Improving e-book access via a library-developed full-text search tool*

PubMed Central

Foust, Jill E.; Bergen, Phillip; Maxeiner, Gretchen L.; Pawlowski, Peter N.

2007-01-01

Purpose: This paper reports on the development of a tool for searching the contents of licensed full-text electronic book (e-book) collections. Setting: The Health Sciences Library System (HSLS) provides services to the University of Pittsburgh's medical programs and large academic health system. Brief Description: The HSLS has developed an innovative tool for federated searching of its e-book collections. Built using the XML-based Vivísimo development environment, the tool enables a user to perform a full-text search of over 2,500 titles from the library's seven most highly used e-book collections. From a single “Google-style” query, results are returned as an integrated set of links pointing directly to relevant sections of the full text. Results are also grouped into categories that enable more precise retrieval without reformulation of the search. Results/Evaluation: A heuristic evaluation demonstrated the usability of the tool and a web server log analysis indicated an acceptable level of usage. Based on its success, there are plans to increase the number of online book collections searched. Conclusion: This library's first foray into federated searching has produced an effective tool for searching across large collections of full-text e-books and has provided a good foundation for the development of other library-based federated searching products. PMID:17252065

Estimating Missing Features to Improve Multimedia Information Retrieval

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

Bagherjeiran, A; Love, N S; Kamath, C

Retrieval in a multimedia database usually involves combining information from different modalities of data, such as text and images. However, all modalities of the data may not be available to form the query. The retrieval results from such a partial query are often less than satisfactory. In this paper, we present an approach to complete a partial query by estimating the missing features in the query. Our experiments with a database of images and their associated captions show that, with an initial text-only query, our completion method has similar performance to a full query with both image and text features.more » In addition, when we use relevance feedback, our approach outperforms the results obtained using a full query.« less

[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.

A Current Approach to Halitosis and Oral Malodor- A Mini Review.

PubMed

Bicak, Damla Aksit

2018-01-01

Halitosis, in other words, oral malodor is an important multifactorial health problem affecting the psychological and social life of individuals and is the most common reason for referral to dentists after dental caries and periodontal diseases. The objective of this review was to present and discuss conventional and recently introduced information about the types, causes, detection and treatment methods of halitosis. An expanded literature review was conducted which targeted all articles published in peer-reviewed journals relating to the topic of halitosis. Only articles written in Turkish and English languages were considered. The review itself began with a search of relevant subject headings such as 'halitosis, oral malodor, volatile sulfur compounds in PubMed/Medline, Scopus, Google Scholar and Tubitak Ulakbim databases. A hand search of references was also performed. When search results are combined, the total number of relevant literature was found to be 4646 abstracts and 978 full-text articles. Abstracts, editorial letters were not included and about half of full-text articles were not related to dental practice. Among the remaining 124 full-text articles, duplicated articles and articles written other than Turkish and English languages were removed and 54 full-text articles were used for this review. According to the reviewed articles, both conventional and new methods were introduced in the management of halitosis. However, conventional methods seem to be more effective and widely used in the diagnosis and treatment of halitosis. As being first line professionals, dentists must analyze and treat oral problems which may be responsible for the patient's malodor, and should inform the patient about halitosis causes and oral hygiene procedures (tooth flossing, tongue cleaning, appropriate mouthwash and toothpaste selection and use) and if the problem persists, they should consult to a medical specialist.

An exploratory analysis of PubMed's free full-text limit on citation retrieval for clinical questions.

PubMed

Krieger, Mary M; Richter, Randy R; Austin, Tricia M

2008-10-01

The research sought to determine (1) how use of the PubMed free full-text (FFT) limit affects citation retrieval and (2) how use of the FFT limit impacts the types of articles and levels of evidence retrieved. Four clinical questions based on a research agenda for physical therapy were searched in PubMed both with and without the use of the FFT limit. Retrieved citations were examined for relevancy to each question. Abstracts of relevant citations were reviewed to determine the types of articles and levels of evidence. Descriptive analysis was used to compare the total number of citations, number of relevant citations, types of articles, and levels of evidence both with and without the use of the FFT limit. Across all 4 questions, the FFT limit reduced the number of citations to 11.1% of the total number of citations retrieved without the FFT limit. Additionally, high-quality evidence such as systematic reviews and randomized controlled trials were missed when the FFT limit was used. Health sciences librarians play a key role in educating users about the potential impact the FFT limit has on the number of citations, types of articles, and levels of evidence retrieved.

12 years on - Is the NLM medical text indexer still useful and relevant?

PubMed

Mork, James; Aronson, Alan; Demner-Fushman, Dina

2017-02-23

Facing a growing workload and dwindling resources, the US National Library of Medicine (NLM) created the Indexing Initiative project in 1996. This cross-library team's mission is to explore indexing methodologies for ensuring quality and currency of NLM document collections. The NLM Medical Text Indexer (MTI) is the main product of this project and has been providing automated indexing recommendations since 2002. After all of this time, the questions arise whether MTI is still useful and relevant. To answer the question about MTI usefulness, we track a wide variety of statistics related to how frequently MEDLINE indexers refer to MTI recommendations, how well MTI performs against human indexing, and how often MTI is used. To answer the question of MTI relevancy compared to other available tools, we have participated in the 2013 and 2014 BioASQ Challenges. The BioASQ Challenges have provided us with an unbiased comparison between the MTI system and other systems performing the same task. Indexers have continually increased their use of MTI recommendations over the years from 15.75% of the articles they index in 2002 to 62.44% in 2014 showing that the indexers find MTI to be increasingly useful. The MTI performance statistics show significant improvement in Precision (+0.2992) and F 1 (+0.1997) with modest gains in Recall (+0.0454) over the years. MTI consistency is comparable to the available indexer consistency studies. MTI performed well in both of the BioASQ Challenges ranking within the top tier teams. Based on our findings, yes, MTI is still relevant and useful, and needs to be improved and expanded. The BioASQ Challenge results have shown that we need to incorporate more machine learning into MTI while still retaining the indexing rules that have earned MTI the indexers' trust over the years. We also need to expand MTI through the use of full text, when and where it is available, to provide coverage of indexing terms that are typically only found in the full text. The role of MTI at NLM is also expanding into new areas, further reinforcing the idea that MTI is increasingly useful and relevant.

World Wide Web Search Engines: AltaVista and Yahoo.

ERIC Educational Resources Information Center

Machovec, George S., Ed.

1996-01-01

Examines the history, structure, and search capabilities of Internet search tools AltaVista and Yahoo. AltaVista provides relevance-ranked feedback on full-text searches. Yahoo indexes Web "citations" only but does organize information hierarchically into predefined categories. Yahoo has recently become a publicly held company and…

Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining.

PubMed

Kreula, Sanna M; Kaewphan, Suwisa; Ginter, Filip; Jones, Patrik R

2018-01-01

The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from 'reading the literature'. The utility of text-mining for well-studied species is obvious though the utility for less studied species, or those with no prior track-record at all, is not clear. Here we present a concept for how advanced text-mining can be used to create information-rich networks even for less well studied species and apply it to generate an open-access gene-gene association network resource for Synechocystis sp. PCC 6803, a representative model organism for cyanobacteria and first case-study for the methodology. By merging the text-mining network with networks generated from species-specific experimental data, network integration was used to enhance the accuracy of predicting novel interactions that are biologically relevant. A rule-based algorithm (filter) was constructed in order to automate the search for novel candidate genes with a high degree of likely association to known target genes by (1) ignoring established relationships from the existing literature, as they are already 'known', and (2) demanding multiple independent evidences for every novel and potentially relevant relationship. Using selected case studies, we demonstrate the utility of the network resource and filter to ( i ) discover novel candidate associations between different genes or proteins in the network, and ( ii ) rapidly evaluate the potential role of any one particular gene or protein. The full network is provided as an open-source resource.

An exploratory analysis of PubMed's free full-text limit on citation retrieval for clinical questions

PubMed Central

Krieger, Mary M.; Richter, Randy R.; Austin, Tricia M.

2008-01-01

Objective: The research sought to determine (1) how use of the PubMed free full-text (FFT) limit affects citation retrieval and (2) how use of the FFT limit impacts the types of articles and levels of evidence retrieved. Methods: Four clinical questions based on a research agenda for physical therapy were searched in PubMed both with and without the use of the FFT limit. Retrieved citations were examined for relevancy to each question. Abstracts of relevant citations were reviewed to determine the types of articles and levels of evidence. Descriptive analysis was used to compare the total number of citations, number of relevant citations, types of articles, and levels of evidence both with and without the use of the FFT limit. Results: Across all 4 questions, the FFT limit reduced the number of citations to 11.1% of the total number of citations retrieved without the FFT limit. Additionally, high-quality evidence such as systematic reviews and randomized controlled trials were missed when the FFT limit was used. Conclusions: Health sciences librarians play a key role in educating users about the potential impact the FFT limit has on the number of citations, types of articles, and levels of evidence retrieved. PMID:18974812

Semi automatic indexing of PostScript files using Medical Text Indexer in medical education.

PubMed

Mollah, Shamim Ara; Cimino, Christopher

2007-10-11

At Albert Einstein College of Medicine a large part of online lecture materials contain PostScript files. As the collection grows it becomes essential to create a digital library to have easy access to relevant sections of the lecture material that is full-text indexed; to create this index it is necessary to extract all the text from the document files that constitute the originals of the lectures. In this study we present a semi automatic indexing method using robust technique for extracting text from PostScript files and National Library of Medicine's Medical Text Indexer (MTI) program for indexing the text. This model can be applied to other medical schools for indexing purposes.

Mining protein function from text using term-based support vector machines

PubMed Central

Rice, Simon B; Nenadic, Goran; Stapley, Benjamin J

2005-01-01

Background Text mining has spurred huge interest in the domain of biology. The goal of the BioCreAtIvE exercise was to evaluate the performance of current text mining systems. We participated in Task 2, which addressed assigning Gene Ontology terms to human proteins and selecting relevant evidence from full-text documents. We approached it as a modified form of the document classification task. We used a supervised machine-learning approach (based on support vector machines) to assign protein function and select passages that support the assignments. As classification features, we used a protein's co-occurring terms that were automatically extracted from documents. Results The results evaluated by curators were modest, and quite variable for different problems: in many cases we have relatively good assignment of GO terms to proteins, but the selected supporting text was typically non-relevant (precision spanning from 3% to 50%). The method appears to work best when a substantial set of relevant documents is obtained, while it works poorly on single documents and/or short passages. The initial results suggest that our approach can also mine annotations from text even when an explicit statement relating a protein to a GO term is absent. Conclusion A machine learning approach to mining protein function predictions from text can yield good performance only if sufficient training data is available, and significant amount of supporting data is used for prediction. The most promising results are for combined document retrieval and GO term assignment, which calls for the integration of methods developed in BioCreAtIvE Task 1 and Task 2. PMID:15960835

Effects of OCR Errors on Ranking and Feedback Using the Vector Space Model.

ERIC Educational Resources Information Center

Taghva, Kazem; And Others

1996-01-01

Reports on the performance of the vector space model in the presence of OCR (optical character recognition) errors in information retrieval. Highlights include precision and recall, a full-text test collection, smart vector representation, impact of weighting parameters, ranking variability, and the effect of relevance feedback. (Author/LRW)

Understanding disciplinary vocabularies using a full-text enabled domain-independent term extraction approach.

PubMed

Yan, Erjia; Williams, Jake; Chen, Zheng

2017-01-01

Publication metadata help deliver rich analyses of scholarly communication. However, research concepts and ideas are more effectively expressed through unstructured fields such as full texts. Thus, the goals of this paper are to employ a full-text enabled method to extract terms relevant to disciplinary vocabularies, and through them, to understand the relationships between disciplines. This paper uses an efficient, domain-independent term extraction method to extract disciplinary vocabularies from a large multidisciplinary corpus of PLoS ONE publications. It finds a power-law pattern in the frequency distributions of terms present in each discipline, indicating a semantic richness potentially sufficient for further study and advanced analysis. The salient relationships amongst these vocabularies become apparent in application of a principal component analysis. For example, Mathematics and Computer and Information Sciences were found to have similar vocabulary use patterns along with Engineering and Physics; while Chemistry and the Social Sciences were found to exhibit contrasting vocabulary use patterns along with the Earth Sciences and Chemistry. These results have implications to studies of scholarly communication as scholars attempt to identify the epistemological cultures of disciplines, and as a full text-based methodology could lead to machine learning applications in the automated classification of scholarly work according to disciplinary vocabularies.

Understanding disciplinary vocabularies using a full-text enabled domain-independent term extraction approach

PubMed Central

Williams, Jake; Chen, Zheng

2017-01-01

Publication metadata help deliver rich analyses of scholarly communication. However, research concepts and ideas are more effectively expressed through unstructured fields such as full texts. Thus, the goals of this paper are to employ a full-text enabled method to extract terms relevant to disciplinary vocabularies, and through them, to understand the relationships between disciplines. This paper uses an efficient, domain-independent term extraction method to extract disciplinary vocabularies from a large multidisciplinary corpus of PLoS ONE publications. It finds a power-law pattern in the frequency distributions of terms present in each discipline, indicating a semantic richness potentially sufficient for further study and advanced analysis. The salient relationships amongst these vocabularies become apparent in application of a principal component analysis. For example, Mathematics and Computer and Information Sciences were found to have similar vocabulary use patterns along with Engineering and Physics; while Chemistry and the Social Sciences were found to exhibit contrasting vocabulary use patterns along with the Earth Sciences and Chemistry. These results have implications to studies of scholarly communication as scholars attempt to identify the epistemological cultures of disciplines, and as a full text-based methodology could lead to machine learning applications in the automated classification of scholarly work according to disciplinary vocabularies. PMID:29186141

The Impact of Mobile Apps on Alcohol Use Disorder: A Systematic Review Protocol.

PubMed

Sawares, Antoine Sa; Shen, Nelson; Xue, Yunlin; Abi-Jaoude, Alexxa; Wiljer, David

2017-04-04

Alcohol use disorder (AUD) is among the most prevalent mental disorders worldwide and is associated with a diverse range of physical and psychological comorbidities. Despite various types of treatment, there are many barriers to accessing treatment (ie, stigma, cost, accessibility of service, etc). Mobile apps have the potential to overcome these barriers and provide support to those who need it. The purpose of this systematic review is to assess the effectiveness of mobile apps in reducing alcohol consumption for individuals with AUD and understand the psychological outcomes of using the apps (ie, client empowerment, self-efficacy, etc). The search strategy was applied to 7 health sciences and interdisciplinary databases. Two reviewers will independently assess all titles and abstracts for relevance and then full texts of relevant articles for eligibility. To be included, the article must be a quantitative evaluation of clinical outcomes using the intervention and the intervention must be a consumer-facing app focused on supporting individuals with AUD. Two reviewers will independently extract data from all eligible articles using a standardized extraction worksheet and will independently assess the study quality. A meta-analysis will be conducted if appropriate. Depending on outcomes reported, pooled risk ratios or standardized mean differences will be calculated and reported in the review. The search strategy yielded 699 unique citations. Of those, 63 (9.0%, 63/699) articles were assessed as relevant for full-text review. The full-text reviews are currently underway and the final review is projected to be completed in the summer of 2017. There is potential for mobile apps to support individuals with AUD to reduce their alcohol consumption. This review will be the first to assess the effectiveness of AUD mobile apps and client experiences using the apps. ©Antoine SA Sawares, Nelson Shen, Yunlin Xue, Alexxa Abi-Jaoude, David Wiljer. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 04.04.2017.

Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining

PubMed Central

Kreula, Sanna M.; Kaewphan, Suwisa; Ginter, Filip

2018-01-01

The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from ‘reading the literature’. The utility of text-mining for well-studied species is obvious though the utility for less studied species, or those with no prior track-record at all, is not clear. Here we present a concept for how advanced text-mining can be used to create information-rich networks even for less well studied species and apply it to generate an open-access gene-gene association network resource for Synechocystis sp. PCC 6803, a representative model organism for cyanobacteria and first case-study for the methodology. By merging the text-mining network with networks generated from species-specific experimental data, network integration was used to enhance the accuracy of predicting novel interactions that are biologically relevant. A rule-based algorithm (filter) was constructed in order to automate the search for novel candidate genes with a high degree of likely association to known target genes by (1) ignoring established relationships from the existing literature, as they are already ‘known’, and (2) demanding multiple independent evidences for every novel and potentially relevant relationship. Using selected case studies, we demonstrate the utility of the network resource and filter to (i) discover novel candidate associations between different genes or proteins in the network, and (ii) rapidly evaluate the potential role of any one particular gene or protein. The full network is provided as an open-source resource. PMID:29844966

Updates in venous thromboembolism management: evidence published in 2017.

PubMed

Bartlett, Matthew A; Bierle, Dennis M; Saadiq, Rayya A; Mauck, Karen F; Daniels, Paul R

2018-06-20

Venous thromboembolism (VTE) management is rapidly evolving and staying up-to-date is challenging. We identified the most practice-informing articles published in 2017 relevant to the nonspecialist provider managing VTE. We performed a systematic search of the literature (Appendix A), limiting the search to a publication date of 2017. Two reviewers screened the 2735 resulting abstracts to identify high-quality, clinically relevant publications related to VTE management. One-hundred and six full-text articles were considered for inclusion. The five authors used a modified Delphi method to reach consensus on inclusion of seven articles for in-depth appraisal, following predetermined criteria of clinical relevance to nonspecialist providers, potential for practice change, and strength of the evidence.

Mining the pharmacogenomics literature—a survey of the state of the art

PubMed Central

Cohen, K. Bretonnel; Garten, Yael; Shah, Nigam H.

2012-01-01

This article surveys efforts on text mining of the pharmacogenomics literature, mainly from the period 2008 to 2011. Pharmacogenomics (or pharmacogenetics) is the field that studies how human genetic variation impacts drug response. Therefore, publications span the intersection of research in genotypes, phenotypes and pharmacology, a topic that has increasingly become a focus of active research in recent years. This survey covers efforts dealing with the automatic recognition of relevant named entities (e.g. genes, gene variants and proteins, diseases and other pathological phenomena, drugs and other chemicals relevant for medical treatment), as well as various forms of relations between them. A wide range of text genres is considered, such as scientific publications (abstracts, as well as full texts), patent texts and clinical narratives. We also discuss infrastructure and resources needed for advanced text analytics, e.g. document corpora annotated with corresponding semantic metadata (gold standards and training data), biomedical terminologies and ontologies providing domain-specific background knowledge at different levels of formality and specificity, software architectures for building complex and scalable text analytics pipelines and Web services grounded to them, as well as comprehensive ways to disseminate and interact with the typically huge amounts of semiformal knowledge structures extracted by text mining tools. Finally, we consider some of the novel applications that have already been developed in the field of pharmacogenomic text mining and point out perspectives for future research. PMID:22833496

Mining the pharmacogenomics literature--a survey of the state of the art.

PubMed

Hahn, Udo; Cohen, K Bretonnel; Garten, Yael; Shah, Nigam H

2012-07-01

This article surveys efforts on text mining of the pharmacogenomics literature, mainly from the period 2008 to 2011. Pharmacogenomics (or pharmacogenetics) is the field that studies how human genetic variation impacts drug response. Therefore, publications span the intersection of research in genotypes, phenotypes and pharmacology, a topic that has increasingly become a focus of active research in recent years. This survey covers efforts dealing with the automatic recognition of relevant named entities (e.g. genes, gene variants and proteins, diseases and other pathological phenomena, drugs and other chemicals relevant for medical treatment), as well as various forms of relations between them. A wide range of text genres is considered, such as scientific publications (abstracts, as well as full texts), patent texts and clinical narratives. We also discuss infrastructure and resources needed for advanced text analytics, e.g. document corpora annotated with corresponding semantic metadata (gold standards and training data), biomedical terminologies and ontologies providing domain-specific background knowledge at different levels of formality and specificity, software architectures for building complex and scalable text analytics pipelines and Web services grounded to them, as well as comprehensive ways to disseminate and interact with the typically huge amounts of semiformal knowledge structures extracted by text mining tools. Finally, we consider some of the novel applications that have already been developed in the field of pharmacogenomic text mining and point out perspectives for future research.

Drug therapy for symptoms associated with anxiety in adult palliative care patients.

PubMed

Salt, Susan; Mulvaney, Caroline A; Preston, Nancy J

2017-05-18

This is an update of a Cochrane Review first published in 2004 (Issue 1) and previously updated in 2012 (Issue 10). Anxiety is common in palliative care patients. It can be a natural response to the complex uncertainty of having a life-limiting illness or impending death, but it may represent a clinically significant issue in its own right. To assess the effectiveness of drug therapy for treating symptoms of anxiety in adults with a progressive life-limiting illness who are thought to be in their last year of life. We ran the searches for this update to May 2016. We searched the CENTRAL, MEDLINE (Ovid), Embase (Ovid), CINAHL (EBSCO), PsychLIT (Silver Platter) and PsycINFO (Ovid). We searched seven trials registers and seven pharmaceutical industry trials registers. We handsearched the conference abstracts of the European Association of Palliative Care. Randomised controlled trials which examined the effect of drug therapy for the treatment of symptoms of anxiety in adult palliative care patients, that is, people with a known progressive life-limiting illness that is no longer responsive to curative treatment, including advanced heart, respiratory and neurological diseases (including dementia). Comparator treatments included placebo; another drug therapy or different dose schedule; or a non-drug intervention such as counselling, cognitive behaviour therapies or relaxation therapies. Two review authors independently screened titles and abstracts to identify potentially relevant papers for inclusion in the review. We sought full-text reports for all papers retained at this stage and two reviews authors independently assessed these for inclusion in the review. We planned to assess risk of bias and extract data including information on adverse events. We planned to assess the evidence using GRADE and to create a 'Summary of findings' table. In this update, we identified 707 potentially relevant papers and of these we sought the full-text reports of 10 papers. On examination of these full-text reports, we excluded eight and two are awaiting classification as we have insufficient information to make a decision. Thus, in this update, we found no studies which met our inclusion criteria. For the original review, we identified, and then excluded, the full-text reports of six potentially relevant studies. For the 2012 update, we sought, and excluded, two full-text reports. Thus, we found no studies that assessed the effectiveness of drugs to treat symptoms of anxiety in palliative care patients. There is a lack of evidence to draw a conclusion about the effectiveness of drug therapy for symptoms of anxiety in adult palliative care patients. To date, we have found no studies that meet the inclusion criteria for this review. We are awaiting further information for two studies which may be included in a future update. Randomised controlled trials which assess management of anxiety as a primary endpoint are required to establish the benefits and harms of drug therapy for the treatment of anxiety in palliative care.

PaperBLAST: Text Mining Papers for Information about Homologs

DOE PAGES

Price, Morgan N.; Arkin, Adam P.

2017-08-15

Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources (Swiss-Prot, GeneRIF, and EcoCyc) that link protein sequences to scientific articles. PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quicklymore » finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. We hope that PaperBLAST will make it easier for biologists to predict proteins’ functions.« less

PaperBLAST: Text Mining Papers for Information about Homologs

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

Price, Morgan N.; Arkin, Adam P.

Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources (Swiss-Prot, GeneRIF, and EcoCyc) that link protein sequences to scientific articles. PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quicklymore » finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. We hope that PaperBLAST will make it easier for biologists to predict proteins’ functions.« less

PaperBLAST: Text Mining Papers for Information about Homologs

PubMed Central

Arkin, Adam P.

2017-01-01

ABSTRACT Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources (Swiss-Prot, GeneRIF, and EcoCyc) that link protein sequences to scientific articles. PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. PaperBLAST is available at http://papers.genomics.lbl.gov/. IMPORTANCE With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. We hope that PaperBLAST will make it easier for biologists to predict proteins’ functions. PMID:28845458

PaperBLAST: Text Mining Papers for Information about Homologs.

PubMed

Price, Morgan N; Arkin, Adam P

2017-01-01

Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources (Swiss-Prot, GeneRIF, and EcoCyc) that link protein sequences to scientific articles. PaperBLAST's database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. PaperBLAST is available at http://papers.genomics.lbl.gov/. IMPORTANCE With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. We hope that PaperBLAST will make it easier for biologists to predict proteins' functions.

Essential Annotation Schema for Ecology (EASE)-A framework supporting the efficient data annotation and faceted navigation in ecology.

PubMed

Pfaff, Claas-Thido; Eichenberg, David; Liebergesell, Mario; König-Ries, Birgitta; Wirth, Christian

2017-01-01

Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines.

Quantity and Quality of Economic Evaluations in U.S. Nursing Research, 1997-2015: A Systematic Review.

PubMed

Cook, Wendy A; Morrison, Megan L; Eaton, Linda H; Theodore, Brian R; Doorenbos, Ardith Z

The United States has a complex healthcare system that is undergoing substantial reformations. There is a need for high-quality, economic evaluations of nursing practice. An updated review of completed economic evaluations relevant to the field of nursing within the U.S. healthcare system is timely and needed. The purpose of this study was to evaluate and describe the quantity and quality of economic evaluations in nursing-relevant research performed in the United States between 1997 and 2015. Four databases were searched. Titles, abstracts, and full-text content were reviewed to identify studies that analyzed both costs and outcomes, relevant to nursing, performed in the United States, and used the quality-adjusted life year to measure effectiveness. For included studies, data were extracted from full-text articles using criteria from U.S. Public Health Service's Panel on Cost-Effectiveness in Health and Medicine. Twenty-eight studies met the inclusion criteria. Most (n = 25, 89%) were published in the last decade of the analysis, from 2006 to 2015. Assessment of quality, based on selected items from the panel guidelines, found that the evaluations did not consistently use the recommended societal perspective, use multiple resource utilization categories, use constant dollars, discount future costs and outcomes, use a lifetime horizon, or include an indication of uncertainty in results. The only resource utilization category consistently included across studies was healthcare resources. Only 28 nursing-related studies meeting the inclusion criteria were identified as meeting robust health economic evaluation methodological criteria, and most did not include all important guideline items. Despite increases in absolute numbers of published studies over the past decade, economic evaluation has been underutilized in U.S. nursing-relevant research in the past two decades.

Closing the loop: from paper to protein annotation using supervised Gene Ontology classification.

PubMed

Gobeill, Julien; Pasche, Emilie; Vishnyakova, Dina; Ruch, Patrick

2014-01-01

Gene function curation of the literature with Gene Ontology (GO) concepts is one particularly time-consuming task in genomics, and the help from bioinformatics is highly requested to keep up with the flow of publications. In 2004, the first BioCreative challenge already designed a task of automatic GO concepts assignment from a full text. At this time, results were judged far from reaching the performances required by real curation workflows. In particular, supervised approaches produced the most disappointing results because of lack of training data. Ten years later, the available curation data have massively grown. In 2013, the BioCreative IV GO task revisited the automatic GO assignment task. For this issue, we investigated the power of our supervised classifier, GOCat. GOCat computes similarities between an input text and already curated instances contained in a knowledge base to infer GO concepts. The subtask A consisted in selecting GO evidence sentences for a relevant gene in a full text. For this, we designed a state-of-the-art supervised statistical approach, using a naïve Bayes classifier and the official training set, and obtained fair results. The subtask B consisted in predicting GO concepts from the previous output. For this, we applied GOCat and reached leading results, up to 65% for hierarchical recall in the top 20 outputted concepts. Contrary to previous competitions, machine learning has this time outperformed standard dictionary-based approaches. Thanks to BioCreative IV, we were able to design a complete workflow for curation: given a gene name and a full text, this system is able to select evidence sentences for curation and to deliver highly relevant GO concepts. Contrary to previous competitions, machine learning this time outperformed dictionary-based systems. Observed performances are sufficient for being used in a real semiautomatic curation workflow. GOCat is available at http://eagl.unige.ch/GOCat/. http://eagl.unige.ch/GOCat4FT/. © The Author(s) 2014. Published by Oxford University Press.

California state information handbook: formerly utilized sites remedial action program

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

None

This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the state of California. It contains: a description of themore » state executive branch structure; a summary of relevant state statutes and regulations; a description of the structure of the state legislature, identification of the officers and committee chairmen, and a summary of recent relevant legislative action; the full text of relevant statutes and regulations.« less

Oregon state information handbook formerly utilized sites remedial action program

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

None

This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administater, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the State of Oregon. It contains: a description of themore » state executive branch structure; a summary of relevant state statutes and regulations; a description of the structure of the state legislature, identification of the officers and committee chairmen, and a summary of recent relevant legislative action; and the full text of relevant statutes and regulations.« less

Oregon state information handbook: formerly utilized sites remedial action program

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

None

This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the State of Oregon. It contains a description of themore » state executive branch structure; a summary of relevant state statutes and regulations; a description of the structure of the state legislature, identification of the officers and committee chairmen, and a summary of recent relevant legislative action; and the full text of relevant statutes and regulations.« less

Pennsylvania state information handbook: formerly utilized sites remedial action program

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

None

This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and State levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the State of Pennsylvania. It contains a description of themore » state executive branch structure; a summary of relevant state statutes and regulations; a description of the structure of the state legislature, identification of the officers and committee chairmen, and a summary of recent relevant legislative action; and the full text of relevant statutes and regulations.« less

Florida state information handbook: formerly utilized sites remedial action program

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

None

This volume is one of a series produced under contract with DOE, Office of Nuclear Waste Management, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the federal and state levels, the pertinent programs they administer, each affected state legislature, and current federal and state legislative and regulatory initiatives. This volume is a compilation of information about the State of Florida. It contains a description ofmore » the state executive branch structure; a summary of relevant state statutes and regulations; a description of the structure of the state legislature, identification of the officers and committee chairmen, and a summary of recent relevant legislative action; and the full text of relevant statutes and regulations.« less

New Mexico state information handbook: formerly utilized sites remedial action program

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

None

This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the State of New Mexico. It contains a description ofmore » the state executive branch structure; a summary of relevant state statutes and regulations; a description of the structure of the state legislature, identification of the officers and committee chairmen, and a summary of recent relevant legislative action; and the full text of relevant statutes and regulations.« less

Essential Annotation Schema for Ecology (EASE)—A framework supporting the efficient data annotation and faceted navigation in ecology

PubMed Central

Eichenberg, David; Liebergesell, Mario; König-Ries, Birgitta; Wirth, Christian

2017-01-01

Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines. PMID:29023519

Effects of Coherence and Relevance on Shallow and Deep Text Processing.

ERIC Educational Resources Information Center

Lehman, Stephen; Schraw, Gregory

2002-01-01

Examines the effects of coherence and relevance on shallow and deeper text processing, testing the hypothesis that enhancing the relevance of text segments compensates for breaks in local and global coherence. Results reveal that breaks in local coherence had no effect on any outcome measures, whereas relevance enhanced deeper processing.…

Enamel color changes following orthodontic treatment.

PubMed

Pandian, Akshaya; Ranganathan, Sukanya; Padmanabhan, Sridevi

2017-01-01

To evaluate and compare the effect of various orthodontic bonding systems and clean up procedures on quantitative enamel colour change. A literature search was done to identify the studies that assessed the quantitative enamel colour change associated with the various bonding systems and cleanup procedures. Electronic database (Pub Med, Cochrane and Google Scholar) were searched. First stage screening was performed and the abstracts were selected according to the initial selection criteria. Full text articles were retrieved and analyzed during second stage screening. The bibliographies were reviewed to identify additional relevant studies. Sixteen full text articles were retrieved. Six were rejected because the methodology was different. There was significant enamel colour change following orthodontic bonding, debonding and clean up procedures. Self-etching primers produce less enamel colour change compared to conventional etching. Resin Modified GIC produces least colour change compared to other light cure and chemical cure systems. Polishing following the clean-up procedure reduces the colour change of the enamel.

Dentin Hypersensitivity: Etiology, Diagnosis and Treatment; A Literature Review

PubMed Central

Davari, AR; Ataei, E; Assarzadeh, H

2013-01-01

The objective of this review is to inform practitioners about dentin hypersensitivity (DH); to provide a brief overview of the diagnosis, etiology and clinical management of dentin hypersensitivity and to discuss technical approaches to relieve sensitivity. This clinical information is described in the context of the underlying biology. The author used PUBMED to find relevant English-language literature published in the period 1999 to 2010. The author used combinations of the search terms “dentin*”, “tooth”, “teeth”, “hypersensit*”, “desensitiz*”. Abstracts and also full text articles to identify studies describing etiology, prevalence, clinical features, controlled clinical trials of treatments and relevant laboratory research on mechanisms of action were used. PMID:24724135

[Oral health in the printed media: analysis of newspaper articles in the years 2004-2009].

PubMed

Cavaca, Aline Guio; Gentilli, Victor; Zandonade, Eliana; Cortellete Júnior, Moacyr; Emmerich, Adauto

2012-05-01

This study seeks to outline the main characteristics of the texts on oral health that appeared in the printed media in the State of Espírito Santo from 2004 to 2009, in order to analyze and compare the issues, approaches and journalistic relevance related to the theme prioritized in A Tribuna and A Gazeta newspapers. Exploratory documentary research was conducted, based on quantitative content analysis of the material, which established that the issues included ranged from information about oral health policies, community service and prevention of oral health diseases, to the "aesthetic tendencies" of the smile. It also covered the dissemination of new technologies and dental specialties and there was a predominance of even-numbered pages, fewer first page texts and full-page coverage. This implies a moderate appreciation of these issues, different editorial projects, plus the difference in target audience that determined the journalistic standard and the predominance of specialized sources. Despite the oral health articles not revealing journalistic "scoops", they can be reworked using conscious journalistic techniques, in order to elicit the extraordinary from the ordinary, giving rise to texts of social relevance in both newspapers.

The healing properties of medicinal plants used in the Brazilian public health system: a systematic review.

PubMed

Marmitt, Diorge Jônatas; Bitencourt, Shanna; Silva, Amanda do Couto E; Rempel, Claudete; Goettert, Márcia Inês

2018-06-01

The aim of this study was to conduct a systematic review of the healing potential of medicinal plants belonging to the Brazilian National List of Medicinal Plants of Interest to the Unified Health System (RENISUS). PubMed and ScienceDirect databases were searched for relevant articles, regardless of the language, from 2010 to June 2016. Two reviewers independently assessed study eligibility. Articles were included if they presented evidence of healing potential of medicinal plants. Only those available as full and open access texts were considered. A total of 1381 articles met the inclusion criteria. Of these, 156 studies were considered eligible and were reviewed as full text. Following full analysis, 64 studies were included in this review. The studies covered 27 of the 71 plants belonging to RENISUS, nine of which are native to Brazil. In addition, two species are currently available in the Brazilian public health system as herbal medicine. This review may encourage and contribute to the appropriate use of medicinal plants in the public health system in Brazil.

Flowable Resin Composites: A Systematic Review and Clinical Considerations

PubMed Central

Rodrigues, Jean C.

2015-01-01

Background Little is known about flowable composite materials. Most literature mentions conventional composite materials at large, giving minimal emphasis to flowables in particular. This paper briefly gives an in depth insight to the multiple facets of this versatile material. Aim To exclusively review the most salient features of flowable composite materials in comparison to conventional composites and to give clinicians a detailed understanding of the advantages, drawbacks, indications and contraindications based on composition and physical/mechanical properties. Methodology Data Sources: A thorough literature search from the year 1996 up to January 2015 was done on PubMed Central, The Cochrane Library, Science Direct, Wiley Online Library, and Google Scholar. Grey literature (pending patents, technical reports etc.) was also screened. The search terms used were “dental flowable resin composites”. Search Strategy After omitting the duplicates/repetitions, a total of 491 full text articles were assessed. As including all articles were out of the scope of this paper. Only relevant articles that fulfilled the reviewer’s objectives {mentioning indications, contraindications, applications, assessment of physical/mechanical/biological properties (in vitro/ in vivo /ex vivo)} were considered. A total of 92 full text articles were selected. Conclusion Flowable composites exhibit a variable composition and consequently variable mechanical/ physical properties. Clinicians must be aware of this aspect to make a proper material selection based on specific properties and indications of each material relevant to a particular clinical situation. PMID:26266238

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.

PubMed

Krallinger, Martin; Vazquez, Miguel; Leitner, Florian; Salgado, David; Chatr-Aryamontri, Andrew; Winter, Andrew; Perfetto, Livia; Briganti, Leonardo; Licata, Luana; Iannuccelli, Marta; Castagnoli, Luisa; Cesareni, Gianni; Tyers, Mike; Schneider, Gerold; Rinaldi, Fabio; Leaman, Robert; Gonzalez, Graciela; Matos, Sergio; Kim, Sun; Wilbur, W John; Rocha, Luis; Shatkay, Hagit; Tendulkar, Ashish V; Agarwal, Shashank; Liu, Feifan; Wang, Xinglong; Rak, Rafal; Noto, Keith; Elkan, Charles; Lu, Zhiyong; Dogan, Rezarta Islamaj; Fontaine, Jean-Fred; Andrade-Navarro, Miguel A; Valencia, Alfonso

2011-10-03

Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional metrics. The BioCreative III Protein-Protein Interaction (PPI) tasks were motivated by such considerations, trying to address aspects including how the end user would oversee the generated output, for instance by providing ranked results, textual evidence for human interpretation or measuring time savings by using automated systems. Detecting articles describing complex biological events like PPIs was addressed in the Article Classification Task (ACT), where participants were asked to implement tools for detecting PPI-describing abstracts. Therefore the BCIII-ACT corpus was provided, which includes a training, development and test set of over 12,000 PPI relevant and non-relevant PubMed abstracts labeled manually by domain experts and recording also the human classification times. The Interaction Method Task (IMT) went beyond abstracts and required mining for associations between more than 3,500 full text articles and interaction detection method ontology concepts that had been applied to detect the PPIs reported in them. A total of 11 teams participated in at least one of the two PPI tasks (10 in ACT and 8 in the IMT) and a total of 62 persons were involved either as participants or in preparing data sets/evaluating these tasks. Per task, each team was allowed to submit five runs offline and another five online via the BioCreative Meta-Server. From the 52 runs submitted for the ACT, the highest Matthew's Correlation Coefficient (MCC) score measured was 0.55 at an accuracy of 89% and the best AUC iP/R was 68%. Most ACT teams explored machine learning methods, some of them also used lexical resources like MeSH terms, PSI-MI concepts or particular lists of verbs and nouns, some integrated NER approaches. For the IMT, a total of 42 runs were evaluated by comparing systems against manually generated annotations done by curators from the BioGRID and MINT databases. The highest AUC iP/R achieved by any run was 53%, the best MCC score 0.55. In case of competitive systems with an acceptable recall (above 35%) the macro-averaged precision ranged between 50% and 80%, with a maximum F-Score of 55%. The results of the ACT task of BioCreative III indicate that classification of large unbalanced article collections reflecting the real class imbalance is still challenging. Nevertheless, text-mining tools that report ranked lists of relevant articles for manual selection can potentially reduce the time needed to identify half of the relevant articles to less than 1/4 of the time when compared to unranked results. Detecting associations between full text articles and interaction detection method PSI-MI terms (IMT) is more difficult than might be anticipated. This is due to the variability of method term mentions, errors resulting from pre-processing of articles provided as PDF files, and the heterogeneity and different granularity of method term concepts encountered in the ontology. However, combining the sophisticated techniques developed by the participants with supporting evidence strings derived from the articles for human interpretation could result in practical modules for biological annotation workflows.

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

PubMed Central

2011-01-01

Background Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional metrics. The BioCreative III Protein-Protein Interaction (PPI) tasks were motivated by such considerations, trying to address aspects including how the end user would oversee the generated output, for instance by providing ranked results, textual evidence for human interpretation or measuring time savings by using automated systems. Detecting articles describing complex biological events like PPIs was addressed in the Article Classification Task (ACT), where participants were asked to implement tools for detecting PPI-describing abstracts. Therefore the BCIII-ACT corpus was provided, which includes a training, development and test set of over 12,000 PPI relevant and non-relevant PubMed abstracts labeled manually by domain experts and recording also the human classification times. The Interaction Method Task (IMT) went beyond abstracts and required mining for associations between more than 3,500 full text articles and interaction detection method ontology concepts that had been applied to detect the PPIs reported in them. Results A total of 11 teams participated in at least one of the two PPI tasks (10 in ACT and 8 in the IMT) and a total of 62 persons were involved either as participants or in preparing data sets/evaluating these tasks. Per task, each team was allowed to submit five runs offline and another five online via the BioCreative Meta-Server. From the 52 runs submitted for the ACT, the highest Matthew's Correlation Coefficient (MCC) score measured was 0.55 at an accuracy of 89% and the best AUC iP/R was 68%. Most ACT teams explored machine learning methods, some of them also used lexical resources like MeSH terms, PSI-MI concepts or particular lists of verbs and nouns, some integrated NER approaches. For the IMT, a total of 42 runs were evaluated by comparing systems against manually generated annotations done by curators from the BioGRID and MINT databases. The highest AUC iP/R achieved by any run was 53%, the best MCC score 0.55. In case of competitive systems with an acceptable recall (above 35%) the macro-averaged precision ranged between 50% and 80%, with a maximum F-Score of 55%. Conclusions The results of the ACT task of BioCreative III indicate that classification of large unbalanced article collections reflecting the real class imbalance is still challenging. Nevertheless, text-mining tools that report ranked lists of relevant articles for manual selection can potentially reduce the time needed to identify half of the relevant articles to less than 1/4 of the time when compared to unranked results. Detecting associations between full text articles and interaction detection method PSI-MI terms (IMT) is more difficult than might be anticipated. This is due to the variability of method term mentions, errors resulting from pre-processing of articles provided as PDF files, and the heterogeneity and different granularity of method term concepts encountered in the ontology. However, combining the sophisticated techniques developed by the participants with supporting evidence strings derived from the articles for human interpretation could result in practical modules for biological annotation workflows. PMID:22151929

A Systematic Review of the Relationships between Intimate Partner Violence and HIV/AIDS

PubMed Central

Kouyoumdjian, Fiona G.; Findlay, Nicole; Schwandt, Michael; Calzavara, Liviana M.

2013-01-01

Background Intimate partner violence (IPV) is a significant health problem that has been associated with HIV infection in numerous studies. We aimed to systematically review the literature on relationships between IPV and HIV in order to describe the prevalence of IPV in people with HIV, the prevalence of HIV in people experiencing IPV, the association between IPV and HIV, and evidence regarding mechanisms of risk and interventions. Methods Data sources were 10 electronic databases and reference lists. Studies were included if they reported data on the relationship between IPV and HIV. All records were independently reviewed by two authors at the stages of title and abstract review and full text review. Any abstract considered eligible by either reviewer was reviewed in full, and any disagreement regarding eligibility of full texts or data extracted was resolved by discussion. Results 101 articles were included. Experiencing IPV and HIV infection were associated in unadjusted analyses in most studies, as well as in adjusted analyses in many studies. The findings of qualitative and quantitative studies assessing potential mechanisms linking IPV and HIV were variable. Few interventions have been assessed, but two identified in this review were promising in terms of preventing IPV, though not HIV infection. Conclusions Experiencing IPV and HIV infection tend to be associated in unadjusted analyses, suggesting that IPV screening and linkage with relevant programs and services may be valuable. It is unclear whether there is a causal association between experiencing IPV and HIV infection. Research should focus on defining parameters of IPV which are relevant to HIV infection, including type of IPV and period of exposure and risk, on assessing potential mechanisms, and on developing and assessing interventions which build on the strengths of existing studies. PMID:24282566

Smart-Glasses: Exposing and Elucidating the Ethical Issues.

PubMed

Hofmann, Bjørn; Haustein, Dušan; Landeweerd, Laurens

2017-06-01

The objective of this study is to provide an overview over the ethical issues relevant to the assessment, implementation, and use of smart-glasses. The purpose of the overview is to facilitate deliberation, decision making, and the formation of knowledge and norms for this emerging technology. An axiological question-based method for human cognitive enhancement including an extensive literature search on smart-glasses is used to identify relevant ethical issues. The search is supplemented with relevant ethical issues identified in the literature on human cognitive enhancement (in general) and in the study of the technical aspects of smart-glasses. Identified papers were subject to traditional content analysis: 739 references were identified of which 247 were regarded as relevant for full text examinations, and 155 were included in the study. A wide variety of ethical issues with smart-glasses have been identified, such as issues related to privacy, safety, justice, change in human agency, accountability, responsibility, social interaction, power and ideology. Smart-glasses are envisioned to change individual human identity and behavior as well as social interaction. Taking these issues into account appears to be relevant when developing, deliberating, deciding on, implementing, and using smart-glasses.

The Implementation of Cosine Similarity to Calculate Text Relevance between Two Documents

NASA Astrophysics Data System (ADS)

Gunawan, D.; Sembiring, C. A.; Budiman, M. A.

2018-03-01

Rapidly increasing number of web pages or documents leads to topic specific filtering in order to find web pages or documents efficiently. This is a preliminary research that uses cosine similarity to implement text relevance in order to find topic specific document. This research is divided into three parts. The first part is text-preprocessing. In this part, the punctuation in a document will be removed, then convert the document to lower case, implement stop word removal and then extracting the root word by using Porter Stemming algorithm. The second part is keywords weighting. Keyword weighting will be used by the next part, the text relevance calculation. Text relevance calculation will result the value between 0 and 1. The closer value to 1, then both documents are more related, vice versa.

Interministerial Circular, 2 June 1988.

PubMed

1988-01-01

The text of this Circular on resolving the question of Vietnamese citizens wanting to leave the country to join their families or for other humanitarian reasons is as follows: "1) Those Vietnamese citizens applying for exit visas to resettle abroad must complete all procedures established by the Ministry of Interior. The Ministry of the Interior is responsible for considering and solving applications for exit visas and for notifying the applicants of the results. It must issue exit visas and do other paperwork for those Vietnamese citizens applying for exit visas. 2) The Foreign Affairs Ministry is responsible for cooperating with immigrant-accepting countries and other relevant international organizations in solving entry procedures for those already approved by the interior ministry for leaving the country." full text

Ontology-based content analysis of US patent applications from 2001-2010.

PubMed

Weber, Lutz; Böhme, Timo; Irmer, Matthias

2013-01-01

Ontology-based semantic text analysis methods allow to automatically extract knowledge relationships and data from text documents. In this review, we have applied these technologies for the systematic analysis of pharmaceutical patents. Hierarchical concepts from the knowledge domains of chemical compounds, diseases and proteins were used to annotate full-text US patent applications that deal with pharmacological activities of chemical compounds and filed in the years 2001-2010. Compounds claimed in these applications have been classified into their respective compound classes to review the distribution of scaffold types or general compound classes such as natural products in a time-dependent manner. Similarly, the target proteins and claimed utility of the compounds have been classified and the most relevant were extracted. The method presented allows the discovery of the main areas of innovation as well as emerging fields of patenting activities - providing a broad statistical basis for competitor analysis and decision-making efforts.

Walk-in clinics versus physician offices and emergency rooms for urgent care and chronic disease management.

PubMed

Chen, Connie E; Chen, Christopher T; Hu, Jia; Mehrotra, Ateev

2017-02-17

Walk-in clinics are growing in popularity around the world as a substitute for traditional medical care delivered in physician offices and emergency rooms, but their clinical efficacy is unclear. To assess the quality of care and patient satisfaction of walk-in clinics compared to that of traditional physician offices and emergency rooms for people who present with basic medical complaints for either acute or chronic issues. We searched CENTRAL, MEDLINE, Embase, six other databases, and two trials registers on 22 March 2016 together with reference checking, citation searching, and contact with study authors to identify additional studies. We applied no restrictions on language, publication type, or publication year. Study design: randomized trials, non-randomized trials, and controlled before-after studies. standalone physical clinics not requiring advance appointments or registration, that provided basic medical care without expectation of follow-up. Comparisons: traditional primary care practices or emergency rooms. We used standard methodological procedures expected by Cochrane and the Cochrane Effective Practice and Organisation of Care (EPOC) Group. The literature search identified 6587 citations, of which we considered 65 to be potentially relevant. We reviewed the abstracts of all 65 potentially relevant studies and retrieved the full texts of 12 articles thought to fit our study criteria. However, following independent author assessment of the full texts, we excluded all 12 articles. Controlled trial evidence about the mortality, morbidity, quality of care, and patient satisfaction of walk-in clinics is currently not available.

Searching for Mirrors: Preservice Teachers' Journey toward More Culturally Relevant Pedagogy

ERIC Educational Resources Information Center

Christ, Tanya; Sharma, Sue Ann

2018-01-01

Culturally relevant text selection and pedagogy support students' motivation, engagement, literacy outcomes, and positive identity formation. Nevertheless, there is limited research on teacher preparation that fosters these outcomes. We explore 17 preservice teachers' challenges and successes with culturally relevant text selection and pedagogy…

Texts as Mirrors, Texts as Windows: Black Adolescent Boys and the Complexities of Textual Relevance

ERIC Educational Resources Information Center

Sciurba, Katie

2015-01-01

Discussions of culturally relevant and "boy" literature stress the importance of offering readers occasions to see themselves in texts. However, young men of color have had few opportunities within this discourse to reveal their own experiences with literature. Rather than make presumptions about how texts serve as mirrors to them, as…

PathText: a text mining integrator for biological pathway visualizations

PubMed Central

Kemper, Brian; Matsuzaki, Takuya; Matsuoka, Yukiko; Tsuruoka, Yoshimasa; Kitano, Hiroaki; Ananiadou, Sophia; Tsujii, Jun'ichi

2010-01-01

Motivation: Metabolic and signaling pathways are an increasingly important part of organizing knowledge in systems biology. They serve to integrate collective interpretations of facts scattered throughout literature. Biologists construct a pathway by reading a large number of articles and interpreting them as a consistent network, but most of the models constructed currently lack direct links to those articles. Biologists who want to check the original articles have to spend substantial amounts of time to collect relevant articles and identify the sections relevant to the pathway. Furthermore, with the scientific literature expanding by several thousand papers per week, keeping a model relevant requires a continuous curation effort. In this article, we present a system designed to integrate a pathway visualizer, text mining systems and annotation tools into a seamless environment. This will enable biologists to freely move between parts of a pathway and relevant sections of articles, as well as identify relevant papers from large text bases. The system, PathText, is developed by Systems Biology Institute, Okinawa Institute of Science and Technology, National Centre for Text Mining (University of Manchester) and the University of Tokyo, and is being used by groups of biologists from these locations. Contact: brian@monrovian.com. PMID:20529930

Migration Amendment Act 1987 (No. 133 of 1987), 16 December 1987.

PubMed

1988-01-01

This Act does the following, among other things: 1) requires that certain requests relating to entry permits, visas, and return endorsements are not considered to have been made unless in writing in accordance with the relevant approved forms and unless any fee payable has been made; 2) makes "operators," as well as charterers, liable for the carriage of persons to Australia without documentation; and 3) provides that international air operators shall pay immigration clearance fees payable by passengers whether or not the operator has collected the fees from the passengers. full text

Processing and memory of information presented in narrative or expository texts.

PubMed

Wolfe, Michael B W; Woodwyk, Joshua M

2010-09-01

Previous research suggests that narrative and expository texts differ in the extent to which they prompt students to integrate to-be-learned content with relevant prior knowledge during comprehension. We expand on previous research by examining on-line processing and representation in memory of to-be-learned content that is embedded in narrative or expository texts. We are particularly interested in how differences in the use of relevant prior knowledge leads to differences in terms of levels of discourse representation (textbase vs. situation model). A total of 61 university undergraduates in Expt 1, and 160 in Expt 2. In Expt 1, subjects thought out loud while comprehending circulatory system content embedded in a narrative or expository text, followed by free recall of text content. In Expt 2, subjects read silently and completed a sentence recognition task to assess memory. In Expt 1, subjects made more associations to prior knowledge while reading the expository text, and recalled more content. Content recall was also correlated with amount of relevant prior knowledge for subjects who read the expository text but not the narrative text. In Expt 2, subjects reading the expository text (compared to the narrative text) had a weaker textbase representation of the to-be-learned content, but a marginally stronger situation model. Results suggest that in terms of to-be-learned content, expository texts trigger students to utilize relevant prior knowledge more than narrative texts.

Dynamic "inline" images: context-sensitive retrieval and integration of images into Web documents.

PubMed

Kahn, Charles E

2008-09-01

Integrating relevant images into web-based information resources adds value for research and education. This work sought to evaluate the feasibility of using "Web 2.0" technologies to dynamically retrieve and integrate pertinent images into a radiology web site. An online radiology reference of 1,178 textual web documents was selected as the set of target documents. The ARRS GoldMiner image search engine, which incorporated 176,386 images from 228 peer-reviewed journals, retrieved images on demand and integrated them into the documents. At least one image was retrieved in real-time for display as an "inline" image gallery for 87% of the web documents. Each thumbnail image was linked to the full-size image at its original web site. Review of 20 randomly selected Collaborative Hypertext of Radiology documents found that 69 of 72 displayed images (96%) were relevant to the target document. Users could click on the "More" link to search the image collection more comprehensively and, from there, link to the full text of the article. A gallery of relevant radiology images can be inserted easily into web pages on any web server. Indexing by concepts and keywords allows context-aware image retrieval, and searching by document title and subject metadata yields excellent results. These techniques allow web developers to incorporate easily a context-sensitive image gallery into their documents.

A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records

PubMed Central

Weissenbacher, Davy; Rivera, Robert; Beard, Rachel; Firago, Mari; Wallstrom, Garrick; Scotch, Matthew; Gonzalez, Graciela

2016-01-01

Objective The metadata reflecting the location of the infected host (LOIH) of virus sequences in GenBank often lacks specificity. This work seeks to enhance this metadata by extracting more specific geographic information from related full-text articles and mapping them to their latitude/longitudes using knowledge derived from external geographical databases. Materials and Methods We developed a rule-based information extraction framework for linking GenBank records to the latitude/longitudes of the LOIH. Our system first extracts existing geospatial metadata from GenBank records and attempts to improve it by seeking additional, relevant geographic information from text and tables in related full-text PubMed Central articles. The final extracted locations of the records, based on data assimilated from these sources, are then disambiguated and mapped to their respective geo-coordinates. We evaluated our approach on a manually annotated dataset comprising of 5728 GenBank records for the influenza A virus. Results We found the precision, recall, and f-measure of our system for linking GenBank records to the latitude/longitudes of their LOIH to be 0.832, 0.967, and 0.894, respectively. Discussion Our system had a high level of accuracy for linking GenBank records to the geo-coordinates of the LOIH. However, it can be further improved by expanding our database of geospatial data, incorporating spell correction, and enhancing the rules used for extraction. Conclusion Our system performs reasonably well for linking GenBank records for the influenza A virus to the geo-coordinates of their LOIH based on record metadata and information extracted from related full-text articles. PMID:26911818

A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records.

PubMed

Tahsin, Tasnia; Weissenbacher, Davy; Rivera, Robert; Beard, Rachel; Firago, Mari; Wallstrom, Garrick; Scotch, Matthew; Gonzalez, Graciela

2016-09-01

The metadata reflecting the location of the infected host (LOIH) of virus sequences in GenBank often lacks specificity. This work seeks to enhance this metadata by extracting more specific geographic information from related full-text articles and mapping them to their latitude/longitudes using knowledge derived from external geographical databases. We developed a rule-based information extraction framework for linking GenBank records to the latitude/longitudes of the LOIH. Our system first extracts existing geospatial metadata from GenBank records and attempts to improve it by seeking additional, relevant geographic information from text and tables in related full-text PubMed Central articles. The final extracted locations of the records, based on data assimilated from these sources, are then disambiguated and mapped to their respective geo-coordinates. We evaluated our approach on a manually annotated dataset comprising of 5728 GenBank records for the influenza A virus. We found the precision, recall, and f-measure of our system for linking GenBank records to the latitude/longitudes of their LOIH to be 0.832, 0.967, and 0.894, respectively. Our system had a high level of accuracy for linking GenBank records to the geo-coordinates of the LOIH. However, it can be further improved by expanding our database of geospatial data, incorporating spell correction, and enhancing the rules used for extraction. Our system performs reasonably well for linking GenBank records for the influenza A virus to the geo-coordinates of their LOIH based on record metadata and information extracted from related full-text articles. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Managing Acute Behavioural Disturbances in the Emergency Department Using the Environment, Policies and Practices: A Systematic Review.

PubMed

Weiland, Tracey J; Ivory, Sean; Hutton, Jennie

2017-06-01

Effective strategies for managing acute behavioural disturbances (ABDs) within emergency departments (EDs) are needed given their rising occurrence and negative impact on safety, psychological wellbeing, and staff turnover. Non-pharmacological interventions for ABD management generally fall into four categories: environmental modifications; policies; practice changes; and education. Our objective was to systematically review the efficacy of strategies for ABD management within EDs that involved changes to environment, architecture, policy and practice. We performed systematic searches of CINAHL Plus with Full Text, PsycINFO, MEDLINE, and EMBASE, as well as reference lists of relevant review articles to identify relevant studies published between January 1985 - April 2016. We included studies written in English, which reported management of behavioural disturbances in adults associated with the ED through the use of environmental modifiers (including seclusion, restraint, specialised rooms, architectural changes), policy, and practice-based interventions excepting education-only interventions. Efficacy outcomes of interest included incidence, severity, and duration of ABD, incidence of injuries, staff absenteeism, restraint use, restraint duration, and staff and patient perceptions. Two reviewers independently screened titles and abstracts, and assessed the relevancy and eligibility of studies based on full-text articles. Two authors independently appraised included studies. A narrative synthesis of findings was undertaken. Studies reporting interventions for managing ABDs within the ED are limited in number and quality. The level of evidence for efficacy is low, requiring caution in conclusions. While there is preliminary evidence for environmental change in the form of specialised behavioural rooms, security upgrades and ED modifications, these are not supported by evidence from controlled studies. Many of these "common sense" environmental changes recommended in many guidelines have been widely implemented in EDs. There is an unambiguous gap in the literature regarding the efficacy of interventions for ABD management in EDs involving environmental, policy or practice-based changes. With growing demand on EDs, and with increasing numbers of ABDs, identification of robust evidence-based interventions for safe and effective ABD management is vital.

New approach for correction of error associated with keratometric estimation of corneal power in keratoconus.

PubMed

Camps, Vicente J; Piñero, David P; Caravaca-Arens, Esteban; de Fez, Dolores; Pérez-Cambrodí, Rafael J; Artola, Alberto

2014-09-01

The aim of this study was to obtain the exact value of the keratometric index (nkexact) and to clinically validate a variable keratometric index (nkadj) that minimizes this error. The nkexact value was determined by obtaining differences (ΔPc) between keratometric corneal power (Pk) and Gaussian corneal power ((Equation is included in full-text article.)) equal to 0. The nkexact was defined as the value associated with an equivalent difference in the magnitude of ΔPc for extreme values of posterior corneal radius (r2c) for each anterior corneal radius value (r1c). This nkadj was considered for the calculation of the adjusted corneal power (Pkadj). Values of r1c ∈ (4.2, 8.5) mm and r2c ∈ (3.1, 8.2) mm were considered. Differences of True Net Power with (Equation is included in full-text article.), Pkadj, and Pk(1.3375) were calculated in a clinical sample of 44 eyes with keratoconus. nkexact ranged from 1.3153 to 1.3396 and nkadj from 1.3190 to 1.3339 depending on the eye model analyzed. All the nkadj values adjusted perfectly to 8 linear algorithms. Differences between Pkadj and (Equation is included in full-text article.)did not exceed ±0.7 D (Diopter). Clinically, nk = 1.3375 was not valid in any case. Pkadj and True Net Power and Pk(1.3375) and Pkadj were statistically different (P < 0.01), whereas no differences were found between (Equation is included in full-text article.)and Pkadj (P > 0.01). The use of a single value of nk for the calculation of the total corneal power in keratoconus has been shown to be imprecise, leading to inaccuracies in the detection and classification of this corneal condition. Furthermore, our study shows the relevance of corneal thickness in corneal power calculations in keratoconus.

A Text-Mining Framework for Supporting Systematic Reviews.

PubMed

Li, Dingcheng; Wang, Zhen; Wang, Liwei; Sohn, Sunghwan; Shen, Feichen; Murad, Mohammad Hassan; Liu, Hongfang

2016-11-01

Systematic reviews (SRs) involve the identification, appraisal, and synthesis of all relevant studies for focused questions in a structured reproducible manner. High-quality SRs follow strict procedures and require significant resources and time. We investigated advanced text-mining approaches to reduce the burden associated with abstract screening in SRs and provide high-level information summary. A text-mining SR supporting framework consisting of three self-defined semantics-based ranking metrics was proposed, including keyword relevance, indexed-term relevance and topic relevance. Keyword relevance is based on the user-defined keyword list used in the search strategy. Indexed-term relevance is derived from indexed vocabulary developed by domain experts used for indexing journal articles and books. Topic relevance is defined as the semantic similarity among retrieved abstracts in terms of topics generated by latent Dirichlet allocation, a Bayesian-based model for discovering topics. We tested the proposed framework using three published SRs addressing a variety of topics (Mass Media Interventions, Rectal Cancer and Influenza Vaccine). The results showed that when 91.8%, 85.7%, and 49.3% of the abstract screening labor was saved, the recalls were as high as 100% for the three cases; respectively. Relevant studies identified manually showed strong topic similarity through topic analysis, which supported the inclusion of topic analysis as relevance metric. It was demonstrated that advanced text mining approaches can significantly reduce the abstract screening labor of SRs and provide an informative summary of relevant studies.

