and also cross-references of external databases. Different literature searches of MEDLINE abstracts were performed using specific Medical Subject Headings (MeSH terms) for oral, oropharyngeal, hypopharyngeal and laryngeal squamous cell carcinomas. A curated gene-to-publication assignment yielded a total of 1370 genes related to HN cancer. The diversity of results allowed identifying novel and mostly unexplored gene associations, revealing, for example, that processes linked to response to steroid hormone stimulus are significantly enriched in genes related to HN carcinomas. Thus, our database expands the possibilities for gene networks investigation, providing potential hypothesis to be tested. Database URL: http://www.gencapo.famerp.br/hndb PMID:27013077

Ureteral endometriosis: A systematic literature review

PubMed Central

Palla, Viktoria-Varvara; Karaolanis, Georgios; Katafigiotis, Ioannis; Anastasiou, Ioannis

2017-01-01

Introduction: Ureteral endometriosis is a rare disease affecting women of childbearing age which presents with nonspecific symptoms and it may result in severe morbidity. The aim of this study was to review evidence about incidence, pathogenesis, clinical presentation, diagnosis, and management of ureteral endometriosis. Materials and Methods: PubMed Central database was searched to identify studies reporting cases of ureteral endometriosis. “Ureter” or “Ureteral” and “Endometriosis” were used as key words. Database was searched for articles published since 1996, in English without restrictions regarding the study design. Results: From 420 studies obtained through database search, 104 articles were finally included in this review, including a total of 1384 patients with ureteral endometriosis. Data regarding age, location, pathological findings, and interventions were extracted. Mean patients' age was 38.6 years, whereas the therapeutic arsenal included hormonal, endoscopic, and/or surgical treatment. Conclusions: Ureteral endometriosis represents a diagnostic and therapeutic challenge for the clinicians and high clinical suspicion is needed to identify it. PMID:29021650

Implementing the EuroFIR Document and Data Repositories as accessible resources of food composition information.

PubMed

Unwin, Ian; Jansen-van der Vliet, Martine; Westenbrink, Susanne; Presser, Karl; Infanger, Esther; Porubska, Janka; Roe, Mark; Finglas, Paul

2016-02-15

The EuroFIR Document and Data Repositories are being developed as accessible collections of source documents, including grey literature, and the food composition data reported in them. These Repositories will contain source information available to food composition database compilers when selecting their nutritional data. The Document Repository was implemented as searchable bibliographic records in the Europe PubMed Central database, which links to the documents online. The Data Repository will contain original data from source documents in the Document Repository. Testing confirmed the FoodCASE food database management system as a suitable tool for the input, documentation and quality assessment of Data Repository information. Data management requirements for the input and documentation of reported analytical results were established, including record identification and method documentation specifications. Document access and data preparation using the Repositories will provide information resources for compilers, eliminating duplicated work and supporting unambiguous referencing of data contributing to their compiled data. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

Optimizing literature search in systematic reviews - are MEDLINE, EMBASE and CENTRAL enough for identifying effect studies within the area of musculoskeletal disorders?

PubMed

Aagaard, Thomas; Lund, Hans; Juhl, Carsten

2016-11-22

When conducting systematic reviews, it is essential to perform a comprehensive literature search to identify all published studies relevant to the specific research question. The Cochrane Collaborations Methodological Expectations of Cochrane Intervention Reviews (MECIR) guidelines state that searching MEDLINE, EMBASE and CENTRAL should be considered mandatory. The aim of this study was to evaluate the MECIR recommendations to use MEDLINE, EMBASE and CENTRAL combined, and examine the yield of using these to find randomized controlled trials (RCTs) within the area of musculoskeletal disorders. Data sources were systematic reviews published by the Cochrane Musculoskeletal Review Group, including at least five RCTs, reporting a search history, searching MEDLINE, EMBASE, CENTRAL, and adding reference- and hand-searching. Additional databases were deemed eligible if they indexed RCTs, were in English and used in more than three of the systematic reviews. Relative recall was calculated as the number of studies identified by the literature search divided by the number of eligible studies i.e. included studies in the individual systematic reviews. Finally, cumulative median recall was calculated for MEDLINE, EMBASE and CENTRAL combined followed by the databases yielding additional studies. Deemed eligible was twenty-three systematic reviews and the databases included other than MEDLINE, EMBASE and CENTRAL was AMED, CINAHL, HealthSTAR, MANTIS, OT-Seeker, PEDro, PsychINFO, SCOPUS, SportDISCUS and Web of Science. Cumulative median recall for combined searching in MEDLINE, EMBASE and CENTRAL was 88.9% and increased to 90.9% when adding 10 additional databases. Searching MEDLINE, EMBASE and CENTRAL was not sufficient for identifying all effect studies on musculoskeletal disorders, but additional ten databases did only increase the median recall by 2%. It is possible that searching databases is not sufficient to identify all relevant references, and that reviewers must rely upon additional sources in their literature search. However further research is needed.

Comparative study of multimodal biometric recognition by fusion of iris and fingerprint.

PubMed

Benaliouche, Houda; Touahria, Mohamed

2014-01-01

This research investigates the comparative performance from three different approaches for multimodal recognition of combined iris and fingerprints: classical sum rule, weighted sum rule, and fuzzy logic method. The scores from the different biometric traits of iris and fingerprint are fused at the matching score and the decision levels. The scores combination approach is used after normalization of both scores using the min-max rule. Our experimental results suggest that the fuzzy logic method for the matching scores combinations at the decision level is the best followed by the classical weighted sum rule and the classical sum rule in order. The performance evaluation of each method is reported in terms of matching time, error rates, and accuracy after doing exhaustive tests on the public CASIA-Iris databases V1 and V2 and the FVC 2004 fingerprint database. Experimental results prior to fusion and after fusion are presented followed by their comparison with related works in the current literature. The fusion by fuzzy logic decision mimics the human reasoning in a soft and simple way and gives enhanced results.

Comparative Study of Multimodal Biometric Recognition by Fusion of Iris and Fingerprint

PubMed Central

Benaliouche, Houda; Touahria, Mohamed

2014-01-01

This research investigates the comparative performance from three different approaches for multimodal recognition of combined iris and fingerprints: classical sum rule, weighted sum rule, and fuzzy logic method. The scores from the different biometric traits of iris and fingerprint are fused at the matching score and the decision levels. The scores combination approach is used after normalization of both scores using the min-max rule. Our experimental results suggest that the fuzzy logic method for the matching scores combinations at the decision level is the best followed by the classical weighted sum rule and the classical sum rule in order. The performance evaluation of each method is reported in terms of matching time, error rates, and accuracy after doing exhaustive tests on the public CASIA-Iris databases V1 and V2 and the FVC 2004 fingerprint database. Experimental results prior to fusion and after fusion are presented followed by their comparison with related works in the current literature. The fusion by fuzzy logic decision mimics the human reasoning in a soft and simple way and gives enhanced results. PMID:24605065

Electronic Biomedical Literature Search for Budding Researcher

PubMed Central

Thakre, Subhash B.; Thakre S, Sushama S.; Thakre, Amol D.

2013-01-01

Search for specific and well defined literature related to subject of interest is the foremost step in research. When we are familiar with topic or subject then we can frame appropriate research question. Appropriate research question is the basis for study objectives and hypothesis. The Internet provides a quick access to an overabundance of the medical literature, in the form of primary, secondary and tertiary literature. It is accessible through journals, databases, dictionaries, textbooks, indexes, and e-journals, thereby allowing access to more varied, individualised, and systematic educational opportunities. Web search engine is a tool designed to search for information on the World Wide Web, which may be in the form of web pages, images, information, and other types of files. Search engines for internet-based search of medical literature include Google, Google scholar, Scirus, Yahoo search engine, etc., and databases include MEDLINE, PubMed, MEDLARS, etc. Several web-libraries (National library Medicine, Cochrane, Web of Science, Medical matrix, Emory libraries) have been developed as meta-sites, providing useful links to health resources globally. A researcher must keep in mind the strengths and limitations of a particular search engine/database while searching for a particular type of data. Knowledge about types of literature, levels of evidence, and detail about features of search engine as available, user interface, ease of access, reputable content, and period of time covered allow their optimal use and maximal utility in the field of medicine. Literature search is a dynamic and interactive process; there is no one way to conduct a search and there are many variables involved. It is suggested that a systematic search of literature that uses available electronic resource effectively, is more likely to produce quality research. PMID:24179937

Electronic biomedical literature search for budding researcher.

PubMed

Thakre, Subhash B; Thakre S, Sushama S; Thakre, Amol D

2013-09-01

Search for specific and well defined literature related to subject of interest is the foremost step in research. When we are familiar with topic or subject then we can frame appropriate research question. Appropriate research question is the basis for study objectives and hypothesis. The Internet provides a quick access to an overabundance of the medical literature, in the form of primary, secondary and tertiary literature. It is accessible through journals, databases, dictionaries, textbooks, indexes, and e-journals, thereby allowing access to more varied, individualised, and systematic educational opportunities. Web search engine is a tool designed to search for information on the World Wide Web, which may be in the form of web pages, images, information, and other types of files. Search engines for internet-based search of medical literature include Google, Google scholar, Scirus, Yahoo search engine, etc., and databases include MEDLINE, PubMed, MEDLARS, etc. Several web-libraries (National library Medicine, Cochrane, Web of Science, Medical matrix, Emory libraries) have been developed as meta-sites, providing useful links to health resources globally. A researcher must keep in mind the strengths and limitations of a particular search engine/database while searching for a particular type of data. Knowledge about types of literature, levels of evidence, and detail about features of search engine as available, user interface, ease of access, reputable content, and period of time covered allow their optimal use and maximal utility in the field of medicine. Literature search is a dynamic and interactive process; there is no one way to conduct a search and there are many variables involved. It is suggested that a systematic search of literature that uses available electronic resource effectively, is more likely to produce quality research.

Drug interaction databases in medical literature: transparency of ownership, funding, classification algorithms, level of documentation, and staff qualifications. A systematic review.

PubMed

Kongsholm, Gertrud Gansmo; Nielsen, Anna Katrine Toft; Damkier, Per

2015-11-01

It is well documented that drug-drug interaction databases (DIDs) differ substantially with respect to classification of drug-drug interactions (DDIs). The aim of this study was to study online available transparency of ownership, funding, information, classifications, staff training, and underlying documentation of the five most commonly used open access English language-based online DIDs and the three most commonly used subscription English language-based online DIDs in the literature. We conducted a systematic literature search to identify the five most commonly used open access and the three most commonly used subscription DIDs in the medical literature. The following parameters were assessed for each of the databases: Ownership, classification of interactions, primary information sources, and staff qualification. We compared the overall proportion of yes/no answers from open access databases and subscription databases by Fisher's exact test-both prior to and after requesting missing information. Among open access DIDs, 20/60 items could be verified from the webpage directly compared to 24/36 for the subscription DIDs (p = 0.0028). Following personal request, these numbers rose to 22/60 and 30/36, respectively (p < 0.0001). For items within the "classification of interaction" domain, proportions were 3/25 versus 11/15 available from the webpage (P = 0.0001) and 3/25 versus 15/15 (p < 0.0001) available upon personal request. Available information on online available transparency of ownership, funding, information, classifications, staff training, and underlying documentation varies substantially among various DIDs. Open access DIDs had a statistically lower score on parameters assessed.

COMPARISON OF EXERCISE PARTICIPATION RATES FOR CHILDREN IN THE LITERATURE WITH THOSE IN EPA'S CONSOLIDATED HUMAN ACTIVITY DATABASE (CHAD)

EPA Science Inventory

CHAD contains over 22,000 person-days of human activity pattern survey data. Part of the database includes exercise participation rates for children 0-17 years old, as well as for adults. Analyses of this database indicates that approximately 34% of the 0-17 age group (herea...

Semantic Similarities between a Keyword Database and a Controlled Vocabulary Database: An Investigation in the Antibiotic Resistance Literature.

ERIC Educational Resources Information Center

Qin, Jian

2000-01-01

Explores similarities or dissimilarities between citation-semantic and analytic indexing based on a study of records in the Science Citation Index and MEDLINE databases on antibiotic resistance in pneumonia. Concludes that disparate indexing terms may be an advantage for better recall and precision in information retrieval. (Contains 42…

Common Database Interface for Heterogeneous Software Engineering Tools.

DTIC Science & Technology

1987-12-01

SUB-GROUP Database Management Systems ;Programming(Comuters); 1e 05 Computer Files;Information Transfer;Interfaces; 19. ABSTRACT (Continue on reverse...Air Force Institute of Technology Air University In Partial Fulfillment of the Requirements for the Degree of Master of Science in Information Systems ...Literature ..... 8 System 690 Configuration ......... 8 Database Functionis ............ 14 Software Engineering Environments ... 14 Data Manager

[Bibliometrics and visualization analysis of land use regression models in ambient air pollution research].

PubMed

Zhang, Y J; Zhou, D H; Bai, Z P; Xue, F X

2018-02-10

Objective: To quantitatively analyze the current status and development trends regarding the land use regression (LUR) models on ambient air pollution studies. Methods: Relevant literature from the PubMed database before June 30, 2017 was analyzed, using the Bibliographic Items Co-occurrence Matrix Builder (BICOMB 2.0). Keywords co-occurrence networks, cluster mapping and timeline mapping were generated, using the CiteSpace 5.1.R5 software. Relevant literature identified in three Chinese databases was also reviewed. Results: Four hundred sixty four relevant papers were retrieved from the PubMed database. The number of papers published showed an annual increase, in line with the growing trend of the index. Most papers were published in the journal of Environmental Health Perspectives . Results from the Co-word cluster analysis identified five clusters: cluster#0 consisted of birth cohort studies related to the health effects of prenatal exposure to air pollution; cluster#1 referred to land use regression modeling and exposure assessment; cluster#2 was related to the epidemiology on traffic exposure; cluster#3 dealt with the exposure to ultrafine particles and related health effects; cluster#4 described the exposure to black carbon and related health effects. Data from Timeline mapping indicated that cluster#0 and#1 were the main research areas while cluster#3 and#4 were the up-coming hot areas of research. Ninety four relevant papers were retrieved from the Chinese databases with most of them related to studies on modeling. Conclusion: In order to better assess the health-related risks of ambient air pollution, and to best inform preventative public health intervention policies, application of LUR models to environmental epidemiology studies in China should be encouraged.

An online spatial database of Australian Indigenous Biocultural Knowledge for contemporary natural and cultural resource management.

PubMed

Pert, Petina L; Ens, Emilie J; Locke, John; Clarke, Philip A; Packer, Joanne M; Turpin, Gerry

2015-11-15

With growing international calls for the enhanced involvement of Indigenous peoples and their biocultural knowledge in managing conservation and the sustainable use of physical environment, it is timely to review the available literature and develop cross-cultural approaches to the management of biocultural resources. Online spatial databases are becoming common tools for educating land managers about Indigenous Biocultural Knowledge (IBK), specifically to raise a broad awareness of issues, identify knowledge gaps and opportunities, and to promote collaboration. Here we describe a novel approach to the application of internet and spatial analysis tools that provide an overview of publically available documented Australian IBK (AIBK) and outline the processes used to develop the online resource. By funding an AIBK working group, the Australian Centre for Ecological Analysis and Synthesis (ACEAS) provided a unique opportunity to bring together cross-cultural, cross-disciplinary and trans-organizational contributors who developed these resources. Without such an intentionally collaborative process, this unique tool would not have been developed. The tool developed through this process is derived from a spatial and temporal literature review, case studies and a compilation of methods, as well as other relevant AIBK papers. The online resource illustrates the depth and breadth of documented IBK and identifies opportunities for further work, partnerships and investment for the benefit of not only Indigenous Australians, but all Australians. The database currently includes links to over 1500 publically available IBK documents, of which 568 are geo-referenced and were mapped. It is anticipated that as awareness of the online resource grows, more documents will be provided through the website to build the database. It is envisaged that this will become a well-used tool, integral to future natural and cultural resource management and maintenance. Copyright © 2015. Published by Elsevier B.V.

Supplement to the Carcinogenic Potency Database (CPDB): Results ofanimal bioassays published in the general literature through 1997 and bythe National Toxicology Program in 1997-1998

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

Gold, Lois Swirsky; Manley, Neela B.; Slone, Thomas H.

2005-04-08

The Carcinogenic Potency Database (CPDB) is a systematic and unifying resource that standardizes the results of chronic, long-term animal cancer tests which have been conducted since the 1950s. The analyses include sufficient information on each experiment to permit research into many areas of carcinogenesis. Both qualitative and quantitative information is reported on positive and negative experiments that meet a set of inclusion criteria. A measure of carcinogenic potency, TD50 (daily dose rate in mg/kg body weight/day to induce tumors in half of test animals that would have remained tumor-free at zero dose), is estimated for each tissue-tumor combination reported. Thismore » article is the ninth publication of a chronological plot of the CPDB; it presents results on 560 experiments of 188 chemicals in mice, rats, and hamsters from 185 publications in the general literature updated through 1997, and from 15 Reports of the National Toxicology Program in 1997-1998. The test agents cover a wide variety of uses and chemical classes. The CPDB Web Site(http://potency.berkeley.edu/) presents the combined database of all published plots in a variety of formats as well as summary tables by chemical and by target organ, supplemental materials on dosing and survival, a detailed guide to using the plot formats, and documentation of methods and publications. The overall CPDB, including the results in this article, presents easily accessible results of 6153 experiments on 1485 chemicals from 1426 papers and 429 NCI/NTP (National Cancer Institute/National Toxicology program) Technical Reports. A tab-separated format of the full CPDB for reading the data into spreadsheets or database applications is available on the Web Site.« less

Content Analysis of the Increasing Trend of Information Brokers.

ERIC Educational Resources Information Center

Wilson, Luellen

This study tracks the increasing use of the term "information broker" in the professional library literature, and looks at the extent to which the professional literature reflects the increasing trend of information commodification. The content of three online databases was analyzed: LIBRARY LITERATURE, LISA, and ABI/INFORM. Four terms…

Social Peer Interactions in Persons with Profound Intellectual and Multiple Disabilities: A Literature Review

ERIC Educational Resources Information Center

Nijs, Sara; Maes, Bea

2014-01-01

Social interactions may positively influence developmental and quality of life outcomes. Research in persons with profound intellectual and multiple disabilities (PIMD) mostly investigated interactions with caregivers. This literature review focuses on peer interactions of persons with PIMD. A computerized literature search of three databases was…

Business English as a Lingua Franca (BELF)

ERIC Educational Resources Information Center

Wu, Yan

2013-01-01

This paper examines BELF (Business English as a Lingua Franca) teaching and researching in China. A literature review is conducted using the China National Knowledge Infrastructure (CNKI) database. This survey includes a cursory literature search on BELF and a thorough literature study of 12 Chinese major academic journals. From the data collected…

The NCBI BioSystems database.