A New Bibliographical Feature for SIMBAD: Highlighting the Most Relevant Papers for One Astronomical Object

NASA Astrophysics Data System (ADS)

Oberto, A.; Lesteven, S.; Derriere, S.; Bonnin, C.; Buga, M.; Brouty, M.; Bruneau, C.; Brunet, C.; Eisele, A.; Genova, F.; Guéhenneux, S.; Neuville, M.; Ochsenbein, F.; Perret, E.; Son, E.; Vannier, P.; Vonflie, P.; Wenger, M.; Woelfel, F.

2015-04-01

The number of bibliographical references attached to an astronomical object in SIMBAD is has been growing continuously over the years. It is important for astronomers to retrieve the most relevant papers, those that give important information about the object of study. This is not easy since there can be many references attached to one object. For instance, in 2014, more than 15,000 objects had been attached to more than 50 references. The location of the object's citations inside the paper and its number of occurrences are important criteria to extract the most relevant papers. Since 2008, because of the DJIN application (a semi-automatic tool to search for object names in full text) this information has been collected. For each article associated with an astronomical object, we know where it is cited and how many times and with which name it appears. Since September 2013, the users of SIMBAD web site can choose to retrieve the most relevant references for an astronomical object depending on its location in the publication. A new formula to sort references by combining all locations, number of occurrences, total number of objects studied, citation count, and year is presented in this paper.

Introducing ADS Labs

NASA Astrophysics Data System (ADS)

Accomazzi, Alberto; Henneken, E.; Grant, C. S.; Kurtz, M. J.; Di Milia, G.; Luker, J.; Thompson, D. M.; Bohlen, E.; Murray, S. S.

2011-05-01

ADS Labs is a platform that ADS is introducing in order to test and receive feedback from the community on new technologies and prototype services. Currently, ADS Labs features a new interface for abstract searches, faceted filtering of results, visualization of co-authorship networks, article-level recommendations, and a full-text search service. The streamlined abstract search interface provides a simple, one-box search with options for ranking results based on a paper relevancy, freshness, number of citations, and downloads. In addition, it provides advanced rankings based on collaborative filtering techniques. The faceted filtering interface allows users to narrow search results based on a particular property or set of properties ("facets"), allowing users to manage large lists and explore the relationship between them. For any set or sub-set of records, the co-authorship network can be visualized in an interactive way, offering a view of the distribution of contributors and their inter-relationships. This provides an immediate way to detect groups and collaborations involved in a particular research field. For a majority of papers in Astronomy, our new interface will provide a list of related articles of potential interest. The recommendations are based on a number of factors, including text similarity, citations, and co-readership information. The new full-text search interface allows users to find all instances of particular words or phrases in the body of the articles in our full-text archive. This includes all of the scanned literature in ADS as well as a select portion of the current astronomical literature, including ApJ, ApJS, AJ, MNRAS, PASP, A&A, and soon additional content from Springer journals. Fulltext search results include a list of the matching papers as well as a list of "snippets" of text highlighting the context in which the search terms were found. ADS Labs is available at http://adslabs.org

Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD).

PubMed

Jiang, Xiangying; Ringwald, Martin; Blake, Judith; Shatkay, Hagit

2017-01-01

The Gene Expression Database (GXD) is a comprehensive online database within the Mouse Genome Informatics resource, aiming to provide available information about endogenous gene expression during mouse development. The information stems primarily from many thousands of biomedical publications that database curators must go through and read. Given the very large number of biomedical papers published each year, automatic document classification plays an important role in biomedical research. Specifically, an effective and efficient document classifier is needed for supporting the GXD annotation workflow. We present here an effective yet relatively simple classification scheme, which uses readily available tools while employing feature selection, aiming to assist curators in identifying publications relevant to GXD. We examine the performance of our method over a large manually curated dataset, consisting of more than 25 000 PubMed abstracts, of which about half are curated as relevant to GXD while the other half as irrelevant to GXD. In addition to text from title-and-abstract, we also consider image captions, an important information source that we integrate into our method. We apply a captions-based classifier to a subset of about 3300 documents, for which the full text of the curated articles is available. The results demonstrate that our proposed approach is robust and effectively addresses the GXD document classification. Moreover, using information obtained from image captions clearly improves performance, compared to title and abstract alone, affirming the utility of image captions as a substantial evidence source for automatically determining the relevance of biomedical publications to a specific subject area. www.informatics.jax.org. © The Author(s) 2017. Published by Oxford University Press.

Raising the IQ in full-text searching via intelligent querying

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

Kero, R.; Russell, L.; Swietlik, C.

1994-11-01

Current Information Retrieval (IR) technologies allow for efficient access to relevant information, provided that user selected query terms coincide with the specific linguistical choices made by the authors whose works constitute the text-base. Therefore, the challenge is to enhance the limited searching capability of state-of-the-practice IR. This can be done either with augmented clients that overcome current server searching deficiencies, or with added capabilities that can augment searching algorithms on the servers. The technology being investigated is that of deductive databases, with a set of new techniques called cooperative answering. This technology utilizes semantic networks to allow for navigation betweenmore » possible query search term alternatives. The augmented search terms are passed to an IR engine and the results can be compared. The project utilizes the OSTI Environment, Safety and Health Thesaurus to populate the domain specific semantic network and the text base of ES&H related documents from the Facility Profile Information Management System as the domain specific search space.« less

Moving beyond Text Highlights: Inferring Users' Interests to Improve the Relevance of Retrieval

ERIC Educational Resources Information Center

Balakrishnan, Vimala; Mehmood, Yasir; Nagappan, Yoganathan

2016-01-01

Introduction: Studies have indicated that users' text highlighting behaviour can be further manipulated to improve the relevance of retrieved results. This article reports on a study that examined users' text highlight frequency, length and users' copy-paste actions. Method: A binary voting mechanism was employed to determine the weights for the…

[Text mining, a method for computer-assisted analysis of scientific texts, demonstrated by an analysis of author networks].

PubMed

Hahn, P; Dullweber, F; Unglaub, F; Spies, C K

2014-06-01

Searching for relevant publications is becoming more difficult with the increasing number of scientific articles. Text mining as a specific form of computer-based data analysis may be helpful in this context. Highlighting relations between authors and finding relevant publications concerning a specific subject using text analysis programs are illustrated graphically by 2 performed examples. © Georg Thieme Verlag KG Stuttgart · New York.

King v. Burwell: Desperately Seeking Ambiguity in Clear Statutory Text.

PubMed

Adler, Jonathan H; Cannon, Michael F

2015-06-01

Does the Patient Protection and Affordable Care Act (ACA) of 2010 authorize tax credits within the thirty-six states that failed to establish health insurance exchanges? That is the question presented in Pruitt v. Burwell, Halbig v. Burwell, King v. Burwell, and Indiana v. IRS. The plaintiffs argue that the statute is clear and forecloses any possibility of tax credits in federal exchanges. The government argues that the statute plainly authorizes tax credits in federal exchanges, or is at least ambiguous on the question. Mere disagreement is not evidence of ambiguity. Reaching the truth requires wading deep into each side's arguments. Whether the relevant text is viewed in isolation or in its full statutory context, the ACA authorizes tax credits only in exchanges established by the states. Copyright © 2015 by Duke University Press.

Automatic evidence retrieval for systematic reviews.

PubMed

Choong, Miew Keen; Galgani, Filippo; Dunn, Adam G; Tsafnat, Guy

2014-10-01

Snowballing involves recursively pursuing relevant references cited in the retrieved literature and adding them to the search results. Snowballing is an alternative approach to discover additional evidence that was not retrieved through conventional search. Snowballing's effectiveness makes it best practice in systematic reviews despite being time-consuming and tedious. Our goal was to evaluate an automatic method for citation snowballing's capacity to identify and retrieve the full text and/or abstracts of cited articles. Using 20 review articles that contained 949 citations to journal or conference articles, we manually searched Microsoft Academic Search (MAS) and identified 78.0% (740/949) of the cited articles that were present in the database. We compared the performance of the automatic citation snowballing method against the results of this manual search, measuring precision, recall, and F1 score. The automatic method was able to correctly identify 633 (as proportion of included citations: recall=66.7%, F1 score=79.3%; as proportion of citations in MAS: recall=85.5%, F1 score=91.2%) of citations with high precision (97.7%), and retrieved the full text or abstract for 490 (recall=82.9%, precision=92.1%, F1 score=87.3%) of the 633 correctly retrieved citations. The proposed method for automatic citation snowballing is accurate and is capable of obtaining the full texts or abstracts for a substantial proportion of the scholarly citations in review articles. By automating the process of citation snowballing, it may be possible to reduce the time and effort of common evidence surveillance tasks such as keeping trial registries up to date and conducting systematic reviews.

Can abstract screening workload be reduced using text mining? User experiences of the tool Rayyan.

PubMed

Olofsson, Hanna; Brolund, Agneta; Hellberg, Christel; Silverstein, Rebecca; Stenström, Karin; Österberg, Marie; Dagerhamn, Jessica

2017-09-01

One time-consuming aspect of conducting systematic reviews is the task of sifting through abstracts to identify relevant studies. One promising approach for reducing this burden uses text mining technology to identify those abstracts that are potentially most relevant for a project, allowing those abstracts to be screened first. To examine the effectiveness of the text mining functionality of the abstract screening tool Rayyan. User experiences were collected. Rayyan was used to screen abstracts for 6 reviews in 2015. After screening 25%, 50%, and 75% of the abstracts, the screeners logged the relevant references identified. A survey was sent to users. After screening half of the search result with Rayyan, 86% to 99% of the references deemed relevant to the study were identified. Of those studies included in the final reports, 96% to 100% were already identified in the first half of the screening process. Users rated Rayyan 4.5 out of 5. The text mining function in Rayyan successfully helped reviewers identify relevant studies early in the screening process. Copyright © 2017 John Wiley & Sons, Ltd.

BELTracker: evidence sentence retrieval for BEL statements

PubMed Central

Rastegar-Mojarad, Majid; Komandur Elayavilli, Ravikumar; Liu, Hongfang

2016-01-01

Biological expression language (BEL) is one of the main formal representation models of biological networks. The primary source of information for curating biological networks in BEL representation has been literature. It remains a challenge to identify relevant articles and the corresponding evidence statements for curating and validating BEL statements. In this paper, we describe BELTracker, a tool used to retrieve and rank evidence sentences from PubMed abstracts and full-text articles for a given BEL statement (per the 2015 task requirements of BioCreative V BEL Task). The system is comprised of three main components, (i) translation of a given BEL statement to an information retrieval (IR) query, (ii) retrieval of relevant PubMed citations and (iii) finding and ranking the evidence sentences in those citations. BELTracker uses a combination of multiple approaches based on traditional IR, machine learning, and heuristics to accomplish the task. The system identified and ranked at least one fully relevant evidence sentence in the top 10 retrieved sentences for 72 out of 97 BEL statements in the test set. BELTracker achieved a precision of 0.392, 0.532 and 0.615 when evaluated with three criteria, namely full, relaxed and context criteria, respectively, by the task organizers. Our team at Mayo Clinic was the only participant in this task. BELTracker is available as a RESTful API and is available for public use. Database URL: http://www.openbionlp.org:8080/BelTracker/finder/Given_BEL_Statement PMID:27173525

Analysis of the Relevance of Posts in Asynchronous Discussions

ERIC Educational Resources Information Center

Azevedo, Breno T.; Reategui, Eliseo; Behar, Patrícia A.

2014-01-01

This paper presents ForumMiner, a tool for the automatic analysis of students' posts in asynchronous discussions. ForumMiner uses a text mining system to extract graphs from texts that are given to students as a basis for their discussion. These graphs contain the most relevant terms found in the texts, as well as the relationships between them.…

Attention Switching and Multimedia Learning: The Impact of Executive Resources on the Integrative Comprehension of Texts and Pictures

ERIC Educational Resources Information Center

Baadte, Christiane; Rasch, Thorsten; Honstein, Helena

2015-01-01

The ability to flexibly allocate attention to goal-relevant information is pivotal for the completion of high-level cognitive processes. For instance, in comprehending illustrated texts, the reader permanently has to switch the attentional focus between the text and the corresponding picture in order to extract relevant information from both…

The BioC-BioGRID corpus: full text articles annotated for curation of protein–protein and genetic interactions

PubMed Central

Kim, Sun; Chatr-aryamontri, Andrew; Chang, Christie S.; Oughtred, Rose; Rust, Jennifer; Wilbur, W. John; Comeau, Donald C.; Dolinski, Kara; Tyers, Mike

2017-01-01

A great deal of information on the molecular genetics and biochemistry of model organisms has been reported in the scientific literature. However, this data is typically described in free text form and is not readily amenable to computational analyses. To this end, the BioGRID database systematically curates the biomedical literature for genetic and protein interaction data. This data is provided in a standardized computationally tractable format and includes structured annotation of experimental evidence. BioGRID curation necessarily involves substantial human effort by expert curators who must read each publication to extract the relevant information. Computational text-mining methods offer the potential to augment and accelerate manual curation. To facilitate the development of practical text-mining strategies, a new challenge was organized in BioCreative V for the BioC task, the collaborative Biocurator Assistant Task. This was a non-competitive, cooperative task in which the participants worked together to build BioC-compatible modules into an integrated pipeline to assist BioGRID curators. As an integral part of this task, a test collection of full text articles was developed that contained both biological entity annotations (gene/protein and organism/species) and molecular interaction annotations (protein–protein and genetic interactions (PPIs and GIs)). This collection, which we call the BioC-BioGRID corpus, was annotated by four BioGRID curators over three rounds of annotation and contains 120 full text articles curated in a dataset representing two major model organisms, namely budding yeast and human. The BioC-BioGRID corpus contains annotations for 6409 mentions of genes and their Entrez Gene IDs, 186 mentions of organism names and their NCBI Taxonomy IDs, 1867 mentions of PPIs and 701 annotations of PPI experimental evidence statements, 856 mentions of GIs and 399 annotations of GI evidence statements. The purpose, characteristics and possible future uses of the BioC-BioGRID corpus are detailed in this report. Database URL: http://bioc.sourceforge.net/BioC-BioGRID.html PMID:28077563

Overview of the gene ontology task at BioCreative IV.

PubMed

Mao, Yuqing; Van Auken, Kimberly; Li, Donghui; Arighi, Cecilia N; McQuilton, Peter; Hayman, G Thomas; Tweedie, Susan; Schaeffer, Mary L; Laulederkind, Stanley J F; Wang, Shur-Jen; Gobeill, Julien; Ruch, Patrick; Luu, Anh Tuan; Kim, Jung-Jae; Chiang, Jung-Hsien; Chen, Yu-De; Yang, Chia-Jung; Liu, Hongfang; Zhu, Dongqing; Li, Yanpeng; Yu, Hong; Emadzadeh, Ehsan; Gonzalez, Graciela; Chen, Jian-Ming; Dai, Hong-Jie; Lu, Zhiyong

2014-01-01

Gene ontology (GO) annotation is a common task among model organism databases (MODs) for capturing gene function data from journal articles. It is a time-consuming and labor-intensive task, and is thus often considered as one of the bottlenecks in literature curation. There is a growing need for semiautomated or fully automated GO curation techniques that will help database curators to rapidly and accurately identify gene function information in full-length articles. Despite multiple attempts in the past, few studies have proven to be useful with regard to assisting real-world GO curation. The shortage of sentence-level training data and opportunities for interaction between text-mining developers and GO curators has limited the advances in algorithm development and corresponding use in practical circumstances. To this end, we organized a text-mining challenge task for literature-based GO annotation in BioCreative IV. More specifically, we developed two subtasks: (i) to automatically locate text passages that contain GO-relevant information (a text retrieval task) and (ii) to automatically identify relevant GO terms for the genes in a given article (a concept-recognition task). With the support from five MODs, we provided teams with >4000 unique text passages that served as the basis for each GO annotation in our task data. Such evidence text information has long been recognized as critical for text-mining algorithm development but was never made available because of the high cost of curation. In total, seven teams participated in the challenge task. From the team results, we conclude that the state of the art in automatically mining GO terms from literature has improved over the past decade while much progress is still needed for computer-assisted GO curation. Future work should focus on addressing remaining technical challenges for improved performance of automatic GO concept recognition and incorporating practical benefits of text-mining tools into real-world GO annotation. http://www.biocreative.org/tasks/biocreative-iv/track-4-GO/. Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

THE GAP BETWEEN ECONOMIC EVALUATIONS AND CLINICAL PRACTICE: A SYSTEMATIC REVIEW OF ECONOMIC EVALUATIONS ON DABIGATRAN FOR ATRIAL FIBRILLATION.

PubMed

Rolden, Herbert J A; van der Wilt, Gert Jan; Maas, Angela H E M; Grutters, Janneke P C

2018-06-18

As model-based economic evaluations (MBEEs) are widely used to make decisions in the context of policy, it is imperative that they represent clinical practice. Here, we assess the relevance of MBEEs on dabigatran for the prevention of stroke in patients with atrial fibrillation (AF). We performed a systematic review on the basis of a developed questionnaire, tailored to oral anticoagulation in patients with AF. Included studies had a full body text in English, compared dabigatran with a vitamin K antagonist, were not dedicated to one or more subgroup(s), and yielded an incremental cost-effectiveness ratio. The relevance of all MBEEs was assessed on the basis of ten context-independent factors, which encompassed clinical outcomes and treatment duration. The MBEEs performed for the United States were assessed on the basis of seventeen context-dependent factors, which were related to the country's target population and clinical environment. The search yielded twenty-nine MBEEs, of which six were performed for the United States. On average, 54 percent of the context-independent factors were included per study, and 37 percent of the seventeen context-dependent factors in the U.S. The share of relevant factors per study did not increase over time. MBEEs on dabigatran leave out several relevant factors, limiting their usefulness to decision makers. We strongly urge health economic researchers to improve the relevance of their MBEEs by including context-independent relevance factors, and modeling context-dependent factors befitting the decision context concerned.

Development of an information retrieval tool for biomedical patents.

PubMed

Alves, Tiago; Rodrigues, Rúben; Costa, Hugo; Rocha, Miguel

2018-06-01

The volume of biomedical literature has been increasing in the last years. Patent documents have also followed this trend, being important sources of biomedical knowledge, technical details and curated data, which are put together along the granting process. The field of Biomedical text mining (BioTM) has been creating solutions for the problems posed by the unstructured nature of natural language, which makes the search of information a challenging task. Several BioTM techniques can be applied to patents. From those, Information Retrieval (IR) includes processes where relevant data are obtained from collections of documents. In this work, the main goal was to build a patent pipeline addressing IR tasks over patent repositories to make these documents amenable to BioTM tasks. The pipeline was developed within @Note2, an open-source computational framework for BioTM, adding a number of modules to the core libraries, including patent metadata and full text retrieval, PDF to text conversion and optical character recognition. Also, user interfaces were developed for the main operations materialized in a new @Note2 plug-in. The integration of these tools in @Note2 opens opportunities to run BioTM tools over patent texts, including tasks from Information Extraction, such as Named Entity Recognition or Relation Extraction. We demonstrated the pipeline's main functions with a case study, using an available benchmark dataset from BioCreative challenges. Also, we show the use of the plug-in with a user query related to the production of vanillin. This work makes available all the relevant content from patents to the scientific community, decreasing drastically the time required for this task, and provides graphical interfaces to ease the use of these tools. Copyright © 2018 Elsevier B.V. All rights reserved.

Zika virus infection in pregnancy: a systematic review of disease course and complications.

PubMed

Chibueze, Ezinne C; Tirado, Veronika; Lopes, Katharina da Silva; Balogun, Olukunmi O; Takemoto, Yo; Swa, Toshiyuki; Dagvadorj, Amarjargal; Nagata, Chie; Morisaki, Naho; Menendez, Clara; Ota, Erika; Mori, Rintaro; Oladapo, Olufemi T

2017-02-28

To characterize maternal Zika virus (ZIKV) infection and complement the evidence base for the WHO interim guidance on pregnancy management in the context of ZIKV infection. We searched the relevant database from inception until March 2016. Two review authors independently screened and assessed full texts of eligible reports and extracted data from relevant studies. The quality of studies was assessed using the Newcastle-Ottawa Scale (NOS) and the National Institute of Health (NIH) tool for observational studies and case series/reports, respectively. Among 142 eligible full-text articles, 18 met the inclusion criteria (13 case series/reports and five cohort studies). Common symptoms among pregnant women with suspected/confirmed ZIKV infection were fever, rash, and arthralgia. One case of Guillain-Barré syndrome was reported among ZIKV-infected mothers, no other case of severe maternal morbidity or mortality reported. Complications reported in association with maternal ZIKV infection included a broad range of fetal and newborn neurological and ocular abnormalities; fetal growth restriction, stillbirth, and perinatal death. Microcephaly was the primary neurological complication reported in eight studies, with an incidence of about 1% among newborns of ZIKV infected women in one study. Given the extensive and variable fetal and newborn presentations/complications associated with prenatal ZIKV infection, and the dearth of information provided, knowledge gaps are evident. Further research and comprehensive reporting may provide a better understanding of ZIKV infection in pregnancy and attendant maternal/fetal complications. This knowledge could inform the creation of effective and evidence-based strategies, guidelines and recommendations aimed at the management of maternal ZIKV infection. Adherence to current best practice guidelines for prenatal care among health providers is encouraged, in the context of maternal ZIKV infection.

Text mining for the biocuration workflow

PubMed Central

Hirschman, Lynette; Burns, Gully A. P. C; Krallinger, Martin; Arighi, Cecilia; Cohen, K. Bretonnel; Valencia, Alfonso; Wu, Cathy H.; Chatr-Aryamontri, Andrew; Dowell, Karen G.; Huala, Eva; Lourenço, Anália; Nash, Robert; Veuthey, Anne-Lise; Wiegers, Thomas; Winter, Andrew G.

2012-01-01

Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on ‘Text Mining for the BioCuration Workflow’ at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community. PMID:22513129

Text mining for the biocuration workflow.

PubMed

Hirschman, Lynette; Burns, Gully A P C; Krallinger, Martin; Arighi, Cecilia; Cohen, K Bretonnel; Valencia, Alfonso; Wu, Cathy H; Chatr-Aryamontri, Andrew; Dowell, Karen G; Huala, Eva; Lourenço, Anália; Nash, Robert; Veuthey, Anne-Lise; Wiegers, Thomas; Winter, Andrew G

2012-01-01

Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on 'Text Mining for the BioCuration Workflow' at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community.

Plasma-Lyte 148: A clinical review

PubMed Central

Weinberg, Laurence; Collins, Neil; Van Mourik, Kiara; Tan, Chong; Bellomo, Rinaldo

2016-01-01

AIM To outline the physiochemical properties and specific clinical uses of Plasma-Lyte 148 as choice of solution for fluid intervention in critical illness, surgery and perioperative medicine. METHODS We performed an electronic literature search from Medline and PubMed (via Ovid), anesthesia and pharmacology textbooks, and online sources including studies that compared Plasma-Lyte 148 to other crystalloid solutions. The following keywords were used: “surgery”, “anaesthesia”, “anesthesia”, “anesthesiology”, “anaesthesiology”, “fluids”, “fluid therapy”, “crystalloid”, “saline”, “plasma-Lyte”, “plasmalyte”, “hartmann’s”, “ringers” “acetate”, “gluconate”, “malate”, “lactate”. All relevant articles were accessed in full. We summarized the data and reported the data in tables and text. RESULTS We retrieved 104 articles relevant to the choice of Plasma-Lyte 148 for fluid intervention in critical illness, surgery and perioperative medicine. We analyzed the data and reported the results in tables and text. CONCLUSION Plasma-Lyte 148 is an isotonic, buffered intravenous crystalloid solution with a physiochemical composition that closely reflects human plasma. Emerging data supports the use of buffered crystalloid solutions in preference to saline in improving physicochemical outcomes. Further large randomized controlled trials assessing the comparative effectiveness of Plasma-Lyte 148 and other crystalloid solutions in measuring clinically important outcomes such as morbidity and mortality are needed. PMID:27896148

Use of near-infrared systems for investigations of hemodynamics in human in vivo bone tissue: A systematic review.

PubMed

Meertens, Robert; Casanova, Francesco; Knapp, Karen M; Thorn, Clare; Strain, William David

2018-05-04

A range of technologies using near infrared (NIR) light have shown promise at providing real time measurements of hemodynamic markers in bone tissue in vivo, an exciting prospect given existing difficulties in measuring hemodynamics in bone tissue. This systematic review aimed to evaluate the evidence for this potential use of NIR systems, establishing their potential as a research tool in this field. Major electronic databases including MEDLINE and EMBASE were searched using pre-planned search strategies with broad scope for any in vivo use of NIR technologies in human bone tissue. Following identification of studies by title and abstract screening, full text inclusion was determined by double blind assessment using predefined criteria. Full text studies for inclusion were data extracted using a predesigned proforma and quality assessed. Narrative synthesis was appropriate given the wide heterogeneity of included studies. Eighty-eight full text studies fulfilled the inclusion criteria, 57 addressing laser Doppler flowmetry (56 intra-operatively), 21 near infrared spectroscopy, and 10 photoplethysmography. The heterogeneity of the methodologies included differing hemodynamic markers, measurement protocols, anatomical locations, and research applications, making meaningful direct comparisons impossible. Further, studies were often limited by small sample sizes with potential selection biases, detection biases, and wide variability in results between participants. Despite promising potential in the use of NIR light to interrogate bone circulation, the application of NIR systems in bone requires rigorous assessment of the reproducibility of potential hemodynamic markers and further validation of these markers against alternative physiologically relevant reference standards. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 9999:1-9, 2018. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Automatic Evidence Retrieval for Systematic Reviews

PubMed Central

Choong, Miew Keen; Galgani, Filippo; Dunn, Adam G

2014-01-01

Background Snowballing involves recursively pursuing relevant references cited in the retrieved literature and adding them to the search results. Snowballing is an alternative approach to discover additional evidence that was not retrieved through conventional search. Snowballing’s effectiveness makes it best practice in systematic reviews despite being time-consuming and tedious. Objective Our goal was to evaluate an automatic method for citation snowballing’s capacity to identify and retrieve the full text and/or abstracts of cited articles. Methods Using 20 review articles that contained 949 citations to journal or conference articles, we manually searched Microsoft Academic Search (MAS) and identified 78.0% (740/949) of the cited articles that were present in the database. We compared the performance of the automatic citation snowballing method against the results of this manual search, measuring precision, recall, and F1 score. Results The automatic method was able to correctly identify 633 (as proportion of included citations: recall=66.7%, F1 score=79.3%; as proportion of citations in MAS: recall=85.5%, F1 score=91.2%) of citations with high precision (97.7%), and retrieved the full text or abstract for 490 (recall=82.9%, precision=92.1%, F1 score=87.3%) of the 633 correctly retrieved citations. Conclusions The proposed method for automatic citation snowballing is accurate and is capable of obtaining the full texts or abstracts for a substantial proportion of the scholarly citations in review articles. By automating the process of citation snowballing, it may be possible to reduce the time and effort of common evidence surveillance tasks such as keeping trial registries up to date and conducting systematic reviews. PMID:25274020

Clinical performance of removable dental prostheses in the moderately reduced dentition: a systematic literature review.

PubMed

Moldovan, Ovidiu; Rudolph, Heike; Luthardt, Ralph G

2016-09-01

Evidence-based therapeutic recommendations for removable dental prostheses are still lacking. The aim of the present study was a systematic review and meta-analysis of the survival rates of removable dentures in the moderately reduced dentition. In 2014, a systematic literature search in established medical databases (MEDLINE, EMBASE, BIOSIS, SciSearch, Cochrane, FIZ Technik Web) and a hand search of relevant dental journals were conducted. The search terms were relevant MeSH terms, free search terms, and combinations of the two. The search included RCTs, prospective and retrospective studies on survival rates of removable dental prostheses in the moderately reduced dentition with at least 15 participants, an observation period of at least 2 years, and a dropout rate of less than 25 %. The selection of relevant publications was carried out at the title, abstract, and full-text level by at least two of the authors involved. The publications included were tabulated and analyzed. Of the original 12,994 matches, 1923 were analyzed by title, 650 by abstract, and 111 according to the full text. The final review included 19 publications, of which 6 were multiple publications. Cast-metal framework dentures exhibited failure rates of between 33 and 50 % after 5 years. One study with a 25-year observation period reported failure rates of 50 %. Better results were obtained with proper pretreatment and a good recall scheme. Bilateral attachment prostheses showed failure rates of between 11 and 30 % after 5 years. Unilateral attachment prostheses showed failure rates of 75 % after 5 years. Double-crown prostheses dentures show failure rates of 0 to 21.7 % after 3 to 6 years. Heterogeneous study designs and data analyses rendered a meta-analysis impossible, so that an evaluation at the highest level of evidence could not be performed. Within the limitations of this study, it would be correct to state that removable dental prostheses, given suitable pretreatment and follow-up regimes, can provide satisfactory solutions. Based on only one paper, they revealed acceptable results even over a very long observation period (25 years).

Task relevance induces momentary changes in the functional visual field during reading.

PubMed

Kaakinen, Johanna K; Hyönä, Jukka

2014-02-01

In the research reported here, we examined whether task demands can induce momentary tunnel vision during reading. More specifically, we examined whether the size of the functional visual field depends on task relevance. Forty participants read an expository text with a specific task in mind while their eye movements were recorded. A display-change paradigm with random-letter strings as preview masks was used to study the size of the functional visual field within sentences that contained task-relevant and task-irrelevant information. The results showed that orthographic parafoveal-on-foveal effects and preview benefits were observed for words within task-irrelevant but not task-relevant sentences. The results indicate that the size of the functional visual field is flexible and depends on the momentary processing demands of a reading task. The higher cognitive processing requirements experienced when reading task-relevant text rather than task-irrelevant text induce momentary tunnel vision, which narrows the functional visual field.

The Role of Reader Characteristics in Processing and Learning from Informational Text

ERIC Educational Resources Information Center

Fox, Emily

2009-01-01

This article considers the role of reader characteristics in processing and learning from informational text, as revealed in think-aloud research. A theoretical framework for relevant aspects of readers' processing and products was developed. These relevant aspects included three attentional foci for processing (comprehension, monitoring, and…

Beyond relevance and recall: testing new user-centred measures of database performance.

PubMed

Stokes, Peter; Foster, Allen; Urquhart, Christine

2009-09-01

Measures of the effectiveness of databases have traditionally focused on recall, precision, with some debate on how relevance can be assessed, and by whom. New measures of database performance are required when users are familiar with search engines, and expect full text availability. This research ascertained which of four bibliographic databases (BNI, CINAHL, MEDLINE and EMBASE) could be considered most useful to nursing and midwifery students searching for information for an undergraduate dissertation. Searches on title were performed for dissertation topics supplied by nursing students (n = 9), who made the relevance judgements. Measures of recall and precision were combined with additional factors to provide measures of effectiveness, while efficiency combined measures of novelty and originality and accessibility combined measures for availability and retrievability, based on obtainability. There were significant differences among the databases in precision, originality and availability, but other differences were not significant (Friedman test). Odds ratio tests indicated that BNI, followed by CINAHL were the most effective, CINAHL the most efficient, and BNI the most accessible. The methodology could help library services in purchase decisions as the measure for accessibility, and odds ratio testing helped to differentiate database performance.

Free software to analyse the clinical relevance of drug interactions with antiretroviral agents (SIMARV®) in patients with HIV/AIDS.

PubMed

Giraldo, N A; Amariles, P; Monsalve, M; Faus, M J

Highly active antiretroviral therapy has extended the expected lifespan of patients with HIV/AIDS. However, the therapeutic benefits of some drugs used simultaneously with highly active antiretroviral therapy may be adversely affected by drug interactions. The goal was to design and develop a free software to facilitate analysis, assessment, and clinical decision making according to the clinical relevance of drug interactions in patients with HIV/AIDS. A comprehensive Medline/PubMed database search of drug interactions was performed. Articles that recognized any drug interactions in HIV disease were selected. The publications accessed were limited to human studies in English or Spanish, with full texts retrieved. Drug interactions were analyzed, assessed, and grouped into four levels of clinical relevance according to gravity and probability. Software to systematize the information regarding drug interactions and their clinical relevance was designed and developed. Overall, 952 different references were retrieved and 446 selected; in addition, 67 articles were selected from the citation lists of identified articles. A total of 2119 pairs of drug interactions were identified; of this group, 2006 (94.7%) were drug-drug interactions, 1982 (93.5%) had an identified pharmacokinetic mechanism, and 1409 (66.5%) were mediated by enzyme inhibition. In terms of clinical relevance, 1285 (60.6%) drug interactions were clinically significant in patients with HIV (levels 1 and 2). With this information, a software program that facilitates identification and assessment of the clinical relevance of antiretroviral drug interactions (SIMARV ® ) was developed. A free software package with information on 2119 pairs of antiretroviral drug interactions was designed and developed that could facilitate analysis, assessment, and clinical decision making according to the clinical relevance of drug interactions in patients with HIV/AIDS. Copyright © 2016 Elsevier Inc. All rights reserved.

Academic Journal Embargoes and Full Text Databases.

ERIC Educational Resources Information Center

Brooks, Sam

2003-01-01

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

The Flip Sides of Full-Text: Superindex and the Harvard Business Review/Online.

ERIC Educational Resources Information Center

Dadlez, Eva M.

1984-01-01

This article illustrates similarities between two different types of full-text databases--Superindex, Harvard Business Review/Online--and uses them as arena to demonstrate search and display applications of full-text. The selection of logical operators, full-text search strategies, and keywords and Bibliographic Retrieval Service's Occurrence…

New Jersey state information handbook: Formerly Utilized Sites Remedial Action Program

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

None

Under the implied authority of the Atomic Energy Act of 1954, as amended, radiological surveys and research work has been conducted to determine radiological conditions at former MED/AEC sites. As of this time, 31 sites in 13 states have been identified that require or may require remedial action. This volume is one of a series produced under contract with DOE, Office of Nuclear Waste Management, by POLITECH CORPORATION to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Remedial Action Program. This Information Handbook seriesmore » contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the state of New Jersey. It contains: a description of the state executive branch structure; a summary of relevant state statutes and regulations; a description of the structure of the state legislature, identification of the officers and committee chairmen, and a summary of recent relevant legislative action; and the full text of relevant statutes and regulations. The loose-leaf format used in these volumes will allow the material to be updated periodically as the Remedial Action Program progresses.« less

[Clinical relevance of drug interactions between nonsteroidal antiinflammatory drugs (NSAIDs) and antihypertensives].

PubMed

Villa, Juan; Cano, Alejandra; Franco, David; Monsalve, Mauricio; Hincapié, Jaime; Amariles, Pedro

2014-11-01

To establish the clinical relevance of drug interactions between nonsteroidal antiinflammatory drugs (NSAIDs) and antihypertensives, based on the interaction severity and probability of occurrence. Systematic review. A PubMed/Medline search was made using the MeSH terms: NSAIDs, Antihypertensive drugs, and Drug interactions. Articles between 2002 and 2012, human studies, in Spanish and English and full text access were included. Found articles were included and some of the references used in this works. Studies with in vitro methods, effects on ocular hypertension and those who do not consider the interaction NSAIDs, antihypertensives were excluded. For the selection of the papers included three independent reviewers were involved. We used a tool for data extraction and for assess of the interaction clinical relevance. Nineteen of 50 papers found were included. There were identified 21 interactions with pharmacodynamic mechanism, classified by their clinical relevance in level-2 high risk (76.2%) and level-3 medium risk (23.8%). In addition, evidence of 16 combinations of no interaction were found. Some NSAIDs may attenuate the effectiveness of antihypertensive drugs when used concurrently, especially with angiotensin converting enzyme inhibitors, diuretics, beta blockers and angiotensin receptorsii blockers. There was no evidence of effect modification of calcium channel antagonists, especially dihydropyridine, by concurrent use of NSAIDs. Copyright © 2013 Elsevier España, S.L.U. All rights reserved.

ExaCT: automatic extraction of clinical trial characteristics from journal publications

PubMed Central

2010-01-01

Background Clinical trials are one of the most important sources of evidence for guiding evidence-based practice and the design of new trials. However, most of this information is available only in free text - e.g., in journal publications - which is labour intensive to process for systematic reviews, meta-analyses, and other evidence synthesis studies. This paper presents an automatic information extraction system, called ExaCT, that assists users with locating and extracting key trial characteristics (e.g., eligibility criteria, sample size, drug dosage, primary outcomes) from full-text journal articles reporting on randomized controlled trials (RCTs). Methods ExaCT consists of two parts: an information extraction (IE) engine that searches the article for text fragments that best describe the trial characteristics, and a web browser-based user interface that allows human reviewers to assess and modify the suggested selections. The IE engine uses a statistical text classifier to locate those sentences that have the highest probability of describing a trial characteristic. Then, the IE engine's second stage applies simple rules to these sentences to extract text fragments containing the target answer. The same approach is used for all 21 trial characteristics selected for this study. Results We evaluated ExaCT using 50 previously unseen articles describing RCTs. The text classifier (first stage) was able to recover 88% of relevant sentences among its top five candidates (top5 recall) with the topmost candidate being relevant in 80% of cases (top1 precision). Precision and recall of the extraction rules (second stage) were 93% and 91%, respectively. Together, the two stages of the extraction engine were able to provide (partially) correct solutions in 992 out of 1050 test tasks (94%), with a majority of these (696) representing fully correct and complete answers. Conclusions Our experiments confirmed the applicability and efficacy of ExaCT. Furthermore, they demonstrated that combining a statistical method with 'weak' extraction rules can identify a variety of study characteristics. The system is flexible and can be extended to handle other characteristics and document types (e.g., study protocols). PMID:20920176

Scholarly Information Extraction Is Going to Make a Quantum Leap with PubMed Central (PMC).

PubMed

Matthies, Franz; Hahn, Udo

2017-01-01

With the increasing availability of complete full texts (journal articles), rather than their surrogates (titles, abstracts), as resources for text analytics, entirely new opportunities arise for information extraction and text mining from scholarly publications. Yet, we gathered evidence that a range of problems are encountered for full-text processing when biomedical text analytics simply reuse existing NLP pipelines which were developed on the basis of abstracts (rather than full texts). We conducted experiments with four different relation extraction engines all of which were top performers in previous BioNLP Event Extraction Challenges. We found that abstract-trained engines loose up to 6.6% F-score points when run on full-text data. Hence, the reuse of existing abstract-based NLP software in a full-text scenario is considered harmful because of heavy performance losses. Given the current lack of annotated full-text resources to train on, our study quantifies the price paid for this short cut.

Biological network extraction from scientific literature: state of the art and challenges.

PubMed

Li, Chen; Liakata, Maria; Rebholz-Schuhmann, Dietrich

2014-09-01

Networks of molecular interactions explain complex biological processes, and all known information on molecular events is contained in a number of public repositories including the scientific literature. Metabolic and signalling pathways are often viewed separately, even though both types are composed of interactions involving proteins and other chemical entities. It is necessary to be able to combine data from all available resources to judge the functionality, complexity and completeness of any given network overall, but especially the full integration of relevant information from the scientific literature is still an ongoing and complex task. Currently, the text-mining research community is steadily moving towards processing the full body of the scientific literature by making use of rich linguistic features such as full text parsing, to extract biological interactions. The next step will be to combine these with information from scientific databases to support hypothesis generation for the discovery of new knowledge and the extension of biological networks. The generation of comprehensive networks requires technologies such as entity grounding, coordination resolution and co-reference resolution, which are not fully solved and are required to further improve the quality of results. Here, we analyse the state of the art for the extraction of network information from the scientific literature and the evaluation of extraction methods against reference corpora, discuss challenges involved and identify directions for future research. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Effects of Task Relevance Instructions and Topic Beliefs on Reading Processes and Memory

ERIC Educational Resources Information Center

Bohn-Gettler, Catherine M.; McCrudden, Matthew T.

2018-01-01

This study investigated the effects of task relevance instructions and topic beliefs on reading processes and memory for belief-related text. Undergraduates received task instructions (focus on arguments for vs. against) before reading a dual-position text. In Experiment 1 (n = 88), a reading time methodology showed no differences in reading time…

Cultural Relevance and Informal Reading Inventory Performance: African-American Primary and Middle School Students

ERIC Educational Resources Information Center

Christ, Tanya; Chiu, Ming Ming; Rider, Stephanie; Kitson, Deborah; Hanser, Katherine; McConnell, Elizabeth; Dipzinski, Renae; Mayernik, Heather

2018-01-01

We explore whether (a) teacher ratings of texts' cultural relevance along various dimensions differ from those of students, (b) these ratings reflect a single construct, and (c) ratings of specific dimensions are related to specific reading outcomes. Fifty African-American students were each administered two text protocols for a total of 100…

Efficient and sparse feature selection for biomedical text classification via the elastic net: Application to ICU risk stratification from nursing notes.

PubMed

Marafino, Ben J; Boscardin, W John; Dudley, R Adams

2015-04-01

Sparsity is often a desirable property of statistical models, and various feature selection methods exist so as to yield sparser and interpretable models. However, their application to biomedical text classification, particularly to mortality risk stratification among intensive care unit (ICU) patients, has not been thoroughly studied. To develop and characterize sparse classifiers based on the free text of nursing notes in order to predict ICU mortality risk and to discover text features most strongly associated with mortality. We selected nursing notes from the first 24h of ICU admission for 25,826 adult ICU patients from the MIMIC-II database. We then developed a pair of stochastic gradient descent-based classifiers with elastic-net regularization. We also studied the performance-sparsity tradeoffs of both classifiers as their regularization parameters were varied. The best-performing classifier achieved a 10-fold cross-validated AUC of 0.897 under the log loss function and full L2 regularization, while full L1 regularization used just 0.00025% of candidate input features and resulted in an AUC of 0.889. Using the log loss (range of AUCs 0.889-0.897) yielded better performance compared to the hinge loss (0.850-0.876), but the latter yielded even sparser models. Most features selected by both classifiers appear clinically relevant and correspond to predictors already present in existing ICU mortality models. The sparser classifiers were also able to discover a number of informative - albeit nonclinical - features. The elastic-net-regularized classifiers perform reasonably well and are capable of reducing the number of features required by over a thousandfold, with only a modest impact on performance. Copyright © 2015 Elsevier Inc. All rights reserved.

Does tooth brushing influence the development and progression of non-inflammatory gingival recession? A systematic review.

PubMed

Rajapakse, P Sunethra; McCracken, Giles I; Gwynnett, Erika; Steen, Nick D; Guentsch, Arndt; Heasman, Peter A

2007-12-01

The aim of this systematic review was to produce the best available evidence and pool appropriate data to evaluate the effect of tooth brushing on the initiation and progression of non-inflammatory gingival recession. A protocol was developed a priori for the question: "Do factors associated with tooth brushing predict the development and progression of non-inflammatory gingival recession in adults?" The search covered six electronic databases between January 1966 and July 2005. Hand searching included searches of the Journal of Clinical Periodontology, Journal of Periodontal Research and the Journal of Periodontology. Bibliographies of narrative reviews, conference proceedings and relevant texts known to the authors were also searched. Inclusion of titles, abstracts and ultimately full texts was based on consensus between three reviewers. The full texts of 29 papers were read and 18 texts were eligible for inclusion. One abstract from EuroPerio 5 reported a randomized-controlled clinical trial [Level I evidence] in which the authors concluded that the toothbrushes significantly reduced recessions on buccal tooth surfaces over 18 months. Of the remaining 17 observational studies, two concluded that there appeared to be no relationship between tooth brushing frequency and gingival recession. Eight studies reported a positive association between tooth brushing frequency and recession. Other potential risk factors were duration of tooth brushing, brushing force, frequency of changing the toothbrush, brush (bristle) hardness and tooth brushing technique. None of the observational studies satisfied all the specified criteria for quality appraisal and a valid appraisal of the quality of the randomized-controlled trial was not possible. The data to support or refute the association between tooth brushing and gingival recession are inconclusive.

Extracting PICO Sentences from Clinical Trial Reports using Supervised Distant Supervision

PubMed Central

Wallace, Byron C.; Kuiper, Joël; Sharma, Aakash; Zhu, Mingxi (Brian); Marshall, Iain J.

2016-01-01

Systematic reviews underpin Evidence Based Medicine (EBM) by addressing precise clinical questions via comprehensive synthesis of all relevant published evidence. Authors of systematic reviews typically define a Population/Problem, Intervention, Comparator, and Outcome (a PICO criteria) of interest, and then retrieve, appraise and synthesize results from all reports of clinical trials that meet these criteria. Identifying PICO elements in the full-texts of trial reports is thus a critical yet time-consuming step in the systematic review process. We seek to expedite evidence synthesis by developing machine learning models to automatically extract sentences from articles relevant to PICO elements. Collecting a large corpus of training data for this task would be prohibitively expensive. Therefore, we derive distant supervision (DS) with which to train models using previously conducted reviews. DS entails heuristically deriving ‘soft’ labels from an available structured resource. However, we have access only to unstructured, free-text summaries of PICO elements for corresponding articles; we must derive from these the desired sentence-level annotations. To this end, we propose a novel method – supervised distant supervision (SDS) – that uses a small amount of direct supervision to better exploit a large corpus of distantly labeled instances by learning to pseudo-annotate articles using the available DS. We show that this approach tends to outperform existing methods with respect to automated PICO extraction. PMID:27746703

Effects of Pre-reading Instructions on the Comprehension of Science Texts

NASA Astrophysics Data System (ADS)

Lyons, Yuna H.

This study examined how three different pre-reading (or relevance) instructions led to different learning outcomes for middle school students reading science texts on the topic of sweetness. The first was a generic instruction to read for understanding. The second prompted students to form a holistic explanation of the topic of sweetness, and the third instruction prompted students to focus on the core scientific principle of the relationship between structure and function. The latter two were specifically designed to align with science disciplinary goals. A comparison of the three treatments found that the generic instruction and the structure-function instruction led to better learning outcomes, measured by recall, short-answer performance questions, and a traditional multiple-choice/short-answer assessment. A qualitative analysis of the data also revealed some small yet notable differences in the recall pattern of students, such as an increased recall of key ideas for the structure-function instruction. This effect was seen predominantly for higher-skilled readers. The results suggest the possibility that relevance instructions targeting core ideas may help to orient students to the key ideas and explanations in scientific text, especially for higher-skilled readers, and indirectly highlights some of the challenges for students with less reading competencies. Overall, this study provides greater insight into how middle-school students read science texts, the effectiveness of instructor-provided relevance instructions in promoting (higher-level) comprehension of science texts, and implications for teachers on how to use texts in science instruction. Keywords: relevance instructions, pre-reading instructions, comprehension, science texts, middle school students, low- versus high-skilled readers.

A strategy for electronic dissemination of NASA Langley technical publications

NASA Technical Reports Server (NTRS)

Roper, Donna G.; Mccaskill, Mary K.; Holland, Scott D.; Walsh, Joanne L.; Nelson, Michael L.; Adkins, Susan L.; Ambur, Manjula Y.; Campbell, Bryan A.

1994-01-01

To demonstrate NASA Langley Research Center's relevance and to transfer technology to external customers in a timely and efficient manner, Langley has formed a working group to study and recommend a course of action for the electronic dissemination of technical reports (EDTR). The working group identified electronic report requirements (e.g., accessibility, file format, search requirements) of customers in U.S. industry through numerous site visits and personal contacts. Internal surveys were also used to determine commonalities in document preparation methods. From these surveys, a set of requirements for an electronic dissemination system was developed. Two candidate systems were identified and evaluated against the set of requirements: the Full-Text Electronic Documents System (FEDS), which is a full-text retrieval system based on the commercial document management package Interleaf, and the Langley Technical Report Server (LTRS), which is a Langley-developed system based on the publicly available World Wide Web (WWW) software system. Factors that led to the selection of LTRS as the vehicle for electronic dissemination included searching and viewing capability, current system operability, and client software availability for multiple platforms at no cost to industry. This report includes the survey results, evaluations, a description of the LTRS architecture, recommended policy statement, and suggestions for future implementations.

Informing clinical policy decision-making practices in ambulance services.

PubMed

Muecke, Sandy; Curac, Nada; Binks, Darryn

2013-12-01

This study aims to identify the processes and frameworks that support an evidence-based approach to clinical policy decision-making practices in ambulance services. This literature review focused on: (i) the setting (pre-hospital); and (ii) the process of evidence translation, for studies published after the year 2000. Searches of Medline, CINAHL and Google were undertaken. Reference lists of eligible publications were searched for relevant articles. A total of 954 articles were identified. Of these, 20 full text articles were assessed for eligibility and seven full text articles met the inclusion criteria. Three provided detailed descriptions of the evidence-based practice processes used to inform ambulance service protocol or guideline development or review. There is little published literature that describes the processes involved, and frameworks required, to inform clinical policy decision making within ambulance services. This review found that processes were iterative and involved collaborations across many internal and external stakeholders. In several jurisdictions, these were coordinated by a dedicated team. Success appears dependent on committed leadership and purposive human and structural resources. Although time consuming, structured processes have been developed in some jurisdictions to assist decision-making processes. Further insight is likely to be obtained from literature published by those from other disciplines. © 2013 The Authors. International Journal of Evidence-Based Healthcare © 2013 The Joanna Briggs Institute.

Full-text publication of abstract-presented work in sport and exercise psychology

PubMed Central

Warden, Stuart

2018-01-01

Objectives Meetings promote information sharing, but do not enable full dissemination of details. A systematic search was conducted for abstracts presented at the 2010 and 2011 Association of Applied Sport Psychology Annual Conferences to determine the full-text dissemination rate of work presented in abstract form and investigate factors influencing this rate. Methods Systematic searches were sequentially conducted to determine whether the abstract-presented work had been published in full-text format in the 5 years following presentation. If a potential full-text publication was identified, information from the conference abstract (eg, results, number of participants in the sample(s), measurement tools used and so on) was compared with the full text to ensure the two entities represented the same body of work. Abstract factors of interest were assessed using logistic regression. Results Ninety-four out of 423 presented abstracts (22.2%) were published in full text. Odds of full-text publication increased if the abstract was from an international institution, presented in certain conference sections or presented as a lecture. Conclusion Those attending professional conferences should be cautious when translating data presented at conferences into their applied work because of the low rate of peer-reviewed and full-text publication of the information. PMID:29629187

Journal searching in non-MEDLINE resources on Internet Web sites.

PubMed

Lingle, V A

1997-01-01

Internet access to the medical journal literature is absorbing the attention of all relevant parties, i.e., publishers, journal vendors, librarians, commercial providers, government agencies, and end users. Journal content on the Web sites spans the range from advertising and ordering information for the print version, to table of contents and abstracts, to downloadable full text and graphics of articles. The searching parameters for systems other than MEDLINE also differ extensively with a wide variety of features and resulting retrieval. This discussion reviews a selection of providers of medical information (particularly the journal literature) on the Internet, making a comparison of what is available on Web sites and how it can be searched.

Using Relevance Prompts: An Exploratory Study to Promote Eighth Graders' Comprehension and Retelling of Narrative Text

ERIC Educational Resources Information Center

Fogarty, Melissa S.; Davis, John L.; Anderson, Leah L.; Myint, Ahmarlay

2017-01-01

This exploratory study investigated the effects of modifying eighth grade students' purposes for reading through a prompt designed to increase engagement with the text. The current study was conducted using a randomized between-subjects design, with a relevance prompt as the between-subjects factor and reader proficiency as a covariate. A sample…

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.

Literature evidence in open targets - a target validation platform.

PubMed

Kafkas, Şenay; Dunham, Ian; McEntyre, Johanna

2017-06-06

We present the Europe PMC literature component of Open Targets - a target validation platform that integrates various evidence to aid drug target identification and validation. The component identifies target-disease associations in documents and ranks the documents based on their confidence from the Europe PMC literature database, by using rules utilising expert-provided heuristic information. The confidence score of a given document represents how valuable the document is in the scope of target validation for a given target-disease association by taking into account the credibility of the association based on the properties of the text. The component serves the platform regularly with the up-to-date data since December, 2015. Currently, there are a total number of 1168365 distinct target-disease associations text mined from >26 million PubMed abstracts and >1.2 million Open Access full text articles. Our comparative analyses on the current available evidence data in the platform revealed that 850179 of these associations are exclusively identified by literature mining. This component helps the platform's users by providing the most relevant literature hits for a given target and disease. The text mining evidence along with the other types of evidence can be explored visually through https://www.targetvalidation.org and all the evidence data is available for download in json format from https://www.targetvalidation.org/downloads/data .

Data Compression in Full-Text Retrieval Systems.

ERIC Educational Resources Information Center

Bell, Timothy C.; And Others

1993-01-01

Describes compression methods for components of full-text systems such as text databases on CD-ROM. Topics discussed include storage media; structures for full-text retrieval, including indexes, inverted files, and bitmaps; compression tools; memory requirements during retrieval; and ranking and information retrieval. (Contains 53 references.)…

The full spectrum of ethical issues in the care of patients with ALS: a systematic qualitative review.

PubMed

Seitzer, F; Kahrass, H; Neitzke, G; Strech, D

2016-02-01

Dealing systematically with ethical issues in amyotrophic lateral sclerosis (ALS) care requires an unbiased awareness of all the relevant ethical issues. The aim of the study was to determine systematically and transparently the full spectrum of ethical issues in ALS care. We conducted a systematic review in Medline and Google Books (restricted to English and German literature published between 1993 and 2014). We applied qualitative text analysis and normative analysis to categorise the spectrum of ethical issues in ALS care. The literature review retrieved 56 references that together mentioned a spectrum of 103 ethical issues in ALS care. The spectrum was structured into six major categories that consist of first and second-order categories of ethical issues. The systematically derived spectrum of ethical issues in ALS care presented in this paper raises awareness and understanding of the complexity of ethical issues in ALS care. It also offers a basis for the systematic development of informational and training materials for health professionals, patients and their relatives, and society as a whole. Finally, it supports a rational and fair selection of all those ethical issues that should be addressed in health policies, position papers and clinical practice guidelines. Further research is needed to identify ways to systematically select the most relevant ethical issues not only in the clinical environment, but also for the development of clinical practice guidelines.

Modifiable workplace risk factors contributing to workplace absence across health conditions: A stakeholder-centered best-evidence synthesis of systematic reviews.

PubMed

White, Marc; Wagner, Shannon; Schultz, Izabela Z; Murray, Eleanor; Bradley, Susan M; Hsu, Vernita; McGuire, Lisa; Schulz, Werner

2013-01-01

A challenge facing stakeholders is the identification and translation of relevant high quality research to inform policy and practice. This study engaged academic and community stakeholders in conducting a best evidence-synthesis to enhance knowledge use. To identify modifiable workplace disability risk and protective factors across common health conditions impacting work-related absence. We searched MEDLINE, Embase, CINHAL, The Cochrane Library, PsycINFO, BusinessSourceComplete, and ABI/Inform from 2000 to 2011. Systematic reviews that employed quantitative, qualitative, or mixed methods of work-focused population were considered for inclusion. Two or more independent reviewers reviewed titles only, titles and abstracts, and/or full articles when assessing eligibility for inclusion. Selected articles underwent methodological screening. The search strategy, expert input and grey literature identified 2,467 unique records from which 142 full text articles underwent comprehensive review. Twenty-seven systematic reviews met eligibility criteria. Modifiable work factors found to have consistent evidence across two or more health conditions included lack of social support, increased physical demands at work, job strain, lack of supervisory support, increased psychological demands, low job satisfaction, low worker control of job, and poor leadership quality. The active engagement of stakeholders led to greater understanding of relevance of the study findings for community stakeholders and appreciation of the mutual benefits of collaboration.

Improving Retrieval Performance by Relevance Feedback.

ERIC Educational Resources Information Center

Salton, Gerard; Buckley, Chris

1990-01-01

Briefly describes the principal relevance feedback methods that have been introduced over the years and evaluates the effectiveness of the methods in producing improved query formulations. Prescriptions are given for conducting text retrieval operations iteratively using relevance feedback. (24 references) (Author/CLB)

SCRIPDB: a portal for easy access to syntheses, chemicals and reactions in patents

PubMed Central

Heifets, Abraham; Jurisica, Igor

2012-01-01

The patent literature is a rich catalog of biologically relevant chemicals; many public and commercial molecular databases contain the structures disclosed in patent claims. However, patents are an equally rich source of metadata about bioactive molecules, including mechanism of action, disease class, homologous experimental series, structural alternatives, or the synthetic pathways used to produce molecules of interest. Unfortunately, this metadata is discarded when chemical structures are deposited separately in databases. SCRIPDB is a chemical structure database designed to make this metadata accessible. SCRIPDB provides the full original patent text, reactions and relationships described within any individual patent, in addition to the molecular files common to structural databases. We discuss how such information is valuable in medical text mining, chemical image analysis, reaction extraction and in silico pharmaceutical lead optimization. SCRIPDB may be searched by exact chemical structure, substructure or molecular similarity and the results may be restricted to patents describing synthetic routes. SCRIPDB is available at http://dcv.uhnres.utoronto.ca/SCRIPDB. PMID:22067445

Prevention of sexually transmitted diseases among visually impaired people: educational text validation 1

PubMed Central

Oliveira, Giselly Oseni Barbosa; Cavalcante, Luana Duarte Wanderley; Pagliuca, Lorita Marlena Freitag; de Almeida, Paulo César; Rebouças, Cristiana Brasil de Almeida

2016-01-01

ABSTRACT Objective: to validate an educational text in the context of Sexually Transmitted Diseases (STD) for visually impaired persons, making it accessible to this population. Method: a validation study, in a virtual environment. Data collection occurred from May to September 2012 by emailing the subjects, and was composed by seven content experts about STDs. Analysis was based on the considerations of the experts about Objectives, Structure and Presentation, and Relevance. Results: on the Objectives and Structure and Presentation blocks, 77 (84.6%) and 48 (85.7%) were fully adequate or appropriate, respectively. In the Relevance block, items 3.2 - Allows transfer and generalization of learning, and 3.5 - Portrays aspects needed to clarify the family, showed bad agreement indices of 0.42 and 0.57, respectively. The analysis was followed by reformulating the text according to the relevant suggestions. Conclusion: the text was validated regarding the content of sexually transmitted diseases. A total of 35 stanzas were removed and nine others included, following the recommendations of the experts. PMID:27556880

Differences in Functional Outcomes for Adult Patients with Prosthodontically-Treated and -Untreated Shortened Dental Arches: A Systematic Review

PubMed Central

Khan, Saadika; Musekiwa, Alfred; Chikte, Usuf M. E.; Omar, Ridwaan

2014-01-01

This review examined differences in functional outcomes and patient satisfaction when shortened dental arches are left untreated compared to their restoration to complete arch lengths with different prosthodontic interventions. Methods A protocol was developed according to the criteria for a systematic review. All relevant databases were searched to identify appropriate clinical trials regardless of language or publication status. Predetermined eligibility criteria were applied, trial quality assessed and data extracted for each study. Relevant outcomes assessed were: functioning ability, patient satisfaction and harmful effects on oral structures. Results Searches yielded 101 articles: 81 from electronic databases and 20 from reference lists of retrieved articles (PEARLing searches). Sixty-nine citations were assessed for eligibility after removing 32 duplicate records. After reading titles and abstracts, a total of 41 records were excluded and the full-texts of the remaining 28 records were read. Only 21 records were included for the SR because 7 records were excluded after reading the full-text reports. These 21 records report the outcomes of four randomized controlled trials (RCTs) and one non-randomized clinical trial (CT) which were pre-specified and used for this review. No on-going studies were found and no eligible studies were excluded for failure to report the reviewer’s pre-specified outcomes. Outcomes were reported in the retrieved 21 articles. A narrative explanation of the pre-specified outcomes is reported for the 3 comparison groups (which were based on the different interventions used for the individual clinical trials). The shortened dental arch as a treatment option is encouraging in terms of functioning, patient satisfaction and cost-effectiveness. By using only high quality studies it was expected that the results would be more reliable when making conclusions and recommendations, but some of the included studies had to be downgraded due to methodological errors. PMID:24992473

Can antiviral treatment for hepatitis C be safely and effectively delivered in primary care?: a narrative systematic review of the evidence base.