PubMed

Geer, Lewis Y; Marchler-Bauer, Aron; Geer, Renata C; Han, Lianyi; He, Jane; He, Siqian; Liu, Chunlei; Shi, Wenyao; Bryant, Stephen H

2010-01-01

The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationships from the literature or multiple experimental datasets.

Mapping the literature of health care chaplaincy.

PubMed

Johnson, Emily; Dodd-McCue, Diane; Tartaglia, Alexander; McDaniel, Jennifer

2013-07-01

This study examined citation patterns and indexing coverage from 2008 to 2010 to determine (1) the core literature of health care chaplaincy and (2) the resources providing optimum coverage for the literature. Citations from three source journals (2008-2010 inclusive) were collected and analyzed according to the protocol created for the Mapping the Literature of Allied Health Professions Project. An analysis of indexing coverage by five databases was conducted. A secondary analysis of self-citations by source journals was also conducted. The 3 source journals--Chaplaincy Today, the Journal of Health Care Chaplaincy, and the Journal of Pastoral Care and Counseling--ranked as the top 3 journals in Zone 1 and provided the highest number of most frequently cited articles for health care chaplaincy. Additional journals that appeared in this highly productive zone covered the disciplines of medicine, psychology, nursing, and religion, which were also represented in the Zones 2 and 3 journals. None of the databases provided complete coverage for the core journals; however, MEDLINE provided the most comprehensive coverage for journals in Zones 1 and 2, followed by Academic Search Complete, CINAHL, PsycINFO, and ATLA. Self-citations for the source journals ranged from 9% to 16%. Health care chaplaincy draws from a diverse body of inter-professional literature. Libraries wishing to provide access to journal literature to support health care chaplaincy at their institutions will be best able to do this by subscribing to databases and journals that cover medical, psychological, nursing, and religion- or spirituality-focused disciplines.

Mapping the literature of clinical laboratory science.

PubMed

Delwiche, Frances A

2003-07-01

This paper describes a citation analysis of the literature of clinical laboratory science (medical technology), conducted as part of a project of the Nursing and Allied Health Resources Section of the Medical Library Association. Three source journals widely read by those in the field were identified, from which cited references were collected for a three-year period. Analysis of the references showed that journals were the predominant format of literature cited and the majority of the references were from the last eleven years. Applying Bradford's Law of Scattering to the list of journals cited, three zones were created, each producing approximately one third of the cited references. Thirteen journals were in the first zone, eighty-one in the second, and 849 in the third. A similar list of journals cited was created for four specialty areas in the field: chemistry, hematology, immunohematology, and microbiology. In comparing the indexing coverage of the Zone 1 and 2 journals by four major databases, MEDLINE provided the most comprehensive coverage, while the Cumulative Index to Nursing and Allied Health Literature was the only database that provided complete coverage of the three source journals. However, to obtain complete coverage of the field, it is essential to search multiple databases.

Mapping the literature of clinical laboratory science

PubMed Central

Delwiche, Frances A.

2003-01-01

This paper describes a citation analysis of the literature of clinical laboratory science (medical technology), conducted as part of a project of the Nursing and Allied Health Resources Section of the Medical Library Association. Three source journals widely read by those in the field were identified, from which cited references were collected for a three-year period. Analysis of the references showed that journals were the predominant format of literature cited and the majority of the references were from the last eleven years. Applying Bradford's Law of Scattering to the list of journals cited, three zones were created, each producing approximately one third of the cited references. Thirteen journals were in the first zone, eighty-one in the second, and 849 in the third. A similar list of journals cited was created for four specialty areas in the field: chemistry, hematology, immunohematology, and microbiology. In comparing the indexing coverage of the Zone 1 and 2 journals by four major databases, MEDLINE provided the most comprehensive coverage, while the Cumulative Index to Nursing and Allied Health Literature was the only database that provided complete coverage of the three source journals. However, to obtain complete coverage of the field, it is essential to search multiple databases. PMID:12883564

The Protein Information Resource: an integrated public resource of functional annotation of proteins

PubMed Central

Wu, Cathy H.; Huang, Hongzhan; Arminski, Leslie; Castro-Alvear, Jorge; Chen, Yongxing; Hu, Zhang-Zhi; Ledley, Robert S.; Lewis, Kali C.; Mewes, Hans-Werner; Orcutt, Bruce C.; Suzek, Baris E.; Tsugita, Akira; Vinayaka, C. R.; Yeh, Lai-Su L.; Zhang, Jian; Barker, Winona C.

2002-01-01

The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the PIR-International Protein Sequence Database (PSD), the major annotated protein sequence database in the public domain, containing about 250 000 proteins. To improve protein annotation and the coverage of experimentally validated data, a bibliography submission system is developed for scientists to submit, categorize and retrieve literature information. Comprehensive protein information is available from iProClass, which includes family classification at the superfamily, domain and motif levels, structural and functional features of proteins, as well as cross-references to over 40 biological databases. To provide timely and comprehensive protein data with source attribution, we have introduced a non-redundant reference protein database, PIR-NREF. The database consists of about 800 000 proteins collected from PIR-PSD, SWISS-PROT, TrEMBL, GenPept, RefSeq and PDB, with composite protein names and literature data. To promote database interoperability, we provide XML data distribution and open database schema, and adopt common ontologies. The PIR web site (http://pir.georgetown.edu/) features data mining and sequence analysis tools for information retrieval and functional identification of proteins based on both sequence and annotation information. The PIR databases and other files are also available by FTP (ftp://nbrfa.georgetown.edu/pir_databases). PMID:11752247

A review on computational systems biology of pathogen–host interactions

PubMed Central

Durmuş, Saliha; Çakır, Tunahan; Özgür, Arzucan; Guthke, Reinhard

2015-01-01

Pathogens manipulate the cellular mechanisms of host organisms via pathogen–host interactions (PHIs) in order to take advantage of the capabilities of host cells, leading to infections. The crucial role of these interspecies molecular interactions in initiating and sustaining infections necessitates a thorough understanding of the corresponding mechanisms. Unlike the traditional approach of considering the host or pathogen separately, a systems-level approach, considering the PHI system as a whole is indispensable to elucidate the mechanisms of infection. Following the technological advances in the post-genomic era, PHI data have been produced in large-scale within the last decade. Systems biology-based methods for the inference and analysis of PHI regulatory, metabolic, and protein–protein networks to shed light on infection mechanisms are gaining increasing demand thanks to the availability of omics data. The knowledge derived from the PHIs may largely contribute to the identification of new and more efficient therapeutics to prevent or cure infections. There are recent efforts for the detailed documentation of these experimentally verified PHI data through Web-based databases. Despite these advances in data archiving, there are still large amounts of PHI data in the biomedical literature yet to be discovered, and novel text mining methods are in development to unearth such hidden data. Here, we review a collection of recent studies on computational systems biology of PHIs with a special focus on the methods for the inference and analysis of PHI networks, covering also the Web-based databases and text-mining efforts to unravel the data hidden in the literature. PMID:25914674

A general structure-property relationship to predict the enthalpy of vaporisation at ambient temperatures.

PubMed

Oberg, T

2007-01-01

The vapour pressure is the most important property of an anthropogenic organic compound in determining its partitioning between the atmosphere and the other environmental media. The enthalpy of vaporisation quantifies the temperature dependence of the vapour pressure and its value around 298 K is needed for environmental modelling. The enthalpy of vaporisation can be determined by different experimental methods, but estimation methods are needed to extend the current database and several approaches are available from the literature. However, these methods have limitations, such as a need for other experimental results as input data, a limited applicability domain, a lack of domain definition, and a lack of predictive validation. Here we have attempted to develop a quantitative structure-property relationship (QSPR) that has general applicability and is thoroughly validated. Enthalpies of vaporisation at 298 K were collected from the literature for 1835 pure compounds. The three-dimensional (3D) structures were optimised and each compound was described by a set of computationally derived descriptors. The compounds were randomly assigned into a calibration set and a prediction set. Partial least squares regression (PLSR) was used to estimate a low-dimensional QSPR model with 12 latent variables. The predictive performance of this model, within the domain of application, was estimated at n=560, q2Ext=0.968 and s=0.028 (log transformed values). The QSPR model was subsequently applied to a database of 100,000+ structures, after a similar 3D optimisation and descriptor generation. Reliable predictions can be reported for compounds within the previously defined applicability domain.

Food composition database development for between country comparisons.

PubMed

Merchant, Anwar T; Dehghan, Mahshid

2006-01-19

Nutritional assessment by diet analysis is a two-stepped process consisting of evaluation of food consumption, and conversion of food into nutrient intake by using a food composition database, which lists the mean nutritional values for a given food portion. Most reports in the literature focus on minimizing errors in estimation of food consumption but the selection of a specific food composition table used in nutrient estimation is also a source of errors. We are conducting a large prospective study internationally and need to compare diet, assessed by food frequency questionnaires, in a comparable manner between different countries. We have prepared a multi-country food composition database for nutrient estimation in all the countries participating in our study. The nutrient database is primarily based on the USDA food composition database, modified appropriately with reference to local food composition tables, and supplemented with recipes of locally eaten mixed dishes. By doing so we have ensured that the units of measurement, method of selection of foods for testing, and assays used for nutrient estimation are consistent and as current as possible, and yet have taken into account some local variations. Using this common metric for nutrient assessment will reduce differential errors in nutrient estimation and improve the validity of between-country comparisons.

PDB-wide collection of binding data: current status of the PDBbind database.

PubMed

Liu, Zhihai; Li, Yan; Han, Li; Li, Jie; Liu, Jie; Zhao, Zhixiong; Nie, Wei; Liu, Yuchen; Wang, Renxiao

2015-02-01

Molecular recognition between biological macromolecules and organic small molecules plays an important role in various life processes. Both structural information and binding data of biomolecular complexes are indispensable for depicting the underlying mechanism in such an event. The PDBbind database was created to collect experimentally measured binding data for the biomolecular complexes throughout the Protein Data Bank (PDB). It thus provides the linkage between structural information and energetic properties of biomolecular complexes, which is especially desirable for computational studies or statistical analyses. Since its first public release in 2004, the PDBbind database has been updated on an annual basis. The latest release (version 2013) provides experimental binding affinity data for 10,776 biomolecular complexes in PDB, including 8302 protein-ligand complexes and 2474 other types of complexes. In this article, we will describe the current methods used for compiling PDBbind and the updated status of this database. We will also review some typical applications of PDBbind published in the scientific literature. All contents of this database are freely accessible at the PDBbind-CN Web server at http://www.pdbbind-cn.org/. wangrx@mail.sioc.ac.cn. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Orthodontic extrusion for pre-implant site enhancement: Principles and clinical guidelines.

PubMed

Alsahhaf, Abdulaziz; Att, Wael

2016-07-01

The aim of this paper is to provide a concise overview about the principles of pre-implant orthodontic extrusion, describe methods and techniques available and provide the clinicians with guidelines about its application. A number of reports describe orthodontic extrusion as a reliable method for pre-implant site enhancement. However, no standard protocols have been provided about the application of this technique. The literature database was searched for studies involving implant site enhancement by means of orthodontic extrusion. Information about the principles, indications and contraindications of this method, type of anchorage, force and time were obtained from the literature. Despite that the scarce data is largely limited to case reports and case series, implant site enhancement by means of orthodontic extrusion seems to be a promising option to improve soft and hard tissue conditions prior to implant placement. Orthodontic extrusion is being implemented as a treatment alternative to enhance hard and soft tissue prior to implant placement. While the current literature does not provide clear guidelines, the decision making for a specific approach seems to be based on the clinician's preferences. Clinical studies are needed to verify the validity of this treatment option. Copyright © 2016 Japan Prosthodontic Society. Published by Elsevier Ltd. All rights reserved.

[Survey of Literature on the Development of an Evidence Database for Hospital-prepared Drugs in Japan].

PubMed

Momo, Kenji

2018-01-01

　Hospital-prepared drugs (HP), known as In'Naiseizai in Japan, are custom-prepared formulations which offer medical professionals an alternative administration pathway by changing the formulation of existing drugs according to a patients' needs. Preparing the HP is one of several roles of pharmacists in providing personalized medicine at hospitals in Japan. In 2012, the Japanese Society of Hospital Pharmacists provided guidelines for the appropriate use of "Hospital-prepared drugs". The following information was included in this guide: 1) documentation of the proper procedures, materials, prescription practices, etc., 2) required approval from the institutional review board of each HP on the risk-based classifications, and 3) to assess the stability, efficacy, and safety of each HP. However, several problems persist for pharmacists trying to prepare or use HP appropriately; the most common is insufficient manpower to both assess and prepare these drugs during routine hospital work. To resolve this problem, we are developing an evidence database for HP based on surveys of the current literature. This database has been developed for 109 drugs to date. Data-driven assessment of the stability of HP showed that 52 out of 109 drugs examined (47.7%). Notably, only 6 of the 109 HP (5.5%) in the database had all three characteristics of "stability", "safety", and "efficacy". In conclusion, the application of this database will save manpower hours for hospital pharmacists in the preparation of HP. In the near future, we will make this database available to the wider medical community via the web or through literature.

Advancing psychobiography: Reply to Young and Collins (2018).

PubMed

Ponterotto, Joseph G

2018-04-01

In this reply to Young and Collins (2018), the author responds to 3 primary concerns raised about integrating psychobiography into mainstream psychology: appropriate historical context and historiographic research methods, avoiding deterministic conclusions and the role of psychobiography in theory testing, and ethical concerns related to lack of informed consent of the identified subject. The author appreciates the thoughtful comments of Young and Collins and hopes that discussion and debate about psychobiography will continue in the literature. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes

NASA Astrophysics Data System (ADS)

Chindelevitch, Leonid; Ziemek, Daniel; Enayetallah, Ahmed; Randhawa, Ranjit; Sidders, Ben; Brockel, Christoph; Huang, Enoch

Over the past decade gene expression data sets have been generated at an increasing pace. In addition to ever increasing data generation, the biomedical literature is growing exponentially. The PubMed database (Sayers et al., 2010) comprises more than 20 million citations as of October 2010. The goal of our method is the prediction of putative upstream regulators of observed expression changes based on a set of over 400,000 causal relationships. The resulting putative regulators constitute directly testable hypotheses for follow-up.

Activity-based costing in services: literature bibliometric review.

PubMed

Stefano, Nara Medianeira; Filho, Nelson Casarotto

2013-12-01

This article is aimed at structuring a bibliography portfolio to treat the application of the ABC method in service and contribute to discussions within the scientific community. The methodology followed a three-stage procedure: Planning, execution and Synthesis. Also, the process ProKnow-C (Knowledge Process Development - Constructivist) was used in the execution stage. International databases were used to collect information (ISI Web of Knowledge and Scopus). As a result, we obtained a bibliography portfolio of 21 articles (with scientific recognition) dealing with the proposed theme.

Injury of the Inferior Alveolar Nerve during Implant Placement: a Literature Review

PubMed Central

Wang, Hom-Lay; Sabalys, Gintautas

2011-01-01

ABSTRACT Objectives The purpose of present article was to review aetiological factors, mechanism, clinical symptoms, and diagnostic methods as well as to create treatment guidelines for the management of inferior alveolar nerve injury during dental implant placement. Material and Methods Literature was selected through a search of PubMed, Embase and Cochrane electronic databases. The keywords used for search were inferior alveolar nerve injury, inferior alveolar nerve injuries, inferior alveolar nerve injury implant, inferior alveolar nerve damage, inferior alveolar nerve paresthesia and inferior alveolar nerve repair. The search was restricted to English language articles, published from 1972 to November 2010. Additionally, a manual search in the major anatomy, dental implant, periodontal and oral surgery journals and books were performed. The publications there selected by including clinical, human anatomy and physiology studies. Results In total 136 literature sources were obtained and reviewed. Aetiological factors of inferior alveolar nerve injury, risk factors, mechanism, clinical sensory nerve examination methods, clinical symptoms and treatment were discussed. Guidelines were created to illustrate the methods used to prevent and manage inferior alveolar nerve injury before or after dental implant placement. Conclusions The damage of inferior alveolar nerve during the dental implant placement can be a serious complication. Clinician should recognise and exclude aetiological factors leading to nerve injury. Proper presurgery planning, timely diagnosis and treatment are the key to avoid nerve sensory disturbances management. PMID:24421983

Teaching Evidence-Based Medicine in the Era of Point-of-Care Databases: The Case of the Giant Bladder Stone.

PubMed

Kash, Melissa J

2016-01-01

In an era where physicians rely on point-of-care databases that provide filtered, pre-appraised, and quickly accessible clinical information by smartphone applications, it is difficult to teach medical students the importance of knowing not only when it is appropriate to search the primary medical literature but also how to do it. This column will describe how librarians at an academic health sciences library use an unusual clinical case to make demonstrations of searching primary medical literature real and meaningful to medical students, and to illustrate vividly the importance of knowing what to do when the answer to a clinical question cannot be found in a point-of-care database.

LiverTox: Clinical and Research Information on Drug-Induced Liver Injury

MedlinePlus

... News Information Resources Glossary Abbreviations SEARCH THE LIVERTOX DATABASE Search for a specific medication, herbal or supplement: ... About Us . Disclaimer. Information presented in the LiverTox database is derived from the scientific literature and public ...

The care pathway: concepts and theories: an introduction.

PubMed

Schrijvers, Guus; van Hoorn, Arjan; Huiskes, Nicolette

2012-01-01

This article addresses first the definition of a (care) pathway, and then follows a description of theories since the 1950s. It ends with a discussion of theoretical advantages and disadvantages of care pathways for patients and professionals. The objective of this paper is to provide a theoretical base for empirical studies on care pathways. The knowledge for this chapter is based on several books on pathways, which we found by searching in the digital encyclopedia Wikipedia. Although this is not usual in scientific publications, this method was used because books are not searchable by databases as Pubmed. From 2005, we performed a literature search on Pubmed and other literature databases, and with the keywords integrated care pathway, clinical pathway, critical pathway, theory, research, and evaluation. One of the inspirational sources was the website of the European Pathway Association (EPA) and its journal International Journal of Care Pathways. The authors visited several sites for this paper. These are mentioned as illustration of a concept or theory. Most of them have English websites with more information. The URLs of these websites are not mentioned in this paper as a reference, because the content of them changes fast, sometimes every day.