PubMed

Brew, Iain F; Butt, Christine; Wright, Nat

2013-12-01

The burden of hepatitis C (HCV) treatment is growing, as is the political resolve to tackle the epidemic. Primary care will need to work more closely with secondary care to succeed in reducing the prevalence of chronic HCV. To identify research relating to the provision of antiviral treatment for HCV in primary care. A narrative systematic review of six databases. Method Medline, Embase, Cinahl, PsycINFO, Web of Science, and Cochrane were searched. Relevant journals were searched by hand for articles to be included in the review. Reference lists of relevant papers were reviewed and full-text papers were retrieved for those deemed to potentially fulfil the inclusion criteria of the review. A total of 683 abstracts led to 77 full-text articles being retrieved, of which 16 were finally included in the review. An evidence base emerged, highlighting that community-based antiviral treatment provision is feasible and can result in clinical outcomes comparable to those achieved in hospital outpatient settings. Such provision can be in mainstream general practice, at community addiction centres, or in prisons. GPs must be trained before offering such a service and there is also a need for ongoing specialist supervision of primary care practice. Such training and supervision can be delivered by teleconference, although, even with such ready availability of training and supervision, only a minority of GPs are likely to want to provide antiviral treatment. There is emerging evidence supporting the effectiveness of antiviral treatment provision for patients with chronic hepatitis C in a wide variety of primary care and wider community settings. Training and ongoing supervision of primary care practitioners by specialists is a prerequisite. There is an opportunity through future research activity to evaluate typologies of patients who would be best served by primary care-based treatment and those for whom hospital-based outpatient treatment would be most appropriate.

The NASA Astrophysics Data System joins the Revolution

NASA Astrophysics Data System (ADS)

Accomazzi, Alberto; Kurtz, Michael J.; Henneken, Edwin; Grant, Carolyn S.; Thompson, Donna M.; Chyla, Roman; Holachek, Alexandra; Sudilovsky, Vladimir; Elliott, Jonathan; Murray, Stephen S.

2015-08-01

Whether or not scholarly publications are going through an evolution or revolution, one comforting certainty remains: the NASA Astrophysics Data System (ADS) is here to help the working astronomer and librarian navigate through the increasingly complex communication environment we find ourselves in. Born as a bibliographic database, today's ADS is best described as a an "aggregator" of scholarly resources relevant to the needs of researchers in astronomy and physics. In addition to indexing content from a variety of publishers, data and software archives, the ADS enriches its records by text-mining and indexing the full-text articles, enriching its metadata through the extraction of citations and acknowledgments and the ingest of bibliographies and data links maintained by astronomy institutions and data archives. In addition, ADS generates and maintains citation and co-readership networks to support discovery and bibliometric analysis.In this talk I will summarize new and ongoing curation activities and technology developments of the ADS in the face of the ever-changing world of scholarly publishing and the trends in information-sharing behavior of astronomers. Recent curation efforts include the indexing of non-standard scholarly content (such as software packages, IVOA documents and standards, and NASA award proposals); the indexing of additional content (full-text of articles, acknowledgments, affiliations, ORCID ids); and enhanced support for bibliographic groups and data links. Recent technology developments include a new Application Programming Interface which provides access to a variety of ADS microservices, a new user interface featuring a variety of visualizations and bibliometric analysis, and integration with ORCID services to support paper claiming.

Learning from Texts: Activation of Information from Previous Texts during Reading

ERIC Educational Resources Information Center

Beker, Katinka; Jolles, Dietsje; Lorch, Robert F., Jr.; van den Broek, Paul

2016-01-01

Learning often involves integration of information from multiple texts. The aim of the current study was to determine whether relevant information from previously read texts is spontaneously activated during reading, allowing for integration between texts (experiment 1 and 2), and whether this process is related to the representation of the texts…

CHROTRAN 1.0: A mathematical and computational model for in situ heavy metal remediation in heterogeneous aquifers

NASA Astrophysics Data System (ADS)

Hansen, Scott K.; Pandey, Sachin; Karra, Satish; Vesselinov, Velimir V.

2017-12-01

Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a multi-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, chrotran, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling, and biomass death. Our software implementation handles heterogeneous flow fields, as well as arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.

In the pursuit of a semantic similarity metric based on UMLS annotations for articles in PubMed Central Open Access.

PubMed

Garcia Castro, Leyla Jael; Berlanga, Rafael; Garcia, Alexander

2015-10-01

Although full-text articles are provided by the publishers in electronic formats, it remains a challenge to find related work beyond the title and abstract context. Identifying related articles based on their abstract is indeed a good starting point; this process is straightforward and does not consume as many resources as full-text based similarity would require. However, further analyses may require in-depth understanding of the full content. Two articles with highly related abstracts can be substantially different regarding the full content. How similarity differs when considering title-and-abstract versus full-text and which semantic similarity metric provides better results when dealing with full-text articles are the main issues addressed in this manuscript. We have benchmarked three similarity metrics - BM25, PMRA, and Cosine, in order to determine which one performs best when using concept-based annotations on full-text documents. We also evaluated variations in similarity values based on title-and-abstract against those relying on full-text. Our test dataset comprises the Genomics track article collection from the 2005 Text Retrieval Conference. Initially, we used an entity recognition software to semantically annotate titles and abstracts as well as full-text with concepts defined in the Unified Medical Language System (UMLS®). For each article, we created a document profile, i.e., a set of identified concepts, term frequency, and inverse document frequency; we then applied various similarity metrics to those document profiles. We considered correlation, precision, recall, and F1 in order to determine which similarity metric performs best with concept-based annotations. For those full-text articles available in PubMed Central Open Access (PMC-OA), we also performed dispersion analyses in order to understand how similarity varies when considering full-text articles. We have found that the PubMed Related Articles similarity metric is the most suitable for full-text articles annotated with UMLS concepts. For similarity values above 0.8, all metrics exhibited an F1 around 0.2 and a recall around 0.1; BM25 showed the highest precision close to 1; in all cases the concept-based metrics performed better than the word-stem-based one. Our experiments show that similarity values vary when considering only title-and-abstract versus full-text similarity. Therefore, analyses based on full-text become useful when a given research requires going beyond title and abstract, particularly regarding connectivity across articles. Visualization available at ljgarcia.github.io/semsim.benchmark/, data available at http://dx.doi.org/10.5281/zenodo.13323. Copyright © 2015 Elsevier Inc. All rights reserved.

Enterprise Reference Library

NASA Technical Reports Server (NTRS)

Bickham, Grandin; Saile, Lynn; Havelka, Jacque; Fitts, Mary

2011-01-01

Introduction: Johnson Space Center (JSC) offers two extensive libraries that contain journals, research literature and electronic resources. Searching capabilities are available to those individuals residing onsite or through a librarian s search. Many individuals have rich collections of references, but no mechanisms to share reference libraries across researchers, projects, or directorates exist. Likewise, information regarding which references are provided to which individuals is not available, resulting in duplicate requests, redundant labor costs and associated copying fees. In addition, this tends to limit collaboration between colleagues and promotes the establishment of individual, unshared silos of information The Integrated Medical Model (IMM) team has utilized a centralized reference management tool during the development, test, and operational phases of this project. The Enterprise Reference Library project expands the capabilities developed for IMM to address the above issues and enhance collaboration across JSC. Method: After significant market analysis for a multi-user reference management tool, no available commercial tool was found to meet this need, so a software program was built around a commercial tool, Reference Manager 12 by The Thomson Corporation. A use case approach guided the requirements development phase. The premise of the design is that individuals use their own reference management software and export to SharePoint when their library is incorporated into the Enterprise Reference Library. This results in a searchable user-specific library application. An accompanying share folder will warehouse the electronic full-text articles, which allows the global user community to access full -text articles. Discussion: An enterprise reference library solution can provide a multidisciplinary collection of full text articles. This approach improves efficiency in obtaining and storing reference material while greatly reducing labor, purchasing and duplication costs. Most importantly, increasing collaboration across research groups provides unprecedented access to information relevant to NASA s mission. Conclusion: This project is an expansion and cost-effective leveraging of the existing JSC centralized library. Adding key word and author search capabilities and an alert function for notifications about new articles, based on users profiles, represent examples of future enhancements.

The Economic Impact of Adult Hearing Loss: A Systematic Review.

PubMed

Huddle, Matthew G; Goman, Adele M; Kernizan, Faradia C; Foley, Danielle M; Price, Carrie; Frick, Kevin D; Lin, Frank R

2017-10-01

Hearing impairment (HI) is highly prevalent in older adults and has been associated with adverse health outcomes. However, the overall economic impact of HI is not well described. The goal of this review was to summarize available data on all relevant costs associated with HI among adults. A literature search of PubMed, Embase, the Cochrane Library, CINAHL, and Scopus was conducted in August 2015. For this systematic review, data extraction and quality assessment were performed by 2 independent reviewers. Eligibility criteria for included studies were presence of quantitative estimation of economic impact or loss of productivity of patients with HI, full-text English-language access, and publication in an academic, peer-reviewed journal or government report prior to August 2015. This review follows the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) statement. A meta-analysis was not performed owing to the studies' heterogeneity in outcomes measures, methodology, and study country. The initial literature search yielded 4595 total references. After 2043 duplicates were removed, 2552 publications underwent title and abstract review, yielding 59 articles for full-text review. After full-text review, 25 articles were included. Of the included articles, 8 incorporated measures of disability; 5 included direct estimates of medical expenditures; 8 included other cost estimates; and 7 were related to noise-induced or work-related HI. Estimates of the economic cost of lost productivity varied widely, from $1.8 to $194 billion in the United States. Excess medical costs resulting from HI ranged from $3.3 to $12.8 billion in the United States. Hearing loss is associated with billions of dollars of excess costs in the United States, but significant variance is seen between studies. A rigorous, comprehensive estimate of the economic impact of hearing loss is needed to help guide policy decisions around the management of hearing loss in adults.

Creating and Using Culturally Sustaining Informational Texts

ERIC Educational Resources Information Center

Watanabe Kganetso, Lynne M.

2017-01-01

Current standards and assessments emphasize the importance of a variety of genres in students' literacy diets, which has placed increased attention on informational texts. Unfortunately, young students' current exposure to and experiences with informational texts are often limited by the texts' availability, quality, and relevance to children's…

A systematic review of the factors that influence the quality and effectiveness of telesupervision for health professionals.

PubMed

Martin, Priya; Lizarondo, Lucylynn; Kumar, Saravana

2018-05-01

Introduction Whilst telesupervision (clinical supervision undertaken using communication technology) is being used more frequently, there is limited information on what factors influence its effectiveness and quality. We undertook this systematic review to address this gap. Methods Eligible telesupervision studies were identified following targeted search of electronic databases and the grey literature. Data were synthesised thematically, resulting in development of core themes. Results We identified 286 papers for initial relevancy screening by title and abstract. The full text of 36 papers were then retrieved and assessed for further relevance. A total of 11 papers were included in the final analysis. We identified eight themes that contribute to effective and high-quality telesupervision: supervisee characteristics, supervisor characteristics, supervision characteristics, supervisory relationship, communication strategies, prior face-to-face contact, environmental factors and technological considerations. Conclusion From the available evidence, telesupervision can be a feasible and acceptable form of clinical supervision if set up well. Further studies with robust designs are required to strengthen the existing evidence on what makes telesupervision effective, as well as to examine its cost-effectiveness.

Supernovas y Cosmología

NASA Astrophysics Data System (ADS)

Folatelli, G.

Supernovae are very relevant astrophysical objects because they indicate the violent end of certain stars and because they alter the interstellar medium. But most importantly, they have become an extremely useful tool for measuring cosmological distances. Based on highly precise distances to type Ia supernovae it was possible to find out that the expansion of the universe is currently accelerated. This led to introducing the concept of ``dark energy'' as a dominant and yet unknown component of the cosmos. In this article we will describe the method of distance measurements that leads to the determination of cosmological parameters. We will briefly review the current status of the field with emphasis on the importance of improving our knowledge about the physical nature of supernovae. FULL TEXT IN SPANISH

Reported estimates of diagnostic accuracy in ophthalmology conference abstracts were not associated with full-text publication

PubMed Central

Korevaar, Daniël A.; Cohen, Jérémie F.; Spijker, René; Saldanha, Ian J.; Dickersin, Kay; Virgili, Gianni; Hooft, Lotty; Bossuyt, Patrick M.M.

2016-01-01

Objective To assess whether conference abstracts that report higher estimates of diagnostic accuracy are more likely to reach full-text publication in a peer-reviewed journal. Study Design and Setting We identified abstracts describing diagnostic accuracy studies, presented between 2007 and 2010 at the Association for Research in Vision and Ophthalmology (ARVO) Annual Meeting. We extracted reported estimates of sensitivity, specificity, area under the receiver operating characteristic curve (AUC), and diagnostic odds ratio (DOR). Between May and July 2015, we searched MEDLINE and EMBASE to identify corresponding full-text publications; if needed, we contacted abstract authors. Cox regression was performed to estimate associations with full-text publication, where sensitivity, specificity, and AUC were logit transformed, and DOR was log transformed. Results A full-text publication was found for 226/399 (57%) included abstracts. There was no association between reported estimates of sensitivity and full-text publication (hazard ratio [HR] 1.09 [95% confidence interval {CI} 0.98, 1.22]). The same applied to specificity (HR 1.00 [95% CI 0.88, 1.14]), AUC (HR 0.91 [95% CI 0.75, 1.09]), and DOR (HR 1.01 [95% CI 0.94, 1.09]). Conclusion Almost half of the ARVO conference abstracts describing diagnostic accuracy studies did not reach full-text publication. Studies in abstracts that mentioned higher accuracy estimates were not more likely to be reported in a full-text publication. PMID:27312228

The Effect of Text Materials with Relevant Language, Illustrations and Content Upon the Reading Achievement and Reading Preference (Attitude) of Black Primary and Intermediate Inner-City Students.

ERIC Educational Resources Information Center

Grant, Gloria W.

The purpose of this study was to examine the effect of text materials with relevant language, illustrations, and content upon the reading achievement and reading preference (attitude) of black primary and intermediate grade inner-city students. The subjects for the study were 330 black students enrolled in three schools in a large urban area. A…

DOE Research and Development Accomplishments Help

Science.gov Websites

be used to search, locate, access, and electronically download full-text research and development (R Browse Downloading, Viewing, and/or Searching Full-text Documents/Pages Searching the Database Search Features Search allows you to search the OCRed full-text document and bibliographic information, the

Where Full-Text Is Viable.

ERIC Educational Resources Information Center

Cotton, P. L.

1987-01-01

Defines two types of online databases: source, referring to those intended to be complete in themselves, whether full-text or abstracts; and bibliographic, meaning those that are not complete. Predictions are made about the future growth rate of these two types of databases, as well as full-text versus abstract databases. (EM)

Searching Harvard Business Review Online. . . Lessons in Searching a Full Text Database.

ERIC Educational Resources Information Center

Tenopir, Carol

1985-01-01

This article examines the Harvard Business Review Online (HBRO) database (bibliographic description fields, abstracts, extracted information, full text, subject descriptors) and reports on 31 sample HBRO searches conducted in Bibliographic Retrieval Services to test differences between searching full text and searching bibliographic record. Sample…

Sub-diffusive scattering parameter maps recovered using wide-field high-frequency structured light imaging.

PubMed

Kanick, Stephen Chad; McClatchy, David M; Krishnaswamy, Venkataramanan; Elliott, Jonathan T; Paulsen, Keith D; Pogue, Brian W

2014-10-01

This study investigates the hypothesis that structured light reflectance imaging with high spatial frequency patterns [Formula: see text] can be used to quantitatively map the anisotropic scattering phase function distribution [Formula: see text] in turbid media. Monte Carlo simulations were used in part to establish a semi-empirical model of demodulated reflectance ([Formula: see text]) in terms of dimensionless scattering [Formula: see text] and [Formula: see text], a metric of the first two moments of the [Formula: see text] distribution. Experiments completed in tissue-simulating phantoms showed that simultaneous analysis of [Formula: see text] spectra sampled at multiple [Formula: see text] in the frequency range [0.05-0.5] [Formula: see text] allowed accurate estimation of both [Formula: see text] in the relevant tissue range [0.4-1.8] [Formula: see text], and [Formula: see text] in the range [1.4-1.75]. Pilot measurements of a healthy volunteer exhibited [Formula: see text]-based contrast between scar tissue and surrounding normal skin, which was not as apparent in wide field diffuse imaging. These results represent the first wide-field maps to quantify sub-diffuse scattering parameters, which are sensitive to sub-microscopic tissue structures and composition, and therefore, offer potential for fast diagnostic imaging of ultrastructure on a size scale that is relevant to surgical applications.

An Enhanced Text-Mining Framework for Extracting Disaster Relevant Data through Social Media and Remote Sensing Data Fusion

NASA Astrophysics Data System (ADS)

Scheele, C. J.; Huang, Q.

2016-12-01

In the past decade, the rise in social media has led to the development of a vast number of social media services and applications. Disaster management represents one of such applications leveraging massive data generated for event detection, response, and recovery. In order to find disaster relevant social media data, current approaches utilize natural language processing (NLP) methods based on keywords, or machine learning algorithms relying on text only. However, these approaches cannot be perfectly accurate due to the variability and uncertainty in language used on social media. To improve current methods, the enhanced text-mining framework is proposed to incorporate location information from social media and authoritative remote sensing datasets for detecting disaster relevant social media posts, which are determined by assessing the textual content using common text mining methods and how the post relates spatiotemporally to the disaster event. To assess the framework, geo-tagged Tweets were collected for three different spatial and temporal disaster events: hurricane, flood, and tornado. Remote sensing data and products for each event were then collected using RealEarthTM. Both Naive Bayes and Logistic Regression classifiers were used to compare the accuracy within the enhanced text-mining framework. Finally, the accuracies from the enhanced text-mining framework were compared to the current text-only methods for each of the case study disaster events. The results from this study address the need for more authoritative data when using social media in disaster management applications.

Graphics in Text: A Bibliography. Monograph No. 6.

ERIC Educational Resources Information Center

Macdonald-Ross, Michael; Smith, Eleanor

This bibliography lists books and articles discussing graphic aspects of human communication. References have been selected for their relevance to the design of self-instructional texts for the adult learner; for the most part, research on younger children, on non-text media, and on non-educational texts is not included. Items are organized into…

RobotReviewer: evaluation of a system for automatically assessing bias in clinical trials.

PubMed

Marshall, Iain J; Kuiper, Joël; Wallace, Byron C

2016-01-01

To develop and evaluate RobotReviewer, a machine learning (ML) system that automatically assesses bias in clinical trials. From a (PDF-formatted) trial report, the system should determine risks of bias for the domains defined by the Cochrane Risk of Bias (RoB) tool, and extract supporting text for these judgments. We algorithmically annotated 12,808 trial PDFs using data from the Cochrane Database of Systematic Reviews (CDSR). Trials were labeled as being at low or high/unclear risk of bias for each domain, and sentences were labeled as being informative or not. This dataset was used to train a multi-task ML model. We estimated the accuracy of ML judgments versus humans by comparing trials with two or more independent RoB assessments in the CDSR. Twenty blinded experienced reviewers rated the relevance of supporting text, comparing ML output with equivalent (human-extracted) text from the CDSR. By retrieving the top 3 candidate sentences per document (top3 recall), the best ML text was rated more relevant than text from the CDSR, but not significantly (60.4% ML text rated 'highly relevant' v 56.5% of text from reviews; difference +3.9%, [-3.2% to +10.9%]). Model RoB judgments were less accurate than those from published reviews, though the difference was <10% (overall accuracy 71.0% with ML v 78.3% with CDSR). Risk of bias assessment may be automated with reasonable accuracy. Automatically identified text supporting bias assessment is of equal quality to the manually identified text in the CDSR. This technology could substantially reduce reviewer workload and expedite evidence syntheses. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

Full-Text Searching on Major Supermarket Systems: Dialog, Data-Star, and Nexis.

ERIC Educational Resources Information Center

Tenopir, Carol; Berglund, Sharon

1993-01-01

Examines the similarities, differences, and full-text features of the three most-used online systems for full-text searching in general libraries: DIALOG, Data-Star, and NEXIS. Overlapping databases, unique sources, search features, proximity operators, set building, language enhancement and word equivalencies, and display features are discussed.…

About / FAQ | DOE PAGES

Science.gov Websites

: + Advanced Search × Advanced Search All Fields: Title: Full Text: Bibliographic Data: Creator / Author: Name discoverable at no charge to users. DOE PAGES offers free public access to the best available full-text version and distributed content, with PAGES maintaining a permanent archive of all full text and metadata. In

The Weaknesses of Full-Text Searching

ERIC Educational Resources Information Center

Beall, Jeffrey

2008-01-01

This paper provides a theoretical critique of the deficiencies of full-text searching in academic library databases. Because full-text searching relies on matching words in a search query with words in online resources, it is an inefficient method of finding information in a database. This matching fails to retrieve synonyms, and it also retrieves…

75 FR 55267 - Airspace Designations; Incorporation By Reference

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-10

... airspace listings in FAA Order 7400.9T in full text as proposed rule documents in the Federal Register. Likewise, all amendments of these listings were published in full text as final rules in the Federal... Order 7400.9U in full text as proposed rule documents in the Federal Register. Likewise, all amendments...

76 FR 53328 - Airspace Designations; Incorporation by Reference

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-26

... proposed changes of the airspace listings in FAA Order 7400.9U in full text as proposed rule documents in the Federal Register. Likewise, all amendments of these listings were published in full text as final... the airspace listings in FAA Order 7400.9V in full text as proposed rule documents in the Federal...

Agreement among readers on what is relevant in self-help psychology books.

PubMed

Forest, James J; Del Ben, Kevin; Toews, Stuart B

2003-12-01

It was hypothesized that text marking in self-help psychology books would indicate that readers agree on which pages and lines contain relevant information. Previously owned copies of two self-help book titles (n=48, n=38), all with marked text, were collected from second-hand book stores and scored for line and page marking. Chi-squares for goodness-of-fit yielded significant differences between observed and chance agreement in marking behavior. Intraclass and KR-20 correlations were significantly different from zero, suggesting that readers agreed on what information was relevant and irrelevant. Actual users of self-help books may have similar standards because of cultural values, social group relations, or common problem experiences.

Keyword extraction by entropy difference between the intrinsic and extrinsic mode

NASA Astrophysics Data System (ADS)

Yang, Zhen; Lei, Jianjun; Fan, Kefeng; Lai, Yingxu

2013-10-01

This paper proposes a new metric to evaluate and rank the relevance of words in a text. The method uses the Shannon’s entropy difference between the intrinsic and extrinsic mode, which refers to the fact that relevant words significantly reflect the author’s writing intention, i.e., their occurrences are modulated by the author’s purpose, while the irrelevant words are distributed randomly in the text. By using The Origin of Species by Charles Darwin as a representative text sample, the performance of our detector is demonstrated and compared to previous proposals. Since a reference text “corpus” is all of an author’s writings, books, papers, etc. his collected works is not needed. Our approach is especially suitable for single documents of which there is no a priori information available.

An Experiment Comparing Lexical and Statistical Methods for Extracting MeSH Terms from Clinical Free Text

PubMed Central

Cooper, Gregory F.; Miller, Randolph A.

1998-01-01

Abstract Objective: A primary goal of the University of Pittsburgh's 1990-94 UMLS-sponsored effort was to develop and evaluate PostDoc (a lexical indexing system) and Pindex (a statistical indexing system) comparatively, and then in combination as a hybrid system. Each system takes as input a portion of the free text from a narrative part of a patient's electronic medical record and returns a list of suggested MeSH terms to use in formulating a Medline search that includes concepts in the text. This paper describes the systems and reports an evaluation. The intent is for this evaluation to serve as a step toward the eventual realization of systems that assist healthcare personnel in using the electronic medical record to construct patient-specific searches of Medline. Design: The authors tested the performances of PostDoc, Pindex, and a hybrid system, using text taken from randomly selected clinical records, which were stratified to include six radiology reports, six pathology reports, and six discharge summaries. They identified concepts in the clinical records that might conceivably be used in performing a patient-specific Medline search. Each system was given the free text of each record as an input. The extent to which a system-derived list of MeSH terms captured the relevant concepts in these documents was determined based on blinded assessments by the authors. Results: PostDoc output a mean of approximately 19 MeSH terms per report, which included about 40% of the relevant report concepts. Pindex output a mean of approximately 57 terms per report and captured about 45% of the relevant report concepts. A hybrid system captured approximately 66% of the relevant concepts and output about 71 terms per report. Conclusion: The outputs of PostDoc and Pindex are complementary in capturing MeSH terms from clinical free text. The results suggest possible approaches to reduce the number of terms output while maintaining the percentage of terms captured, including the use of UMLS semantic types to constrain the output list to contain only clinically relevant MeSH terms. PMID:9452986

Toward a definition of competency-based education in medicine: a systematic review of published definitions.

PubMed

Frank, Jason R; Mungroo, Rani; Ahmad, Yasmine; Wang, Mimi; De Rossi, Stefanie; Horsley, Tanya

2010-01-01

Competency-based education (CBE) has emerged in the health professions to address criticisms of contemporary approaches to training. However, the literature has no clear, widely accepted definition of CBE that furthers innovation, debate, and scholarship in this area. To systematically review CBE-related literature in order to identify key terms and constructs to inform the development of a useful working definition of CBE for medical education. We searched electronic databases and supplemented searches by using authors' files, checking reference lists, contacting relevant organizations and conducting Internet searches. Screening was carried out by duplicate assessment, and disagreements were resolved by consensus. We included any English- or French-language sources that defined competency-based education. Data were analyzed qualitatively and summarized descriptively. We identified 15,956 records for initial relevancy screening by title and abstract. The full text of 1,826 records was then retrieved and assessed further for relevance. A total of 173 records were analyzed. We identified 4 major themes (organizing framework, rationale, contrast with time, and implementing CBE) and 6 sub-themes (outcomes defined, curriculum of competencies, demonstrable, assessment, learner-centred and societal needs). From these themes, a new definition of CBE was synthesized. This is the first comprehensive systematic review of the medical education literature related to CBE definitions. The themes and definition identified should be considered by educators to advance the field.

The Interaction of Knowledge and Text Structure on the Ability to Identify Main Ideas in Texts. Content Knowledge and Reading Comprehension.

ERIC Educational Resources Information Center

Day, Jeanne D.; Engelhardt, Jean

Two studies examined how the factors of content-relevant knowledge and text organization influence students' abilities to study and to remember text information. The first experiment examined the effect of prior content knowledge on students' ability to identify important information in the text. Forty 7th- and forty 11th-grade students, experts…

High-performance information search filters for acute kidney injury content in PubMed, Ovid Medline and Embase.

PubMed

Hildebrand, Ainslie M; Iansavichus, Arthur V; Haynes, R Brian; Wilczynski, Nancy L; Mehta, Ravindra L; Parikh, Chirag R; Garg, Amit X

2014-04-01

We frequently fail to identify articles relevant to the subject of acute kidney injury (AKI) when searching the large bibliographic databases such as PubMed, Ovid Medline or Embase. To address this issue, we used computer automation to create information search filters to better identify articles relevant to AKI in these databases. We first manually reviewed a sample of 22 992 full-text articles and used prespecified criteria to determine whether each article contained AKI content or not. In the development phase (two-thirds of the sample), we developed and tested the performance of >1.3-million unique filters. Filters with high sensitivity and high specificity for the identification of AKI articles were then retested in the validation phase (remaining third of the sample). We succeeded in developing and validating high-performance AKI search filters for each bibliographic database with sensitivities and specificities in excess of 90%. Filters optimized for sensitivity reached at least 97.2% sensitivity, and filters optimized for specificity reached at least 99.5% specificity. The filters were complex; for example one PubMed filter included >140 terms used in combination, including 'acute kidney injury', 'tubular necrosis', 'azotemia' and 'ischemic injury'. In proof-of-concept searches, physicians found more articles relevant to topics in AKI with the use of the filters. PubMed, Ovid Medline and Embase can be filtered for articles relevant to AKI in a reliable manner. These high-performance information filters are now available online and can be used to better identify AKI content in large bibliographic databases.

Teaching ethics and professionalism in plastic surgery: a systematic review.

PubMed

de Blacam, Catherine; Vercler, Christian J

2014-04-01

Maintenance of the highest ethical and professional standards in plastic surgery is in the best interests of our profession and the public whom we serve. Both the American Board of Medical Specialties and the Accreditation Council on Graduate Medical Education mandate training in ethics and professionalism for all residents. Presently there is no gold standard in ethics and professionalism education. A systematic review on teaching ethics and professionalism in plastic surgery was performed for all articles from inception to May 23, 2013 in MEDLINE, Scopus, EMBASE, CENTRAL, and ERIC. References of relevant publications were searched for additional papers. Key journals were hand searched and relevant conference proceedings were also reviewed. Duplicate and non-English articles were excluded. Inclusion and exclusion criteria were applied to find articles that described a curriculum in ethics and/or professionalism in plastic surgery. Two hundred twenty-seven relevant articles were identified. One hundred seventy-four did not meet inclusion criteria based on screening of the title, and 39 of those did not meet inclusion criteria based on screening of the abstract or introductory paragraph. Of the 14 identified for full text review, only 2 articles described a set curriculum in ethics and/or professionalism in plastic surgery training and reported outcomes. A paucity of data exists regarding the structure, content, or relevant measures that can be applied to assess outcomes of a curriculum to teach ethics and professionalism to plastic surgery trainees. Endeavors to teach ethics and professionalism to plastic surgery trainees must rigorously document the process and outcomes to facilitate the maintenance of our profession.

GeoDeepDive: Towards a Machine Reading-Ready Digital Library and Information Integration Resource

NASA Astrophysics Data System (ADS)

Husson, J. M.; Peters, S. E.; Livny, M.; Ross, I.

2015-12-01

Recent developments in machine reading and learning approaches to text and data mining hold considerable promise for accelerating the pace and quality of literature-based data synthesis, but these advances have outpaced even basic levels of access to the published literature. For many geoscience domains, particularly those based on physical samples and field-based descriptions, this limitation is significant. Here we describe a general infrastructure to support published literature-based machine reading and learning approaches to information integration and knowledge base creation. This infrastructure supports rate-controlled automated fetching of original documents, along with full bibliographic citation metadata, from remote servers, the secure storage of original documents, and the utilization of considerable high-throughput computing resources for the pre-processing of these documents by optical character recognition, natural language parsing, and other document annotation and parsing software tools. New tools and versions of existing tools can be automatically deployed against original documents when they are made available. The products of these tools (text/XML files) are managed by MongoDB and are available for use in data extraction applications. Basic search and discovery functionality is provided by ElasticSearch, which is used to identify documents of potential relevance to a given data extraction task. Relevant files derived from the original documents are then combined into basic starting points for application building; these starting points are kept up-to-date as new relevant documents are incorporated into the digital library. Currently, our digital library stores contains more than 360K documents supplied by Elsevier and the USGS and we are actively seeking additional content providers. By focusing on building a dependable infrastructure to support the retrieval, storage, and pre-processing of published content, we are establishing a foundation for complex, and continually improving, information integration and data extraction applications. We have developed one such application, which we present as an example, and invite new collaborations to develop other such applications.

Support Vector Machines: Relevance Feedback and Information Retrieval.

ERIC Educational Resources Information Center

Drucker, Harris; Shahrary, Behzad; Gibbon, David C.

2002-01-01

Compares support vector machines (SVMs) to Rocchio, Ide regular and Ide dec-hi algorithms in information retrieval (IR) of text documents using relevancy feedback. If the preliminary search is so poor that one has to search through many documents to find at least one relevant document, then SVM is preferred. Includes nine tables. (Contains 24…

Full-Text Linking: Affiliated versus Nonaffiliated Access in a Free Database.

ERIC Educational Resources Information Center

Grogg, Jill E.; Andreadis, Debra K.; Kirk, Rachel A.

2002-01-01

Presents a comparison of access to full-text articles from a free bibliographic database (PubSCIENCE) for affiliated and unaffiliated users. Found that affiliated users had access to more full-text articles than unaffiliated users had, and that both types of users could increase their level of access through additional searching and greater…

77 FR 50907 - Airspace Designations; Incorporation by Reference

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-23

... FAA processed all proposed changes of the airspace listings in FAA Order 7400.9V in full text as... in full text as final rules in the Federal Register. This rule reflects the periodic integration of... changes of the airspace listings in FAA Order 7400.9W in full text as proposed rule documents in the...

78 FR 52847 - Airspace Designations; Incorporation by Reference

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-27

... FAA processed all proposed changes of the airspace listings in FAA Order 7400.9W in full text as... in full text as final rules in the Federal Register. This rule reflects the periodic integration of... changes of the airspace listings in FAA Order 7400.9X in full text as proposed rule documents in the...

Full Text Psychology Journals Available from Popular Library Databases

ERIC Educational Resources Information Center

Joswick, Kathleen E.

2006-01-01

The author identified 433 core journals in psychology and investigated their full text availability in popular databases. While 62 percent of the studied journals were available in at least one database, access from individual databases ranged from 1.4 percent to 38.1 percent of the titles. The full text of influential psychology journals is not…

78 FR 48404 - Defense Federal Acquisition Regulation Supplement: Clauses With Alternates-Contract Financing...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-08

... as well as the alternate. In addition, the proposed rule would include the full text of the clause.... The inclusion of the full text of each clause alternate aims to make the terms of a clause alternate... conditions easier to read and understand. By placing alternates in full text, all paragraph substitutions...

Accessing Biomedical Literature in the Current Information Landscape

PubMed Central

Khare, Ritu; Leaman, Robert; Lu, Zhiyong

2015-01-01

i. Summary Biomedical and life sciences literature is unique because of its exponentially increasing volume and interdisciplinary nature. Biomedical literature access is essential for several types of users including biomedical researchers, clinicians, database curators, and bibliometricians. In the past few decades, several online search tools and literature archives, generic as well as biomedicine-specific, have been developed. We present this chapter in the light of three consecutive steps of literature access: searching for citations, retrieving full-text, and viewing the article. The first section presents the current state of practice of biomedical literature access, including an analysis of the search tools most frequently used by the users, including PubMed, Google Scholar, Web of Science, Scopus, and Embase, and a study on biomedical literature archives such as PubMed Central. The next section describes current research and the state-of-the-art systems motivated by the challenges a user faces during query formulation and interpretation of search results. The research solutions are classified into five key areas related to text and data mining, text similarity search, semantic search, query support, relevance ranking, and clustering results. Finally, the last section describes some predicted future trends for improving biomedical literature access, such as searching and reading articles on portable devices, and adoption of the open access policy. PMID:24788259

Mining of relations between proteins over biomedical scientific literature using a deep-linguistic approach.

PubMed

Rinaldi, Fabio; Schneider, Gerold; Kaljurand, Kaarel; Hess, Michael; Andronis, Christos; Konstandi, Ourania; Persidis, Andreas

2007-02-01

The amount of new discoveries (as published in the scientific literature) in the biomedical area is growing at an exponential rate. This growth makes it very difficult to filter the most relevant results, and thus the extraction of the core information becomes very expensive. Therefore, there is a growing interest in text processing approaches that can deliver selected information from scientific publications, which can limit the amount of human intervention normally needed to gather those results. This paper presents and evaluates an approach aimed at automating the process of extracting functional relations (e.g. interactions between genes and proteins) from scientific literature in the biomedical domain. The approach, using a novel dependency-based parser, is based on a complete syntactic analysis of the corpus. We have implemented a state-of-the-art text mining system for biomedical literature, based on a deep-linguistic, full-parsing approach. The results are validated on two different corpora: the manually annotated genomics information access (GENIA) corpus and the automatically annotated arabidopsis thaliana circadian rhythms (ATCR) corpus. We show how a deep-linguistic approach (contrary to common belief) can be used in a real world text mining application, offering high-precision relation extraction, while at the same time retaining a sufficient recall.

MeSH indexing based on automatically generated summaries.

PubMed

Jimeno-Yepes, Antonio J; Plaza, Laura; Mork, James G; Aronson, Alan R; Díaz, Alberto

2013-06-26

MEDLINE citations are manually indexed at the U.S. National Library of Medicine (NLM) using as reference the Medical Subject Headings (MeSH) controlled vocabulary. For this task, the human indexers read the full text of the article. Due to the growth of MEDLINE, the NLM Indexing Initiative explores indexing methodologies that can support the task of the indexers. Medical Text Indexer (MTI) is a tool developed by the NLM Indexing Initiative to provide MeSH indexing recommendations to indexers. Currently, the input to MTI is MEDLINE citations, title and abstract only. Previous work has shown that using full text as input to MTI increases recall, but decreases precision sharply. We propose using summaries generated automatically from the full text for the input to MTI to use in the task of suggesting MeSH headings to indexers. Summaries distill the most salient information from the full text, which might increase the coverage of automatic indexing approaches based on MEDLINE. We hypothesize that if the results were good enough, manual indexers could possibly use automatic summaries instead of the full texts, along with the recommendations of MTI, to speed up the process while maintaining high quality of indexing results. We have generated summaries of different lengths using two different summarizers, and evaluated the MTI indexing on the summaries using different algorithms: MTI, individual MTI components, and machine learning. The results are compared to those of full text articles and MEDLINE citations. Our results show that automatically generated summaries achieve similar recall but higher precision compared to full text articles. Compared to MEDLINE citations, summaries achieve higher recall but lower precision. Our results show that automatic summaries produce better indexing than full text articles. Summaries produce similar recall to full text but much better precision, which seems to indicate that automatic summaries can efficiently capture the most important contents within the original articles. The combination of MEDLINE citations and automatically generated summaries could improve the recommendations suggested by MTI. On the other hand, indexing performance might be dependent on the MeSH heading being indexed. Summarization techniques could thus be considered as a feature selection algorithm that might have to be tuned individually for each MeSH heading.

A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

PubMed Central

Miwa, Makoto; Ohta, Tomoko; Rak, Rafal; Rowley, Andrew; Kell, Douglas B.; Pyysalo, Sampo; Ananiadou, Sophia

2013-01-01

Motivation: To create, verify and maintain pathway models, curators must discover and assess knowledge distributed over the vast body of biological literature. Methods supporting these tasks must understand both the pathway model representations and the natural language in the literature. These methods should identify and order documents by relevance to any given pathway reaction. No existing system has addressed all aspects of this challenge. Method: We present novel methods for associating pathway model reactions with relevant publications. Our approach extracts the reactions directly from the models and then turns them into queries for three text mining-based MEDLINE literature search systems. These queries are executed, and the resulting documents are combined and ranked according to their relevance to the reactions of interest. We manually annotate document-reaction pairs with the relevance of the document to the reaction and use this annotation to study several ranking methods, using various heuristic and machine-learning approaches. Results: Our evaluation shows that the annotated document-reaction pairs can be used to create a rule-based document ranking system, and that machine learning can be used to rank documents by their relevance to pathway reactions. We find that a Support Vector Machine-based system outperforms several baselines and matches the performance of the rule-based system. The success of the query extraction and ranking methods are used to update our existing pathway search system, PathText. Availability: An online demonstration of PathText 2 and the annotated corpus are available for research purposes at http://www.nactem.ac.uk/pathtext2/. Contact: makoto.miwa@manchester.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23813008

Implementing DSpace at NASA Langley Research Center

NASA Technical Reports Server (NTRS)

Lowe, Greta

2007-01-01

This presentation looks at the implementation of the DSpace institutional repository system at the NASA Langley Technical Library. NASA Langley Technical Library implemented DSpace software as a replacement for the Langley Technical Report Server (LTRS). DSpace was also used to develop the Langley Technical Library Digital Repository (LTLDR). LTLDR contains archival copies of core technical reports in the aeronautics area dating back to the NACA era and other specialized collections relevant to the NASA Langley community. Extensive metadata crosswalks were created to facilitate moving data from various systems and formats to DSpace. The Dublin Core metadata screens were also customized. The OpenURL standard and Ex Libris Metalib are being used in this environment to assist our customers with either discovering full-text content or with initiating a request for the item.

Social Media Use Among Nurses: Literature Review.

PubMed

Cordoş, Ariana Anamaria; Bolboacă, Sorana D

2016-01-01

The scope of the research was to increase the understanding of social media's influence among nurses while highlighting gaps in the literature and areas for further research. The search of PubMed database was performed in November 2015, using terms to identify peer-reviewed articles that describe the use of social media for nursing students or nurse practitioners. A systematic approach was used to retrieve papers and extract relevant data. There were identified 23 full text articles involving social media and nurse-related terminology. The majority of the studies were interventional (n = 20) that assessed social media as a teaching tool. Podcasts, Multiplayer virtual worlds and mixed social media platforms has also been assessed. Social media is used as a tool of information for nurses mainly as the means for engaging and communicating.

Integrating GPCR-specific information with full text articles

PubMed Central

2011-01-01

Background With the continued growth in the volume both of experimental G protein-coupled receptor (GPCR) data and of the related peer-reviewed literature, the ability of GPCR researchers to keep up-to-date is becoming increasingly curtailed. Results We present work that integrates the biological data and annotations in the GPCR information system (GPCRDB) with next-generation methods for intelligently exploring, visualising and interacting with the scientific articles used to disseminate them. This solution automatically retrieves relevant information from GPCRDB and displays it both within and as an adjunct to an article. Conclusions This approach allows researchers to extract more knowledge more swiftly from literature. Importantly, it allows reinterpretation of data in articles published before GPCR structure data became widely available, thereby rescuing these valuable data from long-dormant sources. PMID:21910883

78 FR 11815 - Creation of a New Computer Matching Program That Will Expire on August 13, 2014

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-20

... Applications, SSA/OEEAS, 60-0058, full text published at 71 FR 1815 (January 11, 2006); the Master Beneficiary Record, SSA/ ORSIS 60-0090, full text published at 71 FR 1826 (January 11, 2006); and Supplemental Security Income and Special Veterans Benefits SSA/ ODSSIS, 60-0103, full text published at 71 FR 1826...

Text Structure and Retention of Prose.

ERIC Educational Resources Information Center

Zimmer, John W.

1985-01-01

The effects of text structure were studied using two kinds of reading materials: a standard text with headings and illustrations, as well as a nonstructured manuscript. The manuscript readers scored higher on delayed tests, generated more relevant ideas, and wrote better essays both immediately and after a delay. (Author/GDC)

Text Mining Effectively Scores and Ranks the Literature for Improving Chemical-Gene-Disease Curation at the Comparative Toxicogenomics Database

PubMed Central

Johnson, Robin J.; Lay, Jean M.; Lennon-Hopkins, Kelley; Saraceni-Richards, Cynthia; Sciaky, Daniela; Murphy, Cynthia Grondin; Mattingly, Carolyn J.

2013-01-01

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a public resource that curates interactions between environmental chemicals and gene products, and their relationships to diseases, as a means of understanding the effects of environmental chemicals on human health. CTD provides a triad of core information in the form of chemical-gene, chemical-disease, and gene-disease interactions that are manually curated from scientific articles. To increase the efficiency, productivity, and data coverage of manual curation, we have leveraged text mining to help rank and prioritize the triaged literature. Here, we describe our text-mining process that computes and assigns each article a document relevancy score (DRS), wherein a high DRS suggests that an article is more likely to be relevant for curation at CTD. We evaluated our process by first text mining a corpus of 14,904 articles triaged for seven heavy metals (cadmium, cobalt, copper, lead, manganese, mercury, and nickel). Based upon initial analysis, a representative subset corpus of 3,583 articles was then selected from the 14,094 articles and sent to five CTD biocurators for review. The resulting curation of these 3,583 articles was analyzed for a variety of parameters, including article relevancy, novel data content, interaction yield rate, mean average precision, and biological and toxicological interpretability. We show that for all measured parameters, the DRS is an effective indicator for scoring and improving the ranking of literature for the curation of chemical-gene-disease information at CTD. Here, we demonstrate how fully incorporating text mining-based DRS scoring into our curation pipeline enhances manual curation by prioritizing more relevant articles, thereby increasing data content, productivity, and efficiency. PMID:23613709

DataToText: A Consumer-Oriented Approach to Data Analysis

ERIC Educational Resources Information Center

Kenny, David A.

2010-01-01

DataToText is a project developed where the user communicates the relevant information for an analysis and DataToText computer routine produces text output that describes in words, tables, and figures the results from the analyses. Two extended examples are given, one an example of a moderator analysis and the other an example of a dyadic data…

Approaches to teach evidence-based practice among health professionals: an overview of the existing evidence.

PubMed

Patelarou, Athina E; Kyriakoulis, Konstantinos G; Stamou, Aliki A; Laliotis, Aggelos; Sifaki-Pistolla, Dimitra; Matalliotakis, Michail; Prokopakis, Emmanuel; Patelarou, Evridiki

2017-01-01

Health care professionals' adoption of evidence-based practice (EBP) remains limited, although most health care professionals are familiar with EBP and believe in its value. This systematic review aimed to bring together the best methods used to teach EBP to health professionals. The authors conducted a systematic search for the period 2005-2015 (an update of the search took place in October 2016) using PubMed interface (Medline). MeSH terms as well as free-text keywords were used. Studies were analyzed and evaluated by title and abstract. Those studies which fulfilled the inclusion criteria were assessed by full text. References of articles were also taken into consideration for identifying relevant studies not found through algorithm search. Twenty articles were found to be relevant. The majority of the studies were conducted among nurses (n=7) and physicians (n=6), and only a few among professionals from mixed disciplines (n=5). Two studies were conducted among chiropractors (n=1) and faculty members from a naturopathic and classical Chinese medicine institution (n=1). Researchers used a variety of different approaches, which varied with respect to duration and organization. We divided interventions into two categories. Single interventions included either a workshop, or a journal club, or a conference, or a lecture, or online learning tools, whereas multiple interventions included a combination of these approaches. An increase in EBP competencies and attitudes was reported in nine studies. Teaching methods for optimizing EBP among health professionals could become a robust standardized procedure of the medical educational curricula and lifelong learning of health care professionals.

Exploring the views and experiences of HIV positive patients treated for cancer: a systematic review of the literature.

PubMed

Hainsworth, Emma G; Shahmanesh, Maryam; Stevenson, Fiona

2018-05-01

A systematic review of the literature was conducted to find out what is known about patients' experiences of a dual diagnosis of HIV and cancer. We systematically searched the following databases; MEDLINE (Ovid Version); CINAHL Plus; PsycINFO and EMBASE from inception to June 2016 for studies that included patients with a dual diagnosis of cancer and HIV and focused on patient experiences. Studies with a focus on one illness rather than a dual diagnosis, those that focused on treatment strategies and medical management, epidemiology and pathology studies and comparison studies were all excluded. The full text of the included studies were reviewed. Information on location, sample size, study design and a narrative summary of findings were extracted using a standardised format. Studies were combined thematically. 1777 records were screened by title and abstract using the selection criteria described in the methods. Eight records were reviewed in depth in full text and seven selected as eligible. The selected studies suggest that a dual diagnosis of HIV and cancer has a powerful impact on individuals' behaviour. The experience of stigma was a consistent factor in all patient accounts and the strategy of selective disclosure to access support reveals how patient agency can interplay with stigma. This is an area largely unexplored in the published literature; further research into patients' experiences of a dual diagnosis of HIV and cancer will provide relevant knowledge in order to tailor and improve services.

Commercial Database Design vs. Library Terminology Comprehension: Why Do Students Print Abstracts Instead of Full-Text Articles?

ERIC Educational Resources Information Center

Imler, Bonnie; Eichelberger, Michelle

2014-01-01

When asked to print the full text of an article, many undergraduate college students print the abstract instead of the full text. This study seeks to determine the underlying cause(s) of this confusion. In this quantitative study, participants (n = 40) performed five usability tasks to assess ease of use and usefulness of five commercial library…

Development of a full-text information retrieval system

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

Keizo Oyama; AKira Miyazawa, Atsuhiro Takasu; Kouji Shibano

The authors have executed a project to realize a full-text information retrieval system. The system is designed to deal with a document database comprising full text of a large number of documents such as academic papers. The document structures are utilized in searching and extracting appropriate information. The concept of structure handling and the configuration of the system are described in this paper.

Effect of Direction, Text Organization, and Age Level on Reading Comprehension.

ERIC Educational Resources Information Center

Lindsey, Jimmy D.

1980-01-01

Concludes that teacher guidance affects learning disabled students' recall and comprehension of goal-relevant information but that neither text organization nor age level is associated with degree of recall and comprehension. (FL)

Relevance of Non-communicable Comorbidities for the Development of the Severe Forms of Dengue: A Systematic Literature Review.

PubMed

Toledo, Joao; George, Leyanna; Martinez, Eric; Lazaro, Adhara; Han, Wai Wai; Coelho, Giovanini E; Runge Ranzinger, Silvia; Horstick, Olaf

2016-01-01

Patients with dengue fever and comorbidities seem to be at higher risk of developing complications and/or severe dengue compared to healthier individuals. This study systematically reviews the evidence related to comorbidities and dengue. A systematic literature review was performed in five databases (EMBASE, PUBMED, Global Health, SciELO, Cochrane) and grey literature for full-text articles since its inceptions until October 10, 2015. A total of 230 articles were retrieved. Sixteen studies were analysed after applying all inclusion and exclusion criteria. Seven case control studies and nine retrospective cohort studies showed that comorbidities may contribute to severe dengue, especially 1) cardiovascular disease, 2) stroke, 3) diabetes, 4) respiratory disease and 5) renal disease, as well as old age. However, due to heterogeneity in studies, the real estimate effect of comorbidities as modifiers of dengue severity could not be established. Further research in regions with high prevalence of dengue infection would contribute to a better understanding of the relevance of comorbidities in severe dengue, especially with a standardised protocol, for outcomes, specific comorbidities, study design-best using prospective designs-and sample sizes.

Enhanced quality and quantity of retrieval of Critically Appraised Topics using the CAT Crawler.

PubMed

Dong, P; Mondry, A

2004-03-01

As healthcare moves towards the implementation of Evidence-Based Medicine (EBM), Critically Appraised Topics (CATs) become useful in helping physicians to make clinical decisions. A number of academic and healthcare organizations have set up web-based CAT libraries. The primary objective of the presented work is to provide a one-stop search and download site that allows access to multiple CAT libraries. A web-based application, namely the CAT Crawler, was developed to serve physicians with an adequate access to available appraised topics on the Internet. Important information is extracted automatically and regularly from CAT websites, and consolidated by checking the uniqueness and availability. The principle of meta-search is incorporated into the implementation of the search engine, which finds relevant topics following keyword input. The retrieved result directs the physician to the original resource page. A full-text article of a particular topic can be converted into a proper format for downloading to Personal Digital Assistant (PDA) devices. In summary, the application provides physicians with a common interface to retrieve relevant CATs on particular clinical topics from multiple resources, and thus speeds up the decision making process.

A Knowledge Discovery framework for Planetary Defense

NASA Astrophysics Data System (ADS)

Jiang, Y.; Yang, C. P.; Li, Y.; Yu, M.; Bambacus, M.; Seery, B.; Barbee, B.

2016-12-01

Planetary Defense, a project funded by NASA Goddard and the NSF, is a multi-faceted effort focused on the mitigation of Near Earth Object (NEO) threats to our planet. Currently, there exists a dispersion of information concerning NEO's amongst different organizations and scientists, leading to a lack of a coherent system of information to be used for efficient NEO mitigation. In this paper, a planetary defense knowledge discovery engine is proposed to better assist the development and integration of a NEO responding system. Specifically, we have implemented an organized information framework by two means: 1) the development of a semantic knowledge base, which provides a structure for relevant information. It has been developed by the implementation of web crawling and natural language processing techniques, which allows us to collect and store the most relevant structured information on a regular basis. 2) the development of a knowledge discovery engine, which allows for the efficient retrieval of information from our knowledge base. The knowledge discovery engine has been built on the top of Elasticsearch, an open source full-text search engine, as well as cutting-edge machine learning ranking and recommendation algorithms. This proposed framework is expected to advance the knowledge discovery and innovation in planetary science domain.

A Systematic Review of the Causes and Management of Ischaemic Stroke Caused by Nontissue Emboli

PubMed Central

Judge, Ciaran; Mello, Sarah; Bradley, David

2017-01-01

Introduction The inadvertent or purposeful introduction of foreign bodies or substances can lead to cerebral infarction if they embolize to the brain. Individual reports of these events are uncommon but may increase with the increased occurrences of their risk factors, for example, intra-arterial procedures. Method We searched EMBASE and MEDLINE for articles on embolic stroke of nontissue origin. 1889 articles were identified and screened and 216 articles were ultimately reviewed in full text and included in qualitative analysis. Articles deemed relevant were assessed by a second reviewer to confirm compatibility with the inclusion criteria. References of included articles were reviewed for relevant publications. We categorized the pathology of the emboli into the following groups: air embolism (141 reports), other arterial gas embolisms (49 reports), missiles and foreign bodies (16 reports), and others, including drug embolism, cotton wool, and vascular sclerosant agents. Conclusion Air and gaseous embolism are becoming more common with increased use of interventional medical procedures and increased popularity of sports such as diving. There is increasing evidence for the use of hyperbaric oxygen for such events. Causes of solid emboli are diverse. More commonly reported causes include bullets, missiles, and substances used in medical procedures. PMID:29123937

A Systematic Review of the Causes and Management of Ischaemic Stroke Caused by Nontissue Emboli.

PubMed

Judge, Ciaran; Mello, Sarah; Bradley, David; Harbison, Joseph

2017-01-01

The inadvertent or purposeful introduction of foreign bodies or substances can lead to cerebral infarction if they embolize to the brain. Individual reports of these events are uncommon but may increase with the increased occurrences of their risk factors, for example, intra-arterial procedures. We searched EMBASE and MEDLINE for articles on embolic stroke of nontissue origin. 1889 articles were identified and screened and 216 articles were ultimately reviewed in full text and included in qualitative analysis. Articles deemed relevant were assessed by a second reviewer to confirm compatibility with the inclusion criteria. References of included articles were reviewed for relevant publications. We categorized the pathology of the emboli into the following groups: air embolism (141 reports), other arterial gas embolisms (49 reports), missiles and foreign bodies (16 reports), and others, including drug embolism, cotton wool, and vascular sclerosant agents. Air and gaseous embolism are becoming more common with increased use of interventional medical procedures and increased popularity of sports such as diving. There is increasing evidence for the use of hyperbaric oxygen for such events. Causes of solid emboli are diverse. More commonly reported causes include bullets, missiles, and substances used in medical procedures.

Interventions to tackle malnutrition and its risk factors in children living in slums: a scoping review.

PubMed

Goudet, Sophie; Griffiths, Paula; Bogin, Barry; Madise, Nyovani

2017-02-01

Children living in slums are at high risk of being malnourished. There are no published reviews on existing interventions promoting better nutrition for children living in slums and the risk factors for children's malnutrition. Improved understanding of the risk factors for malnutrition in slums communities and the impact of interventions on children's health can provide guidance to practitioners and decision-makers. The present review is designed to provide this information. The search included 30 electronic bibliographic databases and relevant eligible studies published up to December 2013. The search located 1512 citations. Full text relevance screening was conducted on 226 studies and on abstracts for 16 studies. The final 58 unique studies included 22 on interventions and 38 on risk. All of the interventions were nutrition-specific, with nutritional intervention being the most dominant type. Seventy-three per cent of the interventions were assessed effective. The findings stressed the gaps in knowledge in terms of quality assessment and programmatic recommendations to identify children who are the most at risk of malnutrition to appropriately target interventions. Finally, the review helped to inform a systematic review (Cochrane Systematic review protocol 2015) that will examine the impact of interventions on outcome measures.

Reporting guidelines in health research: A review.

PubMed

Simon, Arun K; Rao, Ashwini; Rajesh, Gururaghavendran; Shenoy, Ramya; Pai, Mithun B

2015-01-01

Contemporary health research has come under close scrutiny, exposing alarming flaws in the reporting of research. The reporting guidelines can aid in identification of poorly reported studies and can bring transparency to health research. The guidelines also help journal editors, peer reviewers, funding agencies, and readers to better discern health research. Reporting guidelines encourage accurate and thorough reporting of fundamental aspects of health research so that the results of studies can be replicated by others. Reporting guidelines are potent tools to improve the practice of research and in reducing reporting bias. For the present review, both electronic and manual literature search was carried out. Electronic databases like PubMed, MEDLINE, EBSCO host, and Science Direct were searched for extracting relevant articles. Various key words and their combinations were used for literature search like reporting guidelines, checklist, research, publishing standards, study design, medicine, and dentistry. The search results were scrutinized for relevance to the topic and only full text articles in English were incorporated. Various reporting guidelines were identified and grouped under headings based on study design. This review article attempts to highlight the various reporting guidelines in literature relating to health research, its potential applications, and its limitations.

No. 279-Female Sexual Health Consensus Clinical Guidelines.

PubMed

Lamont, John; Bajzak, Krisztina; Bouchard, Céline; Burnett, Margaret; Byers, Sandra; Cohen, Trevor; Fisher, William; Holzapfel, Stephen; Senikas, Vyta

2018-06-01

To establish national guidelines for the assessment of women's sexual health concerns and the provision of sexual health care for women. Published literature was retrieved through searches of PubMed, CINAHL, and the Cochrane Library from May to October 2010, using appropriate controlled vocabulary (e.g., sexuality, "sexual dysfunction," "physiological," dyspareunia) and key words (e.g., sexual dysfunction, sex therapy, anorgasmia). Results were restricted, where possible, to systematic reviews, randomized control trials/controlled clinical trials, and observational studies. There were no language restrictions. Searches were updated on a regular basis and incorporated in the guideline to December 2010. Grey (unpublished) literature was identified through searching the websites of health technology assessment and health technology assessment-related agencies, clinical practice guideline collections, clinical trial registries, and national and international medical specialty societies. Each article was screened for relevance and the full text acquired if determined to be relevant. The evidence obtained was reviewed and evaluated by the members of the Expert Workgroup established by The Society of Obstetricians and Gynaecologists of Canada. The quality of evidence was evaluated and recommendations made using the use of criteria described by the Canadian Task Force on Preventive Health Care (Table). Copyright © 2018. Published by Elsevier Inc.

Learning of Multimodal Representations With Random Walks on the Click Graph.

PubMed

Wu, Fei; Lu, Xinyan; Song, Jun; Yan, Shuicheng; Zhang, Zhongfei Mark; Rui, Yong; Zhuang, Yueting

2016-02-01

In multimedia information retrieval, most classic approaches tend to represent different modalities of media in the same feature space. With the click data collected from the users' searching behavior, existing approaches take either one-to-one paired data (text-image pairs) or ranking examples (text-query-image and/or image-query-text ranking lists) as training examples, which do not make full use of the click data, particularly the implicit connections among the data objects. In this paper, we treat the click data as a large click graph, in which vertices are images/text queries and edges indicate the clicks between an image and a query. We consider learning a multimodal representation from the perspective of encoding the explicit/implicit relevance relationship between the vertices in the click graph. By minimizing both the truncated random walk loss as well as the distance between the learned representation of vertices and their corresponding deep neural network output, the proposed model which is named multimodal random walk neural network (MRW-NN) can be applied to not only learn robust representation of the existing multimodal data in the click graph, but also deal with the unseen queries and images to support cross-modal retrieval. We evaluate the latent representation learned by MRW-NN on a public large-scale click log data set Clickture and further show that MRW-NN achieves much better cross-modal retrieval performance on the unseen queries/images than the other state-of-the-art methods.

Definition of infection after fracture fixation: A systematic review of randomized controlled trials to evaluate current practice.

PubMed

Metsemakers, W J; Kortram, K; Morgenstern, M; Moriarty, T F; Meex, I; Kuehl, R; Nijs, S; Richards, R G; Raschke, M; Borens, O; Kates, S L; Zalavras, C; Giannoudis, P V; Verhofstad, M H J

2018-03-01

One of the most challenging musculoskeletal complications in modern trauma surgery is infection after fracture fixation (IAFF). Although infections are clinically obvious in many cases, a clear definition of the term IAFF is crucial, not only for the evaluation of published research data but also for the establishment of uniform treatment concepts. The aim of this systematic review was to identify the definitions used in the scientific literature to describe infectious complications after internal fixation of fractures. The hypothesis of this study was that the majority of fracture-related literature do not define IAFF. A comprehensive search was performed in Embase, Cochrane, Google Scholar, Medline (OvidSP), PubMed publisher and Web-of-Science for randomized controlled trials (RCTs) on fracture fixation. Data were collected on the definition of infectious complications after fracture fixation used in each study. Study selection was accomplished through two phases. During the first phase, titles and abstracts were reviewed for relevance, and the full texts of relevant articles were obtained. During the second phase, full-text articles were reviewed. All definitions were literally extracted and collected in a database. Then, a classification was designed to rate the quality of the description of IAFF. A total of 100 RCT's were identified in the search. Of 100 studies, only two (2%) cited a validated definition to describe IAFF. In 28 (28%) RCTs, the authors used a self-designed definition. In the other 70 RCTs, (70%) there was no description of a definition in the Methods section, although all of the articles described infections as an outcome parameter in the Results section. This systematic review shows that IAFF is not defined in a large majority of the fracture-related literature. To our knowledge, this is the first study conducted with the objective to explore this important issue. The lack of a consensus definition remains a problem in current orthopedic trauma research and treatment and this void should be addressed in the near future. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bioactive glass for dentin remineralization: A systematic review.

PubMed

Fernando, Delihta; Attik, Nina; Pradelle-Plasse, Nelly; Jackson, Phil; Grosgogeat, Brigitte; Colon, Pierre

2017-07-01

Strategies to achieve dentin remineralization is at present an important target of restorative dentistry. Remineralization of dentin by a bioactive material is complete only when the tissue regains its functionality. This is achieved when there is adequate apatite formation which most importantly translates into improved mechanical properties of dentin as a result of intrafibrillar mineralization. Bioactive glass (BAG) is a well-known implant material for bone regeneration and is proven to have excellent ability of apatite formation. Hence, recent studies have proposed BAGs as one of the most desired materials for remineralization of dentin. Therefore the aim of this systematic review was to scope the evidence of bioactive glass to remineralize dentin. The following research question was formulated: "Is there strong evidence for bioactive glass to remineralize dentin?" Three databases (Web of science, PubMed and Science direct) were scanned independently following PRISMA guidelines. Inclusion and exclusion criteria were set to identify relevant articles based on title and abstract screening. Finally, potentially relevant articles were downloaded and the full text was scrutinized to select the articles included in this review. The first phase of search returned 303 articles. A total of 19 papers with full text were scrutinized for inclusion, of which 3 papers were chosen for the final synthesis. All three studies confirm that BAG treatment leads to enhanced apatite formation in dentin. Only 1 of the 3 studies has reported the mechanical properties of dentin after BAG treatment and it revealed that the Young's modulus and flexural bend strength of BAG treated dentin were much lower than natural dentin even though they had similar apatite content. This review highlights the importance of assessing the mechanical properties of dentin alongside to the newly formed apatite content in order to prove BAGs efficiency to remineralize this tissue. Though studies have confirmed that BAGs stimulate excellent apatite formation in dentin, it should be concluded that there isn't sufficient evidence for bioactive glass to effectively remineralize this tissue as the mechanical properties of the BAG treated dentin haven't been well explored. Copyright © 2017 Elsevier B.V. All rights reserved.

Intonation Miscues and Apprehension of Text.

ERIC Educational Resources Information Center

Flippo, Rona F.

Working on the theory that intonation miscues caused by confusion over punctuation and other phrase boundaries will make the apprehension of text more difficult than necessary for young developing readers, a study reviewed the research and literature relevant to the effects of location of punctuation, phrasing, and line breaks in text and on the…

The Full Spectrum of Clinical Ethical Issues in Kidney Failure. Findings of a Systematic Qualitative Review.

PubMed

Kahrass, Hannes; Strech, Daniel; Mertz, Marcel

2016-01-01

When treating patients with kidney failure, unavoidable ethical issues often arise. Current clinical practice guidelines some of them, but lack comprehensive information about the full range of relevant ethical issues in kidney failure. A systematic literature review of such ethical issues supports medical professionalism in nephrology, and offers a solid evidential base for efforts that aim to improve ethical conduct in health care. To identify the full spectrum of clinical ethical issues that can arise for patients with kidney failure in a systematic and transparent manner. A systematic review in Medline (publications in English or German between 2000 and 2014) and Google Books (with no restrictions) was conducted. Ethical issues were identified by qualitative text analysis and normative analysis. The literature review retrieved 106 references that together mentioned 27 ethical issues in clinical care of kidney failure. This set of ethical issues was structured into a matrix consisting of seven major categories and further first and second-order categories. The systematically-derived matrix helps raise awareness and understanding of the complexity of ethical issues in kidney failure. It can be used to identify ethical issues that should be addressed in specific training programs for clinicians, clinical practice guidelines, or other types of policies dealing with kidney failure.

The Full Spectrum of Clinical Ethical Issues in Kidney Failure. Findings of a Systematic Qualitative Review

PubMed Central

Kahrass, Hannes; Strech, Daniel; Mertz, Marcel

2016-01-01

Background When treating patients with kidney failure, unavoidable ethical issues often arise. Current clinical practice guidelines some of them, but lack comprehensive information about the full range of relevant ethical issues in kidney failure. A systematic literature review of such ethical issues supports medical professionalism in nephrology, and offers a solid evidential base for efforts that aim to improve ethical conduct in health care. Aim To identify the full spectrum of clinical ethical issues that can arise for patients with kidney failure in a systematic and transparent manner. Method A systematic review in Medline (publications in English or German between 2000 and 2014) and Google Books (with no restrictions) was conducted. Ethical issues were identified by qualitative text analysis and normative analysis. Results The literature review retrieved 106 references that together mentioned 27 ethical issues in clinical care of kidney failure. This set of ethical issues was structured into a matrix consisting of seven major categories and further first and second-order categories. Conclusions The systematically-derived matrix helps raise awareness and understanding of the complexity of ethical issues in kidney failure. It can be used to identify ethical issues that should be addressed in specific training programs for clinicians, clinical practice guidelines, or other types of policies dealing with kidney failure. PMID:26938863

Enhancing biomedical text summarization using semantic relation extraction.

PubMed

Shang, Yue; Li, Yanpeng; Lin, Hongfei; Yang, Zhihao

2011-01-01

Automatic text summarization for a biomedical concept can help researchers to get the key points of a certain topic from large amount of biomedical literature efficiently. In this paper, we present a method for generating text summary for a given biomedical concept, e.g., H1N1 disease, from multiple documents based on semantic relation extraction. Our approach includes three stages: 1) We extract semantic relations in each sentence using the semantic knowledge representation tool SemRep. 2) We develop a relation-level retrieval method to select the relations most relevant to each query concept and visualize them in a graphic representation. 3) For relations in the relevant set, we extract informative sentences that can interpret them from the document collection to generate text summary using an information retrieval based method. Our major focus in this work is to investigate the contribution of semantic relation extraction to the task of biomedical text summarization. The experimental results on summarization for a set of diseases show that the introduction of semantic knowledge improves the performance and our results are better than the MEAD system, a well-known tool for text summarization.

Fostering adolescents' value beliefs for mathematics with a relevance intervention in the classroom.

PubMed

Gaspard, Hanna; Dicke, Anna-Lena; Flunger, Barbara; Brisson, Brigitte Maria; Häfner, Isabelle; Nagengast, Benjamin; Trautwein, Ulrich

2015-09-01

Interventions targeting students' perceived relevance of the learning content have been shown to effectively promote student motivation within science classes (e.g., Hulleman & Harackiewicz, 2009). Yet, further research is warranted to understand better how such interventions should be designed in order to be successfully implemented in the classroom setting. A cluster randomized controlled study was conducted to test whether ninth-grade students' value beliefs for mathematics (i.e., intrinsic value, attainment value, utility value, and cost) could be fostered with relevance interventions in the classroom. Eighty-two classrooms were randomly assigned to 1 of 2 experimental conditions or a waiting control condition. Both experimental groups received a 90-min intervention within the classroom on the relevance of mathematics, consisting of a psychoeducational presentation and relevance-inducing tasks (either writing a text or evaluating interview quotations). Intervention effects were evaluated via self-reports of 1,916 participating students 6 weeks and 5 months after the intervention in the classroom. Both intervention conditions fostered more positive value beliefs among students at both time points. Compared with the control condition, classes in the quotations condition reported higher utility value, attainment value, and intrinsic value, and classes in the text condition reported higher utility value. Thus, stronger effects on students' value beliefs were found for the quotations condition than for the text condition. When assessing intervention effects separately for females and males, some evidence for stronger effects for females than for males was found. (c) 2015 APA, all rights reserved).

US Army Research Laboratory Joint Interagency Field Experimentation 15-2 Final Report

DTIC Science & Technology

2015-12-01

February 2015, at Alameda Island, California. Advanced text analytics capabilities were demonstrated in a logically coherent workflow pipeline that... text processing capabilities allowed the targeted use of a persistent imagery sensor for rapid detection of mission- critical events. The creation of...a very large text database from open source data provides a relevant and unclassified foundation for continued development of text -processing

MeSH indexing based on automatically generated summaries

PubMed Central

2013-01-01

Background MEDLINE citations are manually indexed at the U.S. National Library of Medicine (NLM) using as reference the Medical Subject Headings (MeSH) controlled vocabulary. For this task, the human indexers read the full text of the article. Due to the growth of MEDLINE, the NLM Indexing Initiative explores indexing methodologies that can support the task of the indexers. Medical Text Indexer (MTI) is a tool developed by the NLM Indexing Initiative to provide MeSH indexing recommendations to indexers. Currently, the input to MTI is MEDLINE citations, title and abstract only. Previous work has shown that using full text as input to MTI increases recall, but decreases precision sharply. We propose using summaries generated automatically from the full text for the input to MTI to use in the task of suggesting MeSH headings to indexers. Summaries distill the most salient information from the full text, which might increase the coverage of automatic indexing approaches based on MEDLINE. We hypothesize that if the results were good enough, manual indexers could possibly use automatic summaries instead of the full texts, along with the recommendations of MTI, to speed up the process while maintaining high quality of indexing results. Results We have generated summaries of different lengths using two different summarizers, and evaluated the MTI indexing on the summaries using different algorithms: MTI, individual MTI components, and machine learning. The results are compared to those of full text articles and MEDLINE citations. Our results show that automatically generated summaries achieve similar recall but higher precision compared to full text articles. Compared to MEDLINE citations, summaries achieve higher recall but lower precision. Conclusions Our results show that automatic summaries produce better indexing than full text articles. Summaries produce similar recall to full text but much better precision, which seems to indicate that automatic summaries can efficiently capture the most important contents within the original articles. The combination of MEDLINE citations and automatically generated summaries could improve the recommendations suggested by MTI. On the other hand, indexing performance might be dependent on the MeSH heading being indexed. Summarization techniques could thus be considered as a feature selection algorithm that might have to be tuned individually for each MeSH heading. PMID:23802936

A metric to search for relevant words

NASA Astrophysics Data System (ADS)

Zhou, Hongding; Slater, Gary W.

2003-11-01

We propose a new metric to evaluate and rank the relevance of words in a text. The method uses the density fluctuations of a word to compute an index that measures its degree of clustering. Highly significant words tend to form clusters, while common words are essentially uniformly spread in a text. If a word is not rare, the metric is stable when we move any individual occurrence of this word in the text. Furthermore, we prove that the metric always increases when words are moved to form larger clusters, or when several independent documents are merged. Using the Holy Bible as an example, we show that our approach reduces the significance of common words when compared to a recently proposed statistical metric.

A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts.

PubMed

Westergaard, David; Stærfeldt, Hans-Henrik; Tønsberg, Christian; Jensen, Lars Juhl; Brunak, Søren

2018-02-01

Across academia and industry, text mining has become a popular strategy for keeping up with the rapid growth of the scientific literature. Text mining of the scientific literature has mostly been carried out on collections of abstracts, due to their availability. Here we present an analysis of 15 million English scientific full-text articles published during the period 1823-2016. We describe the development in article length and publication sub-topics during these nearly 250 years. We showcase the potential of text mining by extracting published protein-protein, disease-gene, and protein subcellular associations using a named entity recognition system, and quantitatively report on their accuracy using gold standard benchmark data sets. We subsequently compare the findings to corresponding results obtained on 16.5 million abstracts included in MEDLINE and show that text mining of full-text articles consistently outperforms using abstracts only.

A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts

PubMed Central

Westergaard, David; Stærfeldt, Hans-Henrik

2018-01-01

Across academia and industry, text mining has become a popular strategy for keeping up with the rapid growth of the scientific literature. Text mining of the scientific literature has mostly been carried out on collections of abstracts, due to their availability. Here we present an analysis of 15 million English scientific full-text articles published during the period 1823–2016. We describe the development in article length and publication sub-topics during these nearly 250 years. We showcase the potential of text mining by extracting published protein–protein, disease–gene, and protein subcellular associations using a named entity recognition system, and quantitatively report on their accuracy using gold standard benchmark data sets. We subsequently compare the findings to corresponding results obtained on 16.5 million abstracts included in MEDLINE and show that text mining of full-text articles consistently outperforms using abstracts only. PMID:29447159

“Free Full Text Articles”: Where to Search for Them?

PubMed Central

Singh, Ashish; Singh, Manish; Singh, Ajai Kumar; Singh, Deepti; Singh, Pratibha; Sharma, Abhishek

2011-01-01

References form the backbone of any medical literature. Presently, because of high inflation, it is very difficult for any library/organization/college to purchase all journals. The condition is even worse for an individual person, such as private practitioners. The solution lies in the free availability of full-text articles. Here, the authors share their experiences about the accessibility of free full-text articles. PMID:22223965

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

Fate of abstracts presented at the annual scientific meeting of the Undersea and Hyperbaric Medical Society.

PubMed

Uzun, Günalp; Mutluoğlu, Mesut; Bakir, Alev; Senocak, Mustafa S

2013-01-01

The full-text publication of abstracts presented at any given scientific meeting in peer-reviewed journals is accepted as a measure of scientific quality of that particular meeting. The aim of this study is to determine the full-text publication rate of abstracts presented at the 2005 Scientific Meeting of the Undersea and Hyperbaric Medical Society (UHMS). We identified the scientific abstracts presented at the 2005 UHMS meeting and searched the PubMed database (June 2005 to July 2010) for their corresponding full-text publication. We recorded the following parameters for each of the abstracts: number of authors, number of centers involved in the study, statistical methods used, country of origin of the study, study type, and subject of the abstract. We recorded the time to publication and the title of the journal if the abstract had been published in a peer-reviewed journal. Overall, we identified 187 abstracts presented at the 2005 UHMS meeting. Two of the abstracts were excluded from the study because they had been retracted from the meeting and six more because they had been already published as full-text articles at the time the meeting was held. Of the 179 abstracts, 62 (34.6%) were published as full-text articles within the succeeding five years. The mean (+/- SD) time to publication was 18.5 (+/- 13.6) months. Multivariate analysis with logistic regression identified "country of origin" and "the subject of the abstract" as independent predictors of full-text publication. We found that only one-third of the abstracts presented at the 2005 UHMS meeting were published as full-text articles within the succeeding five years. Although this rate is consistent with similar studies from various disciplines, further research is needed to identify the specific barriers to full-text publication of abstracts in the field of underwater and hyperbaric medicine.

Implementation of the common phrase index method on the phrase query for information retrieval

NASA Astrophysics Data System (ADS)

Fatmawati, Triyah; Zaman, Badrus; Werdiningsih, Indah

2017-08-01

As the development of technology, the process of finding information on the news text is easy, because the text of the news is not only distributed in print media, such as newspapers, but also in electronic media that can be accessed using the search engine. In the process of finding relevant documents on the search engine, a phrase often used as a query. The number of words that make up the phrase query and their position obviously affect the relevance of the document produced. As a result, the accuracy of the information obtained will be affected. Based on the outlined problem, the purpose of this research was to analyze the implementation of the common phrase index method on information retrieval. This research will be conducted in English news text and implemented on a prototype to determine the relevance level of the documents produced. The system is built with the stages of pre-processing, indexing, term weighting calculation, and cosine similarity calculation. Then the system will display the document search results in a sequence, based on the cosine similarity. Furthermore, system testing will be conducted using 100 documents and 20 queries. That result is then used for the evaluation stage. First, determine the relevant documents using kappa statistic calculation. Second, determine the system success rate using precision, recall, and F-measure calculation. In this research, the result of kappa statistic calculation was 0.71, so that the relevant documents are eligible for the system evaluation. Then the calculation of precision, recall, and F-measure produces precision of 0.37, recall of 0.50, and F-measure of 0.43. From this result can be said that the success rate of the system to produce relevant documents is low.

Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature.

PubMed

Müller, H-M; Van Auken, K M; Li, Y; Sternberg, P W

2018-03-09

The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved. We describe the next generation of the Textpresso information retrieval system, Textpresso Central (TPC). TPC builds on the strengths of the original system by expanding the full text corpus to include the PubMed Central Open Access Subset (PMC OA), as well as the WormBase C. elegans bibliography. In addition, TPC allows users to create a customized corpus by uploading and processing documents of their choosing. TPC is UIMA compliant, to facilitate compatibility with external processing modules, and takes advantage of Lucene indexing and search technology for efficient handling of millions of full text documents. Like Textpresso, TPC searches can be performed using keywords and/or categories (semantically related groups of terms), but to provide better context for interpreting and validating queries, search results may now be viewed as highlighted passages in the context of full text. To facilitate biocuration efforts, TPC also allows users to select text spans from the full text and annotate them, create customized curation forms for any data type, and send resulting annotations to external curation databases. As an example of such a curation form, we describe integration of TPC with the Noctua curation tool developed by the Gene Ontology (GO) Consortium. Textpresso Central is an online literature search and curation platform that enables biocurators and biomedical researchers to search and mine the full text of literature by integrating keyword and category searches with viewing search results in the context of the full text. It also allows users to create customized curation interfaces, use those interfaces to make annotations linked to supporting evidence statements, and then send those annotations to any database in the world. Textpresso Central URL: http://www.textpresso.org/tpc.

Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion.

PubMed

Agarwal, Shashank; Yu, Hong

2009-12-01

Biomedical texts can be typically represented by four rhetorical categories: Introduction, Methods, Results and Discussion (IMRAD). Classifying sentences into these categories can benefit many other text-mining tasks. Although many studies have applied different approaches for automatically classifying sentences in MEDLINE abstracts into the IMRAD categories, few have explored the classification of sentences that appear in full-text biomedical articles. We first evaluated whether sentences in full-text biomedical articles could be reliably annotated into the IMRAD format and then explored different approaches for automatically classifying these sentences into the IMRAD categories. Our results show an overall annotation agreement of 82.14% with a Kappa score of 0.756. The best classification system is a multinomial naïve Bayes classifier trained on manually annotated data that achieved 91.95% accuracy and an average F-score of 91.55%, which is significantly higher than baseline systems. A web version of this system is available online at-http://wood.ims.uwm.edu/full_text_classifier/.

Barriers to reporting medication errors and near misses among nurses: A systematic review.

PubMed

Vrbnjak, Dominika; Denieffe, Suzanne; O'Gorman, Claire; Pajnkihar, Majda

2016-11-01

To explore barriers to nurses' reporting of medication errors and near misses in hospital settings. Systematic review. Medline, CINAHL, PubMed and Cochrane Library in addition to Google and Google Scholar and reference lists of relevant studies published in English between January 1981 and April 2015 were searched for relevant qualitative, quantitative or mixed methods empirical studies or unpublished PhD theses. Papers with a primary focus on barriers to reporting medication errors and near misses in nursing were included. The titles and abstracts of the search results were assessed for eligibility and relevance by one of the authors. After retrieval of the full texts, two of the authors independently made decisions concerning the final inclusion and these were validated by the third reviewer. Three authors independently assessed methodological quality of studies. Relevant data were extracted and findings were synthesised using thematic synthesis. From 4038 identified records, 38 studies were included in the synthesis. Findings suggest that organizational barriers such as culture, the reporting system and management behaviour in addition to personal and professional barriers such as fear, accountability and characteristics of nurses are barriers to reporting medication errors. To overcome reported barriers it is necessary to develop a non-blaming, non-punitive and non-fearful learning culture at unit and organizational level. Anonymous, effective, uncomplicated and efficient reporting systems and supportive management behaviour that provides open feedback to nurses is needed. Nurses are accountable for patients' safety, so they need to be educated and skilled in error management. Lack of research into barriers to reporting of near misses' and low awareness of reporting suggests the need for further research and development of educational and management approaches to overcome these barriers. Copyright © 2016 Elsevier Ltd. All rights reserved.

"What is relevant in a text document?": An interpretable machine learning approach

PubMed Central

Arras, Leila; Horn, Franziska; Montavon, Grégoire; Müller, Klaus-Robert

2017-01-01

Text documents can be described by a number of abstract concepts such as semantic category, writing style, or sentiment. Machine learning (ML) models have been trained to automatically map documents to these abstract concepts, allowing to annotate very large text collections, more than could be processed by a human in a lifetime. Besides predicting the text’s category very accurately, it is also highly desirable to understand how and why the categorization process takes place. In this paper, we demonstrate that such understanding can be achieved by tracing the classification decision back to individual words using layer-wise relevance propagation (LRP), a recently developed technique for explaining predictions of complex non-linear classifiers. We train two word-based ML models, a convolutional neural network (CNN) and a bag-of-words SVM classifier, on a topic categorization task and adapt the LRP method to decompose the predictions of these models onto words. Resulting scores indicate how much individual words contribute to the overall classification decision. This enables one to distill relevant information from text documents without an explicit semantic information extraction step. We further use the word-wise relevance scores for generating novel vector-based document representations which capture semantic information. Based on these document vectors, we introduce a measure of model explanatory power and show that, although the SVM and CNN models perform similarly in terms of classification accuracy, the latter exhibits a higher level of explainability which makes it more comprehensible for humans and potentially more useful for other applications. PMID:28800619

Evaluating Open-Source Full-Text Search Engines for Matching ICD-10 Codes.

PubMed

Jurcău, Daniel-Alexandru; Stoicu-Tivadar, Vasile

2016-01-01

This research presents the results of evaluating multiple free, open-source engines on matching ICD-10 diagnostic codes via full-text searches. The study investigates what it takes to get an accurate match when searching for a specific diagnostic code. For each code the evaluation starts by extracting the words that make up its text and continues with building full-text search queries from the combinations of these words. The queries are then run against all the ICD-10 codes until a match indicates the code in question as a match with the highest relative score. This method identifies the minimum number of words that must be provided in order for the search engines choose the desired entry. The engines analyzed include a popular Java-based full-text search engine, a lightweight engine written in JavaScript which can even execute on the user's browser, and two popular open-source relational database management systems.

Preservice Elementary School Teachers' Conceptual Change about Projectile Motion: Refutation Text, Demonstration, Affective Factors, and Relevance.

ERIC Educational Resources Information Center

Hynd, Cynthia; And Others

1997-01-01

Investigates changes in preservice teachers' conceptions about projectile motion brought about by a combination of reading and demonstration and appeal to usefulness. Results indicate the effectiveness of a combined Demo-Text condition on immediate posttests and effectiveness of text in producing long-term change. Analysis also indicates an…

Unkindest Cuts? Some Effects of Picture Editing on Recall of Television News Information.

ERIC Educational Resources Information Center

Davies, Maire Messenger; And Others

1985-01-01

This study examined the effects of pictorial changes on recall of spoken text in a television news broadcast viewed by adolescents and adults. Adult recall of spoken text was impaired by mid-sentence picture editing while adolescents' recall was enhanced so long as accompanying pictures were relevant to verbal text. (MBR)

The effectiveness of noninvasive interventions for musculoskeletal thoracic spine and chest wall pain: a systematic review by the Ontario Protocol for Traffic Injury Management (OPTIMa) collaboration.

PubMed

Southerst, Danielle; Marchand, Andrée-Anne; Côté, Pierre; Shearer, Heather M; Wong, Jessica J; Varatharajan, Sharanya; Randhawa, Kristi; Sutton, Deborah; Yu, Hainan; Gross, Douglas P; Jacobs, Craig; Goldgrub, Rachel; Stupar, Maja; Mior, Silvano; Carroll, Linda J; Taylor-Vaisey, Anne

2015-09-01

The purpose of this study was to critically appraise and synthesize evidence on the effectiveness of noninvasive interventions, excluding pharmacological treatments, for musculoskeletal thoracic pain. Randomized controlled trials (RCTs), cohort studies, and case-control studies evaluating the effectiveness of noninvasive interventions were eligible. We searched MEDLINE, EMBASE, PsycINFO, and the Cochrane Central Register of Controlled Trials accessed through Ovid Technologies, Inc, and CINAHL Plus with Full Text accessed through EBSCOhost from 1990 to 2015. Our search strategies combined controlled vocabulary relevant to each database (eg, MeSH for MEDLINE) and text words relevant to our research question and the inclusion criteria. Random pairs of independent reviewers screened studies for relevance and critically appraised relevant studies using the Scottish Intercollegiate Guidelines Network criteria. Studies with a low risk of bias were synthesized following best evidence synthesis principles. We screened 6988 articles and critically appraised 2 studies. Both studies had a low risk of bias and were included in our synthesis. One RCT compared thoracic spinal manipulation, needle acupuncture, and placebo electrotherapy for recent thoracic spine pain. There were statistically significant but clinically nonimportant short-term reductions in pain favoring manipulation. There were no differences between acupuncture and placebo electrotherapy. Another RCT compared a multimodal program of care and a session of education for recent musculoskeletal chest wall pain. The multimodal care resulted in statistically significant but clinically nonimportant short-term reductions in pain over education. However, participants receiving multimodal care were more likely to report important improvements in chest pain. Quality evidence on the management of musculoskeletal thoracic pain is sparse. The current evidence suggests that compared to placebo, spinal manipulation is associated with a small and clinically nonimportant reduction in pain intensity and that acupuncture leads to similar outcomes as placebo. Furthermore, a multimodal program of care (ie, manual therapy, soft tissue therapy, exercises, heat/ice, and advice) and a single education session lead to similar pain reduction for recent-onset musculoskeletal chest wall pain. However, patients who receive multimodal care are more likely to report pain improvements. Copyright © 2015 National University of Health Sciences. Published by Elsevier Inc. All rights reserved.

Does Bariatric Surgery Affect the Incidence of Endometrial Cancer Development? A Systematic Review.

PubMed

Winder, Alec A; Kularatna, Malsha; MacCormick, Andrew D

2018-05-01

Obesity has been linked to an increased prevalence in multiple cancers. Studies have suggested a reduction in the overall risk of cancer after bariatric surgery. We reviewed the evidence for bariatric surgery reducing the risk of endometrial cancer. Data was extracted from PubMed, EMBASE, and Medline to perform a systematic review. Thirty-one full text articles were identified from 265 abstracts. Nine observational studies were relevant to endometrial cancer. In the five controlled studies, 462 of 113,032 (0.4%) patients receiving bariatric surgery versus 11,997 of 848,864 (1.4%) controls developed endometrial cancer, odds ratio of 0.317 (95% CI 0.161 to 0.627) using random effects model (P < 0.001). Bariatric surgery seems to reduce the risk of endometrial cancer; however, more research is required.

The Case for Lung Cancer Screening: What Nurses Need to Know.

PubMed

Sorrie, Kerrin; Cates, Lisa; Hill, Alethea

2016-06-01

Lung cancer screening with low-dose helical computed tomography (LDCT) can improve high-risk individuals' chances of being diagnosed at an earlier stage and increase survival. The aims of this article are to present the risk factors associated with the development of lung cancer, identify patients at high risk for lung cancer qualifying for LDCT screening, and understand the importance of early lung cancer detection through the use of LDCT screening. PubMed and CINAHL® databases were searched with key words lung cancer screening to identify full-text academic articles from 2004-2014. This resulted in 529 articles from PubMed and 195 from CINAHL. PubMed offered suggestions for additional relevant journal articles. The National Comprehensive Cancer Network guidelines also provided substantial evidence-based information. Nurses need to provide support, education, and resources for patients undergoing lung cancer screening.

Searching for Bill and Jane: Electronic Full-Text Literature.

ERIC Educational Resources Information Center

Still, Julie; Kassabian, Vibiana

1998-01-01

Examines electronic full-text literature available on the World Wide Web and on CD-ROM. Discusses authors and genres, electronic texts, and fees. Highlights Shakespeare, Jane Austen, and nature writing. Provides a bibliography of Web guides, specialized Shakespeare pages, and pages dealing with the Shakespeare authorship debate and secondary…

A bibliometric analysis of systematic reviews on vaccines and immunisation.

PubMed

Fernandes, Silke; Jit, Mark; Bozzani, Fiammetta; Griffiths, Ulla K; Scott, J Anthony G; Burchett, Helen E D

2018-04-19

SYSVAC is an online bibliographic database of systematic reviews and systematic review protocols on vaccines and immunisation compiled by the London School of Hygiene & Tropical Medicine and hosted by the World Health Organization (WHO) through their National Immunization Technical Advisory Groups (NITAG) resource centre (www.nitag-resource.org). Here the development of the database and a bibliometric review of its content is presented, describing trends in the publication of policy-relevant systematic reviews on vaccines and immunisation from 2008 to 2016. Searches were conducted in seven scientific databases according to a standardized search protocol, initially in 2014 with the most recent update in January 2017. Abstracts and titles were screened according to specific inclusion criteria. All included publications were coded into relevant categories based on a standardized protocol and subsequently analysed to look at trends in time, topic, area of focus, population and geographic location. After screening for inclusion criteria, 1285 systematic reviews were included in the database. While in 2008 there were only 34 systematic reviews on a vaccine-related topic, this increased to 322 in 2016. The most frequent pathogens/diseases studied were influenza, human papillomavirus and pneumococcus. There were several areas of duplication and overlap. As more systematic reviews are published it becomes increasingly time-consuming for decision-makers to identify relevant information among the ever-increasing volume available. The risk of duplication also increases, particularly given the current lack of coordination of systematic reviews on vaccine-related questions, both in terms of their commissioning and their execution. The SYSVAC database offers an accessible catalogue of vaccine-relevant systematic reviews with, where possible access or a link to the full-text. SYSVAC provides a freely searchable platform to identify existing vaccine-policy-relevant systematic reviews. Systematic reviews will need to be assessed adequately for each specific question and quality. Copyright © 2018. Published by Elsevier Ltd.

A systematic review identifies shortcomings in the reporting of crossover trials in chronic painful conditions.

PubMed

Straube, Sebastian; Werny, Benedikt; Friede, Tim

2015-12-01

To investigate the reporting of study features of interest in abstracts and full texts of journal publications of crossover trials in chronic painful conditions. Systematic review based on a MEDLINE (PubMed) search (January 1990-August 2014). Ninety-eight publications on crossover studies with 3,513 study participants were eligible for inclusion. Double-blind status and randomized allocation to treatment groups are commonly reported in both abstracts and full texts (90 of 98 publications and 82 of 98 publications, respectively). Adverse events are reported in both abstract and full text in 49 of 98 publications and in the full text only in 44 of 98. A breakdown of results by treatment period is provided only in 23 of 98 publications, and if so, is reported only in the full text, never in the abstract. There is a time trend for the reporting of randomization in abstracts; it is more likely to be reported in recent studies (P = 0.0094). No time trends are detected in the reporting of double-blind status (P = 0.1087) and adverse events (P = 0.6084). The reporting of adverse events in the abstract and the reporting of results specified by crossover period in the full texts of journal publications on crossover pain trials should be improved. Copyright © 2015 Elsevier Inc. All rights reserved.

Full journal publication of abstracts presented at the Nordic Congress of General Practice in 2009 and 2011.

PubMed

Waldorff, Frans Boch; Petersen, Kristine; Vinther, Siri; Sandholdt, Håkon; Siersma, Volkert; Andersen, John Sahl

2017-03-01

To determine the overall publication rates for abstracts presented at two consecutive Nordic Congresses of General Practice and to evaluate determinants for these publication rates. Prospective study. MEDLINE (PubMed) and Google Scholar were searched for relevant publications from 1 January 2009 up until 31 August 2014. Abstracts accepted for oral or poster presentation were identified from the original congress booklets from the Nordic Congresses of General Practice in 2009 and 2011. Based on PubMed and Google Scholar searches, we subsequently identified full journal publications within a 36-month follow-up from both congresses. In cases of doubt, the first author was contacted directly. Full journal publication within 36 months after the congress. A total of 200 abstracts were analyzed. Of these, 85 (42.5%) were identified with a full publication within 36 months after the congress. More abstracts from the 2011 congress were published compared to the 2009 congress odds ratio (OR) 1.97, 95% confidence interval (CI) (1.10; 3.50). Abstracts accepted for oral presentation were more often published OR 1.94, 95% CI (1.08; 3.50) than accepted poster abstracts. In the multivariate analysis, a university affiliation for both first and last author increased the probability for publication OR 4.23, 95% CI (1.71; 10.42), as well as more than two authors. An optimal number, based on the highest OR, seems to be 3-4 authors with OR 2.43, 95% CI (1.07; 5.54). Qualitative studies were published at the same frequency as quantitative studies OR 1.36, 95% CI (0.57; 3.24). Less than half of the abstracts accepted for oral or poster presentation at two consecutive Nordic Congresses of General Practice were published as full text articles within 36 months. Key points Congress abstracts accepted for Nordic Congress of General Practice are not indexed in international search databases. Less than half of the abstracts accepted for oral or poster presentation at two consecutive Nordic Congresses of General Practice were published as full text articles within 36 months. Future congress committees could address this aspect in order to increase the visibility of and accessibility to research within the field of general practice.

Full journal publication of abstracts presented at the Nordic Congress of General Practice in 2009 and 2011

PubMed Central

Waldorff, Frans Boch; Petersen, Kristine; Vinther, Siri; Sandholdt, Håkon; Siersma, Volkert; Andersen, John Sahl

2017-01-01

Objective To determine the overall publication rates for abstracts presented at two consecutive Nordic Congresses of General Practice and to evaluate determinants for these publication rates. Design Prospective study. Setting MEDLINE (PubMed) and Google Scholar were searched for relevant publications from 1 January 2009 up until 31 August 2014. Methods Abstracts accepted for oral or poster presentation were identified from the original congress booklets from the Nordic Congresses of General Practice in 2009 and 2011. Based on PubMed and Google Scholar searches, we subsequently identified full journal publications within a 36-month follow-up from both congresses. In cases of doubt, the first author was contacted directly. Main outcome measures Full journal publication within 36 months after the congress. Results A total of 200 abstracts were analyzed. Of these, 85 (42.5%) were identified with a full publication within 36 months after the congress. More abstracts from the 2011 congress were published compared to the 2009 congress odds ratio (OR) 1.97, 95% confidence interval (CI) (1.10; 3.50). Abstracts accepted for oral presentation were more often published OR 1.94, 95% CI (1.08; 3.50) than accepted poster abstracts. In the multivariate analysis, a university affiliation for both first and last author increased the probability for publication OR 4.23, 95% CI (1.71; 10.42), as well as more than two authors. An optimal number, based on the highest OR, seems to be 3–4 authors with OR 2.43, 95% CI (1.07; 5.54). Qualitative studies were published at the same frequency as quantitative studies OR 1.36, 95% CI (0.57; 3.24). Conclusion Less than half of the abstracts accepted for oral or poster presentation at two consecutive Nordic Congresses of General Practice were published as full text articles within 36 months. Key points Congress abstracts accepted for Nordic Congress of General Practice are not indexed in international search databases. Less than half of the abstracts accepted for oral or poster presentation at two consecutive Nordic Congresses of General Practice were published as full text articles within 36 months. Future congress committees could address this aspect in order to increase the visibility of and accessibility to research within the field of general practice. PMID:28277049

Desktop Access to Full-Text NACA and NASA Reports: Systems Developed by NASA Langley Technical Library

NASA Technical Reports Server (NTRS)

Ambur, Manjula Y.; Adams, David L.; Trinidad, P. Paul

1997-01-01

NASA Langley Technical Library has been involved in developing systems for full-text information delivery of NACA/NASA technical reports since 1991. This paper will describe the two prototypes it has developed and the present production system configuration. The prototype systems are a NACA CD-ROM of thirty-three classic paper NACA reports and a network-based Full-text Electronic Reports Documents System (FEDS) constructed from both paper and electronic formats of NACA and NASA reports. The production system is the DigiDoc System (DIGItal Documents) presently being developed based on the experiences gained from the two prototypes. DigiDoc configuration integrates the on-line catalog database World Wide Web interface and PDF technology to provide a powerful and flexible search and retrieval system. It describes in detail significant achievements and lessons learned in terms of data conversion, storage technologies, full-text searching and retrieval, and image databases. The conclusions from the experiences of digitization and full- text access and future plans for DigiDoc system implementation are discussed.

Libretexts: a flexible online open system for disseminating educational materials relevant to geophysics at all levels

NASA Astrophysics Data System (ADS)

Halpern, J. B.

2017-12-01

Libretexts is an online open system for distributing educational materials with over 5 million page views per month. Covering geophysics, chemistry, physics and more it offers a platform for authors and users including faculty and students to access curated educational materials. Currently there are on line texts covering geology, geobiology, natural hazards and understanding the refusal to accept climate change as well as relevant materials in other sections on aquatic and atmospheric chemistry. In addition to "written" materials Libretexts provides access to simulations and demonstrations that are relevant. Most importantly the Libretext project welcomes new contributors. Faculty can use available materials to construct their own texts or supplementary materials in relatively short order. Since all material is covered by a Creative Commons Copyright, material can be added to as needed for teaching.

A Matter of Relevance: Teaching Classics in the 21st Century

ERIC Educational Resources Information Center

Youssef, Lamiaa

2010-01-01

In a world literature course, an instructor faces the challenge of engaging the students in classical texts that are historically, geographically, and linguistically "alien" to them. Through a three-step instructional model that includes approximation, thematic relevance, and application, the instructor tries to help students identify,…

Dialoging about English Learners: Preparing Teachers through Culturally Relevant Literature Circles

ERIC Educational Resources Information Center

Heineke, Amy J.

2014-01-01

The author describes how culturally relevant children's literature allowed teachers and teacher candidates to explore the lived realities of diverse students. Through the author's qualitative investigation of 23 literature discussions of undergraduate and graduate students across five academic semesters, the author found that texts written by…

Variation in Relevance Judgments and the Measurement of Retrieval Effectiveness.

ERIC Educational Resources Information Center

Voorhees, Ellen M.

2000-01-01

Discusses the test collections developed in the TREC (Text REtrieval Conference) workshops for information retrieval research and describes a study by NIST (National Institute of Standards and Technology) that verified their reliability by investigating the effect changes in the relevance assessments have on the evaluation of retrieval results.…

Applying evidence-based surgery in daily clinical routine: a feasibility study.

PubMed

Krahn, Jan; Sauerland, Stefan; Rixen, Dieter; Gregor, Sven; Bouillon, Bertil; Neugebauer, Edmund A M

2006-03-01

Although the word evidence-based medicine (EBM) has gained wide popularity, only a few studies have evaluated how EBM works in clinical practice. We have prospectively evaluated the feasibility of evidence-based trauma surgery. Orthopaedic trauma surgeons were asked to produce clinical questions related to the treatment of current patients. An informaticist searched the literature (Medline, Cochrane Library, practice guidelines and textbooks) and reported the findings on every following day. The study's main endpoints were the rate of questions for which relevant evidence (>level V) was available and the time necessary to find and critically appraise medical evidence. In total, 44 EBM questions were formulated, mainly concerning treatment options. PubMed was searched for 39 questions, textbooks for 14, the Cochrane Library for 11, online guidelines for 9 and other sources were used for 4 questions. On average, 157 text items (three per questions) were identified as potentially relevant. Journal articles predominated (83%) over textbooks (10%). Sixty-eight percent of the questions (30 of 44) were answered, either on the basis level 1 (n=13 questions), level 2 (n=6), or level 4 evidence (n=14). Trying to answer a question required 53 min on average, split up between 39 min of database searches and 25 min of obtaining full text articles. In four cases, the evidence suggested a change in clinical management. The physicians were very appreciative of our project and found the provided evidence very helpful for their clinical decisions. Time will be the main barrier against the introduction of clinical EBM. It is likely that clinicians reduce EBM to those situations where evidence is likely to be found. Although the impact of EBM on patient-care was limited, the concept of EBM was successfully implemented.

The Islamic tradition and health inequities: A preliminary conceptual model based on a systematic literature review of Muslim health-care disparities

PubMed Central

Padela, Aasim I.; Zaidi, Danish

2018-01-01

Objective: The objective of this study was to identify mechanisms by which Islamic beliefs, values, and Muslim identity might contribute to health inequities among Muslim populations. Methods: A systematic literature review of empirical studies in Medline from 1980 to 2009 was conducted. The search strategy used three terms covering health-care disparities, ethnicity, and location to uncover relevant papers. Results: A total of 171 articles were relevant based on titles and abstracts. Upon subsequent full-text review, most studies did not include religious identity or religiosity as explanatory variables for observed health disparities. Of 29 studies mentioning Islam within the text, 19 implicated Muslim identity or practices as potential explanations for health differences between Muslim and non-Muslim groups. These 19 studies generated six mechanisms that related the Islamic tradition, Muslim practices, and health inequities: (1) Interpretations of health and/or lack of health based on Islamic theology; (2) Ethical and/or cultural challenges within the clinical realm stemming from Islamic values or practices; (3) Perceived discrimination due to, or a lack of cultural accommodation of, religious values or practices in the clinical realm; (4) Health practices rooted within the Islamic tradition; (5) Patterns of health-care seeking based on Islamic values; and (6) Adverse health exposures due to having a Muslim identity. Conclusion: While there is scant empirical research on Muslim health-care disparities, a preliminary conceptual model relating Islam to health inequities can be built from the extant literature. This model can serve to organize research on Muslim health and distinguish different ways in which a Muslim identity might contribute to the patterning of health disparities. PMID:29404267

77 FR 2011 - Reorganization of Regulations on the Adjudication of Department of Homeland Security Practitioner...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-13

... corresponding DHS provision, 8 CFR 292.3. Although the Department is removing the existing text of Sec. 1292.3, it is transferring certain aspects of Sec. 1292.3 by adding new text at 8 CFR 1003.103 and 1003.105... practitioner disciplinary cases, the Department is transferring the relevant text to EOIR's disciplinary...

Enhancing Biomedical Text Summarization Using Semantic Relation Extraction

PubMed Central

Shang, Yue; Li, Yanpeng; Lin, Hongfei; Yang, Zhihao

2011-01-01

Automatic text summarization for a biomedical concept can help researchers to get the key points of a certain topic from large amount of biomedical literature efficiently. In this paper, we present a method for generating text summary for a given biomedical concept, e.g., H1N1 disease, from multiple documents based on semantic relation extraction. Our approach includes three stages: 1) We extract semantic relations in each sentence using the semantic knowledge representation tool SemRep. 2) We develop a relation-level retrieval method to select the relations most relevant to each query concept and visualize them in a graphic representation. 3) For relations in the relevant set, we extract informative sentences that can interpret them from the document collection to generate text summary using an information retrieval based method. Our major focus in this work is to investigate the contribution of semantic relation extraction to the task of biomedical text summarization. The experimental results on summarization for a set of diseases show that the introduction of semantic knowledge improves the performance and our results are better than the MEAD system, a well-known tool for text summarization. PMID:21887336

An Expert System for Searching in Full-Text

DTIC Science & Technology

1989-12-01

2 An Expert System for Searching in Full-Text 00~ TR89-043 -December, 1989 cc D IF L, ~r." T M~ EA 13~ 1991ON- The University of North Carolina at...Full-Text by Susan Evalyn Gauch A dissertation submitted to the faculty of The University of North Carolina at Chapel Hill in partial fulfillment of...MICROARRAS, the retrieval software. MICROARRAS developed at the University of North Carolina under the direction of John B. Smith and Stephen Weiss [Smith et

Scoping meta-review: introducing a new methodology.

PubMed

Sarrami-Foroushani, Pooria; Travaglia, Joanne; Debono, Deborah; Clay-Williams, Robyn; Braithwaite, Jeffrey

2015-02-01

For researchers, policymakers, and practitioners facing a new field, undertaking a systematic review can typically present a challenge due to the enormous number of relevant papers. A scoping review is a method suggested for addressing this dilemma; however, scoping reviews present their own challenges. This paper introduces the "scoping meta-review" (SMR) for expanding current methodologies and is based on our experiences in mapping the field of consumer engagement in healthcare. During this process, we developed the novel SMR method. An SMR combines aspects of a scoping review and a meta-review to establish an evidence-based map of a field. Similar to a scoping review, an SMR offers a practical and flexible methodology. However, unlike in a traditional scoping review, only systematic reviews are included. Stages of the SMR include: undertaking a preliminary nonsystematic review; building a search strategy; interrogating academic literature databases; classifying and excluding studies based on titles and abstracts; saving the refined database of references; revising the search strategy; selecting and reviewing the full text papers; and thematically analyzing the selected texts and writing the report. The main benefit of an SMR is to map a new field based on high-level evidence provided by systematic reviews. © 2014 Wiley Periodicals, Inc.

Multi-Character Tries for Text Searching.

ERIC Educational Resources Information Center

Cooper, Lorraine K. D.; Tharp, Alan L.

1993-01-01

Introduces the multicharacter trie as an index structure that can improve the time needed for retrieving full-text materials stored on CD-ROMs. The advantages of this structure compared to other structures are described, and experimental results comparing it to the widely used B+ tree and other structures used for full-text retrieval are…

Testing of a Natural Language Retrieval System for a Full Text Knowledge Base.

ERIC Educational Resources Information Center

Bernstein, Lionel M.; Williamson, Robert E.

1984-01-01

The Hepatitis Knowledge Base (text of prototype information system) was used for modifying and testing "A Navigator of Natural Language Organized (Textual) Data" (ANNOD), a retrieval system which combines probabilistic, linguistic, and empirical means to rank individual paragraphs of full text for similarity to natural language queries…

Foundations of Full Text Electronic Information Delivery Systems. Implications for Information Professionals.

ERIC Educational Resources Information Center

Kibirige, Harry M.

Information has become an increasingly valuable commodity. Access to full-text information, containing text, images, and in some cases, sound, is becoming vital to decision-making for organizations as well as individuals. The book covers the following topics: (1) the information marketplace in a cyberculture; (2) the telecommunications foundation…

Utility of Equations to Estimate Peak Oxygen Uptake and Work Rate From a 6-Minute Walk Test in Patients With COPD in a Clinical Setting.

PubMed

Kirkham, Amy A; Pauhl, Katherine E; Elliott, Robyn M; Scott, Jen A; Doria, Silvana C; Davidson, Hanan K; Neil-Sztramko, Sarah E; Campbell, Kristin L; Camp, Pat G

2015-01-01

To determine the utility of equations that use the 6-minute walk test (6MWT) results to estimate peak oxygen uptake ((Equation is included in full-text article.)o2) and peak work rate with chronic obstructive pulmonary disease (COPD) patients in a clinical setting. This study included a systematic review to identify published equations estimating peak (Equation is included in full-text article.)o2 and peak work rate in watts in COPD patients and a retrospective chart review of data from a hospital-based pulmonary rehabilitation program. The following variables were abstracted from the records of 42 consecutively enrolled COPD patients: measured peak (Equation is included in full-text article.)o2 and peak work rate achieved during a cycle ergometer cardiopulmonary exercise test, 6MWT distance, age, sex, weight, height, forced expiratory volume in 1 second, forced vital capacity, and lung diffusion capacity. Estimated peak (Equation is included in full-text article.)o2 and peak work rate were estimated from 6MWT distance using published equations. The error associated with using estimated peak (Equation is included in full-text article.)o2 or peak work to prescribe aerobic exercise intensities of 60% and 80% was calculated. Eleven equations from 6 studies were identified. Agreement between estimated and measured values was poor to moderate (intraclass correlation coefficients = 0.11-0.63). The error associated with using estimated peak (Equation is included in full-text article.)o2 or peak work rate to prescribe exercise intensities of 60% and 80% of measured values ranged from mean differences of 12 to 35 and 16 to 47 percentage points, respectively. There is poor to moderate agreement between measured peak (Equation is included in full-text article.)o2 and peak work rate and estimations from equations that use 6MWT distance, and the use of the estimated values for prescription of aerobic exercise intensity would result in large error. Equations estimating peak (Equation is included in full-text article.)o2 and peak work rate are of low utility for prescribing exercise intensity in pulmonary rehabilitation programs.

Delayed Anaerobic Threshold in Heart Failure Patients With Atrial Fibrillation.

PubMed

Palermo, Pietro; Magrì, Damiano; Sciomer, Susanna; Stefanini, Elisa; Agalbato, Cecilia; Compagnino, Elisa; Chircu, Cristina M; Maffessanti, Francesco; Teodoru, Minodora; Agostoni, Piergiuseppe

2016-01-01

To assess whether atrial fibrillation (AF) in heart failure (HF) affects oxygen uptake at anaerobic threshold ((Equation is included in full-text article.)O2 AT) and heart rate (HR) kinetics. A total of 15 patients with HF and AF and 18 with HF and sinus rhythm (SR) performed a maximal incremental and 2 constant workload cycle ergometer cardiopulmonary exercise tests (below and above AT, at 25% and 75% of maximal workload, respectively). At constant workload tests, kinetics of (Equation is included in full-text article.)O2 and HR were assessed by calculating time constant (τ). HF patients with AF showed a similar peak (Equation is included in full-text article.)O2 to those with SR (16.7 ± 4.5 mL/kg/min vs 16.6 ± 3.9 mL/kg/min). However, (Equation is included in full-text article.)O2 AT (11.3 ± 2.9 mL/kg/min vs 9.3 ± 2.8 mL/kg/min; P < .05), peak HR (149 ± 18.8 bpm vs 116.4 ± 20.4 bpm; P < .001), HR AT (125.3 ± 19.1 bpm vs 90.3 ± 15.5 bpm; P < .001), and HR increase during exercise were greater in HF patients with AF. Finally, τHR and τ(Equation is included in full-text article.)O2 below and above AT were not significantly different. In HF patients with AF, despite a similar peak (Equation is included in full-text article.)O2 compared with patients with HF and SR, (Equation is included in full-text article.)O2 AT is higher because of a higher HR and a greater HR increase during exercise. One postulated mechanism would be a greater cardiac output increase at the beginning of exercise in HF patients with AF. The delayed AT generates uncertainty about the meaning of a (Equation is included in full-text article.)O2 value at AT in HF patients with AF, because a higher AT is usually associated with better performance and a better prognosis.

Text mining resources for the life sciences.

PubMed

Przybyła, Piotr; Shardlow, Matthew; Aubin, Sophie; Bossy, Robert; Eckart de Castilho, Richard; Piperidis, Stelios; McNaught, John; Ananiadou, Sophia

2016-01-01

Text mining is a powerful technology for quickly distilling key information from vast quantities of biomedical literature. However, to harness this power the researcher must be well versed in the availability, suitability, adaptability, interoperability and comparative accuracy of current text mining resources. In this survey, we give an overview of the text mining resources that exist in the life sciences to help researchers, especially those employed in biocuration, to engage with text mining in their own work. We categorize the various resources under three sections: Content Discovery looks at where and how to find biomedical publications for text mining; Knowledge Encoding describes the formats used to represent the different levels of information associated with content that enable text mining, including those formats used to carry such information between processes; Tools and Services gives an overview of workflow management systems that can be used to rapidly configure and compare domain- and task-specific processes, via access to a wide range of pre-built tools. We also provide links to relevant repositories in each section to enable the reader to find resources relevant to their own area of interest. Throughout this work we give a special focus to resources that are interoperable-those that have the crucial ability to share information, enabling smooth integration and reusability. © The Author(s) 2016. Published by Oxford University Press.

Text mining resources for the life sciences

PubMed Central

Shardlow, Matthew; Aubin, Sophie; Bossy, Robert; Eckart de Castilho, Richard; Piperidis, Stelios; McNaught, John; Ananiadou, Sophia

2016-01-01

Text mining is a powerful technology for quickly distilling key information from vast quantities of biomedical literature. However, to harness this power the researcher must be well versed in the availability, suitability, adaptability, interoperability and comparative accuracy of current text mining resources. In this survey, we give an overview of the text mining resources that exist in the life sciences to help researchers, especially those employed in biocuration, to engage with text mining in their own work. We categorize the various resources under three sections: Content Discovery looks at where and how to find biomedical publications for text mining; Knowledge Encoding describes the formats used to represent the different levels of information associated with content that enable text mining, including those formats used to carry such information between processes; Tools and Services gives an overview of workflow management systems that can be used to rapidly configure and compare domain- and task-specific processes, via access to a wide range of pre-built tools. We also provide links to relevant repositories in each section to enable the reader to find resources relevant to their own area of interest. Throughout this work we give a special focus to resources that are interoperable—those that have the crucial ability to share information, enabling smooth integration and reusability. PMID:27888231

Use of multimedia in patient and caregiver education for cancer pain management: a literature review.

PubMed

Lam, Michael; Choi, Matthew; Lam, Helen R; Agarwal, Arnav; Chow, Ronald; Chow, Selina; Rowbottom, Leigha; McDonald, Rachel; Lam, Henry; Chan, Stephanie; Chow, Edward; Henry, Blair

2017-01-01

Pain is one of the most prominent symptoms faced by cancer patients. It is known that patient and caregiver-targeted educational interventions addressing the proper use of pain management may provide significant clinical value. This review examines the literature surrounding the use of multimedia interventions for patient and caregiver education (PCE) on pain management compared to traditional educational interventions. A literature search was conducted in Ovid MEDLINE (1946-July Week 2, 2016), Ovid Embase (1947-2016 Week 29), and Ovid Cochrane Central Register of Controlled Trials (up to June 2016). Paired reviewers conducted title and abstract screening and full-text screening to identify experimental, quasi-experimental and cohort studies evaluating one or more multimedia-based PCE interventions focused on cancer pain and pain management and targeting patients and/or caregivers. Findings were extracted by paired reviewers and synthesized qualitatively. Of the 68 full-text papers assessed, 7 were deemed relevant, of which 5 were RCTs and 2 were observational studies. We found limited but convincing quantitative data to suggest that the use of multimedia use in pain management education for patients/caregivers has greater value-added benefit compared to standard education. While there is evidence suggesting a positive effect on pain-related outcomes with the use of multimedia-based patient and caregiver-targeted interventions, it is limited to a small number of lower-quality studies. More robust and large-scale studies are needed to supplement existing evidence and provide more insight regarding the usability and user-friendliness of these tools in practice.

Effects of raloxifene on cognition, mental health, sleep and sexual function in menopausal women: a systematic review of randomized controlled trials.

PubMed

Yang, Z D; Yu, J; Zhang, Q

2013-08-01

Raloxifene has been used as therapy for osteoporosis and ER(+) breast cancer prevention in menopausal women. However, its effects on cognition and climacteric syndrome are controversial. This study reviews the relevant studies and reaches a comprehensive conclusion. We retrieved thirteen electronic databases, read the titles and abstracts to exclude ineligible articles, and then read the full text and references to form a basis for decisions using the inclusion criteria. If full text was not available, we asked the author for a copy of the article. After the data were extracted and recorded, the research quality was evaluated by two authors using the Jadad score and Cochrane handbook. We found seven eligible studies. The design, evaluated items, questionnaires and scales were heterogeneous. The design quality was fair as evaluated by the Cochrane Handbook. We found that 60 mg/day raloxifene could improve verbal memory, and 120 mg/day raloxifene produced a 33% decrease in the risk of mild cognitive impairment and also lowered the risk of Alzheimer's disease. There was not enough evidence to state if raloxifene had any effect on depression, anxiety, sleep, sexual function, vasomotor symptoms, but significantly worsened menstrual symptoms. Raloxifene may have some benefit for cognition, but it is not significant effect on anxiety, depression, sleep, sexual function, vasomotor symptoms and worsens menstrual symptoms. This drug is safe for treating osteoporosis and preventing breast cancer in menopausal women, but it is not suitable for patients who have any arterial stenosis or thrombophilia. Crown Copyright © 2013. Published by Elsevier Ireland Ltd. All rights reserved.

The Age Conundrum: A Scoping Review of Younger Age or Adolescent and Young Adult as a Risk Factor for Clinical Distress, Depression, or Anxiety in Cancer

PubMed Central

David, Victoria; Giese-Davis, Janine

2015-01-01

This scoping review was conducted to understand the extent, range, and nature of current research on adolescents and young adults (AYA) with cancer and distress, depression, and anxiety (DDA). This information is necessary to find and aggregate valuable data on the AYA population embedded in generalized studies of DDA. Keyword searches of six relevant electronic databases identified 2156 articles, with 316 selected for abstract review and 40 for full text review. Full-text reviews and data extraction resulted in 34 studies being included, which ranged widely in design, sample size, age-range categorization, analysis methods, DDA measurement tool, overall study rigor, and quality of evidence. Studies very seldom reported using theory to guide their age categorization, with only four studies giving any rationale for their age-group definitions. All 34 studies found a significant association between at least one DDA construct and the younger age group relative to the older age groups at some point along the cancer trajectory. However, age as an independent risk factor for DDA is still unclear, as the relationship could be confounded by other age-related factors. Despite the wide range of definitions and effect sizes in the studies included in this review, one thing is clear: adolescents and young adults, however defined, are a distinct group within the cancer population with an elevated risk of DDA. Widespread adoption of a standard AYA age-range definition will be essential to any future meta-analytical psycho-oncology research in this population. PMID:26697266

A Systematic Review of Unmet Information and Psychosocial Support Needs of Adults Diagnosed with Thyroid Cancer.

PubMed

Hyun, Yong Gyu; Alhashemi, Ahmad; Fazelzad, Rouhi; Goldberg, Alyse S; Goldstein, David P; Sawka, Anna M

2016-09-01

Patient education and psychosocial support to patients are important elements of comprehensive cancer care, but the needs of thyroid cancer survivors are not well understood. The published English-language quantitative literature on (i) unmet medical information and (ii) psychosocial support needs of thyroid cancer survivors was systematically reviewed. A librarian information specialist searched seven electronic databases and a hand search was conducted. Two reviewers independently screened citations from the electronic search and reviewed relevant full-text papers. There was consensus between reviewers on the included papers, and duplicate independent abstraction was performed. The results were summarized descriptively. A total of 1984 unique electronic citations were screened, and 51 full-text studies were reviewed (three from the hand search). Seven cross-sectional, single-arm, survey studies were included, containing data from 6215 thyroid cancer survivor respondents. The respective study sizes ranged from 57 to 2398 subjects. All of the studies had some methodological limitations. Unmet information needs were variable relating to the disease, diagnostic tests, treatments, and co-ordination of medical care. There were relatively high unmet information needs related to aftercare (especially long-term effects of the disease or its treatment and its management) and psychosocial concerns (including practical and financial matters). Psychosocial support needs were incompletely met. Patient information on complementary and alternative medicine was very limited. In conclusion, thyroid cancer survivors perceive many unmet information needs, and these needs extend to aftercare. Psychosocial information and supportive care needs may be insufficiently met in this population. More work is needed to improve knowledge translation and psychosocial support for thyroid cancer survivors.

The Age Conundrum: A Scoping Review of Younger Age or Adolescent and Young Adult as a Risk Factor for Clinical Distress, Depression, or Anxiety in Cancer.

PubMed

Lang, Michael J; David, Victoria; Giese-Davis, Janine

2015-12-01

This scoping review was conducted to understand the extent, range, and nature of current research on adolescents and young adults (AYA) with cancer and distress, depression, and anxiety (DDA). This information is necessary to find and aggregate valuable data on the AYA population embedded in generalized studies of DDA. Keyword searches of six relevant electronic databases identified 2156 articles, with 316 selected for abstract review and 40 for full text review. Full-text reviews and data extraction resulted in 34 studies being included, which ranged widely in design, sample size, age-range categorization, analysis methods, DDA measurement tool, overall study rigor, and quality of evidence. Studies very seldom reported using theory to guide their age categorization, with only four studies giving any rationale for their age-group definitions. All 34 studies found a significant association between at least one DDA construct and the younger age group relative to the older age groups at some point along the cancer trajectory. However, age as an independent risk factor for DDA is still unclear, as the relationship could be confounded by other age-related factors. Despite the wide range of definitions and effect sizes in the studies included in this review, one thing is clear: adolescents and young adults, however defined, are a distinct group within the cancer population with an elevated risk of DDA. Widespread adoption of a standard AYA age-range definition will be essential to any future meta-analytical psycho-oncology research in this population.

Maxillary complete denture outcome with two-implant supported mandibular overdentures. A systematic review.

PubMed

Rutkunas, Vygandas; Mizutani, Hiroshi; Peciuliene, Vytaute; Bendinskaite, Ruta; Linkevicius, Tomas

2008-01-01

Research data regarding maxillary complete denture outcome with two-implant supported mandibular overdentures are not consistent. Considering multiple publications on implant supported mandibular overdentures, it was decided to summarize currently present evidence on the maxillary complete dentures opposed by implant-supported mandibular overdentures, and analyze factors that could potentially influence the outcomes. The articles from 1985 to 2007 related to the topic were identified in the online MEDLINE/Pubmed and other databases and manually. Primary articles were scanned, and irrelevant studies were excluded from the further review process. Potentially relevant titles and abstracts were provisionally included for consideration on the basis of full text articles. Full text articles were obtained from on-line and printed sources. The data from the studies were extracted and reviewed. The study has failed to identify any prospective satisfying inclusion/exclusion criteria RCT reporting on maxillary bone resorption. The number of maxillary complete denture relining incidences per patient was constantly increasing during the 10-year period. Maxillary complete denture remake incidences comprised 16-33 % of the number of patients followed during the 10-year period. Comparing patient satisfaction with upper dentures at the baseline and after two years, no decrease in satisfaction was noticed. There is no evidence that maxillary ridge resorption is accelerated with certain types of two-implant supported mandibular overdenture attachments. Most common complication for the maxilla - prosthetic maintenance. There is a risk of decreased patient satisfaction with bar-supported mandibular overdenture. Further studies are needed to provide evidence for the maxillary complete denture outcome with two-implant supported mandibular overdentures.

76 FR 17353 - Aviation Communications

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-29

... publication). The full text of this document is available for public inspection and copying during regular... Printing, Inc., 445 12th Street, SW., Room CY-B402, Washington, DC 20554. The full text may also be...