Which Fecal Immunochemical Test Should I Choose?

PubMed Central

Daly, Jeanette M.; Xu, Yinghui; Levy, Barcey T.

2017-01-01

Objectives: To summarize the fecal immunochemical tests (FITs) available in the United States, the 2014 pathology proficiency testing (PT) program FIT results, and the literature related to the test characteristics of FITs available in the United States to detect advanced adenomatous polyps (AAP) and/or colorectal cancer (CRC). Methods: Detailed review of the Food and Drug Administration’s Clinical Laboratory Improvement Amendments (CLIA) database of fecal occult blood tests, the 2014 FIT PT program results, and the literature related to FIT accuracy. Results: A search of the CLIA database identified 65 FITs, with 26 FITs available for purchase in the United States. Thirteen of these FITs were evaluated on a regular basis by PT programs, with an overall sensitivity of 99.1% and specificity of 99.2% for samples spiked with hemoglobin. Automated FITs had better sensitivity and specificity than CLIA-waived FITs for detection of AAP and CRC in human studies using colonoscopy as the gold standard. Conclusion: Although many FITs are available in the United States, few have been tested in proficiency testing programs. Even fewer have data in humans on sensitivity and specificity for AAP or CRC. Our review indicates that automated FITs have the best test characteristics for AAP and CRC. PMID:28447866

The care pathway: concepts and theories: an introduction

PubMed Central

Schrijvers, Guus; van Hoorn, Arjan; Huiskes, Nicolette

2012-01-01

This article addresses first the definition of a (care) pathway, and then follows a description of theories since the 1950s. It ends with a discussion of theoretical advantages and disadvantages of care pathways for patients and professionals. The objective of this paper is to provide a theoretical base for empirical studies on care pathways. The knowledge for this chapter is based on several books on pathways, which we found by searching in the digital encyclopedia Wikipedia. Although this is not usual in scientific publications, this method was used because books are not searchable by databases as Pubmed. From 2005, we performed a literature search on Pubmed and other literature databases, and with the keywords integrated care pathway, clinical pathway, critical pathway, theory, research, and evaluation. One of the inspirational sources was the website of the European Pathway Association (EPA) and its journal International Journal of Care Pathways. The authors visited several sites for this paper. These are mentioned as illustration of a concept or theory. Most of them have English websites with more information. The URLs of these websites are not mentioned in this paper as a reference, because the content of them changes fast, sometimes every day. PMID:23593066

Informal employment in high-income countries for a health inequalities research: A scoping review.

PubMed

Julià, Mireia; Tarafa, Gemma; O'Campo, Patricia; Muntaner, Carles; Jódar, Pere; Benach, Joan

2015-01-01

Informal employment (IE) is one of the least studied employment conditions in public health research, mainly due to the difficulty of its conceptualization and its measurement, producing a lack of a unique concept and a common method of measurement. The aim of this review is to identify literature on IE in order to improve its definition and methods of measurement, with special attention given to high-income countries, to be able to study the possible impact on health inequalities within and between countries. A scoping review of definitions and methods of measurement of IE was conducted reviewing relevant databases and grey literature and analyzing selected articles. We found a wide spectrum of terms for describing IE as well as definitions and methods of measurement. We provide a definition of IE to be used in health inequalities research in high-income countries. Direct methods such as surveys can capture more information about workers and firms in order to estimate IE. These results can be used in further investigations about the impacts of this IE on health inequalities. Public health research must improve monitoring and analysis of IE in order to know the impacts of this employment condition on health inequalities.

[A novel compound heterozygous mutation in ABCA3 gene in a child with diffuse parenchymal lung disease].

PubMed

Bao, Y M; Liu, X L; Liu, X L; Chen, J H; Zheng, Y J

2017-11-02

Objective: To summarize the clinical characteristics of the diffuse parenchymal lung diseases in a child caused by a novel compound heterozygous ABCA3 mutation and explore the association between the phenotype and ABCA3 mutation. Method: The clinical material of a patient diagnosed with diffuse parenchymal lung disease with ABCA3 mutation in December 2016 in Shenzhen Children's Hospital was analyzed. The information about ABCA3 gene mutation updated before April, 2017 was searched and collected from the gene databases (including 1000Genomes, HGMD, EXAC) and the literatures (including Wanfang Chinese database and Pubmed). Result: The girl was one year and nine months old. She presented with chronic cough, tachypnea, cyanosis and failure to thrive since she was one year and three months old. Her condition gradually deteriorated after she was empirically treated. Physical examination showed malnutrition, tachypnea and clubbed-fingers. Her high resolution computed tomography (HRCT) revealed diffused ground-glass opacities, thickened interlobular septum, and multiple subpleural small air-filled lung cysts. The second generation sequencing study identified a novel compound heterozygous mutation (c.1755delC+c.2890G>A) in her ABCA3 gene, which derived respectively from her parents and has not been reported in the database and the literatures mentioned above. Conclusion: c.1755delC+c.2890G>A is a new kind of compound heterozygous mutation in ABCA3, which can cause children's diffuse parenchymal lung disease. Its phenotype is related to its genotype.

Research Trend Visualization by MeSH Terms from PubMed.

PubMed

Yang, Heyoung; Lee, Hyuck Jai

2018-05-30

Motivation : PubMed is a primary source of biomedical information comprising search tool function and the biomedical literature from MEDLINE which is the US National Library of Medicine premier bibliographic database, life science journals and online books. Complimentary tools to PubMed have been developed to help the users search for literature and acquire knowledge. However, these tools are insufficient to overcome the difficulties of the users due to the proliferation of biomedical literature. A new method is needed for searching the knowledge in biomedical field. Methods : A new method is proposed in this study for visualizing the recent research trends based on the retrieved documents corresponding to a search query given by the user. The Medical Subject Headings (MeSH) are used as the primary analytical element. MeSH terms are extracted from the literature and the correlations between them are calculated. A MeSH network, called MeSH Net, is generated as the final result based on the Pathfinder Network algorithm. Results : A case study for the verification of proposed method was carried out on a research area defined by the search query (immunotherapy and cancer and "tumor microenvironment"). The MeSH Net generated by the method is in good agreement with the actual research activities in the research area (immunotherapy). Conclusion : A prototype application generating MeSH Net was developed. The application, which could be used as a "guide map for travelers", allows the users to quickly and easily acquire the knowledge of research trends. Combination of PubMed and MeSH Net is expected to be an effective complementary system for the researchers in biomedical field experiencing difficulties with search and information analysis.

MPD3: a useful medicinal plants database for drug designing.

PubMed

Mumtaz, Arooj; Ashfaq, Usman Ali; Ul Qamar, Muhammad Tahir; Anwar, Farooq; Gulzar, Faisal; Ali, Muhammad Amjad; Saari, Nazamid; Pervez, Muhammad Tariq

2017-06-01

Medicinal plants are the main natural pools for the discovery and development of new drugs. In the modern era of computer-aided drug designing (CADD), there is need of prompt efforts to design and construct useful database management system that allows proper data storage, retrieval and management with user-friendly interface. An inclusive database having information about classification, activity and ready-to-dock library of medicinal plant's phytochemicals is therefore required to assist the researchers in the field of CADD. The present work was designed to merge activities of phytochemicals from medicinal plants, their targets and literature references into a single comprehensive database named as Medicinal Plants Database for Drug Designing (MPD3). The newly designed online and downloadable MPD3 contains information about more than 5000 phytochemicals from around 1000 medicinal plants with 80 different activities, more than 900 literature references and 200 plus targets. The designed database is deemed to be very useful for the researchers who are engaged in medicinal plants research, CADD and drug discovery/development with ease of operation and increased efficiency. The designed MPD3 is a comprehensive database which provides most of the information related to the medicinal plants at a single platform. MPD3 is freely available at: http://bioinform.info .

The NCBI BioSystems database

PubMed Central

Geer, Lewis Y.; Marchler-Bauer, Aron; Geer, Renata C.; Han, Lianyi; He, Jane; He, Siqian; Liu, Chunlei; Shi, Wenyao; Bryant, Stephen H.

2010-01-01

The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI’s Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationships from the literature or multiple experimental datasets. PMID:19854944

A database of natural products and chemical entities from marine habitat

PubMed Central

Babu, Padavala Ajay; Puppala, Suma Sree; Aswini, Satyavarapu Lakshmi; Vani, Metta Ramya; Kumar, Chinta Narasimha; Prasanna, Tallapragada

2008-01-01

Marine compound database consists of marine natural products and chemical entities, collected from various literature sources, which are known to possess bioactivity against human diseases. The database is constructed using html code. The 12 categories of 182 compounds are provided with the source, compound name, 2-dimensional structure, bioactivity and clinical trial information. The database is freely available online and can be accessed at http://www.progenebio.in/mcdb/index.htm PMID:19238254

Review of Research on Student-Facing Learning Analytics Dashboards and Educational Recommender Systems

ERIC Educational Resources Information Center

Bodily, Robert; Verbert, Katrien

2017-01-01

This article is a comprehensive literature review of student-facing learning analytics reporting systems that track learning analytics data and report it directly to students. This literature review builds on four previously conducted literature reviews in similar domains. Out of the 945 articles retrieved from databases and journals, 93 articles…

Referencing Science: Teaching Undergraduates to Identify, Validate, and Utilize Peer-Reviewed Online Literature

ERIC Educational Resources Information Center

Berzonsky, William A.; Richardson, Katherine D.

2008-01-01

Accessibility of online scientific literature continues to expand due to the advent of scholarly databases and search engines. Studies have shown that undergraduates favor using online scientific literature to address research questions, but they often do not have the skills to assess the validity of research articles. Undergraduates generally are…

Ranking the whole MEDLINE database according to a large training set using text indexing.

PubMed

Suomela, Brian P; Andrade, Miguel A

2005-03-24

The MEDLINE database contains over 12 million references to scientific literature, with about 3/4 of recent articles including an abstract of the publication. Retrieval of entries using queries with keywords is useful for human users that need to obtain small selections. However, particular analyses of the literature or database developments may need the complete ranking of all the references in the MEDLINE database as to their relevance to a topic of interest. This report describes a method that does this ranking using the differences in word content between MEDLINE entries related to a topic and the whole of MEDLINE, in a computational time appropriate for an article search query engine. We tested the capabilities of our system to retrieve MEDLINE references which are relevant to the subject of stem cells. We took advantage of the existing annotation of references with terms from the MeSH hierarchical vocabulary (Medical Subject Headings, developed at the National Library of Medicine). A training set of 81,416 references was constructed by selecting entries annotated with the MeSH term stem cells or some child in its sub tree. Frequencies of all nouns, verbs, and adjectives in the training set were computed and the ratios of word frequencies in the training set to those in the entire MEDLINE were used to score references. Self-consistency of the algorithm, benchmarked with a test set containing the training set and an equal number of references randomly selected from MEDLINE was better using nouns (79%) than adjectives (73%) or verbs (70%). The evaluation of the system with 6,923 references not used for training, containing 204 articles relevant to stem cells according to a human expert, indicated a recall of 65% for a precision of 65%. This strategy appears to be useful for predicting the relevance of MEDLINE references to a given concept. The method is simple and can be used with any user-defined training set. Choice of the part of speech of the words used for classification has important effects on performance. Lists of words, scripts, and additional information are available from the web address http://www.ogic.ca/projects/ks2004/.

Towards pathogenomics: a web-based resource for pathogenicity islands

PubMed Central

Yoon, Sung Ho; Park, Young-Kyu; Lee, Soohyun; Choi, Doil; Oh, Tae Kwang; Hur, Cheol-Goo; Kim, Jihyun F.

2007-01-01

Pathogenicity islands (PAIs) are genetic elements whose products are essential to the process of disease development. They have been horizontally (laterally) transferred from other microbes and are important in evolution of pathogenesis. In this study, a comprehensive database and search engines specialized for PAIs were established. The pathogenicity island database (PAIDB) is a comprehensive relational database of all the reported PAIs and potential PAI regions which were predicted by a method that combines feature-based analysis and similarity-based analysis. Also, using the PAI Finder search application, a multi-sequence query can be analyzed onsite for the presence of potential PAIs. As of April 2006, PAIDB contains 112 types of PAIs and 889 GenBank accessions containing either partial or all PAI loci previously reported in the literature, which are present in 497 strains of pathogenic bacteria. The database also offers 310 candidate PAIs predicted from 118 sequenced prokaryotic genomes. With the increasing number of prokaryotic genomes without functional inference and sequenced genetic regions of suspected involvement in diseases, this web-based, user-friendly resource has the potential to be of significant use in pathogenomics. PAIDB is freely accessible at . PMID:17090594

Assessment of the periodontal health status in patients undergoing orthodontic treatment with fixed appliances and Invisalign system

PubMed Central

Lu, Haili; Tang, Haifang; Zhou, Tian; Kang, Na

2018-01-01

Abstract Background: At present, many scholars have studied the periodontal health status of patients undergoing orthodontic treatment with fixed appliances and invisalign. However, those results are inconsistent. Therefore, we conducted this meta-analysis, and then provide reference for clinical treatment. Methods: Most databases, such as the Cochrane Library, EMBASE, PubMed, Medline, Chinese Biomedical Literature Database, CNKI, and Wan Fang Data were retrieved for related articles from the establishment of the database to October 2017. Meanwhile, we also searched the references of the related literatures manually, in order to increase the included literatures. Two researchers screened the related literatures according to the inclusion criteria and exclusion criteria. Stata 12.0 software was used for data analysis, and results are estimated by odds ratio (OR) and 95% confidence interval (CI). Results: Finally, 7 articles, including 368 patients, were included into our meta-analysis. Meta-analysis results showed that there was no statistically significant difference of gingival index (GI) and sulcus probing depth (SPD) status between the invisalign group and the control group, including at 1, 3, and 6 months (all P > .05). When compared with the control group, the invisalign group presented a lower plaque index (PLI) and sulcus bleeding index (SBI) status at 1 month (OR = −0.53, 95% CI: −0.89 to −0.18; OR = −0.44, 95% CI: −0.70 to −0.19, respectively), 3 months (OR = −0.69, 95% CI: −1.12 to −0.27; OR = −0.49, 95% CI: −0.93 to −0.05, respectively), and 6 months (OR = −0.91, 95% CI: −1.47 to −0.35; OR = −0.40, 95% CI: −0.63 to −0.07, respectively). Subgroup analysis showed that the SPD status was lower in the invisalign group at 6 months when measured the teeth using Ramfjord index (OR = −0.74, 95% CI: −1.35 to −0.12). However, there was no statistically significant difference between the 2 groups when using other measure methods (OR = 0.12, 95% CI: −0.26 to 0.17). Conclusion: Our meta-analysis suggests that comparing with the traditional fixed appliances, patients treated with invisalign have a better periodontal health. However, more studies are needed to confirm this conclusion in the future. PMID:29595680

Medical devices early assessment methods: systematic literature review.

PubMed

Markiewicz, Katarzyna; van Til, Janine A; IJzerman, Maarten J

2014-04-01

The aim of this study was to get an overview of current theory and practice in early assessments of medical devices, and to identify aims and uses of early assessment methods used in practice. A systematic literature review was conducted in September 2013, using computerized databases (PubMed, Science Direct, and Scopus), and references list search. Selected articles were categorized based on their type, objective, and main target audience. The methods used in the application studies were extracted and mapped throughout the early stages of development and for their particular aims. Of 1,961 articles identified, eighty-three studies passed the inclusion criteria, and thirty were included by searching reference lists. There were thirty-one theoretical papers, and eighty-two application papers included. Most studies investigated potential applications/possible improvement of medical devices, developed early assessment framework or included stakeholder perspective in early development stages. Among multiple qualitative and quantitative methods identified, only few were used more than once. The methods aim to inform strategic considerations (e.g., literature review), economic evaluation (e.g., cost-effectiveness analysis), and clinical effectiveness (e.g., clinical trials). Medical devices were often in the prototype product development stage, and the results were usually aimed at informing manufacturers. This study showed converging aims yet widely diverging methods for early assessment during medical device development. For early assessment to become an integral part of activities in the development of medical devices, methods need to be clarified and standardized, and the aims and value of assessment itself must be demonstrated to the main stakeholders for assuring effective and efficient medical device development.

Image Retrieval using Integrated Features of Binary Wavelet Transform

NASA Astrophysics Data System (ADS)

Agarwal, Megha; Maheshwari, R. P.

2011-12-01

In this paper a new approach for image retrieval is proposed with the application of binary wavelet transform. This new approach facilitates the feature calculation with the integration of histogram and correlogram features extracted from binary wavelet subbands. Experiments are performed to evaluate and compare the performance of proposed method with the published literature. It is verified that average precision and average recall of proposed method (69.19%, 41.78%) is significantly improved compared to optimal quantized wavelet correlogram (OQWC) [6] (64.3%, 38.00%) and Gabor wavelet correlogram (GWC) [10] (64.1%, 40.6%). All the experiments are performed on Corel 1000 natural image database [20].

Data Content and Exchange in General Practice: a Review

PubMed Central

Kalankesh, Leila R; Farahbakhsh, Mostafa; Rahimi, Niloofar

2014-01-01

Background: efficient communication of data is inevitable requirement for general practice. Any issue in data content and its exchange among GP and other related entities hinders continuity of patient care. Methods: literature search for this review was conducted on three electronic databases including Medline, Scopus and Science Direct. Results: through reviewing papers, we extracted information on the GP data content, use cases of GP information exchange, its participants, tools and methods, incentives and barriers. Conclusion: considering importance of data content and exchange for GP systems, it seems that more research is needed to be conducted toward providing a comprehensive framework for data content and exchange in GP systems. PMID:25648317

Motion Pattern Encapsulation for Data-Driven Constraint-Based Motion Editing

NASA Astrophysics Data System (ADS)

Carvalho, Schubert R.; Boulic, Ronan; Thalmann, Daniel

The growth of motion capture systems have contributed to the proliferation of human motion database, mainly because human motion is important in many applications, ranging from games entertainment and films to sports and medicine. However, the captured motions normally attend specific needs. As an effort for adapting and reusing captured human motions in new tasks and environments and improving the animator's work, we present and discuss a new data-driven constraint-based animation system for interactive human motion editing. This method offers the compelling advantage that it provides faster deformations and more natural-looking motion results compared to goal-directed constraint-based methods found in the literature.

LGscore: A method to identify disease-related genes using biological literature and Google data.

PubMed

Kim, Jeongwoo; Kim, Hyunjin; Yoon, Youngmi; Park, Sanghyun

2015-04-01

Since the genome project in 1990s, a number of studies associated with genes have been conducted and researchers have confirmed that genes are involved in disease. For this reason, the identification of the relationships between diseases and genes is important in biology. We propose a method called LGscore, which identifies disease-related genes using Google data and literature data. To implement this method, first, we construct a disease-related gene network using text-mining results. We then extract gene-gene interactions based on co-occurrences in abstract data obtained from PubMed, and calculate the weights of edges in the gene network by means of Z-scoring. The weights contain two values: the frequency and the Google search results. The frequency value is extracted from literature data, and the Google search result is obtained using Google. We assign a score to each gene through a network analysis. We assume that genes with a large number of links and numerous Google search results and frequency values are more likely to be involved in disease. For validation, we investigated the top 20 inferred genes for five different diseases using answer sets. The answer sets comprised six databases that contain information on disease-gene relationships. We identified a significant number of disease-related genes as well as candidate genes for Alzheimer's disease, diabetes, colon cancer, lung cancer, and prostate cancer. Our method was up to 40% more accurate than existing methods. Copyright © 2015 Elsevier Inc. All rights reserved.

Multiple endocrine neoplasia type 1 (MEN1): An update of 208 new germline variants reported in the last nine years.

PubMed

Concolino, Paola; Costella, Alessandra; Capoluongo, Ettore

2016-01-01

This review will focus on the germline MEN1 mutations that have been reported in patients with MEN1 and other hereditary endocrine disorders from 2007 to September 2015. A comprehensive review regarding the analysis of 1336 MEN1 mutations reported in the first decade following the gene's identification was performed by Lemos and Thakker in 2008. No other similar papers are available in literature apart from these data. We also checked for the list of Locus-Specific DataBases (LSDBs) and we found five MEN1 free-online mutational databases. 151 articles from the NCBI PubMed literature database were read and evaluated and a total of 75 MEN1 variants were found. On the contrary, 67, 22 and 44 novel MEN1 variants were obtained from ClinVar, MEN1 at Café Variome and HGMD (The Human Gene Mutation Database) databases respectively. A final careful analysis of MEN1 mutations affecting the coding region was performed. Copyright © 2016 Elsevier Inc. All rights reserved.

[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.

WEANING AND EXTUBATION READINESS IN PEDIATRIC PATIENTS

PubMed Central

Newth, Christopher J. L.; Venkataraman, Shekhar; Willson, Douglas F.; Meert, Kathleen L.; Harrison, Rick; Dean, J. Michael; Pollack, Murray; Zimmerman, Jerry; Anand, K. J. S.; Carcillo, Joseph A.; Nicholson, Carol E.

2010-01-01

Objective A systematic review of weaning and extubation for pediatric patients on mechanical ventilation. Data Selection Pediatric and Adult Literature, English language Study Selection Invited review Data Sources Literature review using National Library of Medicine PubMed from January 1972 until April 2008, earlier cross-referenced article citations, the Cochrane Database of Systematic Reviews and the Internet. Conclusions Despite the importance of minimizing time on mechanical ventilation, only limited guidance on weaning and extubation is available from the pediatric literature. A significant proportion of patients being evaluated for weaning are actually ready for extubation, suggesting that weaning is often not considered early enough in the course of ventilation. Indications for extubation are even less clear, although a trial of spontaneous breathing would seem a prerequisite. Several indices have been developed in an attempt to predict weaning and extubation success but the available literature would suggest they offer no improvement over clinical judgment. Extubation failure rates range from 2–20% and bear little relationship to the duration of mechanical ventilation. Upper airway obstruction is the single most common cause of extubation failure. A reliable method of assessing readiness for weaning and predicting extubation success is not evident from the pediatric literature. PMID:19057432

Chinese literatures of radiation oncology covered by PubMed over the past five years.

PubMed

Niu, Dao-Li; Zhen, Jun-Jie; He, Fen

2010-04-01

PubMed is generally acknowledged for its scientificity in literature coverage and authority of literature retrieval . In recent years, many studies have been published in China about radiation oncology. We aimed to investigate the literatures about radiation oncology in China covered by PubMed over the past five years. We collected primary data by searching the PubMed database using the related subject words. The collected data were analyzed and evaluated by bibliometric methods. In the past five years, 550 articles by Chinese authors related to radiotherapy were indexed in PubMed. These articles were published in 160 journals among 26 Chinese provinces/cities. These articles mainly focused on radiation dose and computer-aided radiation therapy. Sixty-four articles were published by Chinese Journal of Cancer , which ranked the top. Forty-four articles were published by the International Journal of Radiation Oncology Biology Physics (IF=4.29), with the largest number among SCI journals. One hundred and sixteen articles from Guangdong Province were covered, accounting for 21.09%. Over the past five years, the discipline of radiation oncology has been greatly developed. The literatures mainly focus on clinical radiation oncology and their regional distribution is uneven.

[Educational practices for diabetes mellitus: integrative literature review].

PubMed

Borba, Anna Karla de Oliveira Tito; Marques, Ana Paula de Oliveira; Leal, Márcia Carréra Campos; Ramos, Roberta Souza Pereira da Silva

2012-03-01

This is an integrative literature review which aims to identify the multi-professional scientific production on educational practices for individuals with diabetes available in the databases: Latin American Literature in Health Sciences (Literatura Latino Americana em Ciências da Saúde-LILACS), Medical Literature and Retrieval System online (Medline), Spanish Bibliographical Index in Health Sciences (Indice Bibliográfico Español en Ciencias de la Salud-Ibecs) and the Database on Nursing (Base de Dados em Enfermagem-BDENF), from 1999 to 2009. Results show that educational practices are developed mainly for adults and seniors up to 80 years of age, and involve themes that reflect the daily ife of living with diabetes. These practices are spread mainly through groups, bringing benefits not only for the individual with diabetes but also for the healthcare professional. Thus, we can see the process of changing the traditional education paradigm to a problem-based dialogical education, with a view for promoting health.

A narrative review of undergraduate peer-based healthcare ethics teaching.

PubMed

Hindmarch, Thomas; Allikmets, Silvia; Knights, Felicity

2015-12-12

This study explores the literature in establishing the value of undergraduate peer-based healthcare ethics teaching as an educational methodology. A narrative review of the literature concerning peer-based ethics teaching was conducted. MEDLINE, EMBASE, CINAHL, SCOPUS databases, and the Cochrane Library, were systematically searched for studies of peer-based ethics or professionalism teaching. Selected studies related peer-based teaching to ethics education outcomes. Ten publications were identified. Selected studies were varied in their chosen intervention methodology and analysis. Collectively, the identified studies suggest peer-based ethics education is an effective and valued educational methodology in training healthcare professionals. One paper suggests peer-based ethics teaching has advantages over traditional didactic methods. Peer-based ethics teaching also receives positive feedback from student participants. However, the limited literature base demonstrates a clear need for more evaluation of this pedagogy. The current literature base suggests that undergraduate peer based healthcare ethics teaching is valuable in terms of efficacy and student satisfaction. We conclude that the medical community should invest in further study in order to capitalise upon the potential of peer-based ethics teaching in undergraduate healthcare education.

Mapping the literature of rehabilitation nursing

PubMed Central

Spasser, Mark A.; Weismantel, Arlene

2006-01-01

Objective: This paper describes a citation analysis of the literature of rehabilitation nursing, conducted as part of the Medical Library Association's Nursing and Allied Health Section's the “Mapping the Literature of Nursing Project.” Methods: One core journal, Rehabilitation Nursing, was selected, being both the official journal of the Association of Rehabilitation Nurses and the only journal devoted exclusively to rehabilitation nursing. Citations were analyzed according to format and date and stratified according to Bradford's Law of Scattering. Results: The nineteen journals that constitute Zone 1 contribute the same number of citations as the eighty-six journals that make up Zone 2. OCLC ArticleFirst, PubMed/MEDLINE, and CINAHL provide the most inclusive coverage of the rehabilitation literature. The source journal, Rehabilitation Nursing, is the most important journal in Zone 1 and thus the most influential rehabilitation nursing journal. Relative degrees of database coverage do not change between Zones 1 and 2. Conclusion: The journals in Zones 1 and 2 collectively represent most of the important subspecialties of rehabilitation nursing, such as the physiological, sociopsychological, and community reintegration issues involved in the long-term rehabilitation process. PMID:16710460

Properties of publications on anatomy in medical education literature.

PubMed

Vorstenbosch, Marc; Bolhuis, Sanneke; van Kuppeveld, Sascha; Kooloos, Jan; Laan, Roland

2011-01-01

Publications on anatomy in medical education appear to be largely anecdotal. To explore this, we investigated the literature on anatomy in medical education, aiming first to evaluate the contribution of the literature on anatomy in medical education to "best evidence medical education" (BEME) and second to evaluate the development of this literature toward more "best evidence" between 1985 and 2009. Four databases were searched for publications on anatomy in medical education published between 1985 and 2009, resulting in 525 references. Hundred publications were characterized by five variables (journal category, paper subject, paper category, author perspective, and paper perspective). Statements from these publications were characterized by two variables (category and foundation). The publications contained 797 statements that involved the words "anatomy," "anatomical," or "anatomist." Forty-five percent of the publications contained no explicit research question. Forty percent of the statements made were about "teaching methods" and 17% about "teaching content," 8% referred to "practical value," and 10% to "side effects" of anatomy education. Ten percent of the statements were "positional," five percent "traditional," four percent "self-evident," and two percent referred to "quality of care." Fifty-six percent of the statements had no foundation, 17% were founded on empirical data, and 27% by references. These results substantiated the critical comments about the anecdotal nature of the literature. However, it is encouraging to see that between 1985 and 2009 the number of publications is rising that these publications increasingly focus on teaching methods and that an academic writing style is developing. This suggests a growing body of empirical literature about anatomy education. Copyright © 2011 American Association of Anatomists.

Is Health-Related Quality of Life after Radical Cystectomy Using Validated Questionnaires Really Better in Patients with Ileal Orthotopic Neobladder Compared to Ileal Conduit: A Meta-Analysis of Retrospective Comparative Studies

PubMed Central

Cerruto, Maria A.; D'Elia, Carolina; Siracusano, Salvatore; Porcaro, Antonio B.; Cacciamani, Giovanni; De Marchi, Davide; Niero, Mauro; Lonardi, Cristina; Iafrate, Massimo; Bassi, Pierfrancesco; Belgrano, Emanuele; Imbimbo, Ciro; Racioppi, Marco; Talamini, Renato; Ciciliato, Stefano; Toffoli, Laura; Rizzo, Michele; Visalli, Francesco; Verze, Paolo; Artibani, Walter

2017-01-01

Introduction From the most recent systematic revision of the literature, an orthotopic neobladder would seem to show marginally better health related quality of life (HR-QoL) scores compared with an ileal conduit. The aim of this study was to review all relevant published studies about the comparison between ileal orthotopic neobladder (IONB) and ileal conduit using validated HR-QoL questionnaires. Materials and Methods Studies were identified by searching multiple literature databases. Data were synthesized using meta-analytic methods conformed to the PRISMA statement. Results The literature search identified 10 papers; pooled effect sizes of combined quality of life outcomes for ileal conduit versus IONB showed a significantly better HR-QoL in patients with IONB (Hedges' g = 0.278; p = 0.000);. The present study has an important limitation due to the type of the analyzed comparative studies, all retrospective and not randomized. Conclusion This meta-analysis of not-randomized, retrospective comparative studies on the impact of ileal conduit versus IONB on HR-QoL showed a significant advantage of IONB subgroups. PMID:28785189

Using mixed methods when researching communities.

PubMed

Ochieng, Bertha M N; Meetoo, Danny

2015-09-01

To argue for the use of mixed methods when researching communities. Although research involving minority communities is now advanced, not enough effort has been made to formulate methodological linkages between qualitative and quantitative methods in most studies. For instance, the quantitative approaches used by epidemiologists and others in examining the wellbeing of communities are usually empirical. While the rationale for this is sound, quantitative findings can be expanded with data from in-depth qualitative approaches, such as interviews or observations, which are likely to provide insights into the experiences of people in those communities and their relationships with their wellbeing. Academic databases including The Cochrane Library, MEDLINE, CINAHL, AMED, INTERNURSE, Science Direct, Web of Knowledge and PubMed. An iterative process of identifying eligible literature was carried out by comprehensively searching electronic databases. Using mixed-methods approaches is likely to address any potential drawbacks of individual methods by exploiting the strengths of each at the various stages of research. Combining methods can provide additional ways of looking at a complex problem and improve the understanding of a community's experiences. However, it is important for researchers to use the different methods interactively during their research. The use of qualitative and quantitative methods is likely to enrich our understanding of the interrelationship between wellbeing and the experiences of communities. This should help researchers to explore socio-cultural factors and experiences of health and healthcare practice more effectively.

All Information Is Not Equal: Using the Literature Databases PubMed and The Cochrane Library for Identifying the Evidence on Granulocyte Transfusion Therapy

PubMed Central

Metzendorf, Maria-Inti; Schulz, Manuela; Braun, Volker

2014-01-01

Summary To be able to take well-informed decisions or carry out sound research, clinicians and researchers alike require specific information seeking skills matching their respective information needs. Biomedical information is traditionally available via different literature databases. This article gives an introduction to two diverging sources, PubMed (23 million references) and The Cochrane Library (800,000 references), both of which offer sophisticated instruments for searching an increasing amount of medical publications of varied quality and ambition. Whereas PubMed as an unfiltered source of primary literature comprises all different kinds of publication types occurring in academic journals, The Cochrane Library is a pre-filtered source which offers access to either synthesized publication types or critically appraised and carefully selected references. A search approach has to be carried out deliberately and requires a good knowledge on the scope and features of the databases as well as on the ability to build a search strategy in a structured way. We present a specific and a sensitive search approach, making use of both databases within two application case scenarios in order to identify the evidence on granulocyte transfusions for infections in adult patients with neutropenia. PMID:25538539

Mapping selected general literature of international nursing.

PubMed

Shams, Marie-Lise Antoun; Dixon, Lana S

2007-01-01

This study, part of a wider project to map the literature of nursing, identifies core journals cited in non-US nursing journals and determines the extent of their coverage by indexing services. Four general English-language journals were analyzed for format types and publication dates. Core titles were identified and nine bibliographic databases were scanned for indexing coverage. Findings show that 57.5% (13,391/23,271) of the cited references from the 4 core journals were to journal articles, 27.8% (6,471/23,271) to books, 9.5% (2,208/23,271) to government documents, 4.9% (1,131/23,271) to miscellaneous sources, and less than 1% (70/23,271) to Internet resources. Eleven journals produced one-third of the citations; the next third included 146 journals, followed by a dispersion of 1,622 titles. PubMed received the best database coverage scores, followed by CINAHL and Science Citation Index. None of the databases provided complete coverage of all 11 core titles. The four source journals contain a diverse group of cited references. The currency of citations to government documents makes these journals a good source for regulatory and legislative awareness. Nurses consult nursing and biomedical journals and must search both nursing and biomedical databases to cover the literature.

Airport take-off noise assessment aimed at identify responsible aircraft classes.

PubMed

Sanchez-Perez, Luis A; Sanchez-Fernandez, Luis P; Shaout, Adnan; Suarez-Guerra, Sergio

2016-01-15

Assessment of aircraft noise is an important task of nowadays airports in order to fight environmental noise pollution given the recent discoveries on the exposure negative effects on human health. Noise monitoring and estimation around airports mostly use aircraft noise signals only for computing statistical indicators and depends on additional data sources so as to determine required inputs such as the aircraft class responsible for noise pollution. In this sense, the noise monitoring and estimation systems have been tried to improve by creating methods for obtaining more information from aircraft noise signals, especially real-time aircraft class recognition. Consequently, this paper proposes a multilayer neural-fuzzy model for aircraft class recognition based on take-off noise signal segmentation. It uses a fuzzy inference system to build a final response for each class p based on the aggregation of K parallel neural networks outputs Op(k) with respect to Linear Predictive Coding (LPC) features extracted from K adjacent signal segments. Based on extensive experiments over two databases with real-time take-off noise measurements, the proposed model performs better than other methods in literature, particularly when aircraft classes are strongly correlated to each other. A new strictly cross-checked database is introduced including more complex classes and real-time take-off noise measurements from modern aircrafts. The new model is at least 5% more accurate with respect to previous database and successfully classifies 87% of measurements in the new database. Copyright © 2015 Elsevier B.V. All rights reserved.

A Cross-Species Analysis of Animal Models for the Investigation of Preterm Birth Mechanisms

PubMed Central

Nielsen, Brian W.; Bonney, Elizabeth A.; Pearce, Bradley D.; Donahue, Leah Rae; Sarkar, Indra Neil

2015-01-01

Background: Spontaneous preterm birth is the leading cause of neonatal morbidity and mortality worldwide. The ability to examine the exact mechanisms underlying this syndrome in humans is limited. Therefore, the study of animal models is critical to unraveling the key physiologic mechanisms that control the timing of birth. The purpose of this review is to facilitate enhanced assimilation of the literature on animal models of preterm birth by a broad range of investigators. Methods: Using classical systematic and informatics search techniques of the available literature through 2012, a database of intact animal models was generated. Research librarians generated a list of articles using multiple databases. From these articles, a comprehensive list of Medical Subject Headings (MeSH) was created. Using mathematical modeling, significant MeSH descriptors were determined, and a MEDLINE search algorithm was created. The articles were reviewed for mechanism of labor induction categorized by species. Results: Existing animal models of preterm birth comprise specific interventions to induce preterm birth, as no animal model was identified that exhibits natural spontaneous preterm birth at an incidence comparable to that of the humans. A search algorithm was developed which when used results in a comprehensive list of agents used to induce preterm delivery in a host of animal species. The evolution of 3 specific animal models—sheep, mice, and rats—has demonstrated a clear shift in focus in the literature from endocrine to inflammatory agents of preterm birth induction. Conclusion: The process of developing a search algorithm to provide efficient access to information on animal models of preterm birth illustrates the need for a more precise organization of the literature to allow the investigator to focus on distinctly maternal versus fetal outcomes. PMID:26377998

Reirradiation spine stereotactic body radiation therapy for spinal metastases: systematic review.