Prevalence, incidence and aetiologies of pulmonary hypertension in Africa: a systematic review and meta-analysis protocol.

PubMed

Bigna, Jean Joel; Noubiap, Jean Jacques; Nansseu, Jobert Richie; Aminde, Leopold Ndemnge

2017-06-16

There are no data summarising the epidemiology of pulmonary hypertension (PH) among adults residing in Africa. Establishment of accurate epidemiological data on PH in this region may guide decision-making toward interventions to curb the burden of PH in Africa. The aim of this systematic review is to determine the prevalence, incidence and aetiologies of PH among people residing in Africa. This systematic review and meta-analysis will follow the MOOSE guidelines for reporting. Relevant abstracts published until 30 September 2016 will be searched in PubMed/Medline, EMBASE (Excerpta Medica Database), African Journals Online and Africa Index Medicus. Full texts of eligible studies will then be accessed through PubMed, Google Scholar, HINARI and the respective journals' websites. Relevant unpublished papers and conference proceedings will also be checked. Data will be analysed using STATA version 13 software. The study-specific estimates will be pooled through a random-effects meta-analysis model to obtain an overall summary estimate of the prevalence/incidence and aetiologies of PH across studies. Heterogeneity of studies will be evaluated by the χ 2 test on Cochrane's Q statistic. Funnel plot analysis and Egger's test will be done to detect publication bias. Results will be presented by geographical region (central, eastern, northern, southern and western Africa). The current study is based on published data; ethical approval is, therefore, not required. This review will guide policy, practice and research by providing information on the magnitude of PH among people residing in Africa. Findings will be presented in evidence tables of individual studies as well as in summary tables. The final report of this systematic review, in the form of a scientific paper, will be published in a peer-reviewed journal. Furthermore, findings will be presented at conferences and submitted to relevant health authorities. PROSPERO CRD42016049351. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

The contribution of nurses to incident disclosure: a narrative review.

PubMed

Harrison, Reema; Birks, Yvonne; Hall, Jill; Bosanquet, Kate; Harden, Melissa; Iedema, Rick

2014-02-01

To explore (a) how nurses feel about disclosing patient safety incidents to patients, (b) the current contribution that nurses make to the process of disclosing patient safety incidents to patients and (c) the barriers that nurses report as inhibiting their involvement in disclosure. A systematic search process was used to identify and select all relevant material. Heterogeneity in study design of the included articles prohibited a meta-analysis and findings were therefore synthesised in a narrative review. A range of text words, synonyms and subject headings were developed in conjunction with the York Centre for Reviews and Dissemination and used to undertake a systematic search of electronic databases (MEDLINE; EMBASE; CENTRAL; PsycINFO; Health Management and Information Consortium; CINAHL; ASSIA; Science Citation Index; Social Science Citation Index; Cochrane Database of Systematic Reviews; Database of Abstracts of Reviews of Effects; Health Technology Assessment Database; Health Systems Evidence; PASCAL; LILACS). Retrieval of studies was restricted to those published after 1980. Further data sources were: websites, grey literature, research in progress databases, hand-searching of relevant journals and author contact. The title and abstract of each citation was independently screened by two reviewers and disagreements resolved by consensus or consultation with a third person. Full text articles retrieved were further screened against the inclusion and exclusion criteria then checked by a second reviewer (YB). Relevant data were extracted and findings were synthesised in a narrative empirical synthesis. The systematic search and selection process identified 15 publications which included 11 unique studies that emerged from a range of locations. Findings suggest that nurses currently support both physicians and patients through incident disclosure, but may be ill-prepared to disclose incidents independently. Barriers to nurse involvement included a lack of opportunities for education and training, and the multiple and sometimes conflicting roles within nursing. Numerous potential benefits were identified that may result from nurses having a greater contribution to the disclosure process, but the provision of support and training is essential to overcome the reported barriers faced by nurses internationally. Copyright © 2013 Elsevier Ltd. All rights reserved.

Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature.

PubMed

Wang, Xinglong; Rak, Rafal; Restificar, Angelo; Nobata, Chikashi; Rupp, C J; Batista-Navarro, Riza Theresa B; Nawaz, Raheel; Ananiadou, Sophia

2011-10-03

The selection of relevant articles for curation, and linking those articles to experimental techniques confirming the findings became one of the primary subjects of the recent BioCreative III contest. The contest's Protein-Protein Interaction (PPI) task consisted of two sub-tasks: Article Classification Task (ACT) and Interaction Method Task (IMT). ACT aimed to automatically select relevant documents for PPI curation, whereas the goal of IMT was to recognise the methods used in experiments for identifying the interactions in full-text articles. We proposed and compared several classification-based methods for both tasks, employing rich contextual features as well as features extracted from external knowledge sources. For IMT, a new method that classifies pair-wise relations between every text phrase and candidate interaction method obtained promising results with an F1 score of 64.49%, as tested on the task's development dataset. We also explored ways to combine this new approach and more conventional, multi-label document classification methods. For ACT, our classifiers exploited automatically detected named entities and other linguistic information. The evaluation results on the BioCreative III PPI test datasets showed that our systems were very competitive: one of our IMT methods yielded the best performance among all participants, as measured by F1 score, Matthew's Correlation Coefficient and AUC iP/R; whereas for ACT, our best classifier was ranked second as measured by AUC iP/R, and also competitive according to other metrics. Our novel approach that converts the multi-class, multi-label classification problem to a binary classification problem showed much promise in IMT. Nevertheless, on the test dataset the best performance was achieved by taking the union of the output of this method and that of a multi-class, multi-label document classifier, which indicates that the two types of systems complement each other in terms of recall. For ACT, our system exploited a rich set of features and also obtained encouraging results. We examined the features with respect to their contributions to the classification results, and concluded that contextual words surrounding named entities, as well as the MeSH headings associated with the documents were among the main contributors to the performance.

Relevans og intention. To analyser af en massemedietekst om okonomisk politik. ROLIG-papir 33 (Relevance and Intention. Two Analyses of a Mass Media Text on Economic Politics. ROLIG-paper 33).

ERIC Educational Resources Information Center

Heltoft, Lars; Geist, Uwe

The three papers in this publication analyze a newspaper article on "economic politics," or more specifically, the devaluing of the Danish kroner. The papers all examine some linguistic or structural feature of the language used in writing the article. Specific focus is on relevance theory and relevance in the article, the use of text…

Motivation and Learning--The Role of Interest in Construction of Representation of Text and Long-Term Retention: Inter- and Intraindividual Analyses

ERIC Educational Resources Information Center

Naceur, Abdelmajid; Schiefele, Ulrich

2005-01-01

The present work examined the influence of topic interest on the strength of different components of text representation and long-term retention according to the model of text processing by van Dijk and Kintsch (1983). A Series of relevant personality characteristics were assessed to control for alternative explanations of interest effect, A total…

Investigating the Effects of Culturally Relevant Texts on African American Struggling Readers' Progress

ERIC Educational Resources Information Center

Clark, Kathleen F.

2017-01-01

Background/Context: In a recent review of culturally relevant instruction and reading comprehension, Fairbanks, Cooper, Masterson, and Webb (2009) highlighted the paucity of research available to support the widespread claim in the literacy field that "students' social and cultural practices are deeply intertwined with literacy learning"…

Systematic review of guidelines for the physical management of osteoarthritis.

PubMed

Larmer, Peter J; Reay, Nicholas D; Aubert, Elizabeth R; Kersten, Paula

2014-02-01

To undertake a systematic critical appraisal of guidelines to provide a summary of recommendations for the physical management of osteoarthritis (OA). The Cochrane Library, MEDLINE, CINAHL, SPORTDiscus with Full Text, Scopus, ScienceDirect, PEDro, and Google Scholar databases were searched (2000-2013) to identify all guidelines, protocols, and recommendations for the management or treatment of OA. In addition, Internet searches of all relevant arthritis organizations were undertaken. All searches were performed between July 2012 and end of April 2013. Guidelines that included only pharmacological, injection therapy, or surgical interventions were excluded. Guidelines published only in English were retrieved. OA guidelines developed from evidence-based research, consensus, and/or expert opinion were retrieved. There were no restrictions on severity or site of OA, sex, or age. Nineteen guidelines were identified for evaluation. The quality of all guidelines was critically appraised using the Appraisal of Guidelines for REsearch and Evaluation II instrument. Each guideline was independently reviewed. All relevant recommendations for the physical management of OA were synthesized, graded, and ranked according to available evidence. Seventeen guidelines with recommendations on the physical management of OA met the inclusion criteria and underwent a full critical appraisal. There were variations in the interventions, levels of evidence, and strength of recommendations across the guidelines. Forty different interventions were identified. Recommendations were graded from "strongly recommended" to "unsupported." Exercise and education were found to be strongly recommended by most guidelines. Exercise and education were key recommendations supporting the importance of rehabilitation in the physical management of OA. This critical appraisal can assist health care providers who are involved in the management of people with OA. Copyright © 2014 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools

PubMed Central

2012-01-01

Background We introduce the linguistic annotation of a corpus of 97 full-text biomedical publications, known as the Colorado Richly Annotated Full Text (CRAFT) corpus. We further assess the performance of existing tools for performing sentence splitting, tokenization, syntactic parsing, and named entity recognition on this corpus. Results Many biomedical natural language processing systems demonstrated large differences between their previously published results and their performance on the CRAFT corpus when tested with the publicly available models or rule sets. Trainable systems differed widely with respect to their ability to build high-performing models based on this data. Conclusions The finding that some systems were able to train high-performing models based on this corpus is additional evidence, beyond high inter-annotator agreement, that the quality of the CRAFT corpus is high. The overall poor performance of various systems indicates that considerable work needs to be done to enable natural language processing systems to work well when the input is full-text journal articles. The CRAFT corpus provides a valuable resource to the biomedical natural language processing community for evaluation and training of new models for biomedical full text publications. PMID:22901054

[Formula: see text]: Oblivious similarity based searching for encrypted data outsourced to an untrusted domain.

PubMed

Pervez, Zeeshan; Ahmad, Mahmood; Khattak, Asad Masood; Ramzan, Naeem; Khan, Wajahat Ali

2017-01-01

Public cloud storage services are becoming prevalent and myriad data sharing, archiving and collaborative services have emerged which harness the pay-as-you-go business model of public cloud. To ensure privacy and confidentiality often encrypted data is outsourced to such services, which further complicates the process of accessing relevant data by using search queries. Search over encrypted data schemes solve this problem by exploiting cryptographic primitives and secure indexing to identify outsourced data that satisfy the search criteria. Almost all of these schemes rely on exact matching between the encrypted data and search criteria. A few schemes which extend the notion of exact matching to similarity based search, lack realism as those schemes rely on trusted third parties or due to increase storage and computational complexity. In this paper we propose Oblivious Similarity based Search ([Formula: see text]) for encrypted data. It enables authorized users to model their own encrypted search queries which are resilient to typographical errors. Unlike conventional methodologies, [Formula: see text] ranks the search results by using similarity measure offering a better search experience than exact matching. It utilizes encrypted bloom filter and probabilistic homomorphic encryption to enable authorized users to access relevant data without revealing results of search query evaluation process to the untrusted cloud service provider. Encrypted bloom filter based search enables [Formula: see text] to reduce search space to potentially relevant encrypted data avoiding unnecessary computation on public cloud. The efficacy of [Formula: see text] is evaluated on Google App Engine for various bloom filter lengths on different cloud configurations.

48 CFR 52.252-1 - Solicitation Provisions Incorporated by Reference.

Code of Federal Regulations, 2010 CFR

2010-10-01

... and submitted with its quotation or offer. In lieu of submitting the full text of those provisions... with its quotation or offer. Also, the full text of a solicitation provision may be accessed...

Elucidating high-dimensional cancer hallmark annotation via enriched ontology.

PubMed

Yan, Shankai; Wong, Ka-Chun

2017-09-01

Cancer hallmark annotation is a promising technique that could discover novel knowledge about cancer from the biomedical literature. The automated annotation of cancer hallmarks could reveal relevant cancer transformation processes in the literature or extract the articles that correspond to the cancer hallmark of interest. It acts as a complementary approach that can retrieve knowledge from massive text information, advancing numerous focused studies in cancer research. Nonetheless, the high-dimensional nature of cancer hallmark annotation imposes a unique challenge. To address the curse of dimensionality, we compared multiple cancer hallmark annotation methods on 1580 PubMed abstracts. Based on the insights, a novel approach, UDT-RF, which makes use of ontological features is proposed. It expands the feature space via the Medical Subject Headings (MeSH) ontology graph and utilizes novel feature selections for elucidating the high-dimensional cancer hallmark annotation space. To demonstrate its effectiveness, state-of-the-art methods are compared and evaluated by a multitude of performance metrics, revealing the full performance spectrum on the full set of cancer hallmarks. Several case studies are conducted, demonstrating how the proposed approach could reveal novel insights into cancers. https://github.com/cskyan/chmannot. Copyright © 2017 Elsevier Inc. All rights reserved.

The indications for polysomnography and related procedures.

PubMed

Chesson, A L; Ferber, R A; Fry, J M; Grigg-Damberger, M; Hartse, K M; Hurwitz, T D; Johnson, S; Kader, G A; Littner, M; Rosen, G; Sangal, R B; Schmidt-Nowara, W; Sher, A

1997-06-01

This paper is a review of the literature on the use of polysomnography in the diagnosis of sleep disorders in the adult. It is based on a search of MEDLINE from January 1966 through April 1996. It has been reviewed and approved by the Board of Directors of the American Sleep Disorders Association and provides the background for the accompanying ASDA Standards of Practice Committee's Parameters for the Practice of Sleep Medicine in North America. The diagnostic categories reviewed are: sleep-related breathing disorders; other respiratory disorders; narcolepsy; parasomnias and sleep-related epilepsy; restless legs syndrome and periodic limb movement disorders: insomnia; and circadian rhythm sleep disorders. Where appropriate, previously published practice parameters papers are cited and discussed. The relevant published peer-reviewed literature used as the basis for critical decisions was compiled into accompanying evidence tables and is analyzed in the text. In the section on the assessment of sleep apnea syndrome, options for estimating pretest probability to select high risk patients are also reviewed. Sleep-testing procedures other than standard polysomnography are also addressed (daytime polysomnography, split-night studies, oximetry, limited full respiratory recordings, and less-than-full respiratory recording) and treatment-related follow-up studies are discussed.

Identity Texts and Academic Achievement: Connecting the Dots in Multilingual School Contexts

ERIC Educational Resources Information Center

Cummins, Jim; Hu, Shirley; Markus, Paula; Kristiina Montero, M.

2015-01-01

The construct of "identity text" conjoins notions of identity affirmation and literacy engagement as equally relevant to addressing causes of underachievement among low socioeconomic status, multilingual, and marginalized group students. Despite extensive empirical evidence supporting the impact on academic achievement of both identity…

Tuberculosis treatment outcome monitoring in European Union countries: systematic review

PubMed Central

van Hest, Rob; Ködmön, Csaba; Verver, Suzanne; Erkens, Connie G.M.; Straetemans, Masja; Manissero, Davide; de Vries, Gerard

2013-01-01

Treatment success measured by treatment outcome monitoring (TOM) is a key programmatic output of tuberculosis (TB) control programmes. We performed a systematic literature review on national-level TOM in the 30 European Union (EU)/European Economic Areas (EEA) countries to summarise methods used to collect and report data on TOM. Online reference bibliographic databases PubMed/MEDLINE and EMBASE were searched to identify relevant indexed and non-indexed literature published between January 2000 and August 2010. The search strategy resulted in 615 potentially relevant indexed citations, of which 27 full-text national studies (79 data sets) were included for final analysis. The selected studies were performed in 10 EU/EEA countries and gave a fragmented impression of TOM in the EU/EEA. Publication year, study period, sample size, databases, definitions, variables, patient and outcome categories, and population subgroups varied widely, portraying a very heterogeneous picture. This review confirmed previous reports of considerable heterogeneity in publications of TOM results across EU/EEA countries. PubMed/MEDLINE and EMBASE indexed studies are not a suitable instrument to measure representative TOM results for the 30 EU/EEA countries. Uniform and complete reporting to the centralised European Surveillance System will produce the most timely and reliable results of TB treatment outcomes in the EU/EEA. PMID:22790913

The risk of elevated prolactin levels in pediatric patients exposed to antipsychotics for the treatment of schizophrenia and schizophrenia spectrum disorders: protocol for a systematic review and meta-analysis

PubMed Central

2014-01-01

Background Antipsychotic medications, particularly second-generation antipsychotics, are increasingly being used to alleviate the symptoms of schizophrenia and other severe mental disorders in the pediatric population. While evidence-based approaches examining efficacy and safety outcomes have been reported, no review has evaluated prolactin-based adverse events for antipsychotic treatments in schizophrenia and schizophrenia spectrum disorders. Methods/design Searches involving MEDLINE, EMBASE, CENTRAL, PsycINFO, and clinical trial registries (ClinicalTrials.gov, Drug Industry Document Archive [DIDA], International Clinical Trials Registry Platform [ICTRP]) will be used to identify relevant studies. Two reviewers will independently screen abstracts and relevant full-text articles of the papers identified by the initial search according to the prospectively defined eligibility criteria. Data extraction will be conducted in duplicate independently. Pairwise random effects meta-analyses and network meta-analyses will be conducted on individual drug and class effects where appropriate. Discussion This systematic review will evaluate prolactin-based adverse events of first- and second-generation antipsychotics in the pediatric population with schizophrenia and schizophrenia spectrum disorders. It will also seek to strengthen the evidence base of the safety of antipsychotics by incorporating both randomized controlled trials and observational studies. Systematic review registration PROSPERO CRD42014009506 PMID:25312992

Mind-to-paper is an effective method for scientific writing.

PubMed

Rosenberg, Jacob; Burcharth, Jakob; Pommergaard, Hans Christian; Danielsen, Anne Kjærgaard

2013-03-01

The problem of initiating the writing process is a well-known phenomenon, especially for young and inexperienced scientists. The purpose of this paper is to present an effective method to overcome this problem and increase writing efficiency among inexperienced scientists. Twelve young scientists within the medical/surgical fields were introduced to the mind-to-paper concept. The first and last article drafts produced by each of the scientists were scored for language complexity (LIX number, Flesch Reading Ease Scale and Gunning Fog), flow, structure, length and use of references; and the results were compared. All participants produced one full article draft during each of the three dictation days. When comparing the first and last article draft regarding time used, no significant difference was detected. In general, the manuscripts were of high quality on all evaluated parameters, but language complexity had increased in the final manuscript. Mind-to-paper dictation for scientific writing is an effective method for production of scientific papers of good initial quality, even when used for the first time by inexperienced scientists. We conclude that practicing this concept produces papers of an adequate language complexity, and that dictation as a writing tool allows for fast transfer of ideas and thoughts to written text. not relevant. not relevant.

Interventions for attention problems after pediatric traumatic brain injury: what is the evidence?

PubMed

Backeljauw, Barynia; Kurowski, Brad G

2014-09-01

To gain an understanding of the current state of the evidence for management of attention problems after traumatic brain injury (TBI) in children, determine gaps in the literature, and make recommendations for future research. TYPE: Focused systematic review. PubMed/Medline and PsychINFO databases were searched for relevant articles published in English during the last 20 years. Keywords included "attention" "attention deficit and disruptive behavior disorders," and "brain injuries." Studies were limited to children. Titles were examined first and eliminated based on lack of relevancy to attention problems after brain injury in children. This was followed by an abstract and full text review. Article quality was determined based on the US Preventative Services Task Force recommendations for evidence grading. Four pharmacologic and 10 cognitive therapy intervention studies were identified. These studies varied in level of evidence quality but were primarily nonrandomized or cohort studies. There are studies that demonstrate benefits of varying pharmacologic and cognitive therapies for the management of attention problems after TBI. However, there is a paucity of evidence available to definitively guide management of attention problems after pediatric TBI. Larger randomized, controlled trials and multicenter studies are needed to elucidate optimal treatment strategies in this population. Copyright © 2014 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

Deinfibulation for treating urologic complications of type III female genital mutilation: A systematic review.

PubMed

Effa, Emmanuel; Ojo, Olumuyiwa; Ihesie, Austin; Meremikwu, Martin M

2017-02-01

Women and girls who have undergone type III female genital mutilation (FGM) may suffer urologic complications such as recurrent urinary tract infections, obstruction, stones, and incontinence. To assess the effectiveness of deinfibulation for preventing and treating urologic complications in women and girls living with FGM. The following major databases were searched from inception to August 2015: Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, SCOPUS, Web of Science, and ClinicalTrials.gov without language restrictions. Randomized controlled studies (RCTs) or observational studies with controls were considered. We screened the results of the search independently for potentially relevant studies and applied inclusion and exclusion criteria for the full texts of the relevant studies. No RCTs were found. We found three case reports and a retrospective case review, all of which were excluded. There is no evidence on the use of deinfibulation to improve urologic complications among women with type III FGM. Current clinical practice may be informed by anecdotal evidence from case reports. Appropriate RCTs and observational studies with comparison groups in countries where FGM is common are needed. PROSPERO registration: CRD42015024901. © 2017 International Federation of Gynecology and Obstetrics. The World Health Organization retains copyright and all other rights in the manuscript of this article as submitted for publication.

2015 SCAI/ACC/HFSA/STS Clinical Expert Consensus Statement on the Use of Percutaneous Mechanical Circulatory Support Devices in Cardiovascular Care (Endorsed by the American Heart Association, the Cardiological Society of India, and Sociedad Latino Americana de Cardiología Intervencionista; Affirmation of Value by the Canadian Association of Interventional Cardiology-Association Canadienne de Cardiologie d'intervention).

PubMed

Rihal, Charanjit S; Naidu, Srihari S; Givertz, Michael M; Szeto, Wilson Y; Burke, James A; Kapur, Navin K; Kern, Morton; Garratt, Kirk N; Goldstein, James A; Dimas, Vivian; Tu, Thomas

2015-06-01

This article provides a brief summary of the relevant recommendations and references related to percutaneous mechanical circulatory support. The goal was to provide the clinician with concise, evidence-based contemporary recommendations, and the supporting documentation to encourage their application. The full text includes disclosure of all relevant relationships with industry for each writing committee member. A fundamental aspect of all expert consensus statements is that these carefully developed, evidence-based documents can neither encompass all clinical circumstances, nor replace the judgment of individual physicians in management of each patient. The science of medicine is rooted in evidence, and the art of medicine is based on the application of this evidence to the individual patient. This expert consensus statement has adhered to these principles for optimal management of patients requiring percutaneous mechanical circulatory support. © 2015 by The Society for Cardiovascular Angiography and Interventions, The American College of Cardiology Foundation, the Heart Failure Society of America, and The Society for Thoracic Surgery.

Association between foot type and tibial stress injuries: a systematic review.

PubMed

Barnes, A; Wheat, J; Milner, C

2008-02-01

To systematically review published articles investigating the association between structural foot characteristics and tibial stress injuries, and to suggest possible future avenues of research in this area. Literature was identified, selected and appraised in accordance with the methods of a systematic review. Articles potentially relevant to the research question were identified by searching the following electronic databases: Amed, Cinahl, Index to UK theses, Medline, PubMed, Scopus, Sports discus and Web of science. Duplicates were removed and, based on the title and abstract, the full text of relevant studies were retrieved. Two reviewers independently assessed papers; this formed the basis for the inclusion of the most appropriate trials. From the 479 articles originally identified, nine were deemed appropriate for inclusion in the review. In general, specific data relating to this relationship was limited. Outcomes of the nine investigations were difficult to compare due to differing methods used across studies. Results have proved conflicting, with limited evidence found to implicate any specific foot type as a potential risk factor for tibial stress injuries. No definitive conclusions can be drawn relating foot structure or function to an increased risk of tibial stress injuries. Extremes of foot types are likely to pose an increased risk of tibial stress injuries compared to normal arched feet.

Use of Web-based library resources by medical students in community and ambulatory settings.

PubMed

Tannery, Nancy Hrinya; Foust, Jill E; Gregg, Amy L; Hartman, Linda M; Kuller, Alice B; Worona, Paul; Tulsky, Asher A

2002-07-01

The purpose was to evaluate the use of Web-based library resources by third-year medical students. Third-year medical students (147) in a twelve-week multidisciplinary primary care rotation in community and ambulatory settings. Individual user surveys and log file analysis of Website were used. Twenty resource topics were compiled into a Website to provide students with access to electronic library resources from any community-based clerkship location. These resource topics, covering subjects such as hypertension and back pain, linked to curriculum training problems, full-text journal articles, MEDLINE searches, electronic book chapters, and relevant Websites. More than half of the students (69%) accessed the Website on a daily or weekly basis. Over 80% thought the Website was a valuable addition to their clerkship. Web-based information resources can provide curriculum support to students for whom access to the library is difficult and time consuming.

Emerging treatments for primary sclerosing cholangitis.

PubMed

Rodriguez, Eduardo A; Carey, Elizabeth J; Lindor, Keith D

2017-05-01

Primary sclerosing cholangitis (PSC) is a chronic, cholestatic, idiopathic liver disease that can progress to end-stage liver disease, cirrhosis and cholangiocarcinoma. PSC is an uncommon and highly heterogeneous disease, associated with inflammatory bowel disease and a complex pathophysiology. To date, no medical therapies have proved effective. The only available treatment for end-stage PSC is liver transplant, but recurrence is a significant complication. Areas covered: This review will explore previously tested treatments, discuss current treatment strategies and present viewpoints about future emerging therapies in PSC. We searched PubMed using the noted keywords. We included data from full-text articles published in English. Further relevant articles were identified from the reference lists of review articles. Expert commentary: The development of new therapies in PSC has been challenging. However, with greater awareness of the disease nowadays, new insights into the disease may help in the design of future therapeutic agents in PSC and ultimately in effective therapies.

TUTORIAL: Development of a cortical visual neuroprosthesis for the blind: the relevance of neuroplasticity

NASA Astrophysics Data System (ADS)

Fernández, E.; Pelayo, F.; Romero, S.; Bongard, M.; Marin, C.; Alfaro, A.; Merabet, L.

2005-12-01

Clinical applications such as artificial vision require extraordinary, diverse, lengthy and intimate collaborations among basic scientists, engineers and clinicians. In this review, we present the state of research on a visual neuroprosthesis designed to interface with the occipital visual cortex as a means through which a limited, but useful, visual sense could be restored in profoundly blind individuals. We review the most important physiological principles regarding this neuroprosthetic approach and emphasize the role of neural plasticity in order to achieve desired behavioral outcomes. While full restoration of fine detailed vision with current technology is unlikely in the immediate near future, the discrimination of shapes and the localization of objects should be possible allowing blind subjects to navigate in a unfamiliar environment and perhaps even to read enlarged text. Continued research and development in neuroprosthesis technology will likely result in a substantial improvement in the quality of life of blind and visually impaired individuals.

Reprint of: Client interfaces to the Virtual Observatory Registry

NASA Astrophysics Data System (ADS)

Demleitner, M.; Harrison, P.; Taylor, M.; Normand, J.

2015-06-01

The Virtual Observatory Registry is a distributed directory of information systems and other resources relevant to astronomy. To make it useful, facilities to query that directory must be provided to humans and machines alike. This article reviews the development and status of such facilities, also considering the lessons learnt from about a decade of experience with Registry interfaces. After a brief outline of the history of the standards development, it describes the use of Registry interfaces in some popular clients as well as dedicated UIs for interrogating the Registry. It continues with a thorough discussion of the design of the two most recent Registry interface standards, RegTAP on the one hand and a full-text-based interface on the other hand. The article finally lays out some of the less obvious conventions that emerged in the interaction between providers of registry records and Registry users as well as remaining challenges and current developments.

Client interfaces to the Virtual Observatory Registry

NASA Astrophysics Data System (ADS)

Demleitner, M.; Harrison, P.; Taylor, M.; Normand, J.

2015-04-01

The Virtual Observatory Registry is a distributed directory of information systems and other resources relevant to astronomy. To make it useful, facilities to query that directory must be provided to humans and machines alike. This article reviews the development and status of such facilities, also considering the lessons learnt from about a decade of experience with Registry interfaces. After a brief outline of the history of the standards development, it describes the use of Registry interfaces in some popular clients as well as dedicated UIs for interrogating the Registry. It continues with a thorough discussion of the design of the two most recent Registry interface standards, RegTAP on the one hand and a full-text-based interface on the other hand. The article finally lays out some of the less obvious conventions that emerged in the interaction between providers of registry records and Registry users as well as remaining challenges and current developments.

Telemedicine Services for the Arctic: A Systematic Review

PubMed Central

Walderhaug, Ståle; Hartvigsen, Gunnar

2017-01-01

Background Telemedicine services have been successfully used in areas where there are adequate infrastructures such as reliable power and communication lines. However, despite the increasing number of merchants and seafarers, maritime and Arctic telemedicine have had limited success. This might be linked with various factors such as lack of good infrastructure, lack of trained onboard personnel, lack of Arctic-enhanced telemedicine equipment, extreme weather conditions, remoteness, and other geographical challenges. Objective The purpose of this review was to assess and analyze the current status of telemedicine services in the context of maritime conditions, extreme weather (ie, Arctic weather), and remote accidents and emergencies. Moreover, the paper aimed to identify successfully implemented telemedicine services in the Arctic region and in maritime settings and remote emergency situations and present state of the art systems for these areas. Finally, we identified the status quo of telemedicine services in the context of search and rescue (SAR) scenarios in these extreme conditions. Methods A rigorous literature search was conducted between September 7 and October 28, 2015, through various online databases. Peer reviewed journals and articles were considered. Relevant articles were first identified by reviewing the title, keywords, and abstract for a preliminary filter with our selection criteria, and then we reviewed full-text articles that seemed relevant. Information from the selected literature was extracted based on some predefined categories, which were defined based on previous research and further elaborated upon via iterative brainstorming. Results The initial hits were vetted using the title, abstract, and keywords, and we retrieved a total of 471 papers. After removing duplicates from the list, 422 records remained. Then, we did an independent assessment of the articles and screening based on the inclusion and exclusion criteria, which eliminated another 219 papers, leaving 203 relevant papers. After a full-text assessment, 36 articles were left, which were critically analyzed. The inter-rater agreement was measured using Cohen Kappa test, and disagreements were resolved through discussion. Conclusions Despite the increasing number of fishermen and other seafarers, Arctic and maritime working conditions are mainly characterized by an absence of access to health care facilities. The condition is further aggravated for fishermen and seafarers who are working in the Arctic regions. In spite of the existing barriers and challenges, some telemedicine services have recently been successfully delivered in these areas. These services include teleconsultation (9/37, 24%), teleradiology (8/37, 22%), teledermatology and tele-education (3/37, 8%), telemonitoring and telecardiology (telesonography) (1/37, 3%), and others (10/37, 27%). However, the use of telemedicine in relation to search and rescue (SAR) services is not yet fully exploited. Therefore, we foresee that these implemented and evaluated telemedicine services will serve as underlying models for the successful implementation of future search and rescue (SAR) services. PMID:28659257

Are opioid antagonists effective in reducing self-injury in adults with intellectual disability? A systematic review.

PubMed

Roy, A; Roy, M; Deb, S; Unwin, G; Roy, A

2015-01-01

Self-injury in people with intellectual disability (ID) may be due to variety of factors both environmental and biological. As the drive in UK is to manage people with ID and problem behaviours in the community, it is important to critically examine all treatment options available. As abnormalities in the endogenous opioid system may be a factor in some people with ID, we undertook a systematic review to evaluate the evidence for the effectiveness of opioid antagonists. Four electronic databases were searched for relevant journal articles. In addition, cross-referencing of pertinent reviews and a hand search for articles in major international ID journals between the years 2010 and 2012 was carried out to ensure that all relevant articles were identified. We also searched databases for unpublished clinical trials to overcome publication bias. Each database was searched up to present (February 2013) with no restrictions on the date of publication. The search terms consisted of broad expressions used to describe ID and autistic spectrum disorder as well as terms relating to opioid antagonists and specific drugs. All studies identified by the electronic database search and hand search were examined on the basis of title alone for relevance and duplication. The abstracts of the remaining papers were then scrutinised against the inclusion criteria. Where abstracts failed to provide adequate information, the full texts for these papers were obtained. All the full texts were then evaluated against the inclusion proforma. Two reviewers carried out all the stages of the process independently. The reviewers met to discuss their selections and where disagreements arose, these were settled by discussion with a member of the study group. Data from each study meeting the inclusion criteria was extracted on a pre-piloted data extraction form. The quality of each study was further assessed using the Jadad scale, a tool developed to assess the quality of randomised controlled trials. Out of 10 randomised control trials eight reported a reduction in the frequency of self-injurious behaviour. This meant that 62 participants out of 124 (50%) showed an improvement of which 61 were statistically significant. Forty-nine participants had autism. Eleven (9%) had minor side-effects. The improvement was more marked in people with severe and profound ID and was not affected by the coexistence of autism. This review suggests that some people respond to opioid antagonists with a reduction in self-injury but the trials do not predict who they may be. Future research may identify this sub-group when opioid antagonists may prove to be a useful addition in the pharmacotherapy of self-injury. © 2014 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

Mining Tasks from the Web Anchor Text Graph: MSR Notebook Paper for the TREC 2015 Tasks Track

DTIC Science & Technology

2015-11-20

Mining Tasks from the Web Anchor Text Graph: MSR Notebook Paper for the TREC 2015 Tasks Track Paul N. Bennett Microsoft Research Redmond, USA pauben...anchor text graph has proven useful in the general realm of query reformulation [2], we sought to quantify the value of extracting key phrases from...anchor text in the broader setting of the task understanding track. Given a query, our approach considers a simple method for identifying a relevant

75 FR 27926 - Notice of Availability of Interpretive Rule on the Applicability of Current Water Conservation...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-19

... the message. Comments and suggestions should be provided in WordPerfect, Microsoft Word, PDF, or text file format. The full text of the interpretive rule is available at http://www1.eere.energy.gov.... The full text of the interpretive rule is available at http://www1.eere.energy.gov/buildings/appliance...

Social isolation in mental health: a conceptual and methodological review.

PubMed

Wang, Jingyi; Lloyd-Evans, Brynmor; Giacco, Domenico; Forsyth, Rebecca; Nebo, Cynthia; Mann, Farhana; Johnson, Sonia

2017-12-01

Social isolation and related concepts have been discussed increasingly in the field of mental health. Despite this, there is a lack of conceptual clarity and consistency in the definition and operationalisation of these terms. This review aimed to provide a clear framework for social isolation and related concepts, and to identify well-established measures in the field of mental health for each conceptual domain discussed. We used an iterative strategy of expert consultation and literature searching. A multi-disciplinary group of senior academics was consulted both before and after the literature searching to identify relevant terms, conceptual papers, or recommended measures. Our conceptual framework was also validated through expert consultation. We searched the Web of Science database using terms suggested by experts and subsequently identified further relevant studies through review articles and by reading full texts and reference lists of included studies. A narrative synthesis was conducted. We developed a model with five domains incorporating all the concepts relevant to social isolation in regular use in the mental health research literature. These five domains are: social network-quantity; social network-structure; social network-quality; appraisal of relationships-emotional; and appraisal of relationships-resources. We also identified well-developed measures suitable for assessing each of the five conceptual domains or covering multi-domains. Our review proposes a conceptual model to encompass and differentiate all terms relating to social isolation. Potential uses are in allowing researchers and intervention developers to identify precisely the intended outcomes of interventions, and to choose the most appropriate measures to use in mental health settings.

Standards for definitions and use of outcome measures for clinical effectiveness research in perioperative medicine: European Perioperative Clinical Outcome (EPCO) definitions: a statement from the ESA-ESICM joint taskforce on perioperative outcome measures.

PubMed

Jammer, Ib; Wickboldt, Nadine; Sander, Michael; Smith, Andrew; Schultz, Marcus J; Pelosi, Paolo; Leva, Brigitte; Rhodes, Andrew; Hoeft, Andreas; Walder, Bernhard; Chew, Michelle S; Pearse, Rupert M

2015-02-01

There is a need for large trials that test the clinical effectiveness of interventions in the field of perioperative medicine. Clinical outcome measures used in such trials must be robust, clearly defined and patient-relevant. Our objective was to develop standards for the use of clinical outcome measures to strengthen the methodological quality of perioperative medicine research. A literature search was conducted using PubMed and opinion leaders worldwide were invited to nominate papers that they believed the group should consider. The full texts of relevant articles were reviewed by the taskforce members and then discussed to reach a consensus on the required standards. The report was then circulated to opinion leaders for comment and review. This report describes definitions for 22 individual adverse events with a system of severity grading for each. In addition, four composite outcome measures were identified, which were designed to evaluate postoperative outcomes. The group also agreed on standards for four outcome measures for the evaluation of healthcare resource use and quality of life. Guidance for use of these outcome measures is provided, with particular emphasis on appropriate duration of follow-up. This report provides clearly defined and patient-relevant outcome measures for large clinical trials in perioperative medicine. These outcome measures may also be of use in clinical audit. This report is intended to complement and not replace other related work to improve assessment of clinical outcomes following specific surgical procedures.

Current evidence of percutaneous nucleoplasty for the cervical herniated disk: a systematic review.

PubMed

Wullems, Jorgen A; Halim, Willy; van der Weegen, Walter

2014-07-01

Although percutaneous cervical nucleoplasty (PCN) has been shown to be both safe and effective, its application is still debated. PCN applied in disk herniation has not been systematically reviewed before, resulting in a limited insight into its effectiveness and safety, and the quality of available evidence. Therefore, we systematically reviewed the evidence on the efficacy and safety of PCN in patients with a (contained) herniated disk. MEDLINE, EMBASE, and the Cochrane Library (Central Register of Controlled Trials) were searched for randomized controlled trials (RCTs) and nonrandomized studies using the following keywords: "Nucleoplasty," "Cervical," "Hernia," "Herniation," "Prolapse," "Protrusion," "Intervertebral disk," and "Percutaneous disk decompression." First, all articles were appraised for methodological quality, and then, RCTs were graded for the level of evidence according a best-evidence synthesis, because a meta-analysis was not possible. Finally, the RCTs' applicability and clinical relevance also was assessed. Of 75 identified abstracts, 10 full-text articles were included (3 RCTs and 7 nonrandomized studies). These studies represented a total of 1021 patients: 823 patients (≥ 892 disks) were treated by PCN. All studies showed low methodological quality, except for two. The level of evidence of the RCTs was graded as moderate, with low to moderate applicability and clinical relevance. All included studies showed PCN to be an effective and safe procedure in the treatment of (contained) herniated disks at short-, mid-, and long-term follow-up. However, the level of evidence is moderate and shows only low to moderate applicability and clinical relevance. © 2013 World Institute of Pain.

Mentor Texts and Funds of Knowledge: Situating Writing within Our Students' Worlds

ERIC Educational Resources Information Center

Newman, Beatrice Mendez

2012-01-01

The funds of knowledge concept serves as scaffolding for encouraging students to draw on background experiences and home language to generate authentic writing. This article describes and illustrates several classroom strategies, including 1) using culturally relevant mentor texts; 2) applying Nancie Atwell's writing territories concept; 3)…

Illinois School Code, 1998.

ERIC Educational Resources Information Center

Illinois Association of School Boards, Springfield.

This text consists of numerous statutes selected by the Illinois Association of School Boards' staff for their relevance to public school governance and administration. The publication covers legislation enacted as of January 1, 1998, and includes a myriad of education-related topics. The bulk of the text focuses on schools themselves, featuring…

Introduction to the JASIST Special Topic Issue on Web Retrieval and Mining: A Machine Learning Perspective.

ERIC Educational Resources Information Center

Chen, Hsinchun

2003-01-01

Discusses information retrieval techniques used on the World Wide Web. Topics include machine learning in information extraction; relevance feedback; information filtering and recommendation; text classification and text clustering; Web mining, based on data mining techniques; hyperlink structure; and Web size. (LRW)

Semi-Spontaneous Oral Text Production: Measurements in Clinical Practice

ERIC Educational Resources Information Center

Lind, Marianne; Kristoffersen, Kristian Emil; Moen, Inger; Simonsen, Hanne Gram

2009-01-01

Functionally relevant assessment of the language production of speakers with aphasia should include assessment of connected speech production. Despite the ecological validity of everyday conversations, more controlled and monological types of texts may be easier to obtain and analyse in clinical practice. This article discusses some simple…

Vocabulary in First-Year German Texts

ERIC Educational Resources Information Center

Tussing, Marjorie; Zimmermann, Jon

1977-01-01

Vocabulary in first-year high school and college level German texts was studied. It was suggested that textbook authors use published word frequency lists to develop teaching materials that are practical, useful, and relevant to the process of communication. A word list occurring in 12 textbooks is presented in descending frequency. (SW)

Autobiography and Intertextuality.

ERIC Educational Resources Information Center

Smith, Michael W.

To understand literature, it is necessary for a reader to make connections between the text of the literary work and the text of the reader's life. Student autobiographical writing before reading can be used to enhance students' ability to make such connections. Autobiographical writing helps students apply relevant life experience that might not…

Online and offline inferential and textual processing of poor comprehenders: Evidence from a probing method.

PubMed

Yeari, Menahem; Elentok, Shiri; Schiff, Rachel

2017-03-01

Numerous studies have demonstrated that poor inferential processing underlies the specific deficit of poor comprehenders. However, it is still not clear why poor comprehenders have difficulties in generating inferences while reading and whether this impairment is general or specific to one or more types of inferences. The current study employed an online probing method to examine the spontaneous immediate activation of two inference types-forward-predictive inferences and backward-explanatory inferences-during reading. In addition, we examined the ability of poor comprehenders to retain, suppress, and reactivate text information (relevant for inferencing) in working memory. The participants, 10- to 12-year-old good and poor comprehenders, read short narratives and name inference or text word probes following a predictive, intervening, or bridging sentence. Comparing the size of probe-naming facilitations revealed that poor comprehenders generate predictive inferences, albeit more slowly than good comprehenders, and generate explanatory inferences to a lesser extent than good comprehenders. Moreover, we found that this inferior inferential processing is presumably a result of poor retention and reactivation of inference-evoking text information during reading. Finally, poorer reading comprehension was associated with higher activation of information when it was less relevant following the intervening sentences. Taken together, the current findings demonstrate the manner in which poor regulation of relevant and less relevant information during reading underlies the specific comprehension difficulties experienced by poor comprehenders. Copyright © 2016 Elsevier Inc. All rights reserved.

Text Mining for Drugs and Chemical Compounds: Methods, Tools and Applications.

PubMed

Vazquez, Miguel; Krallinger, Martin; Leitner, Florian; Valencia, Alfonso

2011-06-01

Providing prior knowledge about biological properties of chemicals, such as kinetic values, protein targets, or toxic effects, can facilitate many aspects of drug development. Chemical information is rapidly accumulating in all sorts of free text documents like patents, industry reports, or scientific articles, which has motivated the development of specifically tailored text mining applications. Despite the potential gains, chemical text mining still faces significant challenges. One of the most salient is the recognition of chemical entities mentioned in text. To help practitioners contribute to this area, a good portion of this review is devoted to this issue, and presents the basic concepts and principles underlying the main strategies. The technical details are introduced and accompanied by relevant bibliographic references. Other tasks discussed are retrieving relevant articles, identifying relationships between chemicals and other entities, or determining the chemical structures of chemicals mentioned in text. This review also introduces a number of published applications that can be used to build pipelines in topics like drug side effects, toxicity, and protein-disease-compound network analysis. We conclude the review with an outlook on how we expect the field to evolve, discussing its possibilities and its current limitations. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

SKIMMR: facilitating knowledge discovery in life sciences by machine-aided skim reading

PubMed Central

Burns, Gully A.P.C.

2014-01-01

Background. Unlike full reading, ‘skim-reading’ involves the process of looking quickly over information in an attempt to cover more material whilst still being able to retain a superficial view of the underlying content. Within this work, we specifically emulate this natural human activity by providing a dynamic graph-based view of entities automatically extracted from text. For the extraction, we use shallow parsing, co-occurrence analysis and semantic similarity computation techniques. Our main motivation is to assist biomedical researchers and clinicians in coping with increasingly large amounts of potentially relevant articles that are being published ongoingly in life sciences. Methods. To construct the high-level network overview of articles, we extract weighted binary statements from the text. We consider two types of these statements, co-occurrence and similarity, both organised in the same distributional representation (i.e., in a vector-space model). For the co-occurrence weights, we use point-wise mutual information that indicates the degree of non-random association between two co-occurring entities. For computing the similarity statement weights, we use cosine distance based on the relevant co-occurrence vectors. These statements are used to build fuzzy indices of terms, statements and provenance article identifiers, which support fuzzy querying and subsequent result ranking. These indexing and querying processes are then used to construct a graph-based interface for searching and browsing entity networks extracted from articles, as well as articles relevant to the networks being browsed. Last but not least, we describe a methodology for automated experimental evaluation of the presented approach. The method uses formal comparison of the graphs generated by our tool to relevant gold standards based on manually curated PubMed, TREC challenge and MeSH data. Results. We provide a web-based prototype (called ‘SKIMMR’) that generates a network of inter-related entities from a set of documents which a user may explore through our interface. When a particular area of the entity network looks interesting to a user, the tool displays the documents that are the most relevant to those entities of interest currently shown in the network. We present this as a methodology for browsing a collection of research articles. To illustrate the practical applicability of SKIMMR, we present examples of its use in the domains of Spinal Muscular Atrophy and Parkinson’s Disease. Finally, we report on the results of experimental evaluation using the two domains and one additional dataset based on the TREC challenge. The results show how the presented method for machine-aided skim reading outperforms tools like PubMed regarding focused browsing and informativeness of the browsing context. PMID:25097821

Variability in Objective Refraction for Persons with Down Syndrome.

PubMed

Marsack, Jason D; Ravikumar, Ayeswarya; Benoit, Julia S; Anderson, Heather A

2017-05-01

Down syndrome (DS) is associated with ocular and cognitive sequelae, which both have the potential to influence clinical measures of refractive error. This study compares variability of autorefraction among subjects with and without DS. Grand Seiko autorefraction was performed on 139 subjects with DS (age: 8-55, mean: 25 ± 9 yrs) and 138 controls (age: 7-59, mean: 25 ± 10 yrs). Subjects with three refraction measures per eye (DS: 113, control: 136) were included for analysis. Each refraction was converted to power vector notation (M, J0, J45) and a difference in each component (ΔM, ΔJ0, ΔJ45) was calculated for each refraction pairing. From these quantities, average dioptric strength ((Equation is included in full-text article.): square root of the sum of the squares of M, J0, and J45) and average dioptric difference ((Equation is included in full-text article.): square root of the sum of the squares of ΔM, ΔJ0, and ΔJ45) were calculated. The DS group exhibited a greater median (Equation is included in full-text article.)(1Q: 1.38D M: 2.38D 3Q: 3.41D) than control eyes (1Q: 0.47D M: 0.96D 3Q: 2.75D) (P < .001). Likewise, the DS group exhibited a greater median (Equation is included in full-text article.)in refraction (1Q: 0.27D M: 0.42D 3Q: 0.78D) than control eyes (1Q: 0.11D M: 0.15D 3Q: 0.23D) (P < .001) with 97.1% of control eyes exhibiting (Equation is included in full-text article.)≤0.50D, compared to 59.3% of DS eyes. An effect of (Equation is included in full-text article.)on (Equation is included in full-text article.)was not detected (P = .3009) nor was a significant interaction between (Equation is included in full-text article.)and group detected (P = .49). In the current study, comparing three autorefraction readings, median total dioptric difference with autorefraction in DS was 2.8 times the levels observed in controls, indicating greater potential uncertainty in objective measures of refraction for this population. The analysis demonstrates that J45 is highly contributory to the observed variability.

A Joint Probabilistic Classification Model of Relevant and Irrelevant Sentences in Mathematical Word Problems

ERIC Educational Resources Information Center

Cetintas, Suleyman; Si, Luo; Xin, Yan Ping; Zhang, Dake; Park, Joo Young; Tzur, Ron

2010-01-01

Estimating the difficulty level of math word problems is an important task for many educational applications. Identification of relevant and irrelevant sentences in math word problems is an important step for calculating the difficulty levels of such problems. This paper addresses a novel application of text categorization to identify two types of…

User Feedback Procedures; Part III of Scientific Report No. ISR-18, Information Storage and Retrieval...

ERIC Educational Resources Information Center

Cornell Univ., Ithaca, NY. Dept. of Computer Science.

Part Three of this five part report on Salton's Magical Automatic Retriever of Texts (SMART) project contains four papers. The first: "Variations on the Query Splitting Technique with Relevance Feedback" by T. P. Baker discusses some experiments in relevance feedback performed with variations on the technique of query splitting. The…

When Your Mother Asks for Another Book: Fostering Intergenerational Exchange of Culturally Relevant Books.

ERIC Educational Resources Information Center

Packard, Becky Wai-Ling

2001-01-01

Explores the bi-directional benefits of family literacy practices involving English as a Second Language (ESL) immigrant parents and their children. Discusses the literature on family literacy and culturally relevant texts. Shares and analyzes the case of a shared reading practice. Suggests that this informal family literacy practice could help to…

Semi-spontaneous oral text production: measurements in clinical practice.

PubMed

Lind, Marianne; Kristoffersen, Kristian Emil; Moen, Inger; Simonsen, Hanne Gram

2009-12-01

Functionally relevant assessment of the language production of speakers with aphasia should include assessment of connected speech production. Despite the ecological validity of everyday conversations, more controlled and monological types of texts may be easier to obtain and analyse in clinical practice. This article discusses some simple measurements for the analysis of semi-spontaneous oral text production by speakers with aphasia. Specifically, the measurements are related to the production of verbs and nouns, and the realization of different sentence types. The proposed measurements should be clinically relevant, easily applicable, and linguistically meaningful. The measurements have been applied to oral descriptions of the 'Cookie Theft' picture by eight monolingual Norwegian speakers, four with an anomic type of aphasia and four without any type of language impairment. Despite individual differences in both the clinical and the non-clinical group, most of the measurements seem to distinguish between speakers with and without aphasia.

Full-text automated detection of surgical site infections secondary to neurosurgery in Rennes, France.

PubMed

Campillo-Gimenez, Boris; Garcelon, Nicolas; Jarno, Pascal; Chapplain, Jean Marc; Cuggia, Marc

2013-01-01

The surveillance of Surgical Site Infections (SSI) contributes to the management of risk in French hospitals. Manual identification of infections is costly, time-consuming and limits the promotion of preventive procedures by the dedicated teams. The introduction of alternative methods using automated detection strategies is promising to improve this surveillance. The present study describes an automated detection strategy for SSI in neurosurgery, based on textual analysis of medical reports stored in a clinical data warehouse. The method consists firstly, of enrichment and concept extraction from full-text reports using NOMINDEX, and secondly, text similarity measurement using a vector space model. The text detection was compared to the conventional strategy based on self-declaration and to the automated detection using the diagnosis-related group database. The text-mining approach showed the best detection accuracy, with recall and precision equal to 92% and 40% respectively, and confirmed the interest of reusing full-text medical reports to perform automated detection of SSI.

Full-text, Downloading, & Other Issues.

ERIC Educational Resources Information Center

Tenopir, Carol

1983-01-01

Issues having a possible impact on online search services in libraries are discussed including full text databases, front-end processors which translate user's input into the command language of an appropriate system, downloading to create personal files from commercial databases, and pricing. (EJS)

Is More Always Better?

ERIC Educational Resources Information Center

Bell, Steven J.

2003-01-01

Discusses full-text databases and whether existing aggregator databases are meeting user needs. Topics include the need for better search interfaces; concepts of quality research and information retrieval; information overload; full text in electronic journal collections versus aggregator databases; underrepresentation of certain disciplines; and…

Integrated Models of Care for People Living with Hepatitis C Virus and a Substance Use Disorder: Protocol for a Systematic Review.

PubMed

Ti, Lianping; Parent, Stephanie; Socías, María Eugenia

2018-05-09

People living with a substance use disorder (SUD) are a key population within the hepatitis C virus (HCV) epidemic. While integrated and community-based models of care have shown positive outcomes among this population, the literature has been primarily focused on the HIV context. This paper outlines a systematic review protocol on the impact of various integrated models of care, which includes HCV and SUD services, on various treatment, and health-related outcomes among this population. The objective of this review is to determine the impact of integrated models of care on HCV and addiction treatment and health-related outcomes for adults living with HCV and an SUD. We will search 5 databases, article reference lists, and abstracts from relevant conferences that investigate the impact of integrated models of care on treatment and health-related outcomes among people living with HCV and an SUD. Database searches will be conducted and titles, abstracts, and the full-text of the relevant studies will be independently reviewed in separate stages. The methodological quality of included studies will be assessed using a validated tool. Data from included articles will be extracted using a standardized form and synthesized in a narrative account. For this project, we have received funding from the Canadian Institute of Health Research. To date, we have completed the search strategy, reviewed the titles, abstracts, and full-texts. Grading the selected studies and qualitative synthesis of the results are currently under way, and we expect the final results to be submitted for publication in the fall of 2018. The systematic review will describe different integrated models of care that could be effective in improving the health and well-being of people living with HCV and an SUD. Results of this review could also identify quality improvement strategies to minimize the health and cost burden imposed on patients, healthcare professionals, and the healthcare system. PROSPERO CRD42017078445; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=78445 (Archived by WebCite at http://www.webcitation.org/6z4YnkE9G). ©Lianping Ti, Stephanie Parent, María Eugenia Socías. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 09.05.2018.

Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles.

PubMed

Cohen, K Bretonnel; Lanfranchi, Arrick; Choi, Miji Joo-Young; Bada, Michael; Baumgartner, William A; Panteleyeva, Natalya; Verspoor, Karin; Palmer, Martha; Hunter, Lawrence E

2017-08-17

Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction from the scientific literature. In order to better understand the nature of the phenomenon of coreference in biomedical publications and to increase performance on the task, we annotated the Colorado Richly Annotated Full Text (CRAFT) corpus with coreference relations. The corpus was manually annotated with coreference relations, including identity and appositives for all coreferring base noun phrases. The OntoNotes annotation guidelines, with minor adaptations, were used. Interannotator agreement ranges from 0.480 (entity-based CEAF) to 0.858 (Class-B3), depending on the metric that is used to assess it. The resulting corpus adds nearly 30,000 annotations to the previous release of the CRAFT corpus. Differences from related projects include a much broader definition of markables, connection to extensive annotation of several domain-relevant semantic classes, and connection to complete syntactic annotation. Tool performance was benchmarked on the data. A publicly available out-of-the-box, general-domain coreference resolution system achieved an F-measure of 0.14 (B3), while a simple domain-adapted rule-based system achieved an F-measure of 0.42. An ensemble of the two reached F of 0.46. Following the IDENTITY chains in the data would add 106,263 additional named entities in the full 97-paper corpus, for an increase of 76% percent in the semantic classes of the eight ontologies that have been annotated in earlier versions of the CRAFT corpus. The project produced a large data set for further investigation of coreference and coreference resolution in the scientific literature. The work raised issues in the phenomenon of reference in this domain and genre, and the paper proposes that many mentions that would be considered generic in the general domain are not generic in the biomedical domain due to their referents to specific classes in domain-specific ontologies. The comparison of the performance of a publicly available and well-understood coreference resolution system with a domain-adapted system produced results that are consistent with the notion that the requirements for successful coreference resolution in this genre are quite different from those of the general domain, and also suggest that the baseline performance difference is quite large.

The structural and content aspects of abstracts versus bodies of full text journal articles are different

PubMed Central

2010-01-01

Background An increase in work on the full text of journal articles and the growth of PubMedCentral have the opportunity to create a major paradigm shift in how biomedical text mining is done. However, until now there has been no comprehensive characterization of how the bodies of full text journal articles differ from the abstracts that until now have been the subject of most biomedical text mining research. Results We examined the structural and linguistic aspects of abstracts and bodies of full text articles, the performance of text mining tools on both, and the distribution of a variety of semantic classes of named entities between them. We found marked structural differences, with longer sentences in the article bodies and much heavier use of parenthesized material in the bodies than in the abstracts. We found content differences with respect to linguistic features. Three out of four of the linguistic features that we examined were statistically significantly differently distributed between the two genres. We also found content differences with respect to the distribution of semantic features. There were significantly different densities per thousand words for three out of four semantic classes, and clear differences in the extent to which they appeared in the two genres. With respect to the performance of text mining tools, we found that a mutation finder performed equally well in both genres, but that a wide variety of gene mention systems performed much worse on article bodies than they did on abstracts. POS tagging was also more accurate in abstracts than in article bodies. Conclusions Aspects of structure and content differ markedly between article abstracts and article bodies. A number of these differences may pose problems as the text mining field moves more into the area of processing full-text articles. However, these differences also present a number of opportunities for the extraction of data types, particularly that found in parenthesized text, that is present in article bodies but not in article abstracts. PMID:20920264

Relevance, textual unity, and politeness in writing about science

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

Kreml, N.M.P.

1992-01-01

The question of whether there are social implications of linguistic choices in unifying a text is investigated empirically by this study which accounts for the interpretation of implicatures in conversation and written texts. It considers Relevance Theory (Sperber and Wilson 1988, Blakemore 1987, Blass 1990) to be the explanation of the unity of the text, as opposed to semantic theories of cohesion (Halliday and Hasan 1976) or pragmatic theories of coherence (van Dijk 1977). This study presents a model of three types of textual unifiers: overt (referring specifically to the text), embedded (referring to intra- and extra-textual information), and inferencemore » (not referring to the text at all). It hypothesizes that different genres are characterized by the predominance of different types of textual unifiers, and that readers will prefer those texts that rely on inferential unifiers which emphasize the reader's ability to participate in creating the meaning of the text. Eighteen texts of 275 words each are selected from three genres: scientific magazines, introductory science textbooks, and essays on science. The texts are found to vary significantly by genre in the type of textual unifier used. An Overtness Index expresses the ratio of the marked forms: science textbooks have more Overt unifiers (such as connective phrases) and thus a high Overtness Index; essays rely more on Inference unifiers (not represented by words) and thus have a low Overtness Index. The texts are submitted to 188 readers, and a significantly high number of all types of readers prefer the texts with the lower Overtness Indices-the essays. Thus a low Overtness Index is one feature of texts preferred by readers, supporting the hypotheses that genres of texts vary in the type of unifier used and that readers prefer texts that allow them to participate in constructing the meaning of the text.« less

The Importance of Accuracy, Stimulating writing, and Relevance in Middle School Science Textbook Writing

NASA Astrophysics Data System (ADS)

Hubisz, John

2004-05-01

While accuracy in Middle School science texts is most important, the texts should also read well, stimulating the student to want to go on, and the material must be relevant to the subject at hand as the typical student is not yet prepared to ignore that which is irrelevant. We know that children will read if the material is of interest (witness The Lord of the Rings and the Harry Potter book sales) and so we must write in a way that stimulates the student to want to examine the subject further and eliminate that which adds nothing to the discipline. Examples of the good and the bad will be presented.

Selecting Full-Text Undergraduate Periodicals Databases.

ERIC Educational Resources Information Center

Still, Julie M.; Kassabian, Vibiana

1999-01-01

Examines how libraries and librarians can compare full-text general periodical indices, using ProQuest Direct, Periodical Abstracts (via Ovid), and EBSCOhost as examples. Explores breadth and depth of coverage; manipulation of results (email/download/print); ease of use (searching); and indexing quirks. (AEF)

Processing and Memory of Information Presented in Narrative or Expository Texts

ERIC Educational Resources Information Center

Wolfe, Michael B. W.; Woodwyk, Joshua M.

2010-01-01

Background: Previous research suggests that narrative and expository texts differ in the extent to which they prompt students to integrate to-be-learned content with relevant prior knowledge during comprehension. Aims: We expand on previous research by examining on-line processing and representation in memory of to-be-learned content that is…

Content Analysis of Introductory Interior Design College Textbooks: A Study Revisited

ERIC Educational Resources Information Center

Temple, Julie A.; Potthoff, Joy K.

2013-01-01

Introductory interior design texts adopted by design educators present information relevant to both historical and contemporary issues in interior design. According to one author, they provide a "survey of the field of interior design as it now exists" (Pile, 2007). A comparison of the content of contemporary texts with those of more…

Computational Psycholinguistic Analysis and Its Application in Psychological Assessment of College Students

ERIC Educational Resources Information Center

Kucera, Dalibor; Havigerová, Jana M.

2015-01-01

The paper deals with the issue of computational psycholinguistic analysis (CPA) and its experimental application in basic psychological and pedagogical assessment. CPA is a new method which may potentially provide interesting, psychologically relevant information about the author of a particular text, regardless of the text's factual (semantic)…

STATUS/IQ: A Semi-Intelligent Information Retrieval System.