PubMed

Myrehaug, Sten; Sahgal, Arjun; Hayashi, Motohiro; Levivier, Marc; Ma, Lijun; Martinez, Roberto; Paddick, Ian; Régis, Jean; Ryu, Samuel; Slotman, Ben; De Salles, Antonio

2017-10-01

OBJECTIVE Spinal metastases that recur after conventional palliative radiotherapy have historically been difficult to manage due to concerns of spinal cord toxicity in the retreatment setting. Spine stereotactic body radiation therapy (SBRT), also known as stereotactic radiosurgery, is emerging as an effective and safe means of delivering ablative doses to these recurrent tumors. The authors performed a systematic review of the literature to determine the clinical efficacy and safety of spine SBRT specific to previously irradiated spinal metastases. METHODS A systematic literature review was conducted, which was specific to SBRT to the spine, using MEDLINE, Embase, Cochrane Evidence-Based Medicine Database, National Guideline Clearinghouse, and CMA Infobase, with further bibliographic review of appropriate articles. Research questions included: 1) Is retreatment spine SBRT efficacious with respect to local control and symptom control? 2) Is retreatment spine SBRT safe? RESULTS The initial literature search retrieved 2263 articles. Of these articles, 160 were potentially relevant, 105 were selected for in-depth review, and 9 studies met all inclusion criteria for analysis. All studies were single-institution series, including 4 retrospective, 3 retrospective series of prospective databases, 1 prospective, and 1 Phase I/II prospective study (low- or very low-quality data). The results indicated that spine SBRT is effective, with a median 1-year local control rate of 76% (range 66%-90%). Improvement in patients' pain scores post-SBRT ranged from 65% to 81%. Treatment delivery was safe, with crude rates of vertebral body fracture of 12% (range 0%-22%) and radiation-induced myelopathy of 1.2%. CONCLUSIONS This systematic literature review suggests that SBRT to previously irradiated spinal metastases is safe and effective with respect to both local control and pain relief. Although the evidence is limited to low-quality data, SBRT can be a recommended treatment option for reirradiation.

Predicting Adverse Drug Effects from Literature- and Database-Mined Assertions.

PubMed

La, Mary K; Sedykh, Alexander; Fourches, Denis; Muratov, Eugene; Tropsha, Alexander

2018-06-06

Given that adverse drug effects (ADEs) have led to post-market patient harm and subsequent drug withdrawal, failure of candidate agents in the drug development process, and other negative outcomes, it is essential to attempt to forecast ADEs and other relevant drug-target-effect relationships as early as possible. Current pharmacologic data sources, providing multiple complementary perspectives on the drug-target-effect paradigm, can be integrated to facilitate the inference of relationships between these entities. This study aims to identify both existing and unknown relationships between chemicals (C), protein targets (T), and ADEs (E) based on evidence in the literature. Cheminformatics and data mining approaches were employed to integrate and analyze publicly available clinical pharmacology data and literature assertions interrelating drugs, targets, and ADEs. Based on these assertions, a C-T-E relationship knowledge base was developed. Known pairwise relationships between chemicals, targets, and ADEs were collected from several pharmacological and biomedical data sources. These relationships were curated and integrated according to Swanson's paradigm to form C-T-E triangles. Missing C-E edges were then inferred as C-E relationships. Unreported associations between drugs, targets, and ADEs were inferred, and inferences were prioritized as testable hypotheses. Several C-E inferences, including testosterone → myocardial infarction, were identified using inferences based on the literature sources published prior to confirmatory case reports. Timestamping approaches confirmed the predictive ability of this inference strategy on a larger scale. The presented workflow, based on free-access databases and an association-based inference scheme, provided novel C-E relationships that have been validated post hoc in case reports. With refinement of prioritization schemes for the generated C-E inferences, this workflow may provide an effective computational method for the early detection of potential drug candidate ADEs that can be followed by targeted experimental investigations.

Health Informatics via Machine Learning for the Clinical Management of Patients.

PubMed

Clifton, D A; Niehaus, K E; Charlton, P; Colopy, G W

2015-08-13

To review how health informatics systems based on machine learning methods have impacted the clinical management of patients, by affecting clinical practice. We reviewed literature from 2010-2015 from databases such as Pubmed, IEEE xplore, and INSPEC, in which methods based on machine learning are likely to be reported. We bring together a broad body of literature, aiming to identify those leading examples of health informatics that have advanced the methodology of machine learning. While individual methods may have further examples that might be added, we have chosen some of the most representative, informative exemplars in each case. Our survey highlights that, while much research is taking place in this high-profile field, examples of those that affect the clinical management of patients are seldom found. We show that substantial progress is being made in terms of methodology, often by data scientists working in close collaboration with clinical groups. Health informatics systems based on machine learning are in their infancy and the translation of such systems into clinical management has yet to be performed at scale.

GOClonto: an ontological clustering approach for conceptualizing PubMed abstracts.

PubMed

Zheng, Hai-Tao; Borchert, Charles; Kim, Hong-Gee

2010-02-01

Concurrent with progress in biomedical sciences, an overwhelming of textual knowledge is accumulating in the biomedical literature. PubMed is the most comprehensive database collecting and managing biomedical literature. To help researchers easily understand collections of PubMed abstracts, numerous clustering methods have been proposed to group similar abstracts based on their shared features. However, most of these methods do not explore the semantic relationships among groupings of documents, which could help better illuminate the groupings of PubMed abstracts. To address this issue, we proposed an ontological clustering method called GOClonto for conceptualizing PubMed abstracts. GOClonto uses latent semantic analysis (LSA) and gene ontology (GO) to identify key gene-related concepts and their relationships as well as allocate PubMed abstracts based on these key gene-related concepts. Based on two PubMed abstract collections, the experimental results show that GOClonto is able to identify key gene-related concepts and outperforms the STC (suffix tree clustering) algorithm, the Lingo algorithm, the Fuzzy Ants algorithm, and the clustering based TRS (tolerance rough set) algorithm. Moreover, the two ontologies generated by GOClonto show significant informative conceptual structures.

[Research of bleeding volume and method in blood-letting acupuncture therapy based on data mining].

PubMed

Liu, Xin; Jia, Chun-Sheng; Wang, Jian-Ling; Du, Yu-Zhu; Zhang, Xiao-Xu; Shi, Jing; Li, Xiao-Feng; Sun, Yan-Hui; Zhang, Shen; Zhang, Xuan-Ping; Gang, Wei-Juan

2014-03-01

Through computer-based technology and data mining method, with treatment in cases of bloodletting acupuncture therapy in collected literature as sample data, the association rule in data mining was applied. According to self-built database platform, the data was input, arranged and summarized, and eventually required data was acquired to perform the data mining of bleeding volume and method in blood-letting acupuncture therapy, which summarized its application rules and clinical values to provide better guide for clinical practice. There were 9 kinds of blood-letting tools in the literature, in which the frequency of three-edge needle was the highest, accounting for 84.4% (1239/1468). The bleeding volume was classified into six levels, in which less volume (less than 0.1 mL) had the highest frequency (401 times). According to the results of the data mining, blood-letting acupuncture therapy was widely applied in clinical practice of acupuncture, in which use of three-edge needle and less volume (less than 0.1 mL) of blood were the most common, however, there was no central tendency in general.

Workplace bullying in the Australian health context: a systematic review.

PubMed

Chadwick, Sharlene; Travaglia, Joanne

2017-05-15

Purpose During the past decade, there has been increased attention into bullying behaviours in workplaces. Research to date has varied in design, the definition of what constitutes bullying behaviour, as well as the methods used to collect data and measure bullying incidence and prevalence. Nonetheless, studies demonstrate that bullying is a significant issue, which warrants an increased research focus to develop greater understanding of the concept, its effects and implications in, and for, the workplace. The purpose of this paper is to focus on capturing a range of international and Australian literature regarding workplace bullying behaviours in a health context from a management perspective. As a result, this paper identified the gaps in the literature when expanded specifically to an Australian health context. Design/methodology/approach The purpose of this review is to summarise the existing literature, both internationally and in Australia which examines workplace bullying behaviours in a health context from a management perspective. This describes the review of the literature on workplace bullying in a health context undertaken from January to April 2014. The "Preferred Reporting Systematic Reviews and Meta-Analyses" method was used to structure the review, which covered a wide range of literature from databases including MEDLINE, Embase, CINAHL and InformIT, as well as reports, and grey literature. Findings The review included 62 studies that met the inclusion criteria and reported either: factors contributing to workplace bullying, at least one significant example of workplace bullying behaviour or the impact of workplace bullying behaviours in a health context. Originality/value There is limited data on workplace bullying behaviours in an Australian health context. The literature supports there is value in future research to develop consistent definitions, policies, procedures and frameworks, which could help to prevent or address workplace bullying behaviours based on work being undertaken internationally.

Characteristics and outcomes in children with undifferentiated embryonal sarcoma of the liver: A report from the National Cancer Database

PubMed Central

Shi, Yan; Rojas, Yesenia; Zhang, Wei; Beierle, Elizabeth A.; Doski, John J.; Goldfarb, Melanie; Goldin, Adam B.; Gow, Kenneth W.; Langer, Monica; Meyers, Rebecka L.; Nuchtern, Jed G.

2016-01-01

Abstract Objective To examine patient characteristics and outcomes in children with undifferentiated embryonal sarcoma of the liver (UESL) using a multi‐institutional database. Summary Background Data UESL is a rare disease (incidence is one per million). Therefore, the current literature is mostly limited to small case series. Methods The National Cancer Database was queried for primary UESL diagnosed between 1998 and 2012. Results A total of 103 patients (<18 years) were identified. The 5‐year overall survival of the entire group was 86%. The best outcomes were seen in children who had tumors smaller than 15 cm and were able to undergo surgical resection with or without chemotherapy. Margin status did not appear to significantly affect survival. The most common type of resection was hemihepatectomy (37%), followed by sectionectomy (10%) and trisectionectomy (10%). Orthotopic liver transplant was performed in 10 children, all of whom survived to 5 years. Conclusion Surgical resection with or without chemotherapy should be the mainstay of treatment in children with UESL, and is associated with very favorable outcomes. Negative surgical margins were not associated with improved survival. Orthotopic liver transplantation may be a viable method of attaining local control in tumors, which would otherwise be unresectable. PMID:27781381

Variation in population levels of physical activity in European children and adolescents according to cross-European studies: a systematic literature review within DEDIPAC.

PubMed

Van Hecke, Linde; Loyen, Anne; Verloigne, Maïté; van der Ploeg, Hidde P; Lakerveld, Jeroen; Brug, Johannes; De Bourdeaudhuij, Ilse; Ekelund, Ulf; Donnelly, Alan; Hendriksen, Ingrid; Deforche, Benedicte

2016-06-28

Regular physical activity is associated with physical, social and mental health benefits, whilst insufficient physical activity is associated with several negative health outcomes (e.g. metabolic problems). Population monitoring of physical activity is important to gain insight into prevalence of compliance to physical activity recommendations, groups at risk and changes in physical activity patterns. This review aims to provide an overview of all existing studies that measure physical activity in youth, in cross-European studies, to describe the variation in population levels of physical activity and to describe and define challenges regarding assessment methods that are used. A systematic search was performed on six databases (PubMed, EMBASE, CINAHL, PsycINFO, SportDiscus and OpenGrey), supplemental forward- and backward tracking was done and authors' and experts' literature databases were searched to identify relevant articles. Journal articles or reports that reported levels of physical activity in the general population of youth from cross-European studies were included. Data were reviewed, extracted and assessed by two researchers, with disagreements being resolved by a third researcher. The review protocol of this review is published under registration number CRD42014010684 in the PROSPERO database. The search resulted in 9756 identified records of which 30 articles were included in the current review. This review revealed large differences between countries in prevalence of compliance to physical activity recommendations (i.e. 60 min of daily moderate- to vigorous-intensity physical activity (MVPA)) measured subjectively (5-47%) and accelerometer measured minutes of MVPA (23-200 min). Overall boys and children were more active than girls and adolescents. Different measurement methods (subjective n = 12, objective n = 18) and reported outcome variables (n = 17) were used in the included articles. Different accelerometer intensity thresholds used to define MVPA resulted in substantial differences in MVPA between studies conducted in the same countries when assessed objectively. Reported levels of physical activity and prevalence of compliance to physical activity recommendations in youth showed large variation across European countries. This may reflect true variation in physical activity as well as variation in assessment methods and reported outcome variables. Standardization across Europe, of methods to assess physical activity in youth and reported outcome variables is warranted, preferably moving towards a pan-European surveillance system combining objective and self-report methods.

Missing data in substance abuse research? Researchers’ reporting practices of sexual orientation and gender identity

PubMed Central

Bacca, Cristina L.; Cochran, Bryan N.

2014-01-01

Background Lesbian, gay, bisexual, and transgender individuals are at higher risk for substance use and substance use disorders than heterosexual individuals and are more likely to seek substance use treatment, yet sexual orientation and gender identity are frequently not reported in the research literature. The purpose of this study was to identify if sexual orientation and gender identity are being reported in the recent substance use literature, and if this has changed over time. Method The PsycINFO and PubMed databases were searched for articles released in 2007 and 2012 using the term “substance abuse” and 200 articles were randomly selected from each time period and database. Articles were coded for the presence or absence of sexual orientation and gender identity information. Results Participants’ sexual orientation was reported in 3.0% and 4.9% of the 2007 and 2.3% and 6.5% of the 2012 sample, in PsycINFO and PubMed sample articles, respectively, while non-binary gender identity was reported in 0% and 1.0% of the 2007 sample and 2.3% and 1.9% of the 2012 PsycINFO and PubMed sample articles. There were no differences in rates of reporting over time. Conclusions Sexual orientation and gender identity are rarely reported in the substance abuse literature, and there has not been a change in reporting practices between 2007 and 2012. Recommendations for future investigators in reporting sexual orientation and gender identity are included. PMID:25496705

Joy and happiness: a simultaneous and evolutionary concept analysis.

PubMed

Cottrell, Laura

2016-07-01

To report a simultaneous and evolutionary analysis of the concepts of joy and long-term happiness. Joy and happiness are underrepresented in the nursing literature, though negative concepts are well represented. When mentioned in the literature, neither joy nor happiness is adequately defined, explained, or clearly understood. To promote further investigation of these concepts in nursing and to explore their relationship with health and healing, conceptual clarity is an essential first step. Concept analysis. The following databases were searched, without time restrictions, for articles in English: Academic Search Complete, Anthropology Plus; ATLA Religious Database with ATLASerials; Cumulative Index of Nursing and Allied Health Literature (CINAHL); Education Research Complete; Humanities International Complete; Psych EXTRA; and SocINDEX with Full Text. The final sample size consists of 61 articles and one book, published between 1978-2014. An adapted combination of Rodgers' Evolutionary Model and Haase et al.'s Simultaneous Concept Analysis (SCA) method. Though both are positive concepts, joy and happiness have significant differences. Attributes of joy describe a spontaneous, sudden and transient concept associated with connection, awareness, and freedom. Attributes of happiness describe a pursued, long-lasting, stable mental state associated with virtue and self-control. Further exploration of joy and happiness is necessary to ascertain their relationship with health and their value to nursing practice and theory development. Nurses are encouraged to consider the value of positive concepts to all areas of nursing. © 2016 John Wiley & Sons Ltd.

Neuromuscular Electrical Stimulation for Treatment of Muscle Impairment: Critical Review and Recommendations for Clinical Practice

PubMed Central

Houghton, Pamela; Anthony, Joseph; Rennie, Sandy; Shay, Barbara L.; Hoens, Alison M.

2017-01-01

Purpose: In response to requests from physiotherapists for guidance on optimal stimulation of muscle using neuromuscular electrical stimulation (NMES), a review, synthesis, and extraction of key data from the literature was undertaken by six Canadian physical therapy (PT) educators, clinicians, and researchers in the field of electrophysical agents. The objective was to identify commonly treated conditions for which there was a substantial body of literature from which to draw conclusions regarding the effectiveness of NMES. Included studies had to apply NMES with visible and tetanic muscle contractions. Method: Four electronic databases (CINAHL, Embase, PUBMED, and SCOPUS) were searched for relevant literature published between database inceptions until May 2015. Additional articles were identified from bibliographies of the systematic reviews and from personal collections. Results: The extracted data were synthesized using a consensus process among the authors to provide recommendations for optimal stimulation parameters and application techniques to address muscle impairments associated with the following conditions: stroke (upper or lower extremity; both acute and chronic), anterior cruciate ligament reconstruction, patellofemoral pain syndrome, knee osteoarthritis, and total knee arthroplasty as well as critical illness and advanced disease states. Summaries of key details from each study incorporated into the review were also developed. The final sections of the article outline the recommended terminology for describing practice using electrical currents and provide tips for safe and effective clinical practice using NMES. Conclusion: This article provides physiotherapists with a resource to enable evidence-informed, effective use of NMES for PT practice. PMID:29162949

Ethical issues with colorectal cancer screening-a systematic review.

PubMed

Hofmann, Bjørn

2017-06-01

Colorectal cancer (CRC) screening is widely recommended and implemented. However, sometimes CRC screening is not implemented despite good evidence, and some types of CRC screening are implemented despite lack of evidence. The objective of this article is to expose and elucidate relevant ethical issues in the literature on CRC screening that are important for open and transparent deliberation on CRC screening. An axiological question-based method is used for exposing and elucidating ethical issues relevant in HTA. A literature search in MEDLINE, Embase, PsycINFO, PubMed Bioethics subset, ISI Web of Knowledge, Bioethics Literature Database (BELIT), Ethics in Medicine (ETHMED), SIBIL Base dati di bioetica, LEWI Bibliographic Database on Ethics in the Sciences and Humanities, and EUROETHICS identified 870 references of which 114 were found relevant according to title and abstract. The content of the included papers were subject to ethical analysis to highlight the ethical issues, concerns, and arguments. A wide range of important ethical issues were identified. The main benefits are reduced relative CRC mortality rate, and potentially incidence rate, but there is no evidence of reduced absolute mortality rate. Potential harms are bleeding, perforation, false test results, overdetection, overdiagnosis, overtreatment (including unnecessary removal of polyps), and (rarely) death. Other important issues are related to autonomy and informed choice equity, justice, medicalization, and expanding disease. A series of important ethical issues have been identified and need to be addressed in open and transparent deliberation on CRC screening. © 2016 John Wiley & Sons, Ltd.

Barriers to and Facilitators of Research Utilization among Iranian Nurses: a Literature Review

PubMed Central

Heydari, Abbas; Emami Zeydi, Amir

2014-01-01

Introduction: Research utilization (RU), is an important strategy to promote the quality of patient care. The aim of this study was to present a comprehensive literature review describing barriers and facilitators of RU among Iranian nurses. Methods: Literature review was undertaken using the international databases including Pub Med/Medline, Scopus, Science Direct, and Google Scholar. Also, Persian electronic databases such as Magiran, SID and Iran Medex were searched up to May 2014. The search was limited to articles in the English and Persian languages that evaluate the barriers or facilitators of RU among Iranian nurses. Results: A total of 11 articles were in the final dataset. The most important barriers to RU among Iranian nurses were related to the organization factors such as inadequate facilities; insufficient time on the job, lack of authority, physician cooperation, and administrative support. The most frequent facilitators of RU were education in enhancing nurses knowledge and skills in research evaluation, support from knowledgeable nursing colleagues and nursing faculty in the clinical setting, access to an expert committee for clinical appraisal, improving skills in English language and searching for articles, sufficient economic resources to carry out research, and having access to more facilities such as internet. Conclusion: Iranian nurses encounter with the same difficulties as to other countries regarding RU; while setting related barriers were the predominant obstacles to RU among them. Therefore, health managers are expected to plan appropriate strategies to smooth the progress of RU by nurses in their practice. PMID:25717456

Examining the relationship between infectious diseases and flooding in Europe

PubMed Central

Brown, Lisa; Murray, Virginia

2013-01-01

Introduction Many infectious diseases are sensitive to climatic changes; specifically, flooding. This systematic literature review aimed to strengthen the quality and completeness of evidence on infectious diseases following flooding, relevant to Europe. Methods A systematic literature review from 2004–2012 was performed. Focused searches of the following databases were conducted: Medline, Scopus, PubMed, Cochrane Library, and Evidence Aid. Personal communications with key informants were also reviewed. Results Thirty-eight studies met the inclusion criteria. Evidence suggested that water-borne, rodent-borne, and vector-borne diseases have been associated with flooding in Europe, although at a lower incidence than developing countries. Conclusion Disease surveillance and early warning systems, coupled with effective prevention and response capabilities, can reduce current and future vulnerability to infectious diseases following flooding. PMID:28228994

Mapping the literature of occupational therapy: an update

PubMed Central

Potter, Jonathan

2010-01-01

Objectives: This study updated Reed's 1999 “Mapping the Literature of Occupational Therapy.” An analysis of citation patterns and indexing coverage was undertaken to identify the core literature of occupational therapy and to determine access to that literature. Methods: Citations from three source journals for the years 2006 through 2008 were studied following the common methodology of the “Mapping the Literature of Allied Health Project.” Bradford's Law of Scattering was applied to analyze the productivity of cited journals. A comparative analysis of indexing was conducted across three bibliographic databases. Results: A total of 364 articles cited 10,425 references. Journals were the most frequently cited format, accounting for 65.3% of the references, an increase of 4.1% over the 1999 study. Approximately one-third of the journal references cited a cluster of 9 journals, with the American Journal of Occupational Therapy dominating the field. An additional 120 journals were identified as moderately important based on times cited. CINAHL provided the most comprehensive indexing of core journals, while MEDLINE provided the best overall coverage. Conclusions: Occupational therapy is a multidisciplinary field with a strong core identity and an increasingly diverse literature. Indexing has improved overall since 1999, but gaps in the coverage are still evident. PMID:20648258

Minefields Associated with Mining Data from Peer-reviewed Literature

EPA Science Inventory

The USEPA’s ECOTOX database is the largest compilation of ecotoxicity study results, providing information on the adverse effects of single chemical stressors to ecologically relevant aquatic and terrestrial species. The primary source of data included in the ECOTOX database is t...

MaizeGDB: The Maize Genetics and Genomics Database.

USDA-ARS?s Scientific Manuscript database

MaizeGDB is the community database for biological information about the crop plant Zea mays. Genomic, genetic, sequence, gene product, functional characterization, literature reference, and person/organization contact information are among the datatypes stored at MaizeGDB. At the project’s website...

AN EPA SPONSORED LITERATURE REVIEW DATABASE TO SUPPORT STRESSOR IDENTIFICATION

EPA Science Inventory

The Causal Analysis/Diagnosis Decision Information System (CADDIS) is an EPA decision-support system currently under development for evaluating the biological impact of stressors on water bodies. In support of CADDIS, EPA is developing CADLIT, a searchable database of the scient...

Genetic sex determination assays in 53 mammalian species: Literature analysis and guidelines for reporting standardization.

PubMed

Hrovatin, Karin; Kunej, Tanja

2018-01-01

Erstwhile, sex was determined by observation, which is not always feasible. Nowadays, genetic methods are prevailing due to their accuracy, simplicity, low costs, and time-efficiency. However, there is no comprehensive review enabling overview and development of the field. The studies are heterogeneous, lacking a standardized reporting strategy. Therefore, our aim was to collect genetic sexing assays for mammals and assemble them in a catalogue with unified terminology. Publications were extracted from online databases using key words such as sexing and molecular. The collected data were supplemented with species and gene IDs and the type of sex-specific sequence variant (SSSV). We developed a catalogue and graphic presentation of diagnostic tests for molecular sex determination of mammals, based on 58 papers published from 2/1991 to 10/2016. The catalogue consists of five categories: species, genes, SSSVs, methods, and references. Based on the analysis of published literature, we propose minimal requirements for reporting, consisting of: species scientific name and ID, genetic sequence with name and ID, SSSV, methodology, genomic coordinates (e.g., restriction sites, SSSVs), amplification system, and description of detected amplicon and controls. The present study summarizes vast knowledge that has up to now been scattered across databases, representing the first step toward standardization regarding molecular sexing, enabling a better overview of existing tests and facilitating planned designs of novel tests. The project is ongoing; collecting additional publications, optimizing field development, and standardizing data presentation are needed.

Increasing Coverage of Hepatitis B Vaccination in China

PubMed Central

Wang, Shengnan; Smith, Helen; Peng, Zhuoxin; Xu, Biao; Wang, Weibing

2016-01-01

Abstract This study used a system evaluation method to summarize China's experience on improving the coverage of hepatitis B vaccine, especially the strategies employed to improve the uptake of timely birth dosage. Identifying successful methods and strategies will provide strong evidence for policy makers and health workers in other countries with high hepatitis B prevalence. We conducted a literature review included English or Chinese literature carried out in mainland China, using PubMed, the Cochrane databases, Web of Knowledge, China National Knowledge Infrastructure, Wanfang data, and other relevant databases. Nineteen articles about the effectiveness and impact of interventions on improving the coverage of hepatitis B vaccine were included. Strong or moderate evidence showed that reinforcing health education, training and supervision, providing subsidies for facility birth, strengthening the coordination among health care providers, and using out-of-cold-chain storage for vaccines were all important to improving vaccination coverage. We found evidence that community education was the most commonly used intervention, and out-reach programs such as out-of-cold chain strategy were more effective in increasing the coverage of vaccination in remote areas where the facility birth rate was respectively low. The essential impact factors were found to be strong government commitment and the cooperation of the different government departments. Public interventions relying on basic health care systems combined with outreach care services were critical elements in improving the hepatitis B vaccination rate in China. This success could not have occurred without exceptional national commitment. PMID:27175710

Increasing Coverage of Hepatitis B Vaccination in China: A Systematic Review of Interventions and Implementation Experiences.

PubMed

Wang, Shengnan; Smith, Helen; Peng, Zhuoxin; Xu, Biao; Wang, Weibing

2016-05-01

This study used a system evaluation method to summarize China's experience on improving the coverage of hepatitis B vaccine, especially the strategies employed to improve the uptake of timely birth dosage. Identifying successful methods and strategies will provide strong evidence for policy makers and health workers in other countries with high hepatitis B prevalence.We conducted a literature review included English or Chinese literature carried out in mainland China, using PubMed, the Cochrane databases, Web of Knowledge, China National Knowledge Infrastructure, Wanfang data, and other relevant databases.Nineteen articles about the effectiveness and impact of interventions on improving the coverage of hepatitis B vaccine were included. Strong or moderate evidence showed that reinforcing health education, training and supervision, providing subsidies for facility birth, strengthening the coordination among health care providers, and using out-of-cold-chain storage for vaccines were all important to improving vaccination coverage.We found evidence that community education was the most commonly used intervention, and out-reach programs such as out-of-cold chain strategy were more effective in increasing the coverage of vaccination in remote areas where the facility birth rate was respectively low. The essential impact factors were found to be strong government commitment and the cooperation of the different government departments.Public interventions relying on basic health care systems combined with outreach care services were critical elements in improving the hepatitis B vaccination rate in China. This success could not have occurred without exceptional national commitment.

Swallowing sounds in speech therapy practice: a critical analysis of the literature

PubMed Central

Ferrucci, Juliana Lopes; Mangilli, Laura Davison; Sassi, Fernanda Chiarion; Limongi, Suelly Cecilia Olivan; de Andrade, Claudia Regina Furquim

2013-01-01

ABSTRACT This study aimed to investigate international scientific papers published on the subject of cervical auscultation and its use in speech therapy. The study involved a qualitative review of the literature spanning the last 10 years. Articles were selected from the PubMed database using the following keywords: cervical auscultation, swallowing and swallowing disorders. Research was included that was conducted on adult humans (over 18 years of age) and was written in English. Each citation retrieved from the database was analyzed independently by each of the study researchers to ascertain its relevance for inclusion in the study. The methodology involved formulating the research question, locating and selecting studies and critically evaluating the articles according to the precepts of the Cochrane Handbook. As a result, 35 studies were identified; 13 articles were analyzed because they allowed access to the full text and were related directly to the subject. We found that the studies were performed with groups of healthy subjects and subjects with different types of base pathology. Some studies compared the patterns found in the different groups. Some of the research sought to study the pattern of swallowing sounds with different factors - evaluator experience, the specificity and sensitivity of the method and how to improve the technique of cervical auscultation through the use of instruments other than the stethoscope. The conclusion of this critical analysis is that cervical auscultation is an important tool to be used in conjunction with other assessment methods in the routine clinical evaluation of swallowing. PMID:24488399

Mass Casualty Incident Primary Triage Methods in China

PubMed Central

Chen, Jin-Hong; Yang, Jun; Yang, Yu; Zheng, Jing-Chen

2015-01-01

Objective: To evaluate the technical characteristics and application of mass casualty incident (MCI) primary triage (PT) methods applied in China. Data Sources: Chinese literature was searched by Chinese Academic Journal Network Publishing Database (founded in June 2014). The English literature was searched by PubMed (MEDLINE) (1950 to June 2014). We also searched Official Websites of Chinese Central Government's (http://www.gov.cn/), National Health and Family Planning Commission of China (http://www.nhfpc.gov.cn/), and China Earthquake Information (http://www.csi.ac.cn/). Study Selection: We included studies associated with mass casualty events related to China, the PT applied in China, guidelines and standards, and application and development of the carding PT method in China. Results: From 3976 potentially relevant articles, 22 met the inclusion criteria, 20 Chinese, and 2 English. These articles included 13 case reports, 3 retrospective analyses of MCI, two methods introductions, three national or sectoral criteria, and one simulated field testing and validation. There were a total of 19 kinds of MCI PT methods that have been reported in China from 1950 to 2014. In addition, there were 15 kinds of PT methods reported in the literature from the instance of the application. Conclusions: The national and sectoral current triage criteria are developed mainly for earthquake relief. Classification is not clear. Vague criteria (especially between moderate and severe injuries) operability are not practical. There are no triage methods and research for children and special populations. There is no data and evidence supported triage method. We should revise our existing classification and criteria so it is clearer and easier to be grasped in order to build a real, practical, and efficient PT method. PMID:26415807

[Construction of chemical information database based on optical structure recognition technique].

PubMed

Lv, C Y; Li, M N; Zhang, L R; Liu, Z M

2018-04-18

To create a protocol that could be used to construct chemical information database from scientific literature quickly and automatically. Scientific literature, patents and technical reports from different chemical disciplines were collected and stored in PDF format as fundamental datasets. Chemical structures were transformed from published documents and images to machine-readable data by using the name conversion technology and optical structure recognition tool CLiDE. In the process of molecular structure information extraction, Markush structures were enumerated into well-defined monomer molecules by means of QueryTools in molecule editor ChemDraw. Document management software EndNote X8 was applied to acquire bibliographical references involving title, author, journal and year of publication. Text mining toolkit ChemDataExtractor was adopted to retrieve information that could be used to populate structured chemical database from figures, tables, and textual paragraphs. After this step, detailed manual revision and annotation were conducted in order to ensure the accuracy and completeness of the data. In addition to the literature data, computing simulation platform Pipeline Pilot 7.5 was utilized to calculate the physical and chemical properties and predict molecular attributes. Furthermore, open database ChEMBL was linked to fetch known bioactivities, such as indications and targets. After information extraction and data expansion, five separate metadata files were generated, including molecular structure data file, molecular information, bibliographical references, predictable attributes and known bioactivities. Canonical simplified molecular input line entry specification as primary key, metadata files were associated through common key nodes including molecular number and PDF number to construct an integrated chemical information database. A reasonable construction protocol of chemical information database was created successfully. A total of 174 research articles and 25 reviews published in Marine Drugs from January 2015 to June 2016 collected as essential data source, and an elementary marine natural product database named PKU-MNPD was built in accordance with this protocol, which contained 3 262 molecules and 19 821 records. This data aggregation protocol is of great help for the chemical information database construction in accuracy, comprehensiveness and efficiency based on original documents. The structured chemical information database can facilitate the access to medical intelligence and accelerate the transformation of scientific research achievements.

Literature for flight simulator (motion) requirements research

DOT National Transportation Integrated Search

2010-10-29

This is the yearly snapshot of the literature examined in the framework of the Federal Aviation Administration/Volpe Center Flight Simulator Human Factors Program and entered in an EndNote database. It describes 1131 documents, 118 more than last y...

Variation in choice of study design: findings from the Epidemiology Design Decision Inventory and Evaluation (EDDIE) survey.

PubMed

Stang, Paul E; Ryan, Patrick B; Overhage, J Marc; Schuemie, Martijn J; Hartzema, Abraham G; Welebob, Emily

2013-10-01

Researchers using observational data to understand drug effects must make a number of analytic design choices that suit the characteristics of the data and the subject of the study. Review of the published literature suggests that there is a lack of consistency even when addressing the same research question in the same database. To characterize the degree of similarity or difference in the method and analysis choices made by observational database research experts when presented with research study scenarios. On-line survey using research scenarios on drug-effect studies to capture method selection and analysis choices that follow a dependency branching based on response to key questions. Voluntary participants experienced in epidemiological study design solicited for participation through registration on the Observational Medical Outcomes Partnership website, membership in particular professional organizations, or links in relevant newsletters. Description (proportion) of respondents selecting particular methods and making specific analysis choices based on individual drug-outcome scenario pairs. The number of questions/decisions differed based on stem questions of study design, time-at-risk, outcome definition, and comparator. There is little consistency across scenarios, by drug or by outcome of interest, in the decisions made for design and analyses in scenarios using large healthcare databases. The most consistent choice was the cohort study design but variability in the other critical decisions was common. There is great variation among epidemiologists in the design and analytical choices that they make when implementing analyses in observational healthcare databases. These findings confirm that it will be important to generate empiric evidence to inform these decisions and to promote a better understanding of the impact of standardization on research implementation.

Falls from Height in the Construction Industry: A Critical Review of the Scientific Literature

PubMed Central

Nadhim, Evan A.; Hon, Carol; Xia, Bo; Stewart, Ian; Fang, Dongping

2016-01-01

Globally, falls from height (FFH) are a substantial public health jeopardy and are among the important leading causes of serious and fatal injuries for construction workers. A comprehensive understanding of the causal factors in FFH incidents is urgently required; however, the literature appears to lack a scientific review of FFH. In this study, 297 articles that contribute to the topic of fall incidents were reviewed. Seventy-five (75) articles met the criteria for relevance and were aggregated in a database to support a critical review. A synthesis of macro-variables approach was adopted rather than a structured meta-analysis. Such a method of analysis provides the flexibility to combine previous studies' findings. The most common factors associated with FFH are risky activities, individual characteristics, site conditions, organizational characteristics, agents (scaffolds/ladders) and weather conditions. The outcomes contributed to identifying the most significant research area for safety enhancement by improving engineering facilities, behaviour investigations and FFH prevention methods. PMID:27367706

A Recent Advance in the Automatic Indexing of the Biomedical Literature

PubMed Central

Névéol, Aurélie; Shooshan, Sonya E.; Humphrey, Susanne M.; Mork, James G.; Aronson, Alan R.

2009-01-01

The volume of biomedical literature has experienced explosive growth in recent years. This is reflected in the corresponding increase in the size of MEDLINE®, the largest bibliographic database of biomedical citations. Indexers at the U.S. National Library of Medicine (NLM) need efficient tools to help them accommodate the ensuing workload. After reviewing issues in the automatic assignment of Medical Subject Headings (MeSH® terms) to biomedical text, we focus more specifically on the new subheading attachment feature for NLM’s Medical Text Indexer (MTI). Natural Language Processing, statistical, and machine learning methods of producing automatic MeSH main heading/subheading pair recommendations were assessed independently and combined. The best combination achieves 48% precision and 30% recall. After validation by NLM indexers, a suitable combination of the methods presented in this paper was integrated into MTI as a subheading attachment feature producing MeSH indexing recommendations compliant with current state-of-the-art indexing practice. PMID:19166973

Achieving hemostasis in dermatology – Part 1: Preoperative, intraoperative, and postoperative management

PubMed Central

Kaur, Ravneet Ruby; Glick, Jaimie B.; Siegel, Daniel

2013-01-01

As dermatological procedures continue to become increasingly complex, improved methods and tools to achieve appropriate hemostasis become necessary. The methods for achieving adequate hemostasis are variable and depend greatly on the type of procedure performed and the unique characteristics of the individual patient. In Part 1 of this review, we discuss the preoperative, intraoperative, and postoperative management of patients undergoing dermatologic surgery. We address oral medications and supplements that affect hemostasis, hemostatic anesthesia, and intraoperative interventions such as suture ligation and heat-generating cautery devices. In Part 2 of this review, we will discuss topical hemostats. The authors conducted an extensive literature review using the following keywords: “hemostasis,” “dermatology,” “dermatological surgery,” “dermatologic sutures,” “electrosurgery,” “hemostatic anesthesia,” and “laser surgery.” Sources for this article were identified by searching the English literature in the Pubmed database for the time period from 1940 to March 2012. A thorough bibliography search was also conducted and key references were examined. PMID:23741660

Exploring Nursing Students' Experiences of Learning Using Phenomenography: A Literature Review.