ERIC Educational Resources Information Center

Pearsall, Jayne

1990-01-01

Provides background on the problems of traditional text retrieval systems and describes STATUS/IQ, an advanced text retrieval system that incorporates a natural language front-end and an advanced relevance ranking facility. The principles, capabilities, and benefits of the system are discussed, and an example of a STATUS/IQ session is presented…

Exploring Culturally Relevant Texts with Kindergartners and Their Families

ERIC Educational Resources Information Center

Schrodt, Katie; Fain, Jeanne Gilliam; Hasty, Michelle

2015-01-01

This article shares a monthly curricular model that can help teachers and families bridge the gap between home and school by using literature and response inspired from the cultures in the classroom. Integrating culturally responsive texts and family response journals into the classroom and the home can help children, their families, and peers…

Methodology for the Evaluation of the Algorithms for Text Line Segmentation Based on Extended Binary Classification

NASA Astrophysics Data System (ADS)

Brodic, D.

2011-01-01

Text line segmentation represents the key element in the optical character recognition process. Hence, testing of text line segmentation algorithms has substantial relevance. All previously proposed testing methods deal mainly with text database as a template. They are used for testing as well as for the evaluation of the text segmentation algorithm. In this manuscript, methodology for the evaluation of the algorithm for text segmentation based on extended binary classification is proposed. It is established on the various multiline text samples linked with text segmentation. Their results are distributed according to binary classification. Final result is obtained by comparative analysis of cross linked data. At the end, its suitability for different types of scripts represents its main advantage.

The effectiveness of passive physical modalities for the management of soft tissue injuries and neuropathies of the wrist and hand: a systematic review by the Ontario Protocol for Traffic Injury Management (OPTIMa) collaboration.

PubMed

D'Angelo, Kevin; Sutton, Deborah; Côté, Pierre; Dion, Sarah; Wong, Jessica J; Yu, Hainan; Randhawa, Kristi; Southerst, Danielle; Varatharajan, Sharanya; Cox Dresser, Jocelyn; Brown, Courtney; Menta, Roger; Nordin, Margareta; Shearer, Heather M; Ameis, Arthur; Stupar, Maja; Carroll, Linda J; Taylor-Vaisey, Anne

2015-09-01

The purpose of this systematic review was to determine the effectiveness of passive physical modalities compared to other interventions, placebo/sham interventions, or no intervention in improving self-rated recovery, functional recovery, clinical outcomes and/or administrative outcomes (eg, time of disability benefits) in adults and/or children with soft tissue injuries and neuropathies of the wrist and hand. We systematically searched MEDLINE, EMBASE, PsycINFO, and the Cochrane Central Register of Controlled Trials, accessed through Ovid Technologies, Inc, and CINAHL Plus with Full Text, accessed through EBSCO host, from 1990 to 2015. Our search strategies combined controlled vocabulary relevant to each database (eg, MeSH for MEDLINE) and text words relevant to our research question and the inclusion criteria. Randomized controlled trials, cohort studies, and case-control studies were eligible. Random pairs of independent reviewers screened studies for relevance and critically appraised relevant studies using the Scottish Intercollegiate Guidelines Network criteria. Studies with low risk of bias were synthesized following best evidence synthesis principles. We screened 6618 articles and critically appraised 11 studies. Of those, 7 had low risk of bias: 5 addressed carpal tunnel syndrome (CTS) and 2 addressed de Quervain disease. We found evidence that various types of night splints lead to similar outcomes for the management of CTS. The evidence suggests that a night wrist splint is less effective than surgery in the short term but not in the long term. Furthermore, a night wrist splint and needle electroacupuncture lead to similar outcomes immediately postintervention. Finally, low-level laser therapy and placebo low-level laser therapy lead to similar outcomes. The evidence suggests that kinesio tape or a thumb spica cast offers short-term benefit for the management of de Quervain disease. Our search did not identify any low risk of bias studies examining the effectiveness of passive physical modalities for the management of other soft tissue injuries or neuropathies of the wrist and hand. Different night orthoses provided similar outcomes for CTS. Night orthoses offer similar outcomes to electroacupuncture but are less effective than surgery in the short term. This review suggests that kinesio tape or a thumb spica cast may offer short-term benefit for the management of de Quervain disease. Copyright © 2015 National University of Health Sciences. Published by Elsevier Inc. All rights reserved.

Using the Human Activity Profile to Assess Functional Performance in Heart Failure.

PubMed

Ribeiro-Samora, Giane Amorim; Pereira, Danielle Aparecida Gomes; Vieira, Otávia Alves; de Alencar, Maria Clara Noman; Rodrigues, Roseane Santo; Carvalho, Maria Luiza Vieira; Montemezzo, Dayane; Britto, Raquel Rodrigues

2016-01-01

To investigate (1) the validity of using the Human Activity Profile (HAP) in patients with heart failure (HF) to estimate functional capacity; (2) the association between the HAP and 6-Minute Walk Test (6MWT) distance; and (3) the ability of the HAP to differentiate between New York Heart Association (NYHA) functional classes. In a cross-sectional study, we evaluated 62 clinically stable patients with HF (mean age, 47.98 years; NYHA class I-III). Variables included maximal functional capacity as measured by peak oxygen uptake ((Equation is included in full-text article.)O2) using a cardiopulmonary exercise test (CPET), peak (Equation is included in full-text article.)O2 as estimated by the HAP, and exercise capacity as measured by the 6MWT. The difference between the measured (CPET) and estimated (HAP) peak (Equation is included in full-text article.)O2 against the average values showed a bias of 2.18 mL/kg/min (P = .007). No agreement was seen between these measures when applying the Bland-Altman method. Peak (Equation is included in full-text article.)O2 in the HAP showed a moderate association with the 6MWT distance (r = 0.62; P < .0001). Peak (Equation is included in full-text article.)O2 in the HAP was able to statistically differentiate NYHA functional classes I, II, and III (P < .05). The estimated peak (Equation is included in full-text article.)O2 using the HAP was not concordant with the gold standard CPET measure. On the contrary, the HAP was able to differentiate NYHA functional class associated with the 6MWT distance; therefore, the HAP is a useful tool for assessing functional performance in patients with HF.

The impact of social media promotion with infographics and podcasts on research dissemination and readership.

PubMed

Thoma, Brent; Murray, Heather; Huang, Simon York Ming; Milne, William Ken; Martin, Lynsey J; Bond, Christopher M; Mohindra, Rohit; Chin, Alvin; Yeh, Calvin H; Sanderson, William B; Chan, Teresa M

2018-03-01

In 2015 and 2016, the Canadian Journal of Emergency Medicine (CJEM) Social Media (SoMe) Team collaborated with established medical websites to promote CJEM articles using podcasts and infographics while tracking dissemination and readership. CJEM publications in the "Original Research" and "State of the Art" sections were selected by the SoMe Team for podcast and infographic promotion based on their perceived interest to emergency physicians. A control group was composed retrospectively of articles from the 2015 and 2016 issues with the highest Altmetric score that received standard Facebook and Twitter promotions. Studies on SoMe topics were excluded. Dissemination was quantified by January 1, 2017 Altmetric scores. Readership was measured by abstract and full-text views over a 3-month period. The number needed to view (NNV) was calculated by dividing abstract views by full-text views. Twenty-nine of 88 articles that met inclusion were included in the podcast (6), infographic (11), and control (12) groups. Descriptive statistics (mean, 95% confidence interval) were calculated for podcast (Altmetric: 61, 42-80; Abstract: 1795, 1135-2455; Full-text: 431, 0-1031), infographic (Altmetric: 31.5, 19-43; Abstract: 590, 361-819; Full-text: 65, 33-98), and control (Altmetric: 12, 8-15; Abstract: 257, 159-354; Full-Text: 73, 38-109) articles. The NNV was 4.2 for podcast, 9.0 for infographic, and 3.5 for control articles. Discussion Limitations included selection bias, the influence of SoMe promotion on the Altmetric scores, and a lack of generalizability to other journals. Collaboration with established SoMe websites using podcasts and infographics was associated with increased Altmetric scores and abstract views but not full-text article views.

Fate of abstracts presented at a National Turkish Orthopedics and Traumatology Congress: publication rates and consistency of abstracts compared with their subsequent full-text publications.

PubMed

Yalçınkaya, Merter; Bagatur, Erdem

2013-01-01

The aim of this study was to evaluate the publication rates of full-text articles after presentation of abstracts at a Turkish National Orthopaedics and Traumatology Congress, determine the time lag from the congress date to publication of full-text articles and assess the consistency between abstracts and the subsequent publications. All abstracts from the scientific program of the 20th Turkish National Orthopaedics and Traumatology Congress (2007) were identified and computerized PubMed searches were conducted to determine whether an abstract had been followed by publication of a full-text article and key features were compared to evaluate their consistency. The time lag to publication and the impact factors of the journals where the articles were published were noted. Of the 770 abstracts (264 oral, 506 poster presentations), 227 (29.5%) were followed by a full-text and 116 (44%) of the 264 oral and 111 (22%) of the 506 poster presentations were published. The mean time to publication was 14.9±16.075 (range: 33 to 55) months. Thirty-three (14.5%) were published prior to the presentation at the congress. The likelihood of publication decreased after the third year (26 of 227, 11.5%). A total of 182 (80.2%) articles showed inconsistencies with the abstract; 74 (32.6%) minor, 14 (6.2%) major, and 94 (41.4%) minor and major inconsistencies. The mean impact factor of the journals was 1.152±0.858. The vast majority of abstracts presented at this congress were not followed by publication of a full-text article. Additionally, frequent inconsistencies between the final published article and the original abstract indicated the inadequacy of quality of reporting in abstracts.

Recognizing chemicals in patents: a comparative analysis.

PubMed

Habibi, Maryam; Wiegandt, David Luis; Schmedding, Florian; Leser, Ulf

2016-01-01

Recently, methods for Chemical Named Entity Recognition (NER) have gained substantial interest, driven by the need for automatically analyzing todays ever growing collections of biomedical text. Chemical NER for patents is particularly essential due to the high economic importance of pharmaceutical findings. However, NER on patents has essentially been neglected by the research community for long, mostly because of the lack of enough annotated corpora. A recent international competition specifically targeted this task, but evaluated tools only on gold standard patent abstracts instead of full patents; furthermore, results from such competitions are often difficult to extrapolate to real-life settings due to the relatively high homogeneity of training and test data. Here, we evaluate the two state-of-the-art chemical NER tools, tmChem and ChemSpot, on four different annotated patent corpora, two of which consist of full texts. We study the overall performance of the tools, compare their results at the instance level, report on high-recall and high-precision ensembles, and perform cross-corpus and intra-corpus evaluations. Our findings indicate that full patents are considerably harder to analyze than patent abstracts and clearly confirm the common wisdom that using the same text genre (patent vs. scientific) and text type (abstract vs. full text) for training and testing is a pre-requisite for achieving high quality text mining results.

Multicultural Children's Literature as a Context for Teaching Mathematics for Cultural Relevance in Urban Schools

ERIC Educational Resources Information Center

Leonard, Jacqueline; Moore, Cara M.; Brooks, Wanda

2014-01-01

This article reports on a teacher-research study that used multicultural texts as a context for teaching mathematics for cultural relevance during an elementary mathematics methods course. The results of the study reveal that 28% (5 out of 18) of the teacher candidates (TCs) chose books that were culturally contextual or culturally amenable.…

Interactive Effects of Working Memory Self-Regulatory Ability and Relevance Instructions on Text Processing

ERIC Educational Resources Information Center

Hamilton, Nancy Jo

2012-01-01

Reading is a process that requires the enactment of many cognitive processes. Each of these processes uses a certain amount of working memory resources, which are severely constrained by biology. More efficiency in the function of working memory may mediate the biological limits of same. Reading relevancy instructions may be one such method to…

A Practical Guide to Interpretation of Large Collections of Incident Narratives Using the QUORUM Method

NASA Technical Reports Server (NTRS)

McGreevy, Michael W.

1997-01-01

Analysis of incident reports plays an important role in aviation safety. Typically, a narrative description, written by a participant, is a central part of an incident report. Because there are so many reports, and the narratives contain so much detail, it can be difficult to efficiently and effectively recognize patterns among them. Recognizing and addressing recurring problems, however, is vital to continuing safety in commercial aviation operations. A practical way to interpret large collections of incident narratives is to apply the QUORUM method of text analysis, modeling, and relevance ranking. In this paper, QUORUM text analysis and modeling are surveyed, and QUORUM relevance ranking is described in detail with many examples. The examples are based on several large collections of reports from the Aviation Safety Reporting System (ASRS) database, and a collection of news stories describing the disaster of TWA Flight 800, the Boeing 747 which exploded in mid- air and crashed near Long Island, New York, on July 17, 1996. Reader familiarity with this disaster should make the relevance-ranking examples more understandable. The ASRS examples illustrate the practical application of QUORUM relevance ranking.

Clinically significant drug-drug interactions involving opioid analgesics used for pain treatment in patients with cancer: a systematic review.

PubMed

Kotlinska-Lemieszek, Aleksandra; Klepstad, Pål; Haugen, Dagny Faksvåg

2015-01-01

Opioids are the most frequently used drugs to treat pain in cancer patients. In some patients, however, opioids can cause adverse effects and drug-drug interactions. No advice concerning the combination of opioids and other drugs is given in the current European guidelines. To identify studies that report clinically significant drug-drug interactions involving opioids used for pain treatment in adult cancer patients. Systematic review with searches in Embase, MEDLINE, and Cochrane Central Register of Controlled Trials from the start of the databases (Embase from 1980) through January 2014. In addition, reference lists of relevant full-text papers were hand-searched. Of 901 retrieved papers, 112 were considered as potentially eligible. After full-text reading, 17 were included in the final analysis, together with 15 papers identified through hand-searching of reference lists. All of the 32 included publications were case reports or case series. Clinical manifestations of drug-drug interactions involving opioids were grouped as follows: 1) sedation and respiratory depression, 2) other central nervous system symptoms, 3) impairment of pain control and/or opioid withdrawal, and 4) other symptoms. The most common mechanisms eliciting drug-drug interactions were alteration of opioid metabolism by inhibiting the activity of cytochrome P450 3A4 and pharmacodynamic interactions due to the combined effect on opioid, dopaminergic, cholinergic, and serotonergic activity in the central nervous system. Evidence for drug-drug interactions associated with opioids used for pain treatment in cancer patients is very limited. Still, the cases identified in this systematic review give some important suggestions for clinical practice. Physicians prescribing opioids should recognize the risk of drug-drug interactions and if possible avoid polypharmacy.

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.

The effect of rigid and non-rigid connections between implants and teeth on biological and technical complications: a systematic review and a meta-analysis.

PubMed

Tsaousoglou, Phoebus; Michalakis, Konstantinos; Kang, Kiho; Weber, Hans-Peter; Sculean, Anton

2017-07-01

To assess survival, as well as technical and biological complication rates of partial fixed dental prostheses (FDPs) supported by implants and teeth. An electronic Medline search was conducted to identify articles, published in dental journals from January 1980 to August 2015, reporting on partial FDPs supported by implants and teeth. The search terms were categorized into four groups comprising the PICO question. Manual searches of published full-text articles and related reviews were also performed. The initial database search produced 3587 relevant titles. Three hundred and eighty-six articles were retrieved for abstract review, while 39 articles were selected for full-text review. A total of 10 studies were selected for inclusion. Overall survival rate for implants ranged between 90% and 100%, after follow-up periods with a mean range of 18-120 months. The survival of the abutment teeth was 94.1-100%, while the prostheses survival was 85-100% for the same time period. The most frequent complications were "periapical lesions" (11.53%). The most frequent technical complication was "porcelain occlusal fracture" (16.6%), followed by "screw loosening" (15%). According to the meta-analysis, no intrusion was noted on the rigid connection group, while five teeth (8.19%) were intruded in the non-rigid connection group [95% CI (0.013-0.151)]. The tooth-implant FDP seems to be a possible alternative to an implant-supported FDP. There is limited evidence that rigid connection between teeth and implants presents better results when compared with the non-rigid one. The major drawback of non-rigidly connected FDPs is tooth intrusion. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Effectiveness of nonpharmacological interventions to reduce procedural anxiety in children and adolescents undergoing treatment for cancer: A systematic review and meta-analysis.

PubMed

Nunns, Michael; Mayhew, Dominic; Ford, Tamsin; Rogers, Morwenna; Curle, Christine; Logan, Stuart; Moore, Darren

2018-04-30

Children and young people (CYP) with cancer undergo painful and distressing procedures. We aimed to systematically review the effectiveness of nonpharmacological interventions to reduce procedural anxiety in CYP. Extensive literature searches sought randomised controlled trials that quantified the effect of any nonpharmacological intervention for procedural anxiety in CYP with cancer aged 0 to 25. Study selection involved independent title and abstract screening and full text screening by two reviewers. Anxiety, distress, fear, and pain outcomes were extracted from included studies. Where similar intervention, comparator, and outcomes presented, meta-analysis was performed, producing pooled effect sizes (Cohen's d) and 95% confidence intervals (95% CI). All other data were narratively described. Quality and risk of bias appraisal was performed, based on the Cochrane risk of bias tool. Screening of 11 727 records yielded 56 relevant full texts. There were 15 included studies, eight trialling hypnosis, and seven nonhypnosis interventions. There were large, statistically significant reductions in anxiety and pain for hypnosis, particularly compared with treatment as usual (anxiety: d = 2.30; 95% CI, 1.30-3.30; P < .001; pain: d = 2.16; 95% CI, 1.41-2.92; P < .001). Evidence from nonhypnosis interventions was equivocal, with some promising individual studies. There was high risk of bias across included studies limiting confidence in some positive effects. Evidence suggests promise for hypnosis interventions to reduce procedural anxiety in CYP undergoing cancer treatment. These results largely emerge from one research group, therefore wider research is required. Promising evidence for individual nonhypnosis interventions must be evaluated through rigorously conducted randomised controlled trials. Copyright © 2018 John Wiley & Sons, Ltd.

Comprehensive systematic review summary: Disease-modifying therapies for adults with multiple sclerosis: Report of the Guideline Development, Dissemination, and Implementation Subcommittee of the American Academy of Neurology.

PubMed

Rae-Grant, Alexander; Day, Gregory S; Marrie, Ruth Ann; Rabinstein, Alejandro; Cree, Bruce A C; Gronseth, Gary S; Haboubi, Michael; Halper, June; Hosey, Jonathan P; Jones, David E; Lisak, Robert; Pelletier, Daniel; Potrebic, Sonja; Sitcov, Cynthia; Sommers, Rick; Stachowiak, Julie; Getchius, Thomas S D; Merillat, Shannon A; Pringsheim, Tamara

2018-04-24

To review evidence on starting, switching, and stopping disease-modifying therapies (DMTs) for multiple sclerosis (MS) in clinically isolated syndrome (CIS), relapsing-remitting MS (RRMS), and progressive MS forms. Relevant, peer-reviewed research articles, systematic reviews, and abstracts were identified (MEDLINE, CENTRAL, EMBASE searched from inception to November 2016). Studies were rated using the therapeutic classification scheme. Prior published Cochrane reviews were also used. Twenty Cochrane reviews and an additional 73 full-text articles were selected for data extraction through an updated systematic review (completed November 2016). For people with RRMS, many DMTs are superior to placebo (annualized relapses rates [ARRs], new disease activity [new MRI T2 lesion burden], and in-study disease progression) (see summary and full text publications). For people with RRMS who experienced a relapse on interferon-β (IFN-β) or glatiramer acetate, alemtuzumab is more effective than IFN-β-1a 44 μg subcutaneous 3 times per week in reducing the ARR. For people with primary progressive MS, ocrelizumab is probably more effective than placebo (in-study disease progression). DMTs for MS have varying adverse effects. In people with CIS, glatiramer acetate and IFN-β-1a subcutaneous 3 times per week are more effective than placebo in decreasing risk of conversion to MS. Cladribine, immunoglobulins, IFN-β-1a 30 μg intramuscular weekly, IFN-β-1b subcutaneous alternate day, and teriflunomide are probably more effective than placebo in decreasing risk of conversion to MS. Suggestions for future research include studies considering comparative effectiveness, usefulness of high-efficacy treatment vs stepped-care protocols, and research into predictive biomarkers. © 2018 American Academy of Neurology.

Accuracy of early detection of colorectal tumours by stool methylation markers: A meta-analysis

PubMed Central

Zhang, Hu; Qi, Jian; Wu, Ya-Qiong; Zhang, Ping; Jiang, Jun; Wang, Qi-Xian; Zhu, You-Qing

2014-01-01

AIM: To evaluate the accuracy of methylation of genes in stool samples for diagnosing colorectal tumours. METHODS: Electronic databases including PubMed, Web of Science, Chinese Journals Full-Text Database and Wanfang Journals Full-Text Database were searched to find relevant original articles about methylated genes to be used in diagnosing colorectal tumours. A quality assessment of diagnostic accuracy studies tool (QADAS) was used to evaluate the quality of the included articles, and the Meta-disc 1.4 and SPSS 13.0 software programs were used for data analysis. RESULTS: Thirty-seven articles met the inclusion criteria, and 4484 patients were included. The sensitivity and specificity for the detection of colorectal cancer (CRC) were 73% (95%CI: 71%-75%) and 92% (95%CI: 90%-93%), respectively. For adenoma, the sensitivity and specificity were 51% (95%CI: 47%-54%) and 92% (95%CI: 90%-93%), respectively. Pooled diagnostic performance of SFRP2 methylation for CRC provided the following results: the sensitivity was 79% (95%CI: 75%-82%), the specificity was 93% (95%CI: 90%-96%), the diagnostic OR was 47.57 (95%CI: 20.08-112.72), the area under the curve was 0.9565. Additionally, the results of accuracy of SFRP2 methylation for detecting colorectal adenomas were as follows: sensitivity was 43% (95%CI: 38%-49%), specificity was 94% (95%CI: 91%-97%), the diagnostic OR was 11.06 (95%CI: 5.77-21.18), and the area under the curve was 0.9563. CONCLUSION: Stool-based DNA testing may be useful for noninvasively diagnosing colorectal tumours and SFRP2 methylation is a promising marker that has great potential in early CRC diagnosis. PMID:25320544

The economic evidence for advance care planning: Systematic review of evidence.

PubMed

Dixon, Josie; Matosevic, Tihana; Knapp, Martin

2015-12-01

Advance care planning is a process of discussion and review concerning future care in the event of losing capacity. Aimed at improving the appropriateness and quality of care, it is also often considered a means of making better use of healthcare resources at the end of life. To review and summarise economic evidence on advance care planning. A systematic review of the academic literature. We searched for English language, peer-reviewed journal articles, 1990-2014, using relevant research databases: PubMed, ProQuest, CINAHL Plus with Full Text; EconLit, PsycINFO, SocINDEX with Full Text and International Bibliography of the Social Sciences. Empirical studies using statistical methods in which advance care planning and costs are variables were included. There are no published cost-effectiveness studies. Included studies focus on healthcare savings, usually associated with reduced demand for hospital care. Advance care planning appears to be associated with healthcare savings for some people in some circumstances, such as people living with dementia in the community, people in nursing homes or in areas with high end-of-life care spending. There is no evidence that advance care planning is likely to be more expensive. There is need for clearer articulation of the likely mechanisms by which advance care planning can lead to reduced care costs or improved cost-effectiveness, particularly for people who retain capacity. There is also a need to consider wider costs, including the costs of advance care planning facilitation or interventions and the costs of substitute health, social and informal care. Economic outcomes need to be considered in the context of quality benefits. © The Author(s) 2015.

An integrative review: Developing and measuring creativity in nursing.

PubMed

Ma, Xing; Yang, Yuanyuan; Wang, Xue; Zang, Yuli

2018-03-01

To analyze and synthesise the existing evidence on creativity in nursing. An integrative review. A systematic search was conducted using seven English databases (PubMed, Science Direct, Web of Science, Cochrane, EBSCO, Wiley, and Medline) and the top three best Chinese databases (CNKI, Wanfang Data, and VIP). The combined keywords, creativity and nursing/nurse, were used to search for relevant journal articles that were written in English or Chinese from January 1995 to December 2016. The components of articles, i.e. title, abstract, full-text and the cited reference, were screened, filtered, evaluated and recorded according to the PRISMA statements and Joanna Briggs Institute Checklists. Thematic analysis was performed to synthesise evidence from the full-texts of studies. Fifteen quantitative and seven qualitative studies were included in this review. A joyful affective perspective enriched the conceptualization of creativity in nursing. Many intrinsic factors (e.g. learning styles, thinking styles, intrinsic passion, interest in nursing and achievement motivation) or extrinsic factors (mostly workplace problems and nurses' shortage) could influence nurses' and nursing students' creativity. Artistic expressions (e.g. painting, music, and pottery), self-directed learning and group/team work were reported to have a positive effect on creativity enhancement. None of existing instruments can adequately measure nurses' or nursing students' creativity. The concept of creativity requires an explicit definition, which is essential to the development and evaluation of creativity in nursing education and practice. Many factors influencing nurses' and nursing students' creativity can be implemented to achieve positive outcomes through efforts at artistic expressions, self-directed learning and teamwork. An instrument with satisfactory psychometric properties should be available for monitoring creativity development among nurses and nursing students. Copyright © 2017 Elsevier Ltd. All rights reserved.

Reliability and Validity of Survey Instruments to Measure Work-Related Fatigue in the Emergency Medical Services Setting: A Systematic Review.

PubMed

Patterson, P Daniel; Weaver, Matthew D; Fabio, Anthony; Teasley, Ellen M; Renn, Megan L; Curtis, Brett R; Matthews, Margaret E; Kroemer, Andrew J; Xun, Xiaoshuang; Bizhanova, Zhadyra; Weiss, Patricia M; Sequeira, Denisse J; Coppler, Patrick J; Lang, Eddy S; Higgins, J Stephen

2018-02-15

This study sought to systematically search the literature to identify reliable and valid survey instruments for fatigue measurement in the Emergency Medical Services (EMS) occupational setting. A systematic review study design was used and searched six databases, including one website. The research question guiding the search was developed a priori and registered with the PROSPERO database of systematic reviews: "Are there reliable and valid instruments for measuring fatigue among EMS personnel?" (2016:CRD42016040097). The primary outcome of interest was criterion-related validity. Important outcomes of interest included reliability (e.g., internal consistency), and indicators of sensitivity and specificity. Members of the research team independently screened records from the databases. Full-text articles were evaluated by adapting the Bolster and Rourke system for categorizing findings of systematic reviews, and the rated data abstracted from the body of literature as favorable, unfavorable, mixed/inconclusive, or no impact. The Grading of Recommendations, Assessment, Development and Evaluation (GRADE) methodology was used to evaluate the quality of evidence. The search strategy yielded 1,257 unique records. Thirty-four unique experimental and non-experimental studies were determined relevant following full-text review. Nineteen studies reported on the reliability and/or validity of ten different fatigue survey instruments. Eighteen different studies evaluated the reliability and/or validity of four different sleepiness survey instruments. None of the retained studies reported sensitivity or specificity. Evidence quality was rated as very low across all outcomes. In this systematic review, limited evidence of the reliability and validity of 14 different survey instruments to assess the fatigue and/or sleepiness status of EMS personnel and related shift worker groups was identified.

What is the physiological time to recovery after concussion? A systematic review.

PubMed

Kamins, Joshua; Bigler, Erin; Covassin, Tracey; Henry, Luke; Kemp, Simon; Leddy, John J; Mayer, Andrew; McCrea, Michael; Prins, Mayumi; Schneider, Kathryn J; Valovich McLeod, Tamara C; Zemek, Roger; Giza, Christopher C

2017-06-01

The aim of this study is to consolidate studies of physiological measures following sport-related concussion (SRC) to determine if a time course of postinjury altered neurobiology can be outlined. This biological time course was considered with respect to clinically relevant outcomes such as vulnerability to repeat injury and safe timing of return to physical contact risk. Systematic review. PubMed, CINAHL, Cochrane Central, PsychINFO. Studies were included if they reported original research on physiological or neurobiological changes after SRC. Excluded were cases series <5 subjects, reviews, meta-analyses, editorials, animal research and research not pertaining to SRC. A total of 5834 articles were identified, of which 80 were included for full-text data extraction and review. Relatively few longitudinal studies exist that follow both physiological dysfunction and clinical measures to recovery. Modalities of measuring physiological change after SRC were categorised into the following: functional MRI, diffusion tensor imaging, magnetic resonance spectroscopy, cerebral blood flow, electrophysiology, heart rate, exercise, fluid biomarkers and transcranial magnetic stimulation. Due to differences in modalities, time course, study design and outcomes, it is not possible to define a single 'physiological time window' for SRC recovery. Multiple studies suggest physiological dysfunction may outlast current clinical measures of recovery, supporting a buffer zone of gradually increasing activity before full contact risk. Future studies need to use generalisable populations, longitudinal designs following to physiological and clinical recovery and careful correlation of neurobiological modalities with clinical measures. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Accuracy of early detection of colorectal tumours by stool methylation markers: a meta-analysis.

PubMed

Zhang, Hu; Qi, Jian; Wu, Ya-Qiong; Zhang, Ping; Jiang, Jun; Wang, Qi-Xian; Zhu, You-Qing

2014-10-14

To evaluate the accuracy of methylation of genes in stool samples for diagnosing colorectal tumours. Electronic databases including PubMed, Web of Science, Chinese Journals Full-Text Database and Wanfang Journals Full-Text Database were searched to find relevant original articles about methylated genes to be used in diagnosing colorectal tumours. A quality assessment of diagnostic accuracy studies tool (QADAS) was used to evaluate the quality of the included articles, and the Meta-disc 1.4 and SPSS 13.0 software programs were used for data analysis. Thirty-seven articles met the inclusion criteria, and 4484 patients were included. The sensitivity and specificity for the detection of colorectal cancer (CRC) were 73% (95%CI: 71%-75%) and 92% (95%CI: 90%-93%), respectively. For adenoma, the sensitivity and specificity were 51% (95%CI: 47%-54%) and 92% (95%CI: 90%-93%), respectively. Pooled diagnostic performance of SFRP2 methylation for CRC provided the following results: the sensitivity was 79% (95%CI: 75%-82%), the specificity was 93% (95%CI: 90%-96%), the diagnostic OR was 47.57 (95%CI: 20.08-112.72), the area under the curve was 0.9565. Additionally, the results of accuracy of SFRP2 methylation for detecting colorectal adenomas were as follows: sensitivity was 43% (95%CI: 38%-49%), specificity was 94% (95%CI: 91%-97%), the diagnostic OR was 11.06 (95%CI: 5.77-21.18), and the area under the curve was 0.9563. Stool-based DNA testing may be useful for noninvasively diagnosing colorectal tumours and SFRP2 methylation is a promising marker that has great potential in early CRC diagnosis.

Fiber Typing of the Erector Spinae and Multifidus Muscles in Healthy Controls and Back Pain Patients: A Systematic Literature Review.

PubMed

Cagnie, Barbara; Dhooge, Famke; Schumacher, Charline; De Meulemeester, Kayleigh; Petrovic, Mirko; van Oosterwijck, Jessica; Danneels, Lieven

2015-01-01

Understanding the changes in muscle fiber typing is relevant in the context of muscle disorders because it provides information on the metabolic profile and functional capacity. The aim of this study was to systematically review the literature comparing muscle fiber typing in the back muscles of healthy subjects with low back pain (LBP) patients. Predefined keywords regarding muscle fiber typing and back muscles were combined in PubMed and Web of Science electronic search engines from inception to August 2014. Full-text articles were independently screened by 2 independent, blinded researchers. Full texts fulfilling the predefined inclusion criteria were assessed on risk of bias by 2 independent researchers, and relative data were extracted. Data were not pooled because of heterogeneity in biopsy locations and population. From the 214 articles that were identified, 18 met the inclusion criteria. These articles evaluated the muscle fiber type distribution or proportional fiber type area between muscles, muscle layers, men, and women or healthy subjects and LBP patients. Regarding muscle fiber type distribution, findings in healthy subjects and LBP patients show no or inconclusive evidence for intermuscular and interindividual differentiation. Studies evaluating the proportional fiber type area also suggest little intermuscular differentiation but provide plausible evidence that the proportional area occupied by type I fibers is higher in women compared to men. The evidence for differentiation based on the presence of low back pain is conflicting. This study found that the evidence regarding muscle fiber typing in back muscles is either inconclusive or shows little differences. The most plausible evidence exists for differentiation in proportional fiber type area depending on sex. Copyright © 2015 National University of Health Sciences. Published by Elsevier Inc. All rights reserved.

Systematic Review of Results of Kissing Stents in the Treatment of Aortoiliac Occlusive Disease.

PubMed

Groot Jebbink, Erik; Holewijn, Suzanne; Slump, Cornelis H; Lardenoije, Jan-Willem; Reijnen, Michel M P J

2017-07-01

Endovascular treatment of aortoiliac occlusive disease (AIOD) involving the aortic bifurcation is challenging. The gold standard is open surgery with patency rates up to 90% at 5 years, but has considerable morbidity and mortality. The kissing stent (KS) technique was introduced as an alternative. The goal of this review is to give an overview of the current results and role of the KS technique in AIOD treatment. The Cochrane guidelines were used to assure a systematic method. A search query designed in the Scopus search interface was used to identify relevant studies. Abstracts from the search were screened against the inclusion and exclusion criteria. During full-text reading, methodological quality was scored using a critical review list tailored to the topic of AIOD. Thereafter, study data were extracted and pooled for further analysis. In total, 143 abstracts were retrieved using Scopus, 116 were rejected and 7 more were rejected after full-text screening. One study was included after cross referencing. Twenty-one studies presented 1,390 patients. Rutherford classification 1/2/3 was the indication in 76.2% of patients, and 48.4% of the lesions were classified as Trans-Atlantic Inter-Society Consensus C or D. The technical success rate was 98.7%, and the complication rate was 10.8%. Clinical improvement at 30 days was achieved in 89.9%. Primary patency at 12, 24, and 60 months was 89.3%, 78.6%, and 69.0%, respectively. KS treatment of AIOD yields acceptable mid-term results, with high technical success rates and mostly minor complications occur. The long-term patency cannot yet match that of open surgery, underlining the need for further research that provides insight into factors related to reocclusion. Copyright © 2017 Elsevier Inc. All rights reserved.

Performance Indicators in Spine Surgery.

PubMed

St-Pierre, Godefroy Hardy; Yang, Michael H; Bourget-Murray, Jonathan; Thomas, Ken C; Hurlbert, Robin John; Matthes, Nikolas

2018-02-15

Systematic review. To elucidate how performance indicators are currently used in spine surgery. The Patient Protection and Affordable Care Act has given significant traction to the idea that healthcare must provide value to the patient through the introduction of hospital value-based purchasing. The key to implementing this new paradigm is to measure this value notably through performance indicators. MEDLINE, CINAHL Plus, EMBASE, and Google Scholar were searched for studies reporting the use of performance indicators specific to spine surgery. We followed the Prisma-P methodology for a systematic review for entries from January 1980 to July 2016. All full text articles were then reviewed to identify any measure of performance published within the article. This measure was then examined as per the three criteria of established standard, exclusion/risk adjustment, and benchmarking to determine if it constituted a performance indicator. The initial search yielded 85 results among which two relevant studies were identified. The extended search gave a total of 865 citations across databases among which 15 new articles were identified. The grey literature search provided five additional reports which in turn led to six additional articles. A total of 27 full text articles and reports were retrieved and reviewed. We were unable to identify performance indicators. The articles presenting a measure of performance were organized based on how many criteria they lacked. We further examined the next steps to be taken to craft the first performance indicator in spine surgery. The science of performance measurement applied to spine surgery is still in its infancy. Current outcome metrics used in clinical settings require refinement to become performance indicators. Current registry work is providing the necessary foundation, but requires benchmarking to truly measure performance. 1.

Document Delivery from Full-Text Online Files: A Pilot Project.

ERIC Educational Resources Information Center

Gillikin, David P.

1990-01-01

Describes the Electronic Journal Retrieval Project (EJRP) developed at the University of Tennessee, Knoxville Libraries, to provide full-text journal articles from online systems. Highlights include costs of various search strategies; implications for library services; collection development and interlibrary loan considerations; and suggestions…

Full Text Journal Subscriptions: An Evolutionary Process.

ERIC Educational Resources Information Center

Luther, Judy

1997-01-01

Provides an overview of companies offering Web accessible subscriptions to full text electronic versions of scientific, technical, and medical journals (Academic Press, Blackwell, EBSCO, Elsevier, Highwire Press, Information Quest, Institute of Physics, Johns Hopkins University Press, OCLC, OVID, Springer, and SWETS). Also lists guidelines for…

Techniques for identifying cross-disciplinary and 'hard-to-detect' evidence for systematic review.

PubMed

O'Mara-Eves, Alison; Brunton, Ginny; McDaid, David; Kavanagh, Josephine; Oliver, Sandy; Thomas, James

2014-03-01

Driven by necessity in our own complex review, we developed alternative systematic ways of identifying relevant evidence where the key concepts are generally not focal to the primary studies' aims and are found across multiple disciplines-that is, hard-to-detect evidence. Specifically, we sought to identify evidence on community engagement in public health interventions that aim to reduce health inequalities. Our initial search strategy used text mining to identify synonyms for the concept 'community engagement'. We conducted a systematic search for reviews on public health interventions, supplemented by searches of trials databases. We then used information in the reviews' evidence tables to gather more information about the included studies than was evident in the primary studies' own titles or abstracts. We identified 319 primary studies cited in reviews after full-text screening. In this paper, we retrospectively reflect on the challenges and benefits of the approach taken. We estimate that more than a quarter of the studies that were identified would have been missed by typical searching and screening methods. This identification strategy was highly effective and could be useful for reviews of broad research questions, or where the key concepts are unlikely to be the main focus of primary research. Copyright © 2013 John Wiley & Sons, Ltd.

Relevance of Trust Marks and CE Labels in German-Language Store Descriptions of Health Apps: Analysis

PubMed Central

Hillebrand, Uta; von Jan, Ute

2018-01-01

Background In addition to mandatory CE marking (“CE” representing Conformité Européenne, with the CE marking being a symbol of free marketability in the European Economic Area) for medical devices, there are various seals, initiatives, action groups, etc, in the health app context. However, whether manufacturers use them to distinguish their apps and attach relevance to them is unclear. Objective The objective was to take a snapshot of quality seals, regulatory marks, and other orientation aids available on the German app market and to determine whether manufacturers deem such labels relevant enough to apply them to their apps, namely as reflected by mentions in app description texts in a typical app store (ie, Apple’s App Store). Methods A full survey of the metadata of 103,046 apps from Apple’s German App Store in the Medicine and Health & Fitness categories was carried out. For apps with German-language store descriptions (N=8767), these were automatically searched for the occurrence of relevant keywords and validated manually (N=41). In addition, the websites of various app seal providers were checked for assigned seals. Results Few manufacturers referenced seals in the descriptions (5/41), although this would have been expected more often based on the seals we were able to identify from the seal providers’ Web pages, and there were 34 of 41 that mentioned CE status in the descriptions. Two apps referenced an app directory curated by experts; however, this is not an alternative to CE marks and seals of approval. Conclusions Currently, quality seals seem to be irrelevant for manufacturers. In line with regulatory requirements, mentions of medical device status are more frequent; however, neither characteristic is effective for identifying high-quality apps. To improve this situation, a possibly legally obligatory, standardized reporting system should be implemented. PMID:29695374

Analysis of queries sent to PubMed at the point of care: Observation of search behaviour in a medical teaching hospital

PubMed Central

Hoogendam, Arjen; Stalenhoef, Anton FH; Robbé, Pieter F de Vries; Overbeke, A John PM

2008-01-01

Background The use of PubMed to answer daily medical care questions is limited because it is challenging to retrieve a small set of relevant articles and time is restricted. Knowing what aspects of queries are likely to retrieve relevant articles can increase the effectiveness of PubMed searches. The objectives of our study were to identify queries that are likely to retrieve relevant articles by relating PubMed search techniques and tools to the number of articles retrieved and the selection of articles for further reading. Methods This was a prospective observational study of queries regarding patient-related problems sent to PubMed by residents and internists in internal medicine working in an Academic Medical Centre. We analyzed queries, search results, query tools (Mesh, Limits, wildcards, operators), selection of abstract and full-text for further reading, using a portal that mimics PubMed. Results PubMed was used to solve 1121 patient-related problems, resulting in 3205 distinct queries. Abstracts were viewed in 999 (31%) of these queries, and in 126 (39%) of 321 queries using query tools. The average term count per query was 2.5. Abstracts were selected in more than 40% of queries using four or five terms, increasing to 63% if the use of four or five terms yielded 2–161 articles. Conclusion Queries sent to PubMed by physicians at our hospital during daily medical care contain fewer than three terms. Queries using four to five terms, retrieving less than 161 article titles, are most likely to result in abstract viewing. PubMed search tools are used infrequently by our population and are less effective than the use of four or five terms. Methods to facilitate the formulation of precise queries, using more relevant terms, should be the focus of education and research. PMID:18816391

Relevance of Trust Marks and CE Labels in German-Language Store Descriptions of Health Apps: Analysis.

PubMed

Albrecht, Urs-Vito; Hillebrand, Uta; von Jan, Ute

2018-04-25

In addition to mandatory CE marking ("CE" representing Conformité Européenne, with the CE marking being a symbol of free marketability in the European Economic Area) for medical devices, there are various seals, initiatives, action groups, etc, in the health app context. However, whether manufacturers use them to distinguish their apps and attach relevance to them is unclear. The objective was to take a snapshot of quality seals, regulatory marks, and other orientation aids available on the German app market and to determine whether manufacturers deem such labels relevant enough to apply them to their apps, namely as reflected by mentions in app description texts in a typical app store (ie, Apple's App Store). A full survey of the metadata of 103,046 apps from Apple's German App Store in the Medicine and Health & Fitness categories was carried out. For apps with German-language store descriptions (N=8767), these were automatically searched for the occurrence of relevant keywords and validated manually (N=41). In addition, the websites of various app seal providers were checked for assigned seals. Few manufacturers referenced seals in the descriptions (5/41), although this would have been expected more often based on the seals we were able to identify from the seal providers' Web pages, and there were 34 of 41 that mentioned CE status in the descriptions. Two apps referenced an app directory curated by experts; however, this is not an alternative to CE marks and seals of approval. Currently, quality seals seem to be irrelevant for manufacturers. In line with regulatory requirements, mentions of medical device status are more frequent; however, neither characteristic is effective for identifying high-quality apps. To improve this situation, a possibly legally obligatory, standardized reporting system should be implemented. ©Urs-Vito Albrecht, Uta Hillebrand, Ute von Jan. Originally published in JMIR Mhealth and Uhealth (http://mhealth.jmir.org), 25.04.2018.

A Systematic Review of the Impact of Exposure to Internet-Based Alcohol-Related Content on Young People's Alcohol Use Behaviours.

PubMed

Gupta, Himanshu; Pettigrew, Simone; Lam, Tina; Tait, Robert J

2016-11-01

To conduct a systematic review of studies exploring the relationship between exposure to Internet-based alcohol-related content and alcohol use among young people. Searches of electronic databases and reference lists of relevant articles were conducted to retrieve studies of relevance up until December 2015. Full texts of the studies that met the inclusion criteria were read, appraised for quality using the Kmet forms and guidelines, and included in this review. Fifteen relevant studies were identified. The included studies were a mix of cross-sectional, longitudinal, experimental and qualitative studies conducted in the USA, the UK, Australia and New Zealand. The age range of the participants involved in these studies was 12-25 years. Included studies employed a variety of study designs and a range of different exposure variables and outcome measures. Studies demonstrated significant associations between exposure to Internet-based alcohol-related content and intentions to drink and positive attitudes towards alcohol drinking among young people. Exposure to alcohol-related content on the Internet might predispose young people to patterns of alcohol use by promoting alcohol as a natural and vital part of life. However, the research exploring the influence of this novel form of advertising on young people's alcohol use is emergent, and comprised primarily of cross-sectional studies. To evaluate the direction of the association between exposure to online alcohol-related content and alcohol use, we call for further research based on longitudinal designs. From 15 relevant studies identified, this review reports significant associations between exposure to Internet-based alcohol-related content and intentions to drink and positive attitudes towards alcohol drinking among young people, with different influences found at different stages of alcohol use. ©The Author 2016. Medical Council on Alcohol and Oxford University Press. All rights reserved.

Simulating Expert Clinical Comprehension: Adapting Latent Semantic Analysis to Accurately Extract Clinical Concepts from Psychiatric Narrative

PubMed Central

Cohen, Trevor; Blatter, Brett; Patel, Vimla

2008-01-01

Cognitive studies reveal that less-than-expert clinicians are less able to recognize meaningful patterns of data in clinical narratives. Accordingly, psychiatric residents early in training fail to attend to information that is relevant to diagnosis and the assessment of dangerousness. This manuscript presents cognitively motivated methodology for the simulation of expert ability to organize relevant findings supporting intermediate diagnostic hypotheses. Latent Semantic Analysis is used to generate a semantic space from which meaningful associations between psychiatric terms are derived. Diagnostically meaningful clusters are modeled as geometric structures within this space and compared to elements of psychiatric narrative text using semantic distance measures. A learning algorithm is defined that alters components of these geometric structures in response to labeled training data. Extraction and classification of relevant text segments is evaluated against expert annotation, with system-rater agreement approximating rater-rater agreement. A range of biomedical informatics applications for these methods are suggested. PMID:18455483

Integrating unified medical language system and association mining techniques into relevance feedback for biomedical literature search.

PubMed

Ji, Yanqing; Ying, Hao; Tran, John; Dews, Peter; Massanari, R Michael

2016-07-19

Finding highly relevant articles from biomedical databases is challenging not only because it is often difficult to accurately express a user's underlying intention through keywords but also because a keyword-based query normally returns a long list of hits with many citations being unwanted by the user. This paper proposes a novel biomedical literature search system, called BiomedSearch, which supports complex queries and relevance feedback. The system employed association mining techniques to build a k-profile representing a user's relevance feedback. More specifically, we developed a weighted interest measure and an association mining algorithm to find the strength of association between a query and each concept in the article(s) selected by the user as feedback. The top concepts were utilized to form a k-profile used for the next-round search. BiomedSearch relies on Unified Medical Language System (UMLS) knowledge sources to map text files to standard biomedical concepts. It was designed to support queries with any levels of complexity. A prototype of BiomedSearch software was made and it was preliminarily evaluated using the Genomics data from TREC (Text Retrieval Conference) 2006 Genomics Track. Initial experiment results indicated that BiomedSearch increased the mean average precision (MAP) for a set of queries. With UMLS and association mining techniques, BiomedSearch can effectively utilize users' relevance feedback to improve the performance of biomedical literature search.

Semantic Annotation of Complex Text Structures in Problem Reports

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Throop, David R.; Fleming, Land D.

2011-01-01

Text analysis is important for effective information retrieval from databases where the critical information is embedded in text fields. Aerospace safety depends on effective retrieval of relevant and related problem reports for the purpose of trend analysis. The complex text syntax in problem descriptions has limited statistical text mining of problem reports. The presentation describes an intelligent tagging approach that applies syntactic and then semantic analysis to overcome this problem. The tags identify types of problems and equipment that are embedded in the text descriptions. The power of these tags is illustrated in a faceted searching and browsing interface for problem report trending that combines automatically generated tags with database code fields and temporal information.

47 CFR 1.721 - Format and content of complaints.

Code of Federal Regulations, 2014 CFR

2014-10-01

... description of its relevance to the matters contained in the complaint; and (iii) A complete description of...: Before the Federal Communications Commission, Washington, DC 20554 In the matter of Complainant, v... facts as are necessary to give a full understanding of the matter, including relevant legal and...

47 CFR 1.721 - Format and content of complaints.

Code of Federal Regulations, 2013 CFR

2013-10-01

... description of its relevance to the matters contained in the complaint; and (iii) A complete description of...: Before the Federal Communications Commission, Washington, DC 20554 In the matter of Complainant, v... facts as are necessary to give a full understanding of the matter, including relevant legal and...

47 CFR 1.721 - Format and content of complaints.

Code of Federal Regulations, 2012 CFR

2012-10-01

... description of its relevance to the matters contained in the complaint; and (iii) A complete description of...: Before the Federal Communications Commission, Washington, DC 20554 In the matter of Complainant, v... facts as are necessary to give a full understanding of the matter, including relevant legal and...

Fit for purpose: perspectives on rapid reviews from end-user interviews.

PubMed

Hartling, Lisa; Guise, Jeanne-Marie; Hempel, Susanne; Featherstone, Robin; Mitchell, Matthew D; Motu'apuaka, Makalapua L; Robinson, Karen A; Schoelles, Karen; Totten, Annette; Whitlock, Evelyn; Wilt, Timothy J; Anderson, Johanna; Berliner, Elise; Gozu, Aysegul; Kato, Elisabeth; Paynter, Robin; Umscheid, Craig A

2017-02-17

There is increasing demand for rapid reviews and timely evidence synthesis. The goal of this project was to understand end-user perspectives on the utility and limitations of rapid products including evidence inventories, rapid responses, and rapid reviews. Interviews were conducted with key informants representing: guideline developers (n = 3), health care providers/health system organizations (n = 3), research funders (n = 1), and payers/health insurers (n = 1). We elicited perspectives on important characteristics of systematic reviews, acceptable methods to streamline reviews, and uses of rapid products. We analyzed content of the interview transcripts and identified themes and subthemes. Key informants identified the following as critical features of evidence reviews: (1) originating from a reliable source (i.e., conducted by experienced reviewers from an established research organization), (2) addressing clinically relevant questions, and (3) trusted relationship between the user and producer. Key informants expressed strong preference for the following review methods and characteristics: use of evidence tables, quality rating of studies, assessments of total evidence quality/strength, and use of summary tables for results and conclusions. Most acceptable trade-offs to increase efficiencies were limiting the literature search (e.g., limiting search dates or language) and performing single screening of citations and full texts for relevance. Key informants perceived rapid products (particularly evidence inventories and rapid responses) as useful interim products to inform downstream investigation (e.g., whether to proceed with a full review or guideline, direction for future research). Most key informants indicated that evidence analysis/synthesis and quality/strength of evidence assessments were important for decision-making. They reported that rapid reviews in particular were useful for guideline development on narrow topics, policy decisions when a quick turn-around is needed, decision-making for practicing clinicians in nuanced clinical settings, and decisions about coverage by payers/health insurers. Rapid reviews may be more relevant within specific clinical settings or health systems; whereas, broad/national guidelines often need a traditional systematic review. Key informants interviewed in our study indicated that evidence inventories, rapid responses, and rapid reviews have utility in specific decisions and contexts. They indicated that the credibility of the review producer, relevance of key questions, and close working relationship between the end-user and producer are critical for any rapid product. Our findings are limited by the sample size which may have been too small to reach saturation for the themes described.

Assessing healthcare professionals' experiences of integrated care: do surveys tell the full story?

PubMed

Stephenson, Matthew D; Campbell, Jared M; Lisy, Karolina; Aromataris, Edoardo C

2017-09-01

Integrated care is the combination of different healthcare services with the goal to provide comprehensive, seamless, effective and efficient patient care. Assessing the experiences of healthcare professionals (HCPs) is an important aspect when evaluating integrated care strategies. The aim of this rapid review was to investigate if quantitative surveys used to assess HCPs' experiences with integrated care capture all the aspects highlighted as being important in qualitative research, with a view to informing future survey development. The review considered all types of health professionals in primary care, and hospital and specialist services, with a specific focus on the provision of integrated care aimed at improving the patient journey. PubMed, CINAHL and grey literature sources were searched for relevant surveys/program evaluations and qualitative research studies. Full text articles deemed to be of relevance to the review were appraised for methodological quality using abridged critical appraisal instruments from the Joanna Briggs Institute. Data were extracted from included studies using standardized data extraction templates. Findings from included studies were grouped into domains based on similarity of meaning. Similarities and differences in the domains covered in quantitative surveys and those identified as being important in qualitative research were explored. A total of 37 studies (19 quantitative surveys, 14 qualitative studies and four mixed-method studies) were included in the review. A range of healthcare professions participated in the included studies, the majority being primary care providers. Common domains identified from quantitative surveys and qualitative studies included Communication, Agreement on Clear Roles and Responsibilities, Facilities, Information Systems, and Coordination of Care and Access. Qualitative research highlighted domains identified by HCPs as being relevant to their experiences with integrated care that have not routinely being surveyed, including Workload, Clear Leadership/Decision-Making, Management, Flexibility of Integrated Care Model, Engagement, Usefulness of Integrated Care and Collaboration, and Positive Impact/Clinical Benefits/Practice Level Benefits. There were several domains identified from qualitative research that are not routinely included in quantitative surveys to assess health professionals' experiences of integrated care. In addition, the qualitative findings suggest that the experiences of HCPs are often impacted by deeper aspects than those measured by existing surveys. Incorporation of targeted items within these domains in the design of surveys should enhance the capture of data that are relevant to the experiences of HCPs with integrated care, which may assist in more comprehensive evaluation and subsequent improvement of integrated care programs.

OTLA: A New Model for Online Teaching, Learning and Assessment in Higher Education

ERIC Educational Resources Information Center

Ghilay, Yaron; Ghilay, Ruth

2013-01-01

The study examined a new asynchronous model for online teaching, learning and assessment, called OTLA. It is designed for higher-education institutions and is based on LMS (Learning Management System) as well as other relevant IT tools. The new model includes six digital basic components: text, hypertext, text reading, lectures (voice/video),…

Finding the Spirit Within: A Critical Analysis of Film Techniques in "Spirited Away"

ERIC Educational Resources Information Center

Cooper, Damon

2010-01-01

In 2008 the New South Wales Board of Studies included Hayao Miyazaki's film "Spirited Away" as the prescribed text for the Higher School Certificate Japanese Extension course. A study of the film in this context requires students to engage with the text in three distinct ways: through language, cultural symbolism and relevance, and…

The Dissociation of Word Reading and Text Comprehension: Evidence from Component Skills.

ERIC Educational Resources Information Center

Oakhill, J. V.; Cain, K.; Bryant, P. E.

2003-01-01

Discusses the relative contribution of several theoretically relevant skills and abilities in accounting for variance in both word reading and text comprehension. Data is presented from two waves of a longitudinal study. Shows there is a dissociation between the skills and abilities that account for variance in word reading, and those that account…

Promoting an Equality Agenda in Adult Literacy Practice Using Non-Text/Creative Methodologies

ERIC Educational Resources Information Center

Mark, Rob

2007-01-01

This paper examines the relationship between literacy, equality and creativity and the relevance for adult literacy practices. It looks in particular at how literacy tutors can use creative non-text methods to promote an understanding of equality in learners' lives. Through an examination of the findings from the Literacy and Equality in Irish…

Do You Prefer to Have the Text or a Sheet with Your Physics Exams?

ERIC Educational Resources Information Center

Hamed, Kastro M.

2008-01-01

Many high school and introductory college physics instructors ponder the choice between "open text" exams versus "facts and formulae sheet" exams. Other alternatives are closed book/closed notes exams or an instructor-prepared sheet of facts and relevant formulas. There is no agreement on merit. Rehfuss strongly opposes allowing students to use…

Place-Based Science Teaching and Learning: 40 Activities for K-8 Classrooms

ERIC Educational Resources Information Center

Buxton, Cory A.; Provenzo, Eugene F., Jr.

2011-01-01

Grounded in theory and best-practices research, this practical text provides elementary and middle school teachers with 40 place-based activities that will help them to make science learning relevant to their students. This text provides teachers with both a rationale and a set of strategies and activities for teaching science in a local context…

Network analysis of named entity co-occurrences in written texts

NASA Astrophysics Data System (ADS)

Amancio, Diego Raphael

2016-06-01

The use of methods borrowed from statistics and physics to analyze written texts has allowed the discovery of unprecedent patterns of human behavior and cognition by establishing links between models features and language structure. While current models have been useful to unveil patterns via analysis of syntactical and semantical networks, only a few works have probed the relevance of investigating the structure arising from the relationship between relevant entities such as characters, locations and organizations. In this study, we represent entities appearing in the same context as a co-occurrence network, where links are established according to a null model based on random, shuffled texts. Computational simulations performed in novels revealed that the proposed model displays interesting topological features, such as the small world feature, characterized by high values of clustering coefficient. The effectiveness of our model was verified in a practical pattern recognition task in real networks. When compared with traditional word adjacency networks, our model displayed optimized results in identifying unknown references in texts. Because the proposed representation plays a complementary role in characterizing unstructured documents via topological analysis of named entities, we believe that it could be useful to improve the characterization of written texts (and related systems), specially if combined with traditional approaches based on statistical and deeper paradigms.

Recent Research in Science Teaching and Learning

ERIC Educational Resources Information Center

Allen, Deborah

2014-01-01

This feature is designed to point "CBE - Life Sciences Education" readers to current articles of interest in life sciences education as well as more general and noteworthy publications in education research. URLs are provided for the abstracts or full text of articles. For articles listed as "Abstract available," full text may…

Recent Research in Science Teaching and Learning

ERIC Educational Resources Information Center

Allen, Deborah

2013-01-01

This article is designed to point "CBE-Life Sciences Education" readers to current articles of interest in life sciences education as well as more general and noteworthy publications in education research. URLs are provided for the abstracts or full text of articles. For articles listed as "Abstract available," full text may be…

Abstracts versus Full Texts and Patents: A Quantitative Analysis of Biomedical Entities

NASA Astrophysics Data System (ADS)

Müller, Bernd; Klinger, Roman; Gurulingappa, Harsha; Mevissen, Heinz-Theodor; Hofmann-Apitius, Martin; Fluck, Juliane; Friedrich, Christoph M.

In information retrieval, named entity recognition gives the opportunity to apply semantic search in domain specific corpora. Recently, more full text patents and journal articles became freely available. As the information distribution amongst the different sections is unknown, an analysis of the diversity is of interest.

Understanding Student Article Retrieval Behaviors: Instructional Implications

ERIC Educational Resources Information Center

Cook-Cottone, Catherine P.; Dutt-Doner, Karen; Schoen, David

2005-01-01

This study evaluates the use of full-text databases amongst 425 undergraduate and graduate students in western New York. A review of literature implicated convenience, time issues, article retrieval option knowledge, and the appreciation and understanding of research article quality as potential predictors of full-text reliance. These variables…

Subject Retrieval from Full-Text Databases in the Humanities

ERIC Educational Resources Information Center

East, John W.

2007-01-01

This paper examines the problems involved in subject retrieval from full-text databases of secondary materials in the humanities. Ten such databases were studied and their search functionality evaluated, focusing on factors such as Boolean operators, document surrogates, limiting by subject area, proximity operators, phrase searching, wildcards,…

Maths anxiety and medication dosage calculation errors: A scoping review.

PubMed

Williams, Brett; Davis, Samantha

2016-09-01

A student's accuracy on drug calculation tests may be influenced by maths anxiety, which can impede one's ability to understand and complete mathematic problems. It is important for healthcare students to overcome this barrier when calculating drug dosages in order to avoid administering the incorrect dose to a patient when in the clinical setting. The aim of this study was to examine the effects of maths anxiety on healthcare students' ability to accurately calculate drug dosages by performing a scoping review of the existing literature. This review utilised a six-stage methodology using the following databases; CINAHL, Embase, Medline, Scopus, PsycINFO, Google Scholar, Trip database (http://www.tripdatabase.com/) and Grey Literature report (http://www.greylit.org/). After an initial title/abstract review of relevant papers, and then full text review of the remaining papers, six articles were selected for inclusion in this study. Of the six articles included, there were three experimental studies, two quantitative studies and one mixed method study. All studies addressed nursing students and the presence of maths anxiety. No relevant studies from other disciplines were identified in the existing literature. Three studies took place in the U.S, the remainder in Canada, Australia and United Kingdom. Upon analysis of these studies, four factors including maths anxiety were identified as having an influence on a student's drug dosage calculation abilities. Ultimately, the results from this review suggest more research is required in nursing and other relevant healthcare disciplines regarding the effects of maths anxiety on drug dosage calculations. This additional knowledge will be important to further inform development of strategies to decrease the potentially serious effects of errors in drug dosage calculation to patient safety. Copyright © 2016 Elsevier Ltd. All rights reserved.

Health-related quality-of-life outcome measures in paediatric palliative care: A systematic review of psychometric properties and feasibility of use

PubMed Central

Coombes, Lucy H; Wiseman, Theresa; Lucas, Grace; Sangha, Amrit; Murtagh, Fliss EM

2016-01-01

Background: The number of children worldwide requiring palliative care services is increasing due to advances in medical care and technology. The use of outcome measures is important to improve the quality and effectiveness of care. Aim: To systematically identify health-related quality-of-life outcome measures that could be used in paediatric palliative care and examine their feasibility of use and psychometric properties. Design: A systematic literature review and analysis of psychometric properties. Data sources: PsychInfo, Medline and EMBASE were searched from 1 January 1990 to 10 December 2014. Hand searches of the reference list of included studies and relevant reviews were also performed. Results: From 3460 articles, 125 papers were selected for full-text assessment. A total of 41 articles met the eligibility criteria and examined the psychometric properties of 22 health-related quality-of-life measures. Evidence was limited as at least half of the information on psychometric properties per instrument was missing. Measurement error was not analysed in any of the included articles and responsiveness was only analysed in one study. The methodological quality of included studies varied greatly. Conclusion: There is currently no ‘ideal’ outcome assessment measure for use in paediatric palliative care. The domains of generic health-related quality-of-life measures are not relevant to all children receiving palliative care and some domains within disease-specific measures are only relevant for that specific population. Potential solutions include adapting an existing measure or developing more individualized patient-centred outcome and experience measures. Either way, it is important to continue work on outcome measurement in this field. PMID:27247087

Respiratory Manifestations of Hypothyroidism: A Systematic Review.