PubMed

Barry, Sinead; Ward, Louise; Walter, Ruby

2017-10-01

The purpose of this extensive international and national literature review was to explore how phenomenography identifies nursing students' experiences of learning within preregistration (or prelicensure) nursing education. Data were collected utilizing a comprehensive search of electronic databases. Full text, peer-reviewed, and scholarly articles published in English using the search terms phenomengraph*, nurs*, student, education, and learning were reviewed. Two discreet themes emerged exploring students' experiences of learning within preregistration nursing education: (a) Phenomenography was a beneficial method to expose variation in students' understandings of a challenging concept or topic and (b) phenomenography was beneficial to evaluate teaching methods in attempt to improve student learning of challenging and complex concepts. On the basis of these findings, future research utilizing phenomenography within nursing education has potential to uncover variation in students' understandings of mental health, with future consideration of implications to nursing curriculum design and development. [J Nurs Educ. 2017;56(10):591-598.]. Copyright 2017, SLACK Incorporated.

Multilevel library instruction for emerging nursing roles.

PubMed

Francis, B W; Fisher, C C

1995-10-01

As new nursing roles emerge that involve greater decision making than in the past, added responsibility for outcomes and cost control, and increased emphasis on primary care, the information-seeking skills needed by nurses change. A search of library and nursing literature indicates that there is little comprehensive library instruction covering all levels of nursing programs: undergraduate, returning registered nurses, and graduate students. The University of Florida is one of the few places that has such a multilevel, course-integrated curriculum in place for all entrants into the nursing program. Objectives have been developed for each stage of learning. The courses include instruction in the use of the online public access catalog, printed resources, and electronic databases. A library classroom equipped with the latest technology enables student interaction with electronic databases. This paper discusses the program and several methods used to evaluate it.

NETS[middle dot]A Scholarship: A Review of Published Literature

ERIC Educational Resources Information Center

Richardson, Jayson W.; Bathon, Justin; Flora, Kevin L.; Lewis, Wayne D.

2013-01-01

To date, no systematic analysis of the current body of literature has aimed to understand the extent to which school technology leadership is being investigated. This review of the literature presents a content analysis of articles published from 1997 through 2010 housed in the Education Resource Information Center (ERIC) database on the topic of…

Human Resource Development Practices in Russia: A Structured Literature Review

ERIC Educational Resources Information Center

Plakhotnik, Maria S.

2005-01-01

This literature review aimed to investigate the literature on HRD in Russian enterprises, U.S. firms in Russia, or U.S.-Russian joint ventures to determine the role and function of HRD practitioners in creating a successful economic transition. Thirty-three articles were selected through a database search and examined using content analysis. Three…

Full Text Searching and Customization in the NASA ADS Abstract Service

NASA Technical Reports Server (NTRS)

Eichhorn, G.; Accomazzi, A.; Grant, C. S.; Kurtz, M. J.; Henneken, E. A.; Thompson, D. M.; Murray, S. S.

2004-01-01

The NASA-ADS Abstract Service provides a sophisticated search capability for the literature in Astronomy, Planetary Sciences, Physics/Geophysics, and Space Instrumentation. The ADS is funded by NASA and access to the ADS services is free to anybody worldwide without restrictions. It allows the user to search the literature by author, title, and abstract text. The ADS database contains over 3.6 million references, with 965,000 in the Astronomy/Planetary Sciences database, and 1.6 million in the Physics/Geophysics database. 2/3 of the records have full abstracts, the rest are table of contents entries (titles and author lists only). The coverage for the Astronomy literature is better than 95% from 1975. Before that we cover all major journals and many smaller ones. Most of the journal literature is covered back to volume 1. We now get abstracts on a regular basis from most journals. Over the last year we have entered basically all conference proceedings tables of contents that are available at the Harvard Smithsonian Center for Astrophysics library. This has greatly increased the coverage of conference proceedings in the ADS. The ADS also covers the ArXiv Preprints. We download these preprints every night and index all the preprints. They can be searched either together with the other abstracts or separately. There are currently about 260,000 preprints in that database. In January 2004 we have introduced two new services, full text searching and a personal notification service called "myADS". As all other ADS services, these are free to use for anybody.

PIPE: a protein–protein interaction passage extraction module for BioCreative challenge

PubMed Central

Chu, Chun-Han; Su, Yu-Chen; Chen, Chien Chin; Hsu, Wen-Lian

2016-01-01

Identifying the interactions between proteins mentioned in biomedical literatures is one of the frequently discussed topics of text mining in the life science field. In this article, we propose PIPE, an interaction pattern generation module used in the Collaborative Biocurator Assistant Task at BioCreative V (http://www.biocreative.org/) to capture frequent protein-protein interaction (PPI) patterns within text. We also present an interaction pattern tree (IPT) kernel method that integrates the PPI patterns with convolution tree kernel (CTK) to extract PPIs. Methods were evaluated on LLL, IEPA, HPRD50, AIMed and BioInfer corpora using cross-validation, cross-learning and cross-corpus evaluation. Empirical evaluations demonstrate that our method is effective and outperforms several well-known PPI extraction methods. Database URL: PMID:27524807

Devices and tasks involved in the objective assessment of standing dynamic balancing - A systematic literature review.

PubMed

Petró, Bálint; Papachatzopoulou, Alexandra; Kiss, Rita M

2017-01-01

Static balancing assessment is often complemented with dynamic balancing tasks. Numerous dynamic balancing assessment methods have been developed in recent decades with their corresponding balancing devices and tasks. The aim of this systematic literature review is to identify and categorize existing objective methods of standing dynamic balancing ability assessment with an emphasis on the balancing devices and tasks being used. Three major scientific literature databases (Science Direct, Web of Science, PLoS ONE) and additional sources were used. Studies had to use a dynamic balancing device and a task described in detail. Evaluation had to be based on objectively measureable parameters. Functional tests without instrumentation evaluated exclusively by a clinician were excluded. A total of 63 articles were included. The data extracted during full-text assessment were: author and date; the balancing device with the balancing task and the measured parameters; the health conditions, size, age and sex of participant groups; and follow-up measurements. A variety of dynamic balancing assessment devices were identified and categorized as 1) Solid ground, 2) Balance board, 3) Rotating platform, 4) Horizontal translational platform, 5) Treadmill, 6) Computerized Dynamic Posturography, and 7) Other devices. The group discrimination ability of the methods was explored and the conclusions of the studies were briefly summarized. Due to the wide scope of this search, it provides an overview of balancing devices and do not represent the state-of-the-art of any single method. The identified dynamic balancing assessment methods are offered as a catalogue of candidate methods to complement static assessments used in studies involving postural control.

Community‐Academic Partnerships: A Systematic Review of the State of the Literature and Recommendations for Future Research

PubMed Central

MEZA, ROSEMARY D.; BRIKHO, BRIGITTE; NAAF, MEGHAN; ESTABILLO, JASPER A.; GOMEZ, EMILY D.; VEJNOSKA, SARAH F.; DUFEK, SARAH; STAHMER, AUBYN C.; AARONS, GREGORY A.

2016-01-01

Policy Points: Communities, funding agencies, and institutions are increasingly involving community stakeholders as partners in research, to provide firsthand knowledge and insight.Based on our systematic review of major literature databases, we recommend using a single term, community‐academic partnership (CAP), and a conceptual definition to unite multiple research disciplines and strengthen the field.Interpersonal and operational factors that facilitate or hinder the collaborative process have been consistently identified, including “trust among partners” and “respect among partners” (facilitating interpersonal factors) and “excessive time commitment” (hindering operational factor).Once CAP processes and characteristics are better understood, the effectiveness of collaborative partner involvement can be tested. Context Communities, funding agencies, and institutions are increasingly involving community stakeholders as partners in research. Community stakeholders can provide firsthand knowledge and insight, thereby increasing research relevance and feasibility. Despite the greater emphasis and use of community‐academic partnerships (CAP) across multiple disciplines, definitions of partnerships and methodologies vary greatly, and no systematic reviews consolidating this literature have been published. The purpose of this article, then, is to facilitate the continued growth of this field by examining the characteristics of CAPs and the current state of the science, identifying the facilitating and hindering influences on the collaborative process, and developing a common term and conceptual definition for use across disciplines. Methods Our systematic search of 6 major literature databases generated 1,332 unique articles, 50 of which met our criteria for inclusion and provided data on 54 unique CAPs. We then analyzed studies to describe CAP characteristics and to identify the terms and methods used, as well as the common influences on the CAP process and distal outcomes. Findings CAP research spans disciplines, involves a variety of community stakeholders, and focuses on a large range of study topics. CAP research articles, however, rarely report characteristics such as membership numbers or duration. Most studies involved case studies using qualitative methods to collect data on the collaborative process. Although various terms were used to describe collaborative partnerships, few studies provided conceptual definitions. Twenty‐three facilitating and hindering factors influencing the CAP collaboration process emerged from the literature. Outcomes from the CAPs most often included developing or refining tangible products. Conclusions Based on our systematic review, we recommend using a single term, community‐academic partnership, as well as a conceptual definition to unite multiple research disciplines. In addition, CAP characteristics and methods should be reported more systematically to advance the field (eg, to develop CAP evaluation tools). We have identified the most common influences that facilitate and hinder CAPs, which in turn should guide their development and sustainment. PMID:26994713

[Bibliometric analysis of current glaucoma research based on Pubmed database].

PubMed

Huang, Wen-bin; Wang, Wei; Zhou, Min-wen; Chen, Shi-da; Zhang, Xiu-lan

2013-11-01

To survey the distribution pattern and subject domain knowledge of worldwide glaucoma research based on literatures in Pubmed database. Literatures on glaucoma published in 2007 to 2011 were identified in Pubmed database. The analytic items of an article include published year, country, language author, and journal. After core mesh terms had been characterized by BICOMS, the co-occurrence matrix was built. Cluster analysis was finished by SPSS 20.0. Then visualized network was drawn using ucinet 6.0. Totally 6427 literatures were included, the number of annual articles changed slightly between 2007 and 2011. The United States, England, Germany, Australia, and France together accounted for 77.63% of articles. There were 52 high-frequency subjects and hot topics were clustered into the following 10 categories: (1) Pathology of optic disc and nerve fibers and OCT application, (2) METHODS: of visual field (VF) and visual function examination, (3) Glaucoma drug medications, (4) Pathology and physiology of primary open angle glaucoma (POAG) including VF and intraocular pressure (IOP), (5) Glaucoma surgery, (6) Gene research related to POAG, (7) Glaucoma disease pathology and animal models, (8) Ocular hypertension (OHT) induced complications and corneal changes, (9) Etiology of congenital glaucoma and complications, (10) Etiology and epidemiology of glaucoma. The visualized domain knowledge mapping was successfully built. The pathology of optic disc and nerve fibers, medications, and surgery were well developed. Study on IOP and visual field was in the core domain, which have an important link to etiology, diagnosis, and therapy. The researches on glaucomatous gene, disease pathology model, congenital glaucoma, etiology and epidemiology were not developed well, which are of great promotion space. The distribution pattern and subject domain knowledge of worldwide glaucoma research in the recent five years were shown by using bibliometric analysis.Western developed countries play a leading role in the field of glaucoma research, the international influence of related research in China needs to be strengthened.

Measuring quality of life of people with predementia and dementia and their caregivers: a systematic review protocol

PubMed Central

Landeiro, Filipa; Walsh, Katie; Ghinai, Isaac; Mughal, Seher; Nye, Elsbeth; Wace, Helena; Roberts, Nia; Lecomte, Pascal; Wittenberg, Raphael; Wolstenholme, Jane; Handels, Ron; Roncancio-Diaz, Emilse; Potashman, Michele H; Tockhorn-Heidenreich, Antje

2018-01-01

Introduction Dementia is the fastest growing major cause of disability globally and may have a profound impact on the health-related quality of life (HRQoL) of both the patient with dementia and those who care for them. This review aims to systematically identify and synthesise the measurements of HRQoL for people with, and their caregivers across the full spectrum of, dementia from its preceding stage of predementia to end of life. Methods and analysis A systematic literature review was conducted in Medical Literature Analysis and Retrieval System Online, ExcerptaMedicadataBASE, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, Database of Abstracts of Reviews of Effect, National Health Service Economic Evaluation Database and PsycINFO between January 1990 and the end of April 2017. Two reviewers will independently assess each study for inclusion and disagreements will be resolved by a third reviewer. Data will be extracted using a predefined data extraction form following best practice. Study quality will be assessed with the Effective Public Health Practice Project quality assessment tool. HRQoL measurements will be presented separately for people with dementia and caregivers by instrument used and, when possible, HRQoL will be reported by disease type and stage of the disease. Descriptive statistics of the results will be provided. A narrative synthesis of studies will also be provided discussing differences in HRQoL measurements by instrument used to estimate it, type of dementia and disease severity. Ethics and dissemination This systematic literature review is exempt from ethics approval because the work is carried out on published documents. The findings of the review will be disseminated in a related peer-reviewed journal and presented at conferences. They will also contribute to the work developed in the Real World Outcomes across the Alzheimer’s disease spectrum for better care: multimodal data access platform (ROADMAP). Trial registration number CRD42017071416. PMID:29602838

A systematic review of mixed methods research on human factors and ergonomics in health care.

PubMed

Carayon, Pascale; Kianfar, Sarah; Li, Yaqiong; Xie, Anping; Alyousef, Bashar; Wooldridge, Abigail

2015-11-01

This systematic literature review provides information on the use of mixed methods research in human factors and ergonomics (HFE) research in health care. Using the PRISMA methodology, we searched four databases (PubMed, PsycInfo, Web of Science, and Engineering Village) for studies that met the following inclusion criteria: (1) field study in health care, (2) mixing of qualitative and quantitative data, (3) HFE issues, and (4) empirical evidence. Using an iterative and collaborative process supported by a structured data collection form, the six authors identified a total of 58 studies that primarily address HFE issues in health information technology (e.g., usability) and in the work of healthcare workers. About two-thirds of the mixed methods studies used the convergent parallel study design where quantitative and qualitative data were collected simultaneously. A variety of methods were used for collecting data, including interview, survey and observation. The most frequent combination involved interview for qualitative data and survey for quantitative data. The use of mixed methods in healthcare HFE research has increased over time. However, increasing attention should be paid to the formal literature on mixed methods research to enhance the depth and breadth of this research. Copyright © 2015. Published by Elsevier Ltd.

Potential use of routine databases in health technology assessment.

PubMed

Raftery, J; Roderick, P; Stevens, A

2005-05-01

To develop criteria for classifying databases in relation to their potential use in health technology (HT) assessment and to apply them to a list of databases of relevance in the UK. To explore the extent to which prioritized databases could pick up those HTs being assessed by the National Coordinating Centre for Health Technology Assessment (NCCHTA) and the extent to which these databases have been used in HT assessment. To explore the validation of the databases and their cost. Electronic databases. Key literature sources. Experienced users of routine databases. A 'first principles' examination of the data necessary for each type of HT assessment was carried out, supplemented by literature searches and a historical review. The principal investigators applied the criteria to the databases. Comments of the 'keepers' of the prioritized databases were incorporated. Details of 161 topics funded by the NHS R&D Health Technology Assessment (HTA) programme were reviewed iteratively by the principal investigators. Uses of databases in HTAs were identified by literature searches, which included the title of each prioritized database as a keyword. Annual reports of databases were examined and 'keepers' queried. The validity of each database was assessed using criteria based on a literature search and involvement by the authors in a national academic network. The costs of databases were established from annual reports, enquiries to 'keepers' of databases and 'guesstimates' based on cost per record. For assessing effectiveness, equity and diffusion, routine databases were classified into three broad groups: (1) group I databases, identifying both HTs and health states, (2) group II databases, identifying the HTs, but not a health state, and (3) group III databases, identifying health states, but not an HT. Group I datasets were disaggregated into clinical registries, clinical administrative databases and population-oriented databases. Group III were disaggregated into adverse event reporting, confidential enquiries, disease-only registers and health surveys. Databases in group I can be used not only to assess effectiveness but also to assess diffusion and equity. Databases in group II can only assess diffusion. Group III has restricted scope for assessing HTs, except for analysis of adverse events. For use in costing, databases need to include unit costs or prices. Some databases included unit cost as well as a specific HT. A list of around 270 databases was identified at the level of UK, England and Wales or England (over 1000 including Scotland, Wales and Northern Ireland). Allocation of these to the above groups identified around 60 databases with some potential for HT assessment, roughly half to group I. Eighteen clinical registers were identified as having the greatest potential although the clinical administrative datasets had potential mainly owing to their inclusion of a wide range of technologies. Only two databases were identified that could directly be used in costing. The review of the potential capture of HTs prioritized by the UK's NHS R&D HTA programme showed that only 10% would be captured in these databases, mainly drugs prescribed in primary care. The review of the use of routine databases in any form of HT assessment indicated that clinical registers were mainly used for national comparative audit. Some databases have only been used in annual reports, usually time trend analysis. A few peer-reviewed papers used a clinical register to assess the effectiveness of a technology. Accessibility is suggested as a barrier to using most databases. Clinical administrative databases (group Ib) have mainly been used to build population needs indices and performance indicators. A review of the validity of used databases showed that although internal consistency checks were common, relatively few had any form of external audit. Some comparative audit databases have data scrutinised by participating units. Issues around coverage and coding have, in general, received little attention. NHS funding of databases has been mainly for 'Central Returns' for management purposes, which excludes those databases with the greatest potential for HT assessment. Funding for databases was various, but some are unfunded, relying on goodwill. The estimated total cost of databases in group I plus selected databases from groups II and III has been estimated at pound 50 million or around 0.1% of annual NHS spend. A few databases with limited potential for HT assessment account for the bulk of spending. Suggestions for policy include clarification of responsibility for the strategic development of databases, improved resourcing, and issues around coding, confidentiality, ownership and access, maintenance of clinical support, optimal use of information technology, filling gaps and remedying deficiencies. Recommendations for researchers include closer policy links between routine data and R&D, and selective investment in the more promising databases. Recommended research topics include optimal capture and coding of the range of HTs, international comparisons of the role, funding and use of routine data in healthcare systems and use of routine database in trials and in modelling. Independent evaluations are recommended for information strategies (such as those around the National Service Frameworks and various collaborations) and for electronic patient and health records.

Maintaining Research Documents with Database Management Software.

ERIC Educational Resources Information Center

Harrington, Stuart A.

1999-01-01

Discusses taking notes for research projects and organizing them into card files; reviews the literature on personal filing systems; introduces the basic process of database management; and offers a plan for managing research notes. Describes field groups and field definitions, data entry, and creating reports. (LRW)

EPA’s Drinking Water Treatability Database: A Tool for All Drinking Water Professionals

EPA Science Inventory

The Drinking Water Treatability Database (TDB) is being developed by the USEPA Office of Research and Development to allow drinking water professionals and others to access referenced information gathered from thousands of literature sources and assembled on one site. Currently, ...

Hydrocarbon Spectral Database

National Institute of Standards and Technology Data Gateway

SRD 115 Hydrocarbon Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 91 hydrocarbon molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty and reference are given for each transition reported.

Diatomic Spectral Database

National Institute of Standards and Technology Data Gateway

SRD 114 Diatomic Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 121 diatomic molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty, and reference are given for each transition reported.

Triatomic Spectral Database

National Institute of Standards and Technology Data Gateway

SRD 117 Triatomic Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 55 triatomic molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty and reference are given for each transition reported.

Extracting patterns of database and software usage from the bioinformatics literature

PubMed Central

Duck, Geraint; Nenadic, Goran; Brass, Andy; Robertson, David L.; Stevens, Robert

2014-01-01

Motivation: As a natural consequence of being a computer-based discipline, bioinformatics has a strong focus on database and software development, but the volume and variety of resources are growing at unprecedented rates. An audit of database and software usage patterns could help provide an overview of developments in bioinformatics and community common practice, and comparing the links between resources through time could demonstrate both the persistence of existing software and the emergence of new tools. Results: We study the connections between bioinformatics resources and construct networks of database and software usage patterns, based on resource co-occurrence, that correspond to snapshots of common practice in the bioinformatics community. We apply our approach to pairings of phylogenetics software reported in the literature and argue that these could provide a stepping stone into the identification of scientific best practice. Availability and implementation: The extracted resource data, the scripts used for network generation and the resulting networks are available at http://bionerds.sourceforge.net/networks/ Contact: robert.stevens@manchester.ac.uk PMID:25161253

Factors associated with intended and effective settlement of nursing students and newly graduated nurses in a rural setting after graduation: a mixed-methods review.

PubMed

Trépanier, Amélie; Gagnon, Marie-Pierre; Mbemba, Gisèle Irène Claudine; Côté, José; Paré, Guy; Fortin, Jean-Paul; Duplàa, Emmanuel; Courcy, François

2013-03-01

To identify factors that influence the initial plan and final decision to choose a rural area as first employment location in final-year nursing students or newly graduated nurses. We conducted a mixed-methods review of the literature, including both published and gray literature, using established criteria. Two reviewers performed data extraction of relevant information independently. We retrieved empirical studies from the following databases: PubMED, Embase, CINAHL (EBSCO), Web of Science (SCI and SSCI), The Cochrane Library, Business Source Premier (EBSCO), ERIC, Proquest and PsychInfo. We also searched for empirical studies in the technical and gray literature and reviewed journals related to rural health. Additionally, we conducted searches in websites such as the Center for Health Workforce Planning and Analysis, as well as Google and Google Scholar search engines. Of the 523 studies thus screened, 15 were included for data extraction. We identified more than 40 factors associated with initial plans and final decision to settle in a rural area among nursing graduates. Only limited literature is currently available on the factors associated with the intention of nursing students or newly graduated nurses of practicing in rural areas and on the relationship between intention and effective behavior. This review highlights the needs for further research in this field. Copyright © 2012 Elsevier Ltd. All rights reserved.

O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins.

PubMed Central

Hansen, J E; Lund, O; Nilsson, J; Rapacki, K; Brunak, S

1998-01-01

O-GLYCBASE is a revised database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the sequence databases. Entries include information about species, sequence, glycosylation sites and glycan type and is fully cross-referenced. Compared to version 2.0 the number of entries has increased by 20%. Sequence logos displaying the acceptor specificity patterns for the GalNAc, mannose and GlcNAc transferases are shown. The O-GLYCBASE database is available through the WWW at http://www.cbs.dtu. dk/databases/OGLYCBASE/ PMID:9399880

The study of co-citation analysis and knowledge structure on healthcare domain

NASA Astrophysics Data System (ADS)

Chu, Kuo-Chung; Liu, Wen-I.; Tsai, Ming-Yu

2012-11-01

With the prevalence of Internet and digital archives, the online e-journal database facilitates scholars to search literature in a research domain, or to cross-search an inter-disciplined field; the key literature can be efficiently traced out. This study intends to build a Web-based citation analysis system, which consists of four modules, they are: 1) literature search module; (2) statistics module; (3) articles analysis module; and (4) co-citation analysis module. The system focuses on PubMed Central dataset that has 170,000 records. In a research domain, a specific keyword searches in terms of authors, journals, and core issues. In addition, we use data mining techniques for co-citation analysis. The results assist researchers with in-depth understanding of the domain knowledge. Having an automated system for co-citation analysis, it helps to understand changes, trends, and knowledge structure of research domain. For the best of our knowledge, the proposed system differentiates from existing online electronic retrieval database analysis function. Perhaps, the proposed system is going to be a value-added database of healthcare domain, and hope to contribute the researchers.

Searching for disability in electronic databases of published literature.

PubMed

Walsh, Emily S; Peterson, Jana J; Judkins, Dolores Z

2014-01-01

As researchers in disability and health conduct systematic reviews with greater frequency, the definition of disability used in these reviews gains importance. Translating a comprehensive conceptual definition of "disability" into an operational definition that utilizes electronic databases in the health sciences is a difficult step necessary for performing systematic literature reviews in the field. Consistency of definition across studies will help build a body of evidence that is comparable and amenable to synthesis. To illustrate a process for operationalizing the World Health Organization's International Classification of Disability, Functioning, and Health concept of disability for MEDLINE, PsycINFO, and CINAHL databases. We created an electronic search strategy in conjunction with a reference librarian and an expert panel. Quality control steps included comparison of search results to results of a search for a specific disabling condition and to articles nominated by the expert panel. The complete search strategy is presented. Results of the quality control steps indicated that our strategy was sufficiently sensitive and specific. Our search strategy will be valuable to researchers conducting literature reviews on broad populations with disabilities. Copyright © 2014 Elsevier Inc. All rights reserved.

Comparing Amazon's Mechanical Turk Platform to Conventional Data Collection Methods in the Health and Medical Research Literature.

PubMed

Mortensen, Karoline; Hughes, Taylor L

2018-04-01

The goal of this article is to conduct an assessment of the peer-reviewed primary literature with study objectives to analyze Amazon.com 's Mechanical Turk (MTurk) as a research tool in a health services research and medical context. Searches of Google Scholar and PubMed databases were conducted in February 2017. We screened article titles and abstracts to identify relevant articles that compare data from MTurk samples in a health and medical context to another sample, expert opinion, or other gold standard. Full-text manuscript reviews were conducted for the 35 articles that met the study criteria. The vast majority of the studies supported the use of MTurk for a variety of academic purposes. The literature overwhelmingly concludes that MTurk is an efficient, reliable, cost-effective tool for generating sample responses that are largely comparable to those collected via more conventional means. Caveats include survey responses may not be generalizable to the US population.

Perioperative antibiotic usage by facial plastic surgeons: national survey results and comparison with evidence-based guidelines.

PubMed

Grunebaum, Lisa Danielle; Reiter, David

2006-01-01

To determine current practice for use of perioperative antibiotics among facial plastic surgeons, to determine the extent of use of literature support for preferences of facial plastic surgeons, and to compare patterns of use with nationally supported evidence-based guidelines. A link to a Web site containing a questionnaire on perioperative antibiotic use was e-mailed to more than 1000 facial plastic surgeons in the United States. Responses were archived in a dedicated database and analyzed to determine patterns of use and methods of documenting that use. Current literature was used to develop evidence-based recommendations for perioperative antibiotic use, emphasizing current nationally supported guidelines. Preferences varied significantly for medication used, dosage and regimen, time of first dose relative to incision time, setting in which medication was administered, and procedures for which perioperative antibiotic was deemed necessary. Surgical site infection in facial plastic surgery can be reduced by better conformance to currently available evidence-based guidelines. We offer specific recommendations that are supported by the current literature.

Expert opinion: diagnosis and treatment of proximal hamstring tendinopathy

PubMed Central

Lempainen, Lasse; Johansson, Kristian; Banke, Ingo J.; Ranne, Juha; Mäkelä, Keijo; Sarimo, Janne; Niemi, Pekka; Orava, Sakari

2015-01-01

Summary Background: proximal hamstring tendinopathy (PHT) is a disabilitating disease often causing underperformance in the athletically demanding patients. The main symptom of PHT is lower gluteal pain especially during running or while prolonged sitting. Mainly affecting athletically active individuals, PHT is a considerable challenge for treating health care professionals. Purpose: this paper aims to concisely present the literature on PHT to guide health care professionals treating these patients and doing research on the subject. Methods: we reviewed the literature on PHT through literature search of scientific journal databases. Conclusions: as a tendinopathic pathology, it is a rather recently discovered exertion injury. As with other chronic tendon overuse injuries, current treatment strategies are unspecific with uncertain outcomes due to the unknown etiology of the tendon degeneration. Diagnostic features as well as both operative and non-operative treatments are evaluated from a clinical perspective, providing up to date information for clinicians and sports medicine therapists dealing with hamstring problems. Level of evidence: V. PMID:25878983

Medical Utilization of Kiosks in the Delivery of Patient Education: A Systematic Review

PubMed Central

Yvonne Chan, Yu-Feng; Nagurka, Roxanne; Bentley, Suzanne; Ordonez, Edgardo; Sproule, William

2014-01-01

Background: The utilization of kiosks has previously been shown to be effective for collecting information, delivering educational modules, and providing access to health information. We discuss a review of current literature for the utilization of kiosks for the delivery of patient education. Methods: The criteria for inclusion in this literature review were: (1) study discusses the utilization of kiosks for patient health education; (2) study discusses the use of touch screens for patient health information; (3) published in English. Our review includes searches via MEDLINE databases and Google Scholar for the years 1996-2014. Results: Overall, 167 articles were screened for final eligibility, and after discarding duplicates and non-eligible studies with abstract. Full-text review of 28 articles was included in the final analysis. Conclusion: The review of available literature demonstrates the effectiveness of touch screen kiosks to educate patients and to improve healthcare, both at a performance and cost advantage over other modes of patient education. PMID:25097831

Meditation as an Adjunct to the Management of Multiple Sclerosis

PubMed Central

Levin, Adam B.; Hadgkiss, Emily J.; Weiland, Tracey J.; Jelinek, George A.

2014-01-01

Background. Multiple sclerosis (MS) disease course is known to be adversely affected by several factors including stress. A proposed mechanism for decreasing stress and therefore decreasing MS morbidity and improving quality of life is meditation. This review aims to critically analyse the current literature regarding meditation and MS. Methods. Four major databases were used to search for English language papers published before March 2014 with the terms MS, multiple sclerosis, meditation, and mindfulness. Results. 12 pieces of primary literature fitting the selection criteria were selected: two were randomised controlled studies, four were cohort studies, and six were surveys. The current literature varies in quality; however common positive effects of meditation include improved quality of life (QOL) and improved coping skills. Conclusion. All studies suggest possible benefit to the use of meditation as an adjunct to the management of multiple sclerosis. Additional rigorous clinical trials are required to validate the existing findings and determine if meditation has an impact on disease course over time. PMID:25105026

Management of diabetes and diabetes policies in Turkey

PubMed Central

2013-01-01

Background Diabetes and its complications are among the present and future challenges of the Turkish health care system. The objective of this paper is to discuss the current situation of diabetes and its management in Turkey with special emphasis on the changing policy environment. Methods A literature review in databases such as PUBMED was performed from 2000 to 2011. This synthesis was complemented by grey literature, personal communication and contact with national and provincial health authorities and experts in diabetes from Turkey. Results The literature review and expert consultations indicated a growing policy emphasis on diabetes. Both the public and private sectors, non-governmental organizations have initiated policy papers to shape the outlook of diabetes care in the future. This is in line with the current dynamics of the healthcare system. Conclusions Diabetes care will be high on the agenda in future. Evidence based policy-making is the key to implement the policies adopted so far and a supportive environment is needed. PMID:23597065

Exploring nursing educators' use of theory and methods in search for evidence based credibility in nursing education.

PubMed

Beccaria, Lisa; Kek, Megan Y C A; Huijser, Henk

2018-06-01

In this paper, a review of nursing education literature is employed to ascertain the extent to which nursing educators apply theory to their research, as well as the types of theory they employ. In addition, the use of research methodologies in the nursing education literature is explored. An integrative review. A systematic search was conducted for English-language, peer reviewed publications of any research design via Academic Search Complete, Science Direct, CINAHL, and Health Source: Nursing/Academic Edition databases from 2001 to 2016, of which 140 were reviewed. The findings suggest that within current nursing education literature the scholarship of discovery, and the exploration of epistemologies other than nursing, in particular as they relate to teaching and learning, shows significant potential for expansion and diversification. The analysis highlights opportunities for nursing educators to incorporate broader theoretical, pedagogical, methodological and philosophical perspectives within teaching and the scholarship of teaching. Copyright © 2018 Elsevier Ltd. All rights reserved.

Fragment virtual screening based on Bayesian categorization for discovering novel VEGFR-2 scaffolds.

PubMed

Zhang, Yanmin; Jiao, Yu; Xiong, Xiao; Liu, Haichun; Ran, Ting; Xu, Jinxing; Lu, Shuai; Xu, Anyang; Pan, Jing; Qiao, Xin; Shi, Zhihao; Lu, Tao; Chen, Yadong

2015-11-01

The discovery of novel scaffolds against a specific target has long been one of the most significant but challengeable goals in discovering lead compounds. A scaffold that binds in important regions of the active pocket is more favorable as a starting point because scaffolds generally possess greater optimization possibilities. However, due to the lack of sufficient chemical space diversity of the databases and the ineffectiveness of the screening methods, it still remains a great challenge to discover novel active scaffolds. Since the strengths and weaknesses of both fragment-based drug design and traditional virtual screening (VS), we proposed a fragment VS concept based on Bayesian categorization for the discovery of novel scaffolds. This work investigated the proposal through an application on VEGFR-2 target. Firstly, scaffold and structural diversity of chemical space for 10 compound databases were explicitly evaluated. Simultaneously, a robust Bayesian classification model was constructed for screening not only compound databases but also their corresponding fragment databases. Although analysis of the scaffold diversity demonstrated a very unevenly distribution of scaffolds over molecules, results showed that our Bayesian model behaved better in screening fragments than molecules. Through a literature retrospective research, several generated fragments with relatively high Bayesian scores indeed exhibit VEGFR-2 biological activity, which strongly proved the effectiveness of fragment VS based on Bayesian categorization models. This investigation of Bayesian-based fragment VS can further emphasize the necessity for enrichment of compound databases employed in lead discovery by amplifying the diversity of databases with novel structures.

LIVIVO - the Vertical Search Engine for Life Sciences.

PubMed

Müller, Bernd; Poley, Christoph; Pössel, Jana; Hagelstein, Alexandra; Gübitz, Thomas

2017-01-01

The explosive growth of literature and data in the life sciences challenges researchers to keep track of current advancements in their disciplines. Novel approaches in the life science like the One Health paradigm require integrated methodologies in order to link and connect heterogeneous information from databases and literature resources. Current publications in the life sciences are increasingly characterized by the employment of trans-disciplinary methodologies comprising molecular and cell biology, genetics, genomic, epigenomic, transcriptional and proteomic high throughput technologies with data from humans, plants, and animals. The literature search engine LIVIVO empowers retrieval functionality by incorporating various literature resources from medicine, health, environment, agriculture and nutrition. LIVIVO is developed in-house by ZB MED - Information Centre for Life Sciences. It provides a user-friendly and usability-tested search interface with a corpus of 55 Million citations derived from 50 databases. Standardized application programming interfaces are available for data export and high throughput retrieval. The search functions allow for semantic retrieval with filtering options based on life science entities. The service oriented architecture of LIVIVO uses four different implementation layers to deliver search services. A Knowledge Environment is developed by ZB MED to deal with the heterogeneity of data as an integrative approach to model, store, and link semantic concepts within literature resources and databases. Future work will focus on the exploitation of life science ontologies and on the employment of NLP technologies in order to improve query expansion, filters in faceted search, and concept based relevancy rankings in LIVIVO.

MEDLINE versus EMBASE and CINAHL for telemedicine searches.

PubMed

Bahaadinbeigy, Kambiz; Yogesan, Kanagasingam; Wootton, Richard

2010-10-01

Researchers in the domain of telemedicine throughout the world tend to search multiple bibliographic databases to retrieve the highest possible number of publications when conducting review projects. Medical Literature Analysis and Retrieval System Online (MEDLINE), Excerpta Medica Database (EMBASE), and Cumulative Index to Nursing and Allied Health Literature (CINAHL) are three popular databases in the discipline of biomedicine that are used for conducting reviews. Access to the MEDLINE database is free and easy, whereas EMBASE and CINAHL are not free and sometimes not easy to access for researchers in small research centers. This project sought to compare MEDLINE with EMBASE and CINAHL to estimate what proportion of potentially relevant publications would be missed when only MEDLINE is used in a review project, in comparison to when EMBASE and CINAHL are also used. Twelve simple keywords relevant to 12 different telemedicine applications were searched using all three databases, and the results were compared. About 9%-18% of potentially relevant articles would have been missed if MEDLINE had been the only database used. It is preferable if all three or more databases are used when conducting a review in telemedicine. Researchers from developing countries or small research institutions could rely on only MEDLINE, but they would loose 9%-18% of the potentially relevant publications. Searching MEDLINE alone is not ideal, but in a resource-constrained situation, it is definitely better than nothing.