PubMed

Sorensen, Jesper Roed; Winther, Kristian Hillert; Bonnema, Steen Joop; Godballe, Christian; Hegedüs, Laszlo

2016-11-01

Hypothyroidism has been associated with increased pulmonary morbidity and overall mortality. A systematic review was conducted to identify the prevalence and underlying mechanisms of respiratory problems among patients with thyroid insufficiency. PubMed and EMBASE databases were searched for relevant literature from January 1950 through January 2015 with the following study eligibility criteria: English-language publications; adult subclinical or overt hypothyroid patients; intervention, observational, or retrospective studies; and respiratory manifestations. The Preferred Reporting Items for Systematic reviews and Meta-Analyses statement was followed, and Cochrane's risk of bias tool was used. A total of 1699 papers were screened by two independent authors for relevant titles. Of 109 relevant abstracts, 28 papers underwent full-text analyses, of which 22 were included in the review. Possible mechanisms explaining respiratory problems at multiple physiological levels were identified, such as the ventilator control system, diaphragmatic muscle function, pulmonary gas exchange, goiter caused upper airway obstruction, decreased capacity for energy transduction, and reduced glycolytic activity. Obstructive sleep apnea syndrome was found among 30% of newly diagnosed patients with overt hypothyroidism, and demonstrated reversibility following treatment. The evidence for or against a direct effect on pulmonary function was ambiguous. However, each of the above-mentioned areas was only dealt with in a limited number of studies. Therefore, it is not possible to draw any strong conclusions on any of these themes. Moreover, most studies were hampered by considerable risk of bias due for example to small numbers of patients, lack of control groups, randomization and blinding, and differences in body mass index, sex, and age between subjects and controls. Mechanistic data linking hypothyroidism and respiratory function are at best limited. This area of research is therefore open for retesting hypotheses, using appropriate study designs and methods.

Pediatric hydrocephalus: systematic literature review and evidence-based guidelines. Part 3: Endoscopic computer-assisted electromagnetic navigation and ultrasonography as technical adjuvants for shunt placement.

PubMed

Flannery, Ann Marie; Duhaime, Ann-Christine; Tamber, Mandeep S; Kemp, Joanna

2014-11-01

This systematic review was undertaken to answer the following question: Do technical adjuvants such as ventricular endoscopic placement, computer-assisted electromagnetic guidance, or ultrasound guidance improve ventricular shunt function and survival? The US National Library of Medicine PubMed/MEDLINE database and the Cochrane Database of Systematic Reviews were queried using MeSH headings and key words specifically chosen to identify published articles detailing the use of cerebrospinal fluid shunts for the treatment of pediatric hydrocephalus. Articles meeting specific criteria that had been delineated a priori were then examined, and data were abstracted and compiled in evidentiary tables. These data were then analyzed by the Pediatric Hydrocephalus Systematic Review and Evidence-Based Guidelines Task Force to consider evidence-based treatment recommendations. The search yielded 163 abstracts, which were screened for potential relevance to the application of technical adjuvants in shunt placement. Fourteen articles were selected for full-text review. One additional article was selected during a review of literature citations. Eight of these articles were included in the final recommendations concerning the use of endoscopy, ultrasonography, and electromagnetic image guidance during shunt placement, whereas the remaining articles were excluded due to poor evidence or lack of relevance. The evidence included 1 Class I, 1 Class II, and 6 Class III papers. An evidentiary table of relevant articles was created. CONCLUSIONS/RECOMMENDATION: There is insufficient evidence to recommend the use of endoscopic guidance for routine ventricular catheter placement. Level I, high degree of clinical certainty. The routine use of ultrasound-assisted catheter placement is an option. Level III, unclear clinical certainty. The routine use of computer-assisted electromagnetic (EM) navigation is an option. Level III, unclear clinical certainty.

Lifestyle causes of male infertility.

PubMed

Durairajanayagam, Damayanthi

2018-03-01

To examine the potential effects of lifestyle factors on male reproductive health. Evidence of a global decline in human sperm quality over recent decades has been accumulating. Environmental, occupational, and modifiable lifestyle factors may contribute to this decline. This review focuses on key lifestyle factors that are associated with male infertility such as smoking cigarettes, alcohol intake, use of illicit drugs, obesity, psychological stress, advanced paternal age, dietary practices, and coffee consumption. Other factors such as testicular heat stress, intense cycling training, lack of sleep and exposure to electromagnetic radiation from mobile phone use are briefly discussed. A comprehensive literature search was performed to identify and synthesise all relevant information, mainly from within the last decade, on the major lifestyle factors associated with male infertility and semen quality. Database searches were limited to reports published in English only. A manual search of bibliographies of the reports retrieved was conducted to identify additional relevant articles. In all, 1012 articles were identified from the database search and after reviewing the titles and abstract of the reports, 104 articles met the inclusion criteria. Of these, 30 reports were excluded as the full-text could not be retrieved and the abstract did not have relevant data. The remaining 74 reports were reviewed for data on association between a particular lifestyle factor and male infertility and were included in the present review. The major lifestyle factors discussed in the present review are amongst the multiple potential risk factors that could impair male fertility. However, their negative impact may well be mostly overcome by behaviour modification and better lifestyle choices. Greater awareness and recognition of the possible impact of these lifestyle factors are important amongst couples seeking conception.

Development of Performance Dashboards in Healthcare Sector: Key Practical Issues.

PubMed

Ghazisaeidi, Marjan; Safdari, Reza; Torabi, Mashallah; Mirzaee, Mahboobeh; Farzi, Jebraeil; Goodini, Azadeh

2015-10-01

Static nature of performance reporting systems in health care sector has resulted in inconsistent, incomparable, time consuming, and static performance reports that are not able to transparently reflect a round picture of performance and effectively support healthcare managers' decision makings. So, the healthcare sector needs interactive performance management tools such as performance dashboards to measure, monitor, and manage performance more effectively. The aim of this article was to identify key issues that need to be addressed for developing high-quality performance dashboards in healthcare sector. A literature review was established to search electronic research databases, e-journals collections, and printed journals, books, dissertations, and theses for relevant articles. The search strategy interchangeably used the terms of "dashboard", "performance measurement system", and "executive information system" with the term of "design" combined with operator "AND". Search results (n=250) were adjusted for duplications, screened based on their abstract relevancy and full-text availability (n=147) and then assessed for eligibility (n=40). Eligible articles were included if they had explicitly focused on dashboards, performance measurement systems or executive information systems design. Finally, 28 relevant articles included in the study. Creating high-quality performance dashboards requires addressing both performance measurement and executive information systems design issues. Covering these two fields, identified contents were categorized to four main domains: KPIs development, Data Sources and data generation, Integration of dashboards to source systems, and Information presentation issues. This study implies the main steps to develop dashboards for the purpose of performance management. Performance dashboards developed on performance measurement and executive information systems principles and supported by proper back-end infrastructure will result in creation of dynamic reports that help healthcare managers to consistently measure the performance, continuously detect outliers, deeply analyze causes of poor performance, and effectively plan for the future.

Nursing role in well-child care: Systematic review of the literature.

PubMed

Turley, Jolanda; Vanek, Jaclyn; Johnston, Sharon; Archibald, Doug

2018-04-01

To describe and compare well-child care (WCC) in Australia, the Netherlands, and the United Kingdom (UK), focusing on the role of nurses and their interactions with other primary care providers in order to derive relevant lessons for Canada's interprofessional primary care teams. Ovid MEDLINE, EMBASE, and CINAHL were searched broadly using the search terms well child care, nursing role, and delivery of care and other synonymous terms. In addition, Google Scholar was used to search for gray literature, and reference mining revealed a few other relevant articles. The original search identified 929 articles. The inclusion criteria were the following: relevant to WCC delivery; focuses on Canada, the Netherlands, the UK, Australia, or an international comparison; describes care of healthy term infants; describes care provided in the community; and describes the role of the nurse in WCC delivery. An abstract review followed by full-text review condensed the search to 25 selected articles. Selected articles varied in method and scope; thus, a narrative synthesis was generated using thematic analysis. In Australia, the Netherlands, and the UK, many WCC tasks are performed by trained public health nurses in a separate but parallel system to family medicine, with interaction between nurses and FPs varying greatly among countries. In general, nurses' roles in WCC remained in the preventive care and screening domains, including monitoring development, providing health education, and supporting parents. The 3 overarching themes that were identified were around professional development and education, integration of care and interprofessional collaboration, and the nurses' role in an evolving health system. International examples, given Canada's primary care reforms, suggest it is time to examine greater role sharing in WCC between nurses and FPs in interdisciplinary primary care teams. Copyright© the College of Family Physicians of Canada.

JPRS Report, Soviet Union Military Affairs.

DTIC Science & Technology

1988-02-29

similar article on life in a disciplinary battalion was published in SOVETSKIY VOIN in Rus- sian No 23, Dec 87 pp 14-16. The full text ofthat article... Computer " first two paragraphs are KRASNAYA ZVEZDA intro- duction.! [ Text ] On 15 November, Krasnaya Zvezda published S. Belkin’s article "Taking a...in Russian 15 Dec 87 p 1 [Article: "More Concern About People"] [ Text ] Winter is now in full force. Like a stern and impartial examiner, it checks

An assessment of the information-seeking abilities and needs of practicing speech-language pathologists

PubMed Central

Nail-Chiwetalu, Barbara; Bernstein Ratner, Nan

2007-01-01

Objectives: This study assessed the information-seeking practices and needs of speech-language pathologists (SLPs). Improved understanding of these needs can inform librarians and educators to better prepare students in principles and methods of evidence-based practice (EBP) and, through continuing education (CE), promote the integration of EBP into clinical practice of SLPs. Methods: A 16-question survey was mailed to 1,000 certified speech-language pathologists in the United States. Results: Two hundred and eight usable surveys were returned for a response rate of 21%. For clinical questions, SLPs most often consulted with a colleague, participated in CE activities, and searched the open Internet. Few respondents relied on scholarly journal articles for assistance with clinical cases. The most prominent barriers to finding appropriate information were time and knowledge of where and how to find relevant information. Few reported having information literacy instruction by a librarian. Discussion: If EBP is to become a viable practice in clinical decision making, there appears to be a tremendous need for information literacy instruction in the university curriculum, as well as through CE activities for currently practicing SLPs. Given respondents' reported lack of time and limited access to full-text journals containing evidence relevant to clinical practice, the field of speech-language pathology will need to generate readily accessible clinical summaries of research evidence through meta-analyses, systematic reviews, and clinical practice guidelines. PMID:17443251

Major and Minor Classifications for Surgery in People With Hemophilia: A Literature Review.

PubMed

Solimeno, Luigi Piero; Escobar, Miguel A; Krassova, Snejana; Seremetis, Stephanie

2018-05-01

Agents that control bleeding and the usage of bypassing agents have made surgery an option to consider in people with hemophilia. However, the lack of consistent definitions for major or minor surgery may lead to inconsistencies in patient management. This literature review has evaluated how surgical procedures in people with hemophilia were categorized as major or minor surgery and assessed the consistency across publications. After screening 926 potentially relevant articles, 547 were excluded and 379 full-text articles were reviewed. Ninety-five articles categorized major or minor surgical procedures; of these, 35 publications categorized three or more major or minor surgical procedures and were included for analysis. Seven (20%) publications provided varying criteria for defining major or minor surgery, five of which defined surgery according to the level of surgical invasiveness. Across all 35 publications, there was considerable variance in the categorization of major and minor surgical procedures and some overlap in surgical nomenclature (eg, type of synovectomy, arthroscopy, and central venous access device insertion/removals). The lack of consistent guidance when referring to major or minor surgery in people with hemophilia needs to be addressed. Clear and consistent definitions, achieved by consensus and promoted by relevant international hemophilia committees, are desirable, to provide guidance on appropriate treatment, to increase the accuracy of trial data and may confound the interpretation of surgical outcomes.

Can we Build on Social Movement Theories to Develop and Improve Community-Based Participatory Research? A Framework Synthesis Review.

PubMed

Tremblay, Marie-Claude; Martin, Debbie H; Macaulay, Ann C; Pluye, Pierre

2017-06-01

A long-standing challenge in community-based participatory research (CBPR) has been to anchor practice and evaluation in a relevant and comprehensive theoretical framework of community change. This study describes the development of a multidimensional conceptual framework that builds on social movement theories to identify key components of CBPR processes. Framework synthesis was used as a general literature search and analysis strategy. An initial conceptual framework was developed from the theoretical literature on social movement. A literature search performed to identify illustrative CBPR projects yielded 635 potentially relevant documents, from which eight projects (corresponding to 58 publications) were retained after record and full-text screening. Framework synthesis was used to code and organize data from these projects, ultimately providing a refined framework. The final conceptual framework maps key concepts of CBPR mobilization processes, such as the pivotal role of the partnership; resources and opportunities as necessary components feeding the partnership's development; the importance of framing processes; and a tight alignment between the cause (partnership's goal), the collective action strategy, and the system changes targeted. The revised framework provides a context-specific model to generate a new, innovative understanding of CBPR mobilization processes, drawing on existing theoretical foundations. © 2017 The Authors American Journal of Community Psychology published by Wiley Periodicals, Inc. on behalf of Society for Community Research and Action.

Diagnostic value of clinical tests for degenerative rotator cuff disease in medical practice.

PubMed

Lasbleiz, S; Quintero, N; Ea, K; Petrover, D; Aout, M; Laredo, J D; Vicaut, E; Bardin, T; Orcel, P; Beaudreuil, J

2014-06-01

To assess the diagnostic value of clinical tests for degenerative rotator cuff disease (DRCD) in medical practice. Patients with DRCD were prospectively included. Eleven clinical tests of the rotator cuff have been done. One radiologist performed ultrasonography (US) of the shoulder. Results of US were expressed as normal tendon, tendinopathy or full-thickness tear (the reference). For each clinical test and each US criteria, sensitivity, specificity, negative predictive value and positive predictive value, accuracy, negative likelihood ratio (NLR) and positive likelihood ratio (PLR) were calculated. Clinical relevance was defined as PLR ≥2 and NLR ≤0.5. For 35 patients (39 shoulders), Jobe (PLR: 2.08, NLR: 0.31) and full-can (2, 0.5) test results were relevant for diagnosis of supraspinatus tears and resisted lateral rotation (2.42, 0.5) for infraspinatus tears, with weakness as response criteria. The lift-off test (8.50, 0.27) was relevant for subscapularis tears with lag sign as response criteria. Yergason's test (3.7, 0.41) was relevant for tendinopathy of the long head of the biceps with pain as a response criterion. There was no relevant clinical test for diagnosis of tendinopathy of supraspinatus, infraspinatus or subscapularis. Five of 11 clinical tests were relevant for degenerative rotator cuff disease. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Neurobiological bases of reading comprehension: Insights from neuroimaging studies of word level and text level processing in skilled and impaired readers

PubMed Central

Landi, Nicole; Frost, Stephen J.; Menc, W. Einar; Sandak, Rebecca; Pugh, Kenneth R.

2012-01-01

For accurate reading comprehension, readers must first learn to map letters to their corresponding speech sounds and meaning and then they must string the meanings of many words together to form a representation of the text. Furthermore, readers must master the complexities involved in parsing the relevant syntactic and pragmatic information necessary for accurate interpretation. Failure in this process can occur at multiple levels and cognitive neuroscience has been helpful in identifying the underlying causes of success and failure in reading single words and in reading comprehension. In general, neurobiological studies of skilled reading comprehension indicate a highly overlapping language circuit for single word reading, reading comprehension and listening comprehension with largely quantitative differences in a number of reading and language related areas. This paper reviews relevant research from studies employing neuroimaging techniques to study reading with a focus on the relationship between reading skill, single word reading, and text comprehension. PMID:23662034

DeTEXT: A Database for Evaluating Text Extraction from Biomedical Literature Figures

PubMed Central

Yin, Xu-Cheng; Yang, Chun; Pei, Wei-Yi; Man, Haixia; Zhang, Jun; Learned-Miller, Erik; Yu, Hong

2015-01-01

Hundreds of millions of figures are available in biomedical literature, representing important biomedical experimental evidence. Since text is a rich source of information in figures, automatically extracting such text may assist in the task of mining figure information. A high-quality ground truth standard can greatly facilitate the development of an automated system. This article describes DeTEXT: A database for evaluating text extraction from biomedical literature figures. It is the first publicly available, human-annotated, high quality, and large-scale figure-text dataset with 288 full-text articles, 500 biomedical figures, and 9308 text regions. This article describes how figures were selected from open-access full-text biomedical articles and how annotation guidelines and annotation tools were developed. We also discuss the inter-annotator agreement and the reliability of the annotations. We summarize the statistics of the DeTEXT data and make available evaluation protocols for DeTEXT. Finally we lay out challenges we observed in the automated detection and recognition of figure text and discuss research directions in this area. DeTEXT is publicly available for downloading at http://prir.ustb.edu.cn/DeTEXT/. PMID:25951377

A Retrospective and Prospective View of Information Retrieval and Artificial Intelligence in the 21st Century.

ERIC Educational Resources Information Center

Garfield, Eugene

2001-01-01

Traces the development of information retrieval/services and suggests that the creation of large digital libraries seems inevitable. Examines possibilities for increasing electronic access and the role of artificial intelligence. Highlights include: searching full text; sending full texts; selective dissemination of information (SDI) profiling and…

Recent Research in Science Teaching and Learning

ERIC Educational Resources Information Center

Allen, Deborah

2012-01-01

This article features recent research in science teaching and learning. It presents three current articles of interest in life sciences education, as well as more general and noteworthy publications in education research. URLs are provided for the abstracts or full text of articles. For articles listed as "Abstract available," full text may be…

Design of an On-Line Query Language for Full Text Patent Search.

ERIC Educational Resources Information Center

Glantz, Richard S.

The design of an English-like query language and an interactive computer environment for searching the full text of the U.S. patent collection are discussed. Special attention is paid to achieving a transparent user interface, to providing extremely broad search capabilities (including nested substitution classes, Kleene star events, and domain…

Access to Full-Text Journal Articles: Some Practical Considerations.

ERIC Educational Resources Information Center

Racine, Drew

1992-01-01

Discusses some of the issues and problems involved in using electronic full-text journals in the University of Texas at Austin libraries. Issues addressed include different standards; subjects represented and the time period covered; hardware considerations; software; printing; skills and training needed for library staff and for users; and costs.…

Recent Research in Science Teaching and Learning

ERIC Educational Resources Information Center

Dolan, Erin

2010-01-01

This feature is designed to point readers of this journal to current articles of interest in life sciences education as well as more general and noteworthy publications in education research. URLs are provided for the abstracts or full text of articles. For articles listed as "Abstract available," full text may be accessible at the indicated URL…

Reading behind the Lines: The Factors Affecting the Text Reception Threshold in Hearing Aid Users

ERIC Educational Resources Information Center

Zekveld, Adriana A.; Pronk, Marieke; Danielsson, Henrik; Rönnberg, Jerker

2018-01-01

Purpose: The visual Text Reception Threshold (TRT) test (Zekveld et al., 2007) has been designed to assess modality-general factors relevant for speech perception in noise. In the last decade, the test has been adopted in audiology labs worldwide. The 1st aim of this study was to examine which factors best predict interindividual differences in…

The Function of Annotations in the Comprehension of Scientific Texts: Cognitive Load Effects and the Impact of Verbal Ability

ERIC Educational Resources Information Center

Wallen, Erik; Plass, Jan L.; Brunken, Roland

2005-01-01

Students participated in a study (n = 98) investigating the effectiveness of three types of annotations on three learning outcome measures. The annotations were designed to support the cognitive processes in the comprehension of scientific texts, with a function to aid either the process of selecting relevant information, organizing the…

Bayesian Inference: with ecological applications

USGS Publications Warehouse

Link, William A.; Barker, Richard J.

2010-01-01

This text provides a mathematically rigorous yet accessible and engaging introduction to Bayesian inference with relevant examples that will be of interest to biologists working in the fields of ecology, wildlife management and environmental studies as well as students in advanced undergraduate statistics.. This text opens the door to Bayesian inference, taking advantage of modern computational efficiencies and easily accessible software to evaluate complex hierarchical models.

Learner-generated drawing for phonological and orthographic dyslexic readers.

PubMed

Wang, Li-Chih; Yang, Hsien-Ming; Tasi, Hung-Ju; Chan, Shih-Yi

2013-01-01

This study presents an examination of learner-generated drawing for different reading comprehension subtypes of dyslexic students and control students. The participants were 22 phonological dyslexic students, 20 orthographic dyslexic students, 21 double-deficit dyslexic students, and 45 age-, gender-, and IQ-matched control students. The major evaluation tools included word recognition task, orthographic task, phonological awareness task, and scenery texts and questions. Comparisons of the four groups of students showed differences among phonological dyslexia, orthographic dyslexia, double-deficit dyslexia, and the chronological age control groups in pre- and posttest performance of scenery texts. Differences also existed in relevant questions and the effect of the learner-generated drawing method. The pretest performance showed problems in the dyslexic samples in reading the scenery texts and answering relevant questions. The posttest performance revealed certain differences among phonological dyslexia, orthographic dyslexia, double-deficit dyslexia, and the chronological age control group. Finally, all dyslexic groups obtained a great effect from using the learner-generated drawing, particularly orthographic dyslexia. These results suggest that the learner-generated drawing was also useful for dyslexic students, with the potential for use in the classroom for teaching text reading to dyslexic students. Copyright © 2012 Elsevier Ltd. All rights reserved.

State of reporting of primary biomedical research: a scoping review protocol

PubMed Central

Mbuagbaw, Lawrence; Samaan, Zainab; Jin, Yanling; Nwosu, Ikunna; Levine, Mitchell A H; Adachi, Jonathan D; Thabane, Lehana

2017-01-01

Introduction Incomplete or inconsistent reporting remains a major concern in the biomedical literature. Incomplete or inconsistent reporting may yield the published findings unreliable, irreproducible or sometimes misleading. In this study based on evidence from systematic reviews and surveys that have evaluated the reporting issues in primary biomedical studies, we aim to conduct a scoping review with focuses on (1) the state-of-the-art extent of adherence to the emerging reporting guidelines in primary biomedical research, (2) the inconsistency between protocols or registrations and full reports and (3) the disagreement between abstracts and full-text articles. Methods and analyses We will use a comprehensive search strategy to retrieve all available and eligible systematic reviews and surveys in the literature. We will search the following electronic databases: Web of Science, Excerpta Medica Database (EMBASE), MEDLINE and Cumulative Index to Nursing and Allied Health Literature (CINAHL). Our outcomes are levels of adherence to reporting guidelines, levels of consistency between protocols or registrations and full reports and the agreement between abstracts and full reports, all of which will be expressed as percentages, quality scores or categorised rating (such as high, medium and low). No pooled analyses will be performed quantitatively given the heterogeneity of the included systematic reviews and surveys. Likewise, factors associated with improved completeness and consistency of reporting will be summarised qualitatively. The quality of the included systematic reviews will be evaluated using AMSTAR (a measurement tool to assess systematic reviews). Ethics and dissemination All findings will be published in peer-reviewed journals and relevant conferences. These results may advance our understanding of the extent of incomplete and inconsistent reporting, factors related to improved completeness and consistency of reporting and potential recommendations for various stakeholders in the biomedical community. PMID:28360252

Anxiety in medical students: is preparation for full-time clinical attachments more dependent upon differences in maturity or on educational programmes for undergraduate and graduate entry students?

PubMed

Hayes, K; Feather, A; Hall, A; Sedgwick, P; Wannan, G; Wessier-Smith, A; Green, T; McCrorie, P

2004-11-01

The transition to full-time clinical studies holds anxieties for most medical students. While graduate entry medical education has only recently begun in the UK, the parallel undergraduate and graduate entry MBBS courses taught at our school allowed us to study how 2 differently prepared groups perceived this vital time at a comparable stage in their training. An anonymous questionnaire collected demographic data and graded anxiety in 13 statements relating to starting full-time clinical attachments. Two open questions allowed free text comment on the most positive and negative influences perceived during this time. Both a statistical analysis and a qualitative assessment were performed to compare the 2 groups of students. The 2 groups were similar with respect to gender but the graduate entry students were significantly older. The graduate entry students were significantly less anxious about most aspects of the transition period compared to the undergraduates. These course differences remained after adjusting for age and sex. When adjusted for course and age, male students expressed less anxiety. The main positive qualitative statements related to continual clinical and communication skills training in the graduate entry group. The main qualitative concerns in both groups related to 'fitting in' and perceived lack of factual knowledge. These data support the early introduction of clinical skills teaching, backed up by a fully integrated clinically relevant curriculum with continued assessment, in preparing students and reducing levels of anxiety before they start full-time clinical attachments. These course design differences appear to be more important than any differences in maturity between the 2 groups.

Assessment of turbulence models for pulsatile flow inside a heart pump.

PubMed

Al-Azawy, Mohammed G; Turan, A; Revell, A

2016-02-01

Computational fluid dynamics (CFD) is applied to study the unsteady flow inside a pulsatile pump left ventricular assist device, in order to assess the sensitivity to a range of commonly used turbulence models. Levels of strain and wall shear stress are directly relevant to the evaluation of risk from haemolysis and thrombosis, and thus understanding the sensitivity to these turbulence models is important in the assessment of uncertainty in CFD predictions. The study focuses on a positive displacement or pulsatile pump, and the CFD model includes valves and moving pusher plate. An unstructured dynamic layering method was employed to capture this cyclic motion, and valves were simulated in their fully open position to mimic the natural scenario, with in/outflow triggered at control planes away from the valves. Six turbulence models have been used, comprising three relevant to the low Reynolds number nature of this flow and three more intended to investigate different transport effects. In the first group, we consider the shear stress transport (SST) [Formula: see text] model in both its standard and transition-sensitive forms, and the 'laminar' model in which no turbulence model is used. In the second group, we compare the one equation Spalart-Almaras model, the standard two equation [Formula: see text] and the full Reynolds stress model (RSM). Following evaluation of spatial and temporal resolution requirements, results are compared with available experimental data. The model was operated at a systolic duration of 40% of the pumping cycle and a pumping rate of 86 BPM (beats per minute). Contrary to reasonable preconception, the 'transition' model, calibrated to incorporate additional physical modelling specifically for these flow conditions, was not noticeably superior to the standard form of the model. Indeed, observations of turbulent viscosity ratio reveal that the transition model initiates a premature increase of turbulence in this flow, when compared with both experimental and higher order numerical results previously reported in the literature. Furthermore, the RSM is indicated to provide the most accurate prediction over much of the flow, due to its ability to more correctly account for three-dimensional effects. Finally, the clinical relevance of the results is reported along with a discussion on the impact of such modelling uncertainties.

Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature

PubMed Central

2011-01-01

Background The selection of relevant articles for curation, and linking those articles to experimental techniques confirming the findings became one of the primary subjects of the recent BioCreative III contest. The contest’s Protein-Protein Interaction (PPI) task consisted of two sub-tasks: Article Classification Task (ACT) and Interaction Method Task (IMT). ACT aimed to automatically select relevant documents for PPI curation, whereas the goal of IMT was to recognise the methods used in experiments for identifying the interactions in full-text articles. Results We proposed and compared several classification-based methods for both tasks, employing rich contextual features as well as features extracted from external knowledge sources. For IMT, a new method that classifies pair-wise relations between every text phrase and candidate interaction method obtained promising results with an F1 score of 64.49%, as tested on the task’s development dataset. We also explored ways to combine this new approach and more conventional, multi-label document classification methods. For ACT, our classifiers exploited automatically detected named entities and other linguistic information. The evaluation results on the BioCreative III PPI test datasets showed that our systems were very competitive: one of our IMT methods yielded the best performance among all participants, as measured by F1 score, Matthew’s Correlation Coefficient and AUC iP/R; whereas for ACT, our best classifier was ranked second as measured by AUC iP/R, and also competitive according to other metrics. Conclusions Our novel approach that converts the multi-class, multi-label classification problem to a binary classification problem showed much promise in IMT. Nevertheless, on the test dataset the best performance was achieved by taking the union of the output of this method and that of a multi-class, multi-label document classifier, which indicates that the two types of systems complement each other in terms of recall. For ACT, our system exploited a rich set of features and also obtained encouraging results. We examined the features with respect to their contributions to the classification results, and concluded that contextual words surrounding named entities, as well as the MeSH headings associated with the documents were among the main contributors to the performance. PMID:22151769

Level statistics of words: Finding keywords in literary texts and symbolic sequences

NASA Astrophysics Data System (ADS)

Carpena, P.; Bernaola-Galván, P.; Hackenberg, M.; Coronado, A. V.; Oliver, J. L.

2009-03-01

Using a generalization of the level statistics analysis of quantum disordered systems, we present an approach able to extract automatically keywords in literary texts. Our approach takes into account not only the frequencies of the words present in the text but also their spatial distribution along the text, and is based on the fact that relevant words are significantly clustered (i.e., they self-attract each other), while irrelevant words are distributed randomly in the text. Since a reference corpus is not needed, our approach is especially suitable for single documents for which no a priori information is available. In addition, we show that our method works also in generic symbolic sequences (continuous texts without spaces), thus suggesting its general applicability.

Comparing data accuracy between structured abstracts and full-text journal articles: implications in their use for informing clinical decisions.

PubMed

Fontelo, Paul; Gavino, Alex; Sarmiento, Raymond Francis

2013-12-01

The abstract is the most frequently read section of a research article. The use of 'Consensus Abstracts', a clinician-oriented web application formatted for mobile devices to search MEDLINE/PubMed, for informing clinical decisions was proposed recently; however, inaccuracies between abstracts and the full-text article have been shown. Efforts have been made to improve quality. We compared data in 60 recent-structured abstracts and full-text articles from six highly read medical journals. Data inaccuracies were identified and then classified as either clinically significant or not significant. Data inaccuracies were observed in 53.33% of articles ranging from 3.33% to 45% based on the IMRAD format sections. The Results section showed the highest discrepancies (45%) although these were deemed to be mostly not significant clinically except in one. The two most common discrepancies were mismatched numbers or percentages (11.67%) and numerical data or calculations found in structured abstracts but not mentioned in the full text (40%). There was no significant relationship between journals and the presence of discrepancies (Fisher's exact p value =0.3405). Although we found a high percentage of inaccuracy between structured abstracts and full-text articles, these were not significant clinically. The inaccuracies do not seem to affect the conclusion and interpretation overall. Structured abstracts appear to be informative and may be useful to practitioners as a resource for guiding clinical decisions.

BioCreative III interactive task: an overview

PubMed Central

2011-01-01

Background The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. The biocurator community, as an active user of biomedical literature, provides a diverse and engaged end user group for text mining tools. Earlier BioCreative challenges involved many text mining teams in developing basic capabilities relevant to biological curation, but they did not address the issues of system usage, insertion into the workflow and adoption by curators. Thus in BioCreative III (BC-III), the InterActive Task (IAT) was introduced to address the utility and usability of text mining tools for real-life biocuration tasks. To support the aims of the IAT in BC-III, involvement of both developers and end users was solicited, and the development of a user interface to address the tasks interactively was requested. Results A User Advisory Group (UAG) actively participated in the IAT design and assessment. The task focused on gene normalization (identifying gene mentions in the article and linking these genes to standard database identifiers), gene ranking based on the overall importance of each gene mentioned in the article, and gene-oriented document retrieval (identifying full text papers relevant to a selected gene). Six systems participated and all processed and displayed the same set of articles. The articles were selected based on content known to be problematic for curation, such as ambiguity of gene names, coverage of multiple genes and species, or introduction of a new gene name. Members of the UAG curated three articles for training and assessment purposes, and each member was assigned a system to review. A questionnaire related to the interface usability and task performance (as measured by precision and recall) was answered after systems were used to curate articles. Although the limited number of articles analyzed and users involved in the IAT experiment precluded rigorous quantitative analysis of the results, a qualitative analysis provided valuable insight into some of the problems encountered by users when using the systems. The overall assessment indicates that the system usability features appealed to most users, but the system performance was suboptimal (mainly due to low accuracy in gene normalization). Some of the issues included failure of species identification and gene name ambiguity in the gene normalization task leading to an extensive list of gene identifiers to review, which, in some cases, did not contain the relevant genes. The document retrieval suffered from the same shortfalls. The UAG favored achieving high performance (measured by precision and recall), but strongly recommended the addition of features that facilitate the identification of correct gene and its identifier, such as contextual information to assist in disambiguation. Discussion The IAT was an informative exercise that advanced the dialog between curators and developers and increased the appreciation of challenges faced by each group. A major conclusion was that the intended users should be actively involved in every phase of software development, and this will be strongly encouraged in future tasks. The IAT Task provides the first steps toward the definition of metrics and functional requirements that are necessary for designing a formal evaluation of interactive curation systems in the BioCreative IV challenge. PMID:22151968

Global population-level association between herpes simplex virus 2 prevalence and HIV prevalence.

PubMed

Kouyoumjian, Silva P; Heijnen, Marieke; Chaabna, Karima; Mumtaz, Ghina R; Omori, Ryosuke; Vickerman, Peter; Abu-Raddad, Laith J

2018-06-19

Our objective was to assess the population-level association between herpes simplex virus 2 (HSV-2) and HIV prevalence. Reports of HSV-2 and HIV prevalence were systematically reviewed and synthesized following PRISMA guidelines. Spearman rank correlation ((Equation is included in full-text article.)) was used to assess correlations. Risk ratios (RRHSV-2/HIV) and odds ratios (ORHSV-2/HIV) were used to assess HSV-2/HIV epidemiologic overlap. DerSimonian-Laird random-effects meta-analyses were conducted. In total, 939 matched HSV-2/HIV prevalence measures were identified from 77 countries. HSV-2 prevalence was consistently higher than HIV prevalence. Strong HSV-2/HIV prevalence association was found for all data ((Equation is included in full-text article.) = 0.6, P < 0.001), all data excluding people who inject drugs (PWID) and children ((Equation is included in full-text article.) = 0.7, P < 0.001), female sex workers ((Equation is included in full-text article.) = 0.5, P < 0.001), and MSM ((Equation is included in full-text article.) = 0.7, P < 0.001). No association was found for PWID ((Equation is included in full-text article.) = 0.2, P = 0.222) and children ((Equation is included in full-text article.) = 0.3, P = 0.082). A threshold effect was apparent where HIV prevalence was limited at HSV-2 prevalence less than 20%, but grew steadily with HSV-2 prevalence for HSV-2 prevalence greater than 20%. The overall pooled mean RRHSV-2/HIV was 5.0 (95% CI 4.7-5.3) and ORHSV-2/HIV was 9.0 (95% CI 8.4-9.7). The RRHSV-2/HIV and ORHSV-2/HIV showed similar patterns that conveyed inferences about HSV-2 and HIV epidemiology. HSV-2 and HIV prevalence are strongly associated. HSV-2 prevalence can be used as a proxy 'biomarker' of HIV epidemic potential, acting as a 'temperature scale' of the intensity of sexual risk behavior that drive HIV transmission. HSV-2 prevalence can be used to identify populations and/or sexual networks at high-risk of future HIV expansion, and help prioritization, optimization, and resource allocation of cost-effective prevention interventions.

Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction.

PubMed

Santos, Carlos; Eggle, Daniela; States, David J

2005-04-15

Wnt signaling is a very active area of research with highly relevant publications appearing at a rate of more than one per day. Building and maintaining databases describing signal transduction networks is a time-consuming and demanding task that requires careful literature analysis and extensive domain-specific knowledge. For instance, more than 50 factors involved in Wnt signal transduction have been identified as of late 2003. In this work we describe a natural language processing (NLP) system that is able to identify references to biological interaction networks in free text and automatically assembles a protein association and interaction map. A 'gold standard' set of names and assertions was derived by manual scanning of the Wnt genes website (http://www.stanford.edu/~rnusse/wntwindow.html) including 53 interactions involved in Wnt signaling. This system was used to analyze a corpus of peer-reviewed articles related to Wnt signaling including 3369 Pubmed and 1230 full text papers. Names for key Wnt-pathway associated proteins and biological entities are identified using a chi-squared analysis of noun phrases over-represented in the Wnt literature as compared to the general signal transduction literature. Interestingly, we identified several instances where generic terms were used on the website when more specific terms occur in the literature, and one typographic error on the Wnt canonical pathway. Using the named entity list and performing an exhaustive assertion extraction of the corpus, 34 of the 53 interactions in the 'gold standard' Wnt signaling set were successfully identified (64% recall). In addition, the automated extraction found several interactions involving key Wnt-related molecules which were missing or different from those in the canonical diagram, and these were confirmed by manual review of the text. These results suggest that a combination of NLP techniques for information extraction can form a useful first-pass tool for assisting human annotation and maintenance of signal pathway databases. The pipeline software components are freely available on request to the authors. dstates@umich.edu http://stateslab.bioinformatics.med.umich.edu/software.html.

Development of a text messaging system to improve receipt of survivorship care in adolescent and young adult survivors of childhood cancer.

PubMed

Casillas, Jacqueline; Goyal, Anju; Bryman, Jason; Alquaddoomi, Faisal; Ganz, Patricia A; Lidington, Emma; Macadangdang, Joshua; Estrin, Deborah

2017-08-01

This study aimed to develop and examine the acceptability, feasibility, and usability of a text messaging, or Short Message Service (SMS), system for improving the receipt of survivorship care for adolescent and young adult (AYA) survivors of childhood cancer. Researchers developed and refined the text messaging system based on qualitative data from AYA survivors in an iterative three-stage process. In stage 1, a focus group (n = 4) addressed acceptability; in stage 2, key informant interviews (n = 10) following a 6-week trial addressed feasibility; and in stage 3, key informant interviews (n = 23) following a 6-week trial addressed usability. Qualitative data were analyzed using a constant comparative analytic approach exploring in-depth themes. The final system includes programmed reminders to schedule and attend late effect screening appointments, tailored suggestions for community resources for cancer survivors, and messages prompting participant feedback regarding the appointments and resources. Participants found the text messaging system an acceptable form of communication, the screening reminders and feedback prompts feasible for improving the receipt of survivorship care, and the tailored suggestions for community resources usable for connecting survivors to relevant services. Participants suggested supplementing survivorship care visits and forming AYA survivor social networks as future implementations for the text messaging system. The text messaging system may assist AYA survivors by coordinating late effect screening appointments, facilitating a partnership with the survivorship care team, and connecting survivors with relevant community resources. The text messaging system has the potential to improve the receipt of survivorship care.

Two-body decays of gluino at full one-loop level in the quark-flavour violating MSSM.

PubMed

Eberl, Helmut; Ginina, Elena; Hidaka, Keisho

2017-01-01

We study the two-body decays of the gluino at full one-loop level in the Minimal Supersymmetric Standard Model with quark-flavour violation (QFV) in the squark sector. The renormalisation is done in the [Formula: see text] scheme. The gluon and photon radiations are included by adding the corresponding three-body decay widths. We discuss the dependence of the gluino decay widths on the QFV parameters. The main dependence stems from the [Formula: see text]-[Formula: see text] mixing in the decays to up-type squarks, and from the [Formula: see text]-[Formula: see text] mixing in the decays to down-type squarks due to the strong constraints from B-physics on the other quark-flavour-mixing parameters. The full one-loop corrections to the gluino decay widths are mostly negative and of the order of about -10%. The QFV part stays small in the total width but can vary up to -8% for the decay width into the lightest [Formula: see text] squark. For the corresponding branching ratio the effect is somehow washed out by at least a factor of two. The electroweak corrections can be as large as 35% of the SUSY QCD corrections.

A narrative method for consciousness research.

PubMed

Díaz, José-Luis

2013-01-01

Some types of first-person narrations of mental processes that constitute phenomenological accounts and texts, such as internal monolog statements, epitomize the best expressions and representations of human consciousness available and therefore may be used to model phenomenological streams of consciousness. The type of autonomous monolog in which an author or narrator declares actual mental processes in a think aloud manner seems particularly suitable for modeling streams of consciousness. A narrative method to extract and depict conscious processes, operations, contents, and states from an acceptable phenomenological text would require three subsequent steps: operational criteria for producing and/or selecting a phenomenological text, a system for detecting text items that are indicative of conscious contents and processes, and a procedure for representing such items in formal dynamic system devices such as Petri nets. The requirements and restrictions of each of these steps are presented, analyzed, and applied to phenomenological texts in the following manner: (1) the relevance of introspective language and narrative analyses to consciousness research and the idea that specific narratives are of paramount interest for such investigation is justified; (2) some of the obstacles and constraints to attain plausible consciousness inferences from narrative texts and the methodological requirements to extract and depict items relevant to consciousness contents and operations from a suitable phenomenological text are examined; (3) a preliminary exercise of the proposed method is used to analyze and chart a classical interior monolog excerpted from James Joyce's Ulysses, a masterpiece of the stream-of-consciousness literary technique and, finally, (4) an inter-subjective evaluation for inter-observer agreement of mental attributions of another phenomenological text (an excerpt from the Intimate Journal of Miguel de Unamuno) is presented using some mathematical tools.

A narrative method for consciousness research

PubMed Central

Díaz, José-Luis

2013-01-01

Some types of first-person narrations of mental processes that constitute phenomenological accounts and texts, such as internal monolog statements, epitomize the best expressions and representations of human consciousness available and therefore may be used to model phenomenological streams of consciousness. The type of autonomous monolog in which an author or narrator declares actual mental processes in a think aloud manner seems particularly suitable for modeling streams of consciousness. A narrative method to extract and depict conscious processes, operations, contents, and states from an acceptable phenomenological text would require three subsequent steps: operational criteria for producing and/or selecting a phenomenological text, a system for detecting text items that are indicative of conscious contents and processes, and a procedure for representing such items in formal dynamic system devices such as Petri nets. The requirements and restrictions of each of these steps are presented, analyzed, and applied to phenomenological texts in the following manner: (1) the relevance of introspective language and narrative analyses to consciousness research and the idea that specific narratives are of paramount interest for such investigation is justified; (2) some of the obstacles and constraints to attain plausible consciousness inferences from narrative texts and the methodological requirements to extract and depict items relevant to consciousness contents and operations from a suitable phenomenological text are examined; (3) a preliminary exercise of the proposed method is used to analyze and chart a classical interior monolog excerpted from James Joyce’s Ulysses, a masterpiece of the stream-of-consciousness literary technique and, finally, (4) an inter-subjective evaluation for inter-observer agreement of mental attributions of another phenomenological text (an excerpt from the Intimate Journal of Miguel de Unamuno) is presented using some mathematical tools. PMID:24265610

Mobile Phone Apps for Behavioral Interventions for At-Risk Drinkers in Australia: Literature Review.

PubMed

Choo, Carol C; Burton, André A D

2018-02-13

The mobile technology era has ushered in the use of mobile phone apps for behavioral intervention for at-risk drinkers. Our objective was to review recent research relevant to mobile phone apps that can be used for behavioral intervention for at-risk drinkers in Australia. The inclusion criteria for this review were articles published in peer-reviewed journals from 2001 to 2017 with use of the search terms "smartphone application," "alcohol," "substance," "behavioural intervention," "electronic health," and "mobile health." In total, we identified 103 abstracts, screened 90 articles, and assessed 50 full-text articles that fit the inclusion criteria for eligibility. We included 19 articles in this review. This review highlighted the paucity of evidence-based and empirically validated research into effective mobile phone apps that can be used for behavioral interventions with at-risk drinkers in Australia. ©Carol C Choo, André A D Burton. Originally published in JMIR Mhealth and Uhealth (http://mhealth.jmir.org), 13.02.2018.

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.

Cultural Expressions of Intergenerational Trauma and Mental Health Nursing Implications for U.S. Health Care Delivery Following Refugee Resettlement: An Integrative Review of the Literature.

PubMed

Hudson, Christina Camille; Adams, Susie; Lauderdale, Jana

2016-05-01

The purpose of this integrative review of the literature is to examine cultural expressions of intergenerational trauma among refugees following resettlement, and to determine culturally sensitive mental health care practice implications for health care practitioners working in U.S. health care delivery. Data were collected utilizing a comprehensive computer-assisted search in CINAHL and PsychARTICLES/ProQuest from 2003 to 2013 of full text, peer-reviewed, scholarly journal articles, published in English. Eight articles met selection criteria and were analyzed using Gadamer's philosophical interpretation of play, symbolism, and festival in The Relevance of the Beautiful Six recurrent themes were identified important to refugee health care delivery: silence, communication, adaptation, relationship, remembering, and national redress. Practitioners need to consider cultural influences of intergenerational trauma in processing grief related to loss and how artistic modes of expression are experienced, both individually and communally, in refugee health care delivery. © The Author(s) 2015.

Dosimetry in dentistry.

PubMed

Asha, M L; Chatterjee, Ingita; Patil, Preeti; Naveen, S

2015-01-01

The purpose of this paper was to review various dosimeters used in dentistry and the cumulative results of various studies done with various dosimeters. Several relevant PubMed indexed articles from 1999 to 2013 were electronically searched by typing "dosimeters", "dosimeters in dentistry", "properties of dosimeters", "thermoluminescent and optically stimulated dosimeters", "recent advancements in dosimetry in dentistry." The searches were limited to articles in English to prepare a concise review on dental dosimetry. Titles and abstracts were screened, and articles that fulfilled the criteria of use of dosimeters in dental applications were selected for a full-text reading. Article was divided into four groups: (1) Biological effects of radiation, (2) properties of dosimeters, (3) types of dosimeters and (4) results of various studies using different dosimeters. The present review on dosimetry based on various studies done with dosimeters revealed that, with the advent of radiographic technique the effective dose delivered is low. Therefore, selection of radiological technique plays an important role in dental dose delivery.

Extracting semantic representations from word co-occurrence statistics: stop-lists, stemming, and SVD.

PubMed

Bullinaria, John A; Levy, Joseph P

2012-09-01

In a previous article, we presented a systematic computational study of the extraction of semantic representations from the word-word co-occurrence statistics of large text corpora. The conclusion was that semantic vectors of pointwise mutual information values from very small co-occurrence windows, together with a cosine distance measure, consistently resulted in the best representations across a range of psychologically relevant semantic tasks. This article extends that study by investigating the use of three further factors--namely, the application of stop-lists, word stemming, and dimensionality reduction using singular value decomposition (SVD)--that have been used to provide improved performance elsewhere. It also introduces an additional semantic task and explores the advantages of using a much larger corpus. This leads to the discovery and analysis of improved SVD-based methods for generating semantic representations (that provide new state-of-the-art performance on a standard TOEFL task) and the identification and discussion of problems and misleading results that can arise without a full systematic study.

Head and neck squamous cell carcinoma and its correlation with human papillomavirus in people living with HIV: a systematic review.

PubMed

Ceccarelli, Manuela; Rullo, Emmanuele Venanzi; Facciolà, Alessio; Madeddu, Giordano; Cacopardo, Bruno; Taibi, Rosaria; D'Aleo, Francesco; Pinzone, Marilia Rita; Picerno, Isa; di Rosa, Michele; Visalli, Giuseppa; Condorelli, Fabrizio; Nunnari, Giuseppe; Pellicanò, Giovanni Francesco

2018-03-30

Over the last 20 years we assisted to an increase in the mean age of People Living with HIV and their comorbidities. Especially, there was an increase in Human Papillomavirus-related head and neck squamous cell carcinomas. Despite their increasing incidence in HIV-positive people, mechanisms that lead to their development and progression are only partially understood. The aim of this review is to identify key data and factors about HPV-related head and neck squamous cell carcinoma in HIV-seropositive patients. Systematic search and review of the relevant literature-peer-reviewed and grey-was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines. We included in our review only the 35 full-text articles we considered the most substantial. It is mandatory to improve our knowledge about the interactions existing between HPV and HIV, and about their actions on oral mucosa immune system.

Use of Web-based library resources by medical students in community and ambulatory settings*

PubMed Central

Tannery, Nancy Hrinya; Foust, Jill E.; Gregg, Amy L.; Hartman, Linda M.; Kuller, Alice B.; Worona, Paul; Tulsky, Asher A.

2002-01-01

Purpose: The purpose was to evaluate the use of Web-based library resources by third-year medical students. Setting/Participants/Resources: Third-year medical students (147) in a twelve-week multidisciplinary primary care rotation in community and ambulatory settings. Methodology: Individual user surveys and log file analysis of Website were used. Results/Outcomes: Twenty resource topics were compiled into a Website to provide students with access to electronic library resources from any community-based clerkship location. These resource topics, covering subjects such as hypertension and back pain, linked to curriculum training problems, full-text journal articles, MEDLINE searches, electronic book chapters, and relevant Websites. More than half of the students (69%) accessed the Website on a daily or weekly basis. Over 80% thought the Website was a valuable addition to their clerkship. Discussion/Conclusion: Web-based information resources can provide curriculum support to students for whom access to the library is difficult and time consuming. PMID:12113515

Pre-Cancerous Lesions in the Oral and Maxillofacial Region: A Literature Review with Special Focus on Etiopathogenesis

PubMed Central

Irani, Soussan

2016-01-01

Many types of cancers develop in the oral and maxillofacial region. Squamous cell carcinoma is the most common cancer and constitutes over 90 percent of these tumors. Malignant transformation is a genetic process, which later makes a phenotyping change at the cellular level. Some cancers such as oral squamous cell carcinomas (OSCCs) develop from pre-malignant lesions and conditions. Despite advances in the treatment of OSCC, the 5-year survival rate remains approximately 50% due to inability of early detection of OSCC and precursor lesions. Early detection of oral cancer, especially in the premalignant stage, can decrease mortality and morbidity significantly. This article reviews some clinical, histopathological features and etiopathogenesis of pre-cancerous lesions of the oral cavity and skin of face and lip vermilion. A relevant English literature search in Pubmed, Science Direct, and Google Scholar was performed from 1930 to 2015. Full text of 191 articles met the specific inclusion criteria for this review. PMID:28855922

Integrative Therapeutic Approaches for the Management and Control of Nausea in Children Undergoing Cancer Treatment: A Systematic Review of Literature.

PubMed

Momani, Tha'er G; Berry, Donna L

Chemotherapy-induced nausea and vomiting (CINV) continues to be a common symptom experienced by children undergoing cancer treatment despite the use of contemporary antiemetics. Integrative therapeutic approaches in addition to standard pharmacologic antiemetic regimes offer potential to control CINV. The purpose of this review was to identify current evidence on integrative therapeutic approaches for the control of CINV in children with cancer. Online search engines (PubMed, CINAHL, PsychINFO) were queried using MESH terms. Titles, abstracts, and then full-text articles were reviewed for relevance to the review. The search resulted in 53 studies. Twenty-one studies met our review criteria. Integrative therapies identified included acupuncture/acupressure, aromatherapy, herbal supplements, hypnosis, and other cognitive behavioral interventions. Our review identified little information on the effectiveness and safety of most integrative therapeutic approaches for the control and management of CINV in children with cancer. However, evidence from adult cancer studies and some pediatric studies identify promising interventions for further testing.

Prototype of Multifunctional Full-text Library in the Architecture Web-browser / Web-server / SQL-server

NASA Astrophysics Data System (ADS)

Lyapin, Sergey; Kukovyakin, Alexey

Within the framework of the research program "Textaurus" an operational prototype of multifunctional library T-Libra v.4.1. has been created which makes it possible to carry out flexible parametrizable search within a full-text database. The information system is realized in the architecture Web-browser / Web-server / SQL-server. This allows to achieve an optimal combination of universality and efficiency of text processing, on the one hand, and convenience and minimization of expenses for an end user (due to applying of a standard Web-browser as a client application), on the other one. The following principles underlie the information system: a) multifunctionality, b) intelligence, c) multilingual primary texts and full-text searching, d) development of digital library (DL) by a user ("administrative client"), e) multi-platform working. A "library of concepts", i.e. a block of functional models of semantic (concept-oriented) searching, as well as a subsystem of parametrizable queries to a full-text database, which is closely connected with the "library", serve as a conceptual basis of multifunctionality and "intelligence" of the DL T-Libra v.4.1. An author's paragraph is a unit of full-text searching in the suggested technology. At that, the "logic" of an educational / scientific topic or a problem can be built in a multilevel flexible structure of a query and the "library of concepts", replenishable by the developers and experts. About 10 queries of various level of complexity and conceptuality are realized in the suggested version of the information system: from simple terminological searching (taking into account lexical and grammatical paradigms of Russian) to several kinds of explication of terminological fields and adjustable two-parameter thematic searching (a [set of terms] and a [distance between terms] within the limits of an author's paragraph are such parameters correspondingly).

Figure Text Extraction in Biomedical Literature

PubMed Central

Kim, Daehyun; Yu, Hong

2011-01-01

Background Figures are ubiquitous in biomedical full-text articles, and they represent important biomedical knowledge. However, the sheer volume of biomedical publications has made it necessary to develop computational approaches for accessing figures. Therefore, we are developing the Biomedical Figure Search engine (http://figuresearch.askHERMES.org) to allow bioscientists to access figures efficiently. Since text frequently appears in figures, automatically extracting such text may assist the task of mining information from figures. Little research, however, has been conducted exploring text extraction from biomedical figures. Methodology We first evaluated an off-the-shelf Optical Character Recognition (OCR) tool on its ability to extract text from figures appearing in biomedical full-text articles. We then developed a Figure Text Extraction Tool (FigTExT) to improve the performance of the OCR tool for figure text extraction through the use of three innovative components: image preprocessing, character recognition, and text correction. We first developed image preprocessing to enhance image quality and to improve text localization. Then we adapted the off-the-shelf OCR tool on the improved text localization for character recognition. Finally, we developed and evaluated a novel text correction framework by taking advantage of figure-specific lexicons. Results/Conclusions The evaluation on 382 figures (9,643 figure texts in total) randomly selected from PubMed Central full-text articles shows that FigTExT performed with 84% precision, 98% recall, and 90% F1-score for text localization and with 62.5% precision, 51.0% recall and 56.2% F1-score for figure text extraction. When limiting figure texts to those judged by domain experts to be important content, FigTExT performed with 87.3% precision, 68.8% recall, and 77% F1-score. FigTExT significantly improved the performance of the off-the-shelf OCR tool we used, which on its own performed with 36.6% precision, 19.3% recall, and 25.3% F1-score for text extraction. In addition, our results show that FigTExT can extract texts that do not appear in figure captions or other associated text, further suggesting the potential utility of FigTExT for improving figure search. PMID:21249186

Figure text extraction in biomedical literature.

PubMed

Kim, Daehyun; Yu, Hong

2011-01-13

Figures are ubiquitous in biomedical full-text articles, and they represent important biomedical knowledge. However, the sheer volume of biomedical publications has made it necessary to develop computational approaches for accessing figures. Therefore, we are developing the Biomedical Figure Search engine (http://figuresearch.askHERMES.org) to allow bioscientists to access figures efficiently. Since text frequently appears in figures, automatically extracting such text may assist the task of mining information from figures. Little research, however, has been conducted exploring text extraction from biomedical figures. We first evaluated an off-the-shelf Optical Character Recognition (OCR) tool on its ability to extract text from figures appearing in biomedical full-text articles. We then developed a Figure Text Extraction Tool (FigTExT) to improve the performance of the OCR tool for figure text extraction through the use of three innovative components: image preprocessing, character recognition, and text correction. We first developed image preprocessing to enhance image quality and to improve text localization. Then we adapted the off-the-shelf OCR tool on the improved text localization for character recognition. Finally, we developed and evaluated a novel text correction framework by taking advantage of figure-specific lexicons. The evaluation on 382 figures (9,643 figure texts in total) randomly selected from PubMed Central full-text articles shows that FigTExT performed with 84% precision, 98% recall, and 90% F1-score for text localization and with 62.5% precision, 51.0% recall and 56.2% F1-score for figure text extraction. When limiting figure texts to those judged by domain experts to be important content, FigTExT performed with 87.3% precision, 68.8% recall, and 77% F1-score. FigTExT significantly improved the performance of the off-the-shelf OCR tool we used, which on its own performed with 36.6% precision, 19.3% recall, and 25.3% F1-score for text extraction. In addition, our results show that FigTExT can extract texts that do not appear in figure captions or other associated text, further suggesting the potential utility of FigTExT for improving figure search.

Preparing College Students To Search Full-Text Databases: Is Instruction Necessary?

ERIC Educational Resources Information Center

Riley, Cheryl; Wales, Barbara

Full-text databases allow Central Missouri State University's clients to access some of the serials that libraries have had to cancel due to escalating subscription costs; EbscoHost, the subject of this study, is one such database. The database is available free to all Missouri residents. A survey was designed consisting of 21 questions intended…

ScienceCentral: open access full-text archive of scientific journals based on Journal Article Tag Suite regardless of their languages.

PubMed

Huh, Sun

2013-01-01

ScienceCentral, a free or open access, full-text archive of scientific journal literature at the Korean Federation of Science and Technology Societies, was under test in September 2013. Since it is a Journal Article Tag Suite-based full text database, extensible markup language files of all languages can be presented, according to Unicode Transformation Format 8-bit encoding. It is comparable to PubMed Central: however, there are two distinct differences. First, its scope comprises all science fields; second, it accepts all language journals. Launching ScienceCentral is the first step for free access or open access academic scientific journals of all languages to leap to the world, including scientific journals from Croatia.

Semi-Automated Annotation of Biobank Data Using Standard Medical Terminologies in a Graph Database.

PubMed

Hofer, Philipp; Neururer, Sabrina; Goebel, Georg

2016-01-01

Data describing biobank resources frequently contains unstructured free-text information or insufficient coding standards. (Bio-) medical ontologies like Orphanet Rare Diseases Ontology (ORDO) or the Human Disease Ontology (DOID) provide a high number of concepts, synonyms and entity relationship properties. Such standard terminologies increase quality and granularity of input data by adding comprehensive semantic background knowledge from validated entity relationships. Moreover, cross-references between terminology concepts facilitate data integration across databases using different coding standards. In order to encourage the use of standard terminologies, our aim is to identify and link relevant concepts with free-text diagnosis inputs within a biobank registry. Relevant concepts are selected automatically by lexical matching and SPARQL queries against a RDF triplestore. To ensure correctness of annotations, proposed concepts have to be confirmed by medical data administration experts before they are entered into the registry database. Relevant (bio-) medical terminologies describing diseases and phenotypes were identified and stored in a graph database which was tied to a local biobank registry. Concept recommendations during data input trigger a structured description of medical data and facilitate data linkage between heterogeneous systems.

LMSD: LIPID MAPS structure database

PubMed Central

Sud, Manish; Fahy, Eoin; Cotter, Dawn; Brown, Alex; Dennis, Edward A.; Glass, Christopher K.; Merrill, Alfred H.; Murphy, Robert C.; Raetz, Christian R. H.; Russell, David W.; Subramaniam, Shankar

2007-01-01

The LIPID MAPS Structure Database (LMSD) is a relational database encompassing structures and annotations of biologically relevant lipids. Structures of lipids in the database come from four sources: (i) LIPID MAPS Consortium's core laboratories and partners; (ii) lipids identified by LIPID MAPS experiments; (iii) computationally generated structures for appropriate lipid classes; (iv) biologically relevant lipids manually curated from LIPID BANK, LIPIDAT and other public sources. All the lipid structures in LMSD are drawn in a consistent fashion. In addition to a classification-based retrieval of lipids, users can search LMSD using either text-based or structure-based search options. The text-based search implementation supports data retrieval by any combination of these data fields: LIPID MAPS ID, systematic or common name, mass, formula, category, main class, and subclass data fields. The structure-based search, in conjunction with optional data fields, provides the capability to perform a substructure search or exact match for the structure drawn by the user. Search results, in addition to structure and annotations, also include relevant links to external databases. The LMSD is publicly available at PMID:17098933

Comparing deep learning and concept extraction based methods for patient phenotyping from clinical narratives.

PubMed

Gehrmann, Sebastian; Dernoncourt, Franck; Li, Yeran; Carlson, Eric T; Wu, Joy T; Welt, Jonathan; Foote, John; Moseley, Edward T; Grant, David W; Tyler, Patrick D; Celi, Leo A

2018-01-01

In secondary analysis of electronic health records, a crucial task consists in correctly identifying the patient cohort under investigation. In many cases, the most valuable and relevant information for an accurate classification of medical conditions exist only in clinical narratives. Therefore, it is necessary to use natural language processing (NLP) techniques to extract and evaluate these narratives. The most commonly used approach to this problem relies on extracting a number of clinician-defined medical concepts from text and using machine learning techniques to identify whether a particular patient has a certain condition. However, recent advances in deep learning and NLP enable models to learn a rich representation of (medical) language. Convolutional neural networks (CNN) for text classification can augment the existing techniques by leveraging the representation of language to learn which phrases in a text are relevant for a given medical condition. In this work, we compare concept extraction based methods with CNNs and other commonly used models in NLP in ten phenotyping tasks using 1,610 discharge summaries from the MIMIC-III database. We show that CNNs outperform concept extraction based methods in almost all of the tasks, with an improvement in F1-score of up to 26 and up to 7 percentage points in area under the ROC curve (AUC). We additionally assess the interpretability of both approaches by presenting and evaluating methods that calculate and extract the most salient phrases for a prediction. The results indicate that CNNs are a valid alternative to existing approaches in patient phenotyping and cohort identification, and should be further investigated. Moreover, the deep learning approach presented in this paper can be used to assist clinicians during chart review or support the extraction of billing codes from text by identifying and highlighting relevant phrases for various medical conditions.

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text.

PubMed

Baroukh, Caroline; Jenkins, Sherry L; Dannenfelser, Ruth; Ma'ayan, Avi

2011-10-13

Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are faced with the daunting amount of new research data commonly presented in textual formats, word-clouds can be used to summarize and represent biological and/or biomedical content for various applications. Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. It provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice. Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. Genes2WordCloud is freely available for use online; it is open source software and is available for installation on any web-site along with supporting documentation at http://www.maayanlab.net/G2W. Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications.

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text

PubMed Central

2011-01-01

Background Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are faced with the daunting amount of new research data commonly presented in textual formats, word-clouds can be used to summarize and represent biological and/or biomedical content for various applications. Results Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. It provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice. Methods Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. Genes2WordCloud is freely available for use online; it is open source software and is available for installation on any web-site along with supporting documentation at http://www.maayanlab.net/G2W. Conclusions Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications. PMID:21995939

Measuring large scale space perception in literary texts

NASA Astrophysics Data System (ADS)

Rossi, Paolo

2007-07-01

A center and radius of “perception” (in the sense of environmental cognition) can be formally associated with a written text and operationally defined. Simple algorithms for their computation are presented, and indicators for anisotropy in large scale space perception are introduced. The relevance of these notions for the analysis of literary and historical records is briefly discussed and illustrated with an example taken from medieval historiography.

Neurobiological Bases of Reading Comprehension: Insights from Neuroimaging Studies of Word-Level and Text-Level Processing in Skilled and Impaired Readers

ERIC Educational Resources Information Center

Landi, Nicole; Frost, Stephen J.; Mencl, W. Einar; Sandak, Rebecca; Pugh, Kenneth R.

2013-01-01

For accurate reading comprehension, readers must first learn to map letters to their corresponding speech sounds and meaning, and then they must string the meanings of many words together to form a representation of the text. Furthermore, readers must master the complexities involved in parsing the relevant syntactic and pragmatic information…

Teaching English as a Second Language: Perspectives and Practices. A Series of Six Texts. Speaking and Understanding: Second of a Series.

ERIC Educational Resources Information Center

New York State Education Dept., Albany.

This book is designed to assist those who work with non-English dominant students by providing resource information relevant to second language teaching and learning. The articles in the series encompass both theory and practical learning techniques in six general topics. The articles in the second text of the series, concerning speaking and…

Influencing Attitudes and Changing Behavior: A Basic Introduction to Relevant Methodology, Theory, and Applications. Revised Edition.

ERIC Educational Resources Information Center

Zimbardo, Philip; Ebbesen, Ebbe B.

In this introductory text to the field of attitude change, the emphasis is on one of the end products of research in social psychology--manipulation and control of attitudes and related behaviors. The text first defines the concept of attitude, then identifies ideas from the areas of history, literature, law, religion, and the social sciences that…

Hazardous Communication and Tools for Quality: Basic Statistics. Responsive Text. Educational Materials for the Workplace.

ERIC Educational Resources Information Center

Vermont Inst. for Self-Reliance, Rutland.

This guide provides a description of Responsive Text (RT), a method for presenting job-relevant information within a computer-based support system. A summary of what RT is and why it is important is provided first. The first section of the guide provides a brief overview of what research tells about the reading process and how the general design…

Learning to research in first grade: Bridging the transition from narrative to expository texts and tasks

NASA Astrophysics Data System (ADS)

Weise, Richard

Decades of research indicate that students at all academic grade and performance levels perform poorly with informational texts and tasks and particularly with locating assignment-relevant information in expository texts. Students have little understanding of the individual tasks required, the arc of the activity, the hierarchical structure of the information they seek, or how to reconstitute and interpret the information they extract. Poor performance begins with the introduction of textbooks and research assignments in fourth grade and continues into adulthood. However, to date, neither educators nor researchers have substantially addressed this problem. In this quasi-experimental study, we ask if first-grade children can perform essential tasks in identifying, extracting, and integrating assignment-relevant information and if instruction improves their performance. To answer this question, we conducted a 15-week, teacher-led, intervention in two first-grade classrooms in an inner-city Nashville elementary school. We created a computer learning environment (NoteTaker) to facilitate children's creation of a mental model of the research process and a narrative/expository bridge curriculum to support the children's transition from all narrative to all expository texts and tasks. We also created a new scaffolding taxonomy and a reading-to-research model to focus our research. Teachers participated in weekly professional development workshops. The results of this quasi-experimental study indicate that at-risk, first-grade children are able to (a) identify relevant information in an expository text, (b) categorize the information they identify, and (c) justify their choice of category. Children's performance in the first and last tasks significantly improved with instruction, and low-performing readers showed the greatest benefits from instruction. We find that the children's performance in categorizing information depended upon content-specific knowledge that was not taught, as well as on the process knowledge that was taught. We also find that children's narrative reading performance predicted their initial-performance for each assessment measure. We argue that first-grade children are developmentally ready to read expository texts and to learn reading-to-research tasks and that primary-school literacy instruction should not be limited to reading and writing stories.

Microsoft Research at TREC 2009. Web and Relevance Feedback Tracks

DTIC Science & Technology

2009-11-01

Information Processing Systems, pages 193–200, 2006. [2] J . M. Kleinberg. Authoritative sources in a hyperlinked environment. In Proc. of the 9th...Walker, S. Jones, M. Hancock-Beaulieu, and M. Gatford. Okapi at TREC-3. In Proc. of the 3rd Text REtrieval Conference, 1994. [8] J . J . Rocchio. Relevance...feedback in information retrieval. In Gerard Salton , editor, The SMART Retrieval System - Experiments in Automatic Document Processing. Prentice Hall

The Intestinal Microbiome in Infectious Diseases: The Clinical Relevance of a Rapidly Emerging Field.

PubMed

Harris, Vanessa C; Haak, Bastiaan W; Boele van Hensbroek, Michaël; Wiersinga, Willem J

2017-01-01

The field of infectious disease is undergoing a paradigm shift as the intestinal microbiome is becoming understood. The aim of this review is to inform infectious disease physicians of the potential relevance of the intestinal microbiome to their practice. We searched Medline using both index and text words relating to infectious diseases, microbiome, and probiotics. Relevant articles published up through 2017 were reviewed within Rayyan. The review illustrates pathophysiologic concepts linking the microbiome and infectious diseases; specifically, the intestinal microbiome's relevance to early immune development, the microbiome and enteric infections, the microbiome's relevance in compromised hosts, and antimicrobial resistance. Within each subject, there are specific examples of diseases and at-risk patient populations where a role for the microbiome has been strongly established. This provides an overview of the significance of the intestinal microbiome to microbiology, pediatric and adult infectious diseases with an underpinning of concepts useful for the practicing clinician.

Mindfulness predicts less texting while driving among young adults: Examining attention- and emotion-regulation motives as potential mediators

PubMed Central

Feldman, Greg; Greeson, Jeff; Renna, Megan; Robbins-Monteith, Kendra

2011-01-01

Many young adult drivers read and send text messages while driving despite clear safety risks. Understanding predictors of texting-while-driving may help to indentify relevant targets for interventions to reduce this dangerous behavior. The present study examined whether individual differences in mindfulness is associated with texting-while-driving in a sample of young-adult drivers. Using path analysis, we tested whether this relationship would be mediated by the degree to which individuals use text-messaging as a means of reducing unpleasant emotions (emotion-regulation motives) and the degree to which individuals limit texting in order to focus on present-moment experiences (attention-regulation motives). Individuals lower in mindfulness reported more frequent texting-while-driving and this relationship appeared to be mediated primarily by emotion-regulation motives. Results may help inform the development of mindfulness-based interventions to prevent texting-while-driving. PMID:22031789

Using texts in science education: cognitive processes and knowledge representation.

PubMed

van den Broek, Paul

2010-04-23

Texts form a powerful tool in teaching concepts and principles in science. How do readers extract information from a text, and what are the limitations in this process? Central to comprehension of and learning from a text is the construction of a coherent mental representation that integrates the textual information and relevant background knowledge. This representation engenders learning if it expands the reader's existing knowledge base or if it corrects misconceptions in this knowledge base. The Landscape Model captures the reading process and the influences of reader characteristics (such as working-memory capacity, reading goal, prior knowledge, and inferential skills) and text characteristics (such as content/structure of presented information, processing demands, and textual cues). The model suggests factors that can optimize--or jeopardize--learning science from text.

Influence Diffusion Model in Text-Based Communication

NASA Astrophysics Data System (ADS)

Matsumura, Naohiro; Ohsawa, Yukio; Ishizuka, Mitsuru

Business people, especially marketing researchers, are keen to understand peoples' potential sense of value to create fascinating topics stimulating peoples' interest. In this paper, we aim at finding influential people, comments, and terms contributing the discovery of such topics. For this purpose, we propose an Influence Diffusion Model in text-based communication, where the influence of people, comments, and terms are defined as the degree of text-based relevance of messages. We apply this model to Bulletin Board Service(BBS) on the Internet, and present our discoveries on experimental evaluations.

Towards a semantic lexicon for biological language processing

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

Verspoor, K.

It is well understood that natural language processing (NLP) applications require sophisticated lexical resources to support their processing goals. In the biomedical domain, we are privileged to have access to extensive terminological resources in the form of controlled vocabularies and ontologies, which have been integrated into the framework of the National Library of Medicine's Unified Medical Language System's (UMLS) Metathesaurus. However, the existence of such terminological resources does not guarantee their utility for NLP. In particular, we have two core requirements for lexical resources for NLP in addition to the basic enumeration of important domain terms: representation of morphosyntactic informationmore » about those terms, specifically part of speech information and inflectional patterns to support parsing and lemma assignment, and representation of semantic information indicating general categorical information about terms, and significant relations between terms to support text understanding and inference (Hahn et at, 1999). Biomedical vocabularies by and large commonly leave out morphosyntactic information, and where they address semantic considerations, they often do so in an unprincipled manner, for instance by indicating a relation between two concepts without indicating the type of that relation. But all is not lost. The UMLS knowledge sources include two additional resources which are relevant - the SPECIALIST lexicon, a lexicon addressing our morphosyntactic requirements, and the Semantic Network, a representation of core conceptual categories in the biomedical domain. The coverage of these two knowledge sources with respect to the full coverage of the Metathesaurus is, however, not entirely clear. Furthermore, when our goals are specifically to process biological text - and often more specifically, text in the molecular biology domain - it is difficult to say whether the coverage of these resources is meaningful. The utility of the UMLS knowledge sources for medical language processing (MLP) has been explored (Johnson, 1999; Friedman et al 2001); the time has now come to repeat these experiments with respect to biological language processing (BLP). To that end, this paper presents an analysis of ihe UMLS resources, specifically with an eye towards constructing lexical resources suitable for BLP. We follow the paradigm presented in Johnson (1999) for medical language, exploring overlap between the UMLS Metathesaurus and SPECIALIST lexicon to construct a morphosyntactic and semantically-specified lexicon, and then further explore the overlap with a relevant domain corpus for molecular biology.« less

Toward a Model of Text Comprehension and Production.

ERIC Educational Resources Information Center

Kintsch, Walter; Van Dijk, Teun A.

1978-01-01

Described is the system of mental operations occurring in text comprehension and in recall and summarization. A processing model is outlined: 1) the meaning elements of a text become organized into a coherent whole, 2) the full meaning of the text is condensed into its gist, and 3) new texts are generated from the comprehension processes.…

Rating the Relevance of QUORUM-Selected ASRS Incident Narratives to a "Controlled Flight into Terrain" Accident

NASA Technical Reports Server (NTRS)

McGreevy, Michael W.; Statler, Irving C.

1998-01-01

An exploratory study was conducted to identify commercial aviation incidents that are relevant to a "controlled flight into terrain" (CFIT) accident using a NASA-developed text processing method. The QUORUM method was used to rate 67820 incident narratives, virtually all of the narratives in the Aviation Safety Reporting System (ASRS) database, according to their relevance to two official reports on the crash of American Airlines Flight 965 near Cali, Colombia in December 1995. For comparison with QUORUM's ratings, three experienced ASRS analysts read the reports of the crash and independently rated the relevance of the 100 narratives that were most highly rated by QUORUM, as well as 100 narratives randomly selected from the database. Eighty-four of 100 QUORUM-selected narratives were rated as relevant to the Cali accident by one or more of the analysts. The relevant incidents involved a variety of factors, including, over-reliance on automation, confusion and changes during descent/approach, terrain avoidance, and operations in foreign airspace. In addition, the QUORUM collection of incidents was found to be significantly more relevant than the random collection.

NLM Emergency Access Initiative: FAQs

Science.gov Websites

provide temporary free access to full-text articles from over 650 biomedical serial titles and over 4,000 specified on the EAI welcome page can access the free full text resources during the period indicated to will I have access to this site? The dates of the free access period are listed on the home page along

Adopting an Electronic Text Book for a Postgraduate Accounting Course: An Experiential Study

ERIC Educational Resources Information Center

Schoch, Herbert P.; Teoh, Hai Yap; Kropman, Margaret

2006-01-01

Students are becoming accustomed to using the Internet as an information source that supplements or replaces the normal institutional and classroom handout. However, the use of full electronic books through the Internet or CD instead of a printed full text book is a uniquely different experience, not only for these students but also for academics…

On the Creation of Hypertext Links in Full-Text Documents: Measurement of Inter-Linker Consistency.

ERIC Educational Resources Information Center

Ellis, David; And Others

1994-01-01

Describes a study in which several different sets of hypertext links are inserted by different people in full-text documents. The degree of similarity between the sets is measured using coefficients and topological indices. As in comparable studies of inter-indexer consistency, the sets of links used by different people showed little similarity.…

2 CFR Appendix I to Part 200 - Full Text of Notice of Funding Opportunity

Code of Federal Regulations, 2014 CFR

2014-01-01

... PRINCIPLES, AND AUDIT REQUIREMENTS FOR FEDERAL AWARDS Pt. 200, App. I Appendix I to Part 200—Full Text of... section whether that section is required in every announcement or is a Federal awarding agency option. The... sections to describe the types of information that a Federal awarding agency would include in that section...

The End-User Cometh and Cometh Again and Again.

ERIC Educational Resources Information Center

Nicholas, David; Frossling, Ingrid

This article examines the impact of end-users on the information profession and looks ahead to what the future holds. It examines three waves of end-users that emerged with new search technologies: (1) full-text, natural language online systems; (2) CD-ROMs; and (3) the Internet. In the 1980s, when full-text online systems such as Textline, NEXIS,…

Electronic Journals in Aggregated Collections: Providing Access through the Catalog and a Cold Fusion Database

ERIC Educational Resources Information Center

Anderson, Sue

2005-01-01

Patrons in academic libraries want convenient 24-hour access to full-text journals in a rapid, convenient manner. They want "anytime, anywhere" access to information and they do not want to enter a library to obtain it. This article describes how Eastern Washington University Libraries provide access to full-text journals through several…

Ministry of Health clinical practice guidelines: Management of Rhinosinusitis and Allergic Rhinitis.

PubMed

Siow, J K; Alshaikh, N A; Balakrishnan, A; Chan, K O; Chao, S S; Goh, L G; Hwang, S Y; Lee, C Y; Leong, J L; Lim, L; Menon, A; Sethi, D S; Tan, H; Wang, D Y

2010-03-01

The Ministry of Health publishes national clinical practice guidelines to provide doctors and patients in Singapore with evidence-based guidance on managing important medical conditions. This article reproduces the introduction and executive summary (with recommendations from the guidelines) from the Ministry of Health clinical practice guidelines on Management of Rhinosinusitis and Allergic Rhinitis, for the information of readers of the Singapore Medical Journal. Chapters, page and figure numbers mentioned in the reproduced extract refer to the full text of the guidelines, which are available from the Ministry of Health website (http://www.moh.gov.sg/mohcorp/publications.aspx?id=24046). The recommendations should be used with reference to the full text of the guidelines. Following this article are multiple choice questions based on the full text of the guidelines.

ScienceCentral: open access full-text archive of scientific journals based on Journal Article Tag Suite regardless of their languages

PubMed Central

Huh, Sun

2013-01-01

ScienceCentral, a free or open access, full-text archive of scientific journal literature at the Korean Federation of Science and Technology Societies, was under test in September 2013. Since it is a Journal Article Tag Suite-based full text database, extensible markup language files of all languages can be presented, according to Unicode Transformation Format 8-bit encoding. It is comparable to PubMed Central: however, there are two distinct differences. First, its scope comprises all science fields; second, it accepts all language journals. Launching ScienceCentral is the first step for free access or open access academic scientific journals of all languages to leap to the world, including scientific journals from Croatia. PMID:24266292

Automated annotation of functional imaging experiments via multi-label classification

PubMed Central

Turner, Matthew D.; Chakrabarti, Chayan; Jones, Thomas B.; Xu, Jiawei F.; Fox, Peter T.; Luger, George F.; Laird, Angela R.; Turner, Jessica A.

2013-01-01

Identifying the experimental methods in human neuroimaging papers is important for grouping meaningfully similar experiments for meta-analyses. Currently, this can only be done by human readers. We present the performance of common machine learning (text mining) methods applied to the problem of automatically classifying or labeling this literature. Labeling terms are from the Cognitive Paradigm Ontology (CogPO), the text corpora are abstracts of published functional neuroimaging papers, and the methods use the performance of a human expert as training data. We aim to replicate the expert's annotation of multiple labels per abstract identifying the experimental stimuli, cognitive paradigms, response types, and other relevant dimensions of the experiments. We use several standard machine learning methods: naive Bayes (NB), k-nearest neighbor, and support vector machines (specifically SMO or sequential minimal optimization). Exact match performance ranged from only 15% in the worst cases to 78% in the best cases. NB methods combined with binary relevance transformations performed strongly and were robust to overfitting. This collection of results demonstrates what can be achieved with off-the-shelf software components and little to no pre-processing of raw text. PMID:24409112

Toward Routine Automatic Pathway Discovery from On-line Scientific Text Abstracts.

PubMed

Ng; Wong

1999-01-01

We are entering a new era of research where the latest scientific discoveries are often first reported online and are readily accessible by scientists worldwide. This rapid electronic dissemination of research breakthroughs has greatly accelerated the current pace in genomics and proteomics research. The race to the discovery of a gene or a drug has now become increasingly dependent on how quickly a scientist can scan through voluminous amount of information available online to construct the relevant picture (such as protein-protein interaction pathways) as it takes shape amongst the rapidly expanding pool of globally accessible biological data (e.g. GENBANK) and scientific literature (e.g. MEDLINE). We describe a prototype system for automatic pathway discovery from on-line text abstracts, combining technologies that (1) retrieve research abstracts from online sources, (2) extract relevant information from the free texts, and (3) present the extracted information graphically and intuitively. Our work demonstrates that this framework allows us to routinely scan online scientific literature for automatic discovery of knowledge, giving modern scientists the necessary competitive edge in managing the information explosion in this electronic age.

CRL/NMSU and Brandeis: Description of the MucBruce System as Used for MUC-4

DTIC Science & Technology

1992-01-01

developing a method fo r identifying articles of interest and extracting and storing specific kinds of information from large volumes o f Japanese and...performance . Most of the information produced in our MUC template s is arrived at by probing the text which surrounds `significant’ words for the...strings with semantic information . The other two, the Relevant Template Filter and the Relevant Paragraph Filter, perform word frequency analysis to

Layout-aware text extraction from full-text PDF of scientific articles.

PubMed

Ramakrishnan, Cartic; Patnia, Abhishek; Hovy, Eduard; Burns, Gully Apc

2012-05-28

The Portable Document Format (PDF) is the most commonly used file format for online scientific publications. The absence of effective means to extract text from these PDF files in a layout-aware manner presents a significant challenge for developers of biomedical text mining or biocuration informatics systems that use published literature as an information source. In this paper we introduce the 'Layout-Aware PDF Text Extraction' (LA-PDFText) system to facilitate accurate extraction of text from PDF files of research articles for use in text mining applications. Our paper describes the construction and performance of an open source system that extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles and is meant as a baseline for further experiments into more advanced extraction methods that handle multi-modal content, such as images and graphs. The system works in a three-stage process: (1) Detecting contiguous text blocks using spatial layout processing to locate and identify blocks of contiguous text, (2) Classifying text blocks into rhetorical categories using a rule-based method and (3) Stitching classified text blocks together in the correct order resulting in the extraction of text from section-wise grouped blocks. We show that our system can identify text blocks and classify them into rhetorical categories with Precision1 = 0.96% Recall = 0.89% and F1 = 0.91%. We also present an evaluation of the accuracy of the block detection algorithm used in step 2. Additionally, we have compared the accuracy of the text extracted by LA-PDFText to the text from the Open Access subset of PubMed Central. We then compared this accuracy with that of the text extracted by the PDF2Text system, 2commonly used to extract text from PDF. Finally, we discuss preliminary error analysis for our system and identify further areas of improvement. LA-PDFText is an open-source tool for accurately extracting text from full-text scientific articles. The release of the system is available at http://code.google.com/p/lapdftext/.

Layout-aware text extraction from full-text PDF of scientific articles

PubMed Central

2012-01-01

Background The Portable Document Format (PDF) is the most commonly used file format for online scientific publications. The absence of effective means to extract text from these PDF files in a layout-aware manner presents a significant challenge for developers of biomedical text mining or biocuration informatics systems that use published literature as an information source. In this paper we introduce the ‘Layout-Aware PDF Text Extraction’ (LA-PDFText) system to facilitate accurate extraction of text from PDF files of research articles for use in text mining applications. Results Our paper describes the construction and performance of an open source system that extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles and is meant as a baseline for further experiments into more advanced extraction methods that handle multi-modal content, such as images and graphs. The system works in a three-stage process: (1) Detecting contiguous text blocks using spatial layout processing to locate and identify blocks of contiguous text, (2) Classifying text blocks into rhetorical categories using a rule-based method and (3) Stitching classified text blocks together in the correct order resulting in the extraction of text from section-wise grouped blocks. We show that our system can identify text blocks and classify them into rhetorical categories with Precision1 = 0.96% Recall = 0.89% and F1 = 0.91%. We also present an evaluation of the accuracy of the block detection algorithm used in step 2. Additionally, we have compared the accuracy of the text extracted by LA-PDFText to the text from the Open Access subset of PubMed Central. We then compared this accuracy with that of the text extracted by the PDF2Text system, 2commonly used to extract text from PDF. Finally, we discuss preliminary error analysis for our system and identify further areas of improvement. Conclusions LA-PDFText is an open-source tool for accurately extracting text from full-text scientific articles. The release of the system is available at http://code.google.com/p/lapdftext/. PMID:22640904

Teaching nursing research to undergraduates: a text analysis of instructors' intentions.

PubMed

Porter, Eileen J; Mansour, Tamam B

2003-04-01

Reviews of teaching strategies for undergraduate nursing research have been organized according to (a) the type of learning to be achieved, such as learning by doing, or (b) the specific teaching strategy, such as a poster session. For this text analysis, a new tack was taken to reveal the intentions of undergraduate nursing research instructors for student learning. Giorgi's (1985) descriptive phenomenological method was used to analyze 77 narrative reports of instructors about research teaching strategies. Seven intentions were identified, including desensitizing negative perceptions about research and stimulating collaborative learning about research. The intentions were contrasted in scope and relevance to frameworks organized according to learning goals or teaching techniques. The relevance of the intentions was considered in relation to critical trends influencing nursing education. Copyright 2003 Wiley Periodicals, Inc. Res Nurs Health 26:128-142, 2003

The impact of interface design during an initial high-technology AAC experience: a collective case study of people with aphasia.

PubMed

Dietz, Aimee; Weissling, Kristy; Griffith, Julie; McKelvey, Miechelle; Macke, Devan

2014-12-01

The purpose of this collective case study was to describe the communication behaviors of five people with chronic aphasia when they retold personal narratives to an unfamiliar communication partner using four variants of a visual scene display (VSD) interface. The results revealed that spoken language comprised roughly 70% of expressive modality units; variable patterns of use for other modalities emerged. Although inconsistent across participants, several people with aphasia experienced no trouble sources during the retells using VSDs with personally relevant photographs and text boxes. Overall, participants perceived the personally relevant photographs and the text as helpful during the retells. These patterns may serve as a springboard for future experimental investigations regarding how interface design influences the communicative and linguistic performance of people with aphasia.

Relevance, Derogation and Permission

NASA Astrophysics Data System (ADS)

Stolpe, Audun

We show that a recently developed theory of positive permission based on the notion of derogation is hampered by a triviality result that indicates a problem with the underlying full-meet contraction operation. We suggest a solution that presupposes a particular normal form for codes of norms, adapted from the theory of relevance through propositional letter sharing. We then establish a correspondence between contractions on sets of norms in input/output logic (derogations), and AGM-style contractions on sets of formulae, and use it as a bridge to migrate results on propositional relevance from the latter to the former idiom. Changing the concept accordingly we show that positive permission now incorporates a relevance requirement that wards off triviality.

FEMA Database Requirements Assessment and Resource Directory Model.

DTIC Science & Technology

1982-05-01

File (NRCM) -- WContains information on organizations that are information resources on virtually any subject. * NEW YORK TIMES ONLINE -- Full text...version of the New York Times. * Newsearch: The Daily Index (Newsearch) -- Daily indexing of the periodicals in Magazine Index, newspapers in National...a NEXIS -- Full text of all general and business news covered in a variety of news - papers, magazines and wire services. 0 Oceanic Abstracts

A Resolution in Service: SFX Usage Logs as a Basis for Link Resolver Menu Redesign

ERIC Educational Resources Information Center

Highsmith, Anne L.; Ponsford, Bennett Claire

2011-01-01

In this study, three years of SFX usage logs at Texas A&M University were analyzed to determine how patrons use link resolver services. The study contrasts the actions taken by users when full text is and is not available and compares public versus staff usage. The results confirmed users' preference for full-text services but also provided…

Alterations in Aerobic Exercise Performance and Gait Economy Following High-Intensity Dynamic Stepping Training in Persons With Subacute Stroke.

PubMed

Leddy, Abigail L; Connolly, Mark; Holleran, Carey L; Hennessy, Patrick W; Woodward, Jane; Arena, Ross A; Roth, Elliot J; Hornby, T George

2016-10-01

Impairments in metabolic capacity and economy (O2cost) are hallmark characteristics of locomotor dysfunction following stroke. High-intensity (aerobic) training has been shown to improve peak oxygen consumption in this population, with fewer reports of changes in O2cost. However, particularly in persons with subacute stroke, inconsistent gains in walking function are observed with minimal associations with gains in metabolic parameters. The purpose of this study was to evaluate changes in aerobic exercise performance in participants with subacute stroke following high-intensity variable stepping training as compared with conventional therapy. A secondary analysis was performed on data from a randomized controlled trial comparing high-intensity training with conventional interventions, and from the pilot study that formed the basis for the randomized controlled trial. Participants 1 to 6 months poststroke received 40 or fewer sessions of high-intensity variable stepping training (n = 21) or conventional interventions (n = 12). Assessments were performed at baseline (BSL), posttraining, and 2- to 3-month follow-up and included changes in submaximal (Equation is included in full-text article.)O2 ((Equation is included in full-text article.)O2submax) and O2cost at fastest possible treadmill speeds and peak speeds at BSL testing. Significant improvements were observed in (Equation is included in full-text article.)O2submax with less consistent improvements in O2cost, although individual responses varied substantially. Combined changes in both (Equation is included in full-text article.)O2submax and (Equation is included in full-text article.)O2 at matched peak BSL speeds revealed stronger correlations to improvements in walking function as compared with either measure alone. High-intensity stepping training may elicit significant improvements in (Equation is included in full-text article.)O2submax, whereas changes in both peak capacity and economy better reflect gains in walking function. Providing high-intensity training to improve locomotor and aerobic exercise performance may increase the efficiency of rehabilitation sessions.Video Abstract available for more insights from the authors (see Supplemental Digital Content, http://links.lww.com/JNPT/A142).

Randomized Double-blind Trial of Ringer Lactate Versus Normal Saline in Pediatric Acute Severe Diarrheal Dehydration.

PubMed

Kartha, Gayathri Bhuvaneswaran; Rameshkumar, Ramachandran; Mahadevan, Subramanian

2017-12-01

The aim of this study was to compare the effectiveness of Ringer lactate (RL) versus normal saline (NS) in the correction of pediatric acute severe diarrheal dehydration, as measured by improvement in clinical status and pH (≥7.35). A total of 68 children ages 1 month to 12 years with acute severe diarrheal dehydration (World Health Organization [WHO] classification) were randomized into RL (n = 34) and NS groups (n = 34) and received 100 mL/kg of the assigned intravenous fluid according to WHO PLAN-C for the management of diarrheal dehydration. The primary outcome was an improvement in clinical status and pH (≥7.35) at the end of 6 hours. Secondary outcomes were changes in serum electrolytes, renal and blood gas parameters, the volume of fluid required for dehydration correction excluding the first cycle, time to start oral feeding, hospital stay, and cost-effectiveness analysis. Primary outcome was achieved in 38% versus 23% (relative risk = 1.63, 95% confidence interval 0.80-3.40) in RL and NS groups, respectively. No significant differences were observed in secondary outcomes in electrolytes, renal, and blood gas parameters. None required second cycle of dehydration correction. Median (interquartile range) time to start oral feeding (1.0 [0.19-2.0] vs 1.5 [0.5-2.0] hours) and hospital stay (2.0 [1.0-2.0] vs 2.0 [2.0-2.0] days) was similar. The median total cost was higher in RL than NS group ((Equation is included in full-text article.)120 [(Equation is included in full-text article.)120-(Equation is included in full-text article.)180] vs (Equation is included in full-text article.)55 [(Equation is included in full-text article.)55-(Equation is included in full-text article.)82], P ≤ 0.001). In pediatric acute severe diarrheal dehydration, resuscitation with RL and NS was associated with similar clinical improvement and biochemical resolution. Hence, NS is to be considered as the fluid of choice because of the clinical improvement, cost, and availability.

Effect of Coffee and Caffeine Ingestion on Resistance Exercise Performance.

PubMed

Richardson, Darren L; Clarke, Neil D

2016-10-01

Richardson, DL and Clarke, ND. Effect of coffee and caffeine ingestion on resistance exercise performance. J Strength Cond Res 30(10): 2892-2900, 2016-The aim of the present study was to determine the effect of ingesting caffeine dose-matched anhydrous caffeine, coffee, or decaffeinated coffee plus anhydrous caffeine during resistance exercise on performance. Nine resistance-trained men (mean ± SD: age, 24 ± 2 years; weight, 84 ± 8 kg; height, 180 ± 8 cm) completed a squat and bench press exercise protocol at 60% 1 repetition maximum until failure on 5 occasions consuming 0.15 g·kg caffeinated coffee (COF), 0.15 g·kg decaffeinated coffee (DEC), 0.15 g·kg decaffeinated coffee plus 5 mg·kg anhydrous caffeine (D + C), 5 mg·kg anhydrous caffeine (CAF), or a placebo (PLA). Felt arousal and rating of perceived exertion (RPE) were used to assess perceptual variables and heart rate (HR) to assess physiological responses between trials. There were significant differences in total weight lifted for the squat between conditions (p < 0.01; (Equation is included in full-text article.)= 0.54) with a greater amount lifted during D + C compared with DEC (p < 0.01), CAF (p ≤ 0.05), and PLA (p ≤ 0.05) conditions. Total weight lifted during the COF condition was significantly greater than that lifted under PLA (p < 0.01), although not significantly greater than the amount of weight lifted during the DEC condition (p = 0.082). No significant differences were observed in total weight lifted in the bench press protocol between conditions (p = 0.186; (Equation is included in full-text article.)= 0.17). Significant differences in HR (p < 0.01; (Equation is included in full-text article.)= 0.39) but not RPE (squat: p = 0.690; (Equation is included in full-text article.)= 0.07; bench press: p = 0.165; (Equation is included in full-text article.)= 0.18) and felt arousal (p = 0.056; (Equation is included in full-text article.)= 0.24) were observed between conditions. Coffee and decaffeinated coffee plus caffeine have the ability to improve performance during a resistance exercise protocol, although possibly not over multiple bouts.

Penile Fracture: A Meta-Analysis.

PubMed

Amer, Tarik; Wilson, Rebekah; Chlosta, Piotr; AlBuheissi, Salah; Qazi, Hasan; Fraser, Michael; Aboumarzouk, Omar M

2016-01-01

To review the causes and management of penile fracture and to compare between surgical and conservative management as well as immediate and delayed interventions in terms of overall and specific complications. A search of all reported literature was conducted for all articles reporting on the management and outcomes of penile fractures. Full texts of relevant articles were obtained and screened according to the inclusion criteria. Outcomes measures were numbers of patients receiving surgical or conservative management, aetiology of fracture, length of admission, complications as well as the specifics of diagnostic approaches and operative management. Data was collated and where possible meta-analysed using Revman software. A total of 58 relevant studies involving 3,213 patients demonstrated that intercourse accounts for only 48% of cases with masturbation and forced flexion accounting for 39%. Meta-analysis shows that surgical intervention was associated with significantly fewer complications vs. conservative management (p < 0.000001). Surgical intervention results in significantly less erectile dysfunction (ED), curvature and painful erection than conservative management. There was no significant difference in the number of patients developing plaques/nodules (p = 0.94). Meta-analysis shows that overall early surgery is preferable to delayed surgery but that rates of ED are not significantly different. Early surgical intervention is associated with significantly fewer complications than conservative management or delayed surgery. The combined outcome of rapid diagnosis by history and clinical examination and swift surgical intervention is key for reconstruction with minimal long-term complications. © 2016 S. Karger AG, Basel.

An evidence based review of the assessment and management of penetrating neck trauma.

PubMed

Burgess, C A; Dale, O T; Almeyda, R; Corbridge, R J

2012-02-01

Although relatively uncommon, penetrating neck trauma has the potential for serious morbidity and an estimated mortality of up to 6%. The assessment and management of patients who have sustained a penetrating neck injury has historically been an issue surrounded by significant controversy. OBJECTIVES OF REVIEW: To assess recent evidence relating to the assessment and management of penetrating neck trauma, highlighting areas of controversy with an overall aim of formulating clinical guidelines according to a care pathway format. Structured, non-systematic review of recent medical literature. An electronic literature search was performed in May 2011. The Medline database was searched using the Medical Subject Headings terms 'neck injuries' and 'wounds, penetrating' in conjunction with the terms 'assessment' or 'management'. Embase was searched with the terms 'penetrating trauma' and 'neck injury', also in conjunction with the terms 'assessment' and 'management'. Results were limited to articles published in English from 1990 to the present day. Abstracts were reviewed by the first three authors to select full-text articles for further critical appraisal. The references and citation links of these articles were hand-searched to identify further articles of relevance. 147 relevant articles were identified by the electronic literature search, comprising case series, case reports and reviews. 33 were initially selected for further evaluation. Although controversy continues to surround the management of penetrating neck trauma, the role of selective non-operative management and the utility of CT angiography to investigate potential vascular injuries appears to be increasingly accepted. © 2011 Blackwell Publishing Ltd.

The use of the exit interview to reduce turnover amongst healthcare professionals.

PubMed

Flint, Anndrea; Webster, Joan

2011-01-19

Exit interviews are widely used in healthcare organisations to identify reasons for staff attrition, yet their usefulness in limiting turnover is unclear. To determine the effectiveness of various exit interview strategies in decreasing turnover rates amongst healthcare professionals. We used a comprehensive search strategy including an electronic search of the following databases: DARE, CENTRAL, MEDLINE, EMBASE, CINAHL, PsycINFO, ERIC (search date: 7 September 2010) and EPOC Specialised Register (search date: 30 September 2009). We also screened the reference lists of included studies and relevant reviews. Randomised controlled trials, controlled clinical trials, controlled before and after studies and interrupted time series studies comparing turnover rates between healthcare professionals who had undergone one form of exit interview with another form of exit interview or with no interview. Two review authors independently assessed trial quality and extracted data. The search identified 1560 citations of which we considered 19 potentially relevant. The two authors independently reviewed the abstracts of these studies and retrieved the full texts of eight studies. We excluded all eight following independent assessment. They were either interviews, commentaries on how to do an exit interview or descriptive studies about reasons for leaving. We found no trials that matched our inclusion criteria. Evidence about the effectiveness of exit interviews to reduce turnover is currently not available. However, exit interviews may provide useful information about the work environment which, in turn, may be useful in the development of interventions to reduce turnover.

Informatics in radiology: RADTF: a semantic search-enabled, natural language processor-generated radiology teaching file.

PubMed

Do, Bao H; Wu, Andrew; Biswal, Sandip; Kamaya, Aya; Rubin, Daniel L

2010-11-01

Storing and retrieving radiology cases is an important activity for education and clinical research, but this process can be time-consuming. In the process of structuring reports and images into organized teaching files, incidental pathologic conditions not pertinent to the primary teaching point can be omitted, as when a user saves images of an aortic dissection case but disregards the incidental osteoid osteoma. An alternate strategy for identifying teaching cases is text search of reports in radiology information systems (RIS), but retrieved reports are unstructured, teaching-related content is not highlighted, and patient identifying information is not removed. Furthermore, searching unstructured reports requires sophisticated retrieval methods to achieve useful results. An open-source, RadLex(®)-compatible teaching file solution called RADTF, which uses natural language processing (NLP) methods to process radiology reports, was developed to create a searchable teaching resource from the RIS and the picture archiving and communication system (PACS). The NLP system extracts and de-identifies teaching-relevant statements from full reports to generate a stand-alone database, thus converting existing RIS archives into an on-demand source of teaching material. Using RADTF, the authors generated a semantic search-enabled, Web-based radiology archive containing over 700,000 cases with millions of images. RADTF combines a compact representation of the teaching-relevant content in radiology reports and a versatile search engine with the scale of the entire RIS-PACS collection of case material. ©RSNA, 2010

Is video review of patient encounters an effective tool for medical student learning? A review of the literature

PubMed Central

Hammoud, Maya M; Morgan, Helen K; Edwards, Mary E; Lyon, Jennifer A; White, Casey

2012-01-01

Purpose To determine if video review of student performance during patient encounters is an effective tool for medical student learning. Methods Multiple bibliographic databases that include medical, general health care, education, psychology, and behavioral science literature were searched for the following terms: medical students, medical education, undergraduate medical education, education, self-assessment, self-evaluation, self-appraisal, feedback, videotape, video recording, televised, and DVD. The authors examined all abstracts resulting from this search and reviewed the full text of the relevant articles as well as additional articles identified in the reference lists of the relevant articles. Studies were classified by year of student (preclinical or clinical) and study design (controlled or non-controlled). Results A total of 67 articles met the final search criteria and were fully reviewed. Most studies were non-controlled and performed in the clinical years. Although the studies were quite variable in quality, design, and outcomes, in general video recording of performance and subsequent review by students with expert feedback had positive outcomes in improving feedback and ultimate performance. Video review with self-assessment alone was not found to be generally effective, but when linked with expert feedback it was superior to traditional feedback alone. Conclusion There are many methods for integrating effective use of video-captured performance into a program of learning. We recommend combining student self-assessment with feedback from faculty or other trained individuals for maximum effectiveness. We also recommend additional research in this area. PMID:23761999

The effect of the labelled serving size on consumption: A systematic review.

PubMed

Bucher, Tamara; Murawski, Beatrice; Duncanson, Kerith; Labbe, David; Van der Horst, Klazine

2018-06-01

Guidance for food consumption and portion control plays an important role in the global management of overweight and obesity. Carefully conceptualised serving size labelling can contribute to this guidance. However, little is known about the relationship between the information that is provided regarding serving sizes on food packages and levels of actual food consumption. The aim of this systematic review was to investigate how serving size information on food packages influences food consumption. We conducted a systematic review of the evidence published between 1980 and March 2018. Two reviewers screened titles and abstracts for relevance and assessed relevant articles for eligibility in full-text. Five studies were considered eligible for the systematic review. In three of the included studies, changes in serving size labelling resulted in positive health implications for consumers, whereby less discretionary foods were consumed, if serving sizes were smaller or if serving size information was provided alongside contextual information referring to the entire package. One study did not find significant differences between the conditions they tested and one study suggested a potentially negative impact, if the serving size was reduced. The influence of labelled serving size on consumption of non-discretionary foods remains unclear, which is partially due to the absence of studies specifically focusing on non-discretionary food groups. Studies that investigate the impact of serving size labels within the home environment and across a broad demographic cross-section are required. Copyright © 2018. Published by Elsevier Ltd.

An estimate of pocket closure and avoided needs of surgery after scaling and root planing with systemic antibiotics: a systematic review.

PubMed

Kolakovic, Mirela; Held, Ulrike; Schmidlin, Patrick R; Sahrmann, Philipp

2014-12-22

Relevant benefits of adjunctive medication of antibiotica after conventional root surface debridement in terms of enhanced pocket depth (PD) reduction have been shown. However, means and standard deviations of enhanced reductions are difficult to translate into clinical relevant treatment outcomes such as pocket resolution or avoidance of additional surgical interventions. Accordingly, the aim of this systematic review was to calculate odds ratios for relevant cut-off values of PD after mechanical periodontal treatment with and without antibiotics, specifically the combination of amoxicilline and metronidazol, from published studies. As clinical relevant cut-off values "pocket closure" for PD ≤ 3mm and "avoidance of surgical intervention" for PD ≤ 5 mm were determined. The databases PubMed, Embase and Central were searched for randomized clinical studies assessing the beneficial effect of the combination of amoxicillin and metronidazole after non-surgical mechanical debridement. Titles, abstracts and finally full texts were scrutinized for possible inclusion by two independent investigators. Quality and heterogeneity of the studies were assessed and the study designs were examined. From published means and standard deviations for PD after therapy, odds ratios for the clinically relevant cut-off values were calculated using a specific statistical approach. Meta-analyses were performed for the time points 3 and 6 month after mechanical therapy. Generally, a pronounced chance for pocket closure from 3 to 6 months of healing was shown. The administration of antibiotics resulted in a 3.55 and 4.43 fold higher probability of pocket closure after 3 and 6 months as compared to mechanical therapy alone. However, as the estimated risk for residual pockets > 5 mm was 0 for both groups, no odds ratio could be calculated for persistent needs for surgery. Generally, studies showed a moderate to high quality and large heterogeneity regarding treatment protocol, dose of antibiotic medication and maintenance. With the performed statistical approach, a clear benefit in terms of an enhanced chance for pocket closure by co-administration of the combination of amoxicillin and metronidazole as an adjunct to non-surgical mechanical periodontal therapy has been shown. However, data calculation failed to show a benefit regarding the possible avoidance of surgical interventions.

76 FR 63257 - Facilitating the Deployment of Text-to-911 and Other Next Generation 911 Applications; Framework...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-12

... 11-134] Facilitating the Deployment of Text-to-911 and Other Next Generation 911 Applications... 911 Public Safety Answering Points (PSAPs) via text, photos, videos, and data and enhance the... 22, 2011. The full text of this document is available for public inspection during regular business...

The Full and True Value of Campus Heritage

ERIC Educational Resources Information Center

Elefante, Carl

2011-01-01

To gain a full and true understanding of the value of campus heritage requires shifting perspective. On many campuses, heritage resources are perceived to have no relevance whatsoever to the challenges of sustainability. This results largely from a profound misconception about what may constitute a sustainable future and what steps may be needed…

Validation of a virtual source model of medical linac for Monte Carlo dose calculation using multi-threaded Geant4.

PubMed

Aboulbanine, Zakaria; El Khayati, Naïma

2018-04-13

The use of phase space in medical linear accelerator Monte Carlo (MC) simulations significantly improves the execution time and leads to results comparable to those obtained from full calculations. The classical representation of phase space stores directly the information of millions of particles, producing bulky files. This paper presents a virtual source model (VSM) based on a reconstruction algorithm, taking as input a compressed file of roughly 800 kb derived from phase space data freely available in the International Atomic Energy Agency (IAEA) database. This VSM includes two main components; primary and scattered particle sources, with a specific reconstruction method developed for each. Energy spectra and other relevant variables were extracted from IAEA phase space and stored in the input description data file for both sources. The VSM was validated for three photon beams: Elekta Precise 6 MV/10 MV and a Varian TrueBeam 6 MV. Extensive calculations in water and comparisons between dose distributions of the VSM and IAEA phase space were performed to estimate the VSM precision. The Geant4 MC toolkit in multi-threaded mode (Geant4-[mt]) was used for fast dose calculations and optimized memory use. Four field configurations were chosen for dose calculation validation to test field size and symmetry effects, [Formula: see text] [Formula: see text], [Formula: see text] [Formula: see text], and [Formula: see text] [Formula: see text] for squared fields, and [Formula: see text] [Formula: see text] for an asymmetric rectangular field. Good agreement in terms of [Formula: see text] formalism, for 3%/3 mm and 2%/3 mm criteria, for each evaluated radiation field and photon beam was obtained within a computation time of 60 h on a single WorkStation for a 3 mm voxel matrix. Analyzing the VSM's precision in high dose gradient regions, using the distance to agreement concept (DTA), showed also satisfactory results. In all investigated cases, the mean DTA was less than 1 mm in build-up and penumbra regions. In regards to calculation efficiency, the event processing speed is six times faster using Geant4-[mt] compared to sequential Geant4, when running the same simulation code for both. The developed VSM for 6 MV/10 MV beams widely used, is a general concept easy to adapt in order to reconstruct comparable beam qualities for various linac configurations, facilitating its integration for MC treatment planning purposes.

The full spectrum of ethical issues in dementia care: systematic qualitative review.

PubMed

Strech, Daniel; Mertz, Marcel; Knüppel, Hannes; Neitzke, Gerald; Schmidhuber, Martina

2013-06-01

Integrating ethical issues in dementia-specific training material, clinical guidelines and national strategy plans requires an unbiased awareness of all the relevant ethical issues. To determine systematically and transparently the full spectrum of ethical issues in clinical dementia care. We conducted a systematic review in Medline (restricted to English and German literature published between 2000 and 2011) and Google books (with no restrictions). We applied qualitative text analysis and normative analysis to categorise the spectrum of ethical issues in clinical dementia care. The literature review retrieved 92 references that together mentioned a spectrum of 56 ethical issues in clinical dementia care. The spectrum was structured into seven major categories that consist of first- and second-order categories for ethical issues. The systematically derived spectrum of ethical issues in clinical dementia care presented in this paper can be used as training material for healthcare professionals, students and the public for raising awareness and understanding of the complexity of ethical issues in dementia care. It can also be used to identify ethical issues that should be addressed in dementia-specific training programmes, national strategy plans and clinical practice guidelines. Further research should evaluate whether this new genre of systematic reviews can be applied to the identification of ethical issues in other cognitive and somatic diseases. Also, the practical challenges in addressing ethical issues in training material, guidelines and policies need to be evaluated.

Editorial

NASA Astrophysics Data System (ADS)

Wäppling, Roger

2004-01-01

Physicists generally and our readers in particular are only too aware that the availability of scientific material on the Internet has both advantages and disadvantages. The ease with which a scientist can retrieve information from his/her office has greatly assisted the publication process since references, for example, can be searched for, checked for relevance or cross references with increasing ease. At the same time, however, it has become much easier to use materials without giving credit to the originators and this form of scientific misconduct is of growing concern to the publication process. With this in mind I would like to mention that the facility for retrieving information via the Internet is further developing so that major search engines like Google will be directly usable for retrieving, for example, a Physica Scripta article. Non-subscribers gaining access only to title and abstract whilst subscribers can access the full text in the same way as previously—through libraries and publishers. Physica Scripta has been in the vanguard of electronic development and has many thousands of accesses per day to its full on-line archive. These developments, together with some recent cases of scientific fraud, has led to an increased demand for guidelines for proper ethical conduct in the process of science publishing and, to this end, the International Union of Pure and Applied Physics, IUPAP, is working on a recommendation that I expect to be able to display here once adopted.

Stature and jumping height are required in female volleyball, but motor coordination is a key factor for future elite success.

PubMed

Pion, Johan A; Fransen, Job; Deprez, Dieter N; Segers, Veerle I; Vaeyens, Roel; Philippaerts, Renaat M; Lenoir, Matthieu

2015-06-01

It was hypothesized that differences in anthropometry, physical performance, and motor coordination would be found between Belgian elite and sub-elite level female volleyball players using a retrospective analysis of test results gathered over a 5-year period. The test sample in this study consisted of 21 young female volleyball players (15.3 ± 1.5 years) who were selected to train at the Flemish Top Sports Academy for Volleyball in 2008. All players (elite, n = 13; sub-elite, n = 8) were included in the same talent development program, and the elite-level athletes were of a high to very high performance levels according to European competition level in 2013. Five multivariate analyses of variance were used. There was no significant effect of playing level on measures of anthropometry (F = 0.455, p = 0.718, (Equation is included in full-text article.)= 0.07), flexibility (F = 1.861, p = 0.188, (Equation is included in full-text article.)= 0.19), strength (F = 1.218, p = 0.355, (Equation is included in full-text article.)= 0.32); and speed and agility (F = 1.176, p = 0.350, (Equation is included in full-text article.)= 0.18). Multivariate analyses of variance revealed significant multivariate effects between playing levels for motor coordination (F = 3.470, p = 0.036, (Equation is included in full-text article.)= 0.59). A Mann-Whitney U test and a sequential discriminant analysis confirmed these results. Previous research revealed that stature and jump height are prerequisites for talent identification in female volleyball. In addition, the results show that motor coordination is an important factor in determining inclusion into the elite level in female volleyball.

SU-E-J-128: Two-Stage Atlas Selection in Multi-Atlas-Based Image Segmentation

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

Zhao, T; Ruan, D

2015-06-15

Purpose: In the new era of big data, multi-atlas-based image segmentation is challenged by heterogeneous atlas quality and high computation burden from extensive atlas collection, demanding efficient identification of the most relevant atlases. This study aims to develop a two-stage atlas selection scheme to achieve computational economy with performance guarantee. Methods: We develop a low-cost fusion set selection scheme by introducing a preliminary selection to trim full atlas collection into an augmented subset, alleviating the need for extensive full-fledged registrations. More specifically, fusion set selection is performed in two successive steps: preliminary selection and refinement. An augmented subset is firstmore » roughly selected from the whole atlas collection with a simple registration scheme and the corresponding preliminary relevance metric; the augmented subset is further refined into the desired fusion set size, using full-fledged registration and the associated relevance metric. The main novelty of this work is the introduction of an inference model to relate the preliminary and refined relevance metrics, based on which the augmented subset size is rigorously derived to ensure the desired atlases survive the preliminary selection with high probability. Results: The performance and complexity of the proposed two-stage atlas selection method were assessed using a collection of 30 prostate MR images. It achieved comparable segmentation accuracy as the conventional one-stage method with full-fledged registration, but significantly reduced computation time to 1/3 (from 30.82 to 11.04 min per segmentation). Compared with alternative one-stage cost-saving approach, the proposed scheme yielded superior performance with mean and medium DSC of (0.83, 0.85) compared to (0.74, 0.78). Conclusion: This work has developed a model-guided two-stage atlas selection scheme to achieve significant cost reduction while guaranteeing high segmentation accuracy. The benefit in both complexity and performance is expected to be most pronounced with large-scale heterogeneous data.« less

Single-Stage Mastoid Obliteration in Cholesteatoma Surgery and Recurrent and Residual Disease Rates: A Systematic Review.

PubMed

van der Toom, Hylke F E; van der Schroeff, Marc P; Pauw, Robert J

2018-05-01

The ideal surgical treatment of cholesteatoma has been subject to discussion for years because both traditional surgical techniques (canal wall down [CWD] and canal wall up [CWU] tympanoplasty) have their own advantages and disadvantages. A more recently propagated surgical approach, to combine the CWD or CWU tympanoplasty technique with obliteration of the mastoid and epitympanum, is showing promising results. To systematically review the literature on recurrent and residual cholesteatoma rates after single-stage CWU and CWD tympanoplasty with mastoid obliteration. A systematic search of literature was performed to identify relevant publications in multiple electronic databases. The initial search was conducted in December 2016 and was updated in July 2017. Each study was reviewed by 2 independent reviewers on predetermined eligibility criteria. The methodological quality was determined using the methodological index for nonrandomized studies (MINORS) scale, and the relevance to the current topic was determined using a 4-criterion checklist. The searches identified a total of 336 potentially relevant publications; 190 articles were excluded based on title and abstract. The full-text articles of the remaining 146 citations were assessed for eligibility, resulting in 22 articles. After assessing these remaining articles for methodological quality and relevance to the current topic, another 8 studies were excluded, and a total of 13 studies (1534 patients) were included. Of the 1534 patients who underwent CWD or CWU tympanoplasty with mastoid obliteration, the rate of recurrent disease was 4.6%, and the rate of residual disease was 5.4%. In CWU tympanoplasty with mastoid obliteration, these rates were 0.28% and 4.2%, respectively and in CWD tympanoplasty with mastoid obliteration, 5.9% and 5.8%, respectively. We show the recurrent and residual disease rates after either CWU or CWD tympanoplasty with mastoid obliteration to be qualitatively similar to, if not better than, previously reported rates of for nonobliterative techniques. In this study, the lowest recurrent and residual rates were reported when combining the CWU tympanoplasty with mastoid obliteration, on average 0.28 and 4.2%, respectively.

The effectiveness of knowledge translation strategies used in public health: a systematic review

PubMed Central

2012-01-01

Background Literature related to the effectiveness of knowledge translation (KT) strategies used in public health is lacking. The capacity to seek, analyze, and synthesize evidence-based information in public health is linked to greater success in making policy choices that have the best potential to yield positive outcomes for populations. The purpose of this systematic review is to identify the effectiveness of KT strategies used to promote evidence-informed decision making (EIDM) among public health decision makers. Methods A search strategy was developed to identify primary studies published between 2000–2010. Studies were obtained from multiple electronic databases (CINAHL, Medline, EMBASE, and the Cochrane Database of Systematic Reviews). Searches were supplemented by hand searching and checking the reference lists of included articles. Two independent review authors screened studies for relevance, assessed methodological quality of relevant studies, and extracted data from studies using standardized tools. Results After removal of duplicates, the search identified 64, 391 titles related to KT strategies. Following title and abstract review, 346 publications were deemed potentially relevant, of which 5 met all relevance criteria on full text screen. The included publications were of moderate quality and consisted of five primary studies (four randomized controlled trials and one interrupted time series analysis). Results were synthesized narratively. Simple or single KT strategies were shown in some circumstances to be as effective as complex, multifaceted ones when changing practice including tailored and targeted messaging. Multifaceted KT strategies led to changes in knowledge but not practice. Knowledge translation strategies shown to be less effective were passive and included access to registries of pre-processed research evidence or print materials. While knowledge brokering did not have a significant effect generally, results suggested that it did have a positive effect on those organizations that at baseline perceived their organization to place little value on evidence-informed decision making. Conclusions No singular KT strategy was shown to be effective in all contexts. Conclusions about interventions cannot be taken on their own without considering the characteristics of the knowledge that was being transferred, providers, participants and organizations. PMID:22958371

The Global Evidence Mapping Initiative: scoping research in broad topic areas.

PubMed

Bragge, Peter; Clavisi, Ornella; Turner, Tari; Tavender, Emma; Collie, Alex; Gruen, Russell L

2011-06-17

Evidence mapping describes the quantity, design and characteristics of research in broad topic areas, in contrast to systematic reviews, which usually address narrowly-focused research questions. The breadth of evidence mapping helps to identify evidence gaps, and may guide future research efforts. The Global Evidence Mapping (GEM) Initiative was established in 2007 to create evidence maps providing an overview of existing research in Traumatic Brain Injury (TBI) and Spinal Cord Injury (SCI). The GEM evidence mapping method involved three core tasks:1. Setting the boundaries and context of the map: Definitions for the fields of TBI and SCI were clarified, the prehospital, acute inhospital and rehabilitation phases of care were delineated and relevant stakeholders (patients, carers, clinicians, researchers and policymakers) who could contribute to the mapping were identified. Researchable clinical questions were developed through consultation with key stakeholders and a broad literature search. 2. Searching for and selection of relevant studies: Evidence search and selection involved development of specific search strategies, development of inclusion and exclusion criteria, searching of relevant databases and independent screening and selection by two researchers. 3. Reporting on yield and study characteristics: Data extraction was performed at two levels - 'interventions and study design' and 'detailed study characteristics'. The evidence map and commentary reflected the depth of data extraction. One hundred and twenty-nine researchable clinical questions in TBI and SCI were identified. These questions were then prioritised into high (n = 60) and low (n = 69) importance by the stakeholders involved in question development. Since 2007, 58 263 abstracts have been screened, 3 731 full text articles have been reviewed and 1 644 relevant neurotrauma publications have been mapped, covering fifty-three high priority questions. GEM Initiative evidence maps have a broad range of potential end-users including funding agencies, researchers and clinicians. Evidence mapping is at least as resource-intensive as systematic reviewing. The GEM Initiative has made advancements in evidence mapping, most notably in the area of question development and prioritisation. Evidence mapping complements other review methods for describing existing research, informing future research efforts, and addressing evidence gaps.

The Global Evidence Mapping Initiative: Scoping research in broad topic areas

PubMed Central

2011-01-01

Background Evidence mapping describes the quantity, design and characteristics of research in broad topic areas, in contrast to systematic reviews, which usually address narrowly-focused research questions. The breadth of evidence mapping helps to identify evidence gaps, and may guide future research efforts. The Global Evidence Mapping (GEM) Initiative was established in 2007 to create evidence maps providing an overview of existing research in Traumatic Brain Injury (TBI) and Spinal Cord Injury (SCI). Methods The GEM evidence mapping method involved three core tasks: 1. Setting the boundaries and context of the map: Definitions for the fields of TBI and SCI were clarified, the prehospital, acute inhospital and rehabilitation phases of care were delineated and relevant stakeholders (patients, carers, clinicians, researchers and policymakers) who could contribute to the mapping were identified. Researchable clinical questions were developed through consultation with key stakeholders and a broad literature search. 2. Searching for and selection of relevant studies: Evidence search and selection involved development of specific search strategies, development of inclusion and exclusion criteria, searching of relevant databases and independent screening and selection by two researchers. 3. Reporting on yield and study characteristics: Data extraction was performed at two levels - 'interventions and study design' and 'detailed study characteristics'. The evidence map and commentary reflected the depth of data extraction. Results One hundred and twenty-nine researchable clinical questions in TBI and SCI were identified. These questions were then prioritised into high (n = 60) and low (n = 69) importance by the stakeholders involved in question development. Since 2007, 58 263 abstracts have been screened, 3 731 full text articles have been reviewed and 1 644 relevant neurotrauma publications have been mapped, covering fifty-three high priority questions. Conclusions GEM Initiative evidence maps have a broad range of potential end-users including funding agencies, researchers and clinicians. Evidence mapping is at least as resource-intensive as systematic reviewing. The GEM Initiative has made advancements in evidence mapping, most notably in the area of question development and prioritisation. Evidence mapping complements other review methods for describing existing research, informing future research efforts, and addressing evidence gaps. PMID:21682870

Benefits and applications of interdisciplinary digital tools for environmental meta-reviews and analyses

NASA Astrophysics Data System (ADS)

Grubert, Emily; Siders, Anne

2016-09-01

Digitally-aided reviews of large bodies of text-based information, such as academic literature, are growing in capability but are not yet common in environmental fields. Environmental sciences and studies can benefit from application of digital tools to create comprehensive, replicable, interdisciplinary reviews that provide rapid, up-to-date, and policy-relevant reports of existing work. This work reviews the potential for applications of computational text mining and analysis tools originating in the humanities to environmental science and policy questions. Two process-oriented case studies of digitally-aided environmental literature reviews and meta-analyses illustrate potential benefits and limitations. A medium-sized, medium-resolution review (∼8000 journal abstracts and titles) focuses on topic modeling as a rapid way to identify thematic changes over time. A small, high-resolution review (∼300 full text journal articles) combines collocation and network analysis with manual coding to synthesize and question empirical field work. We note that even small digitally-aided analyses are close to the upper limit of what can be done manually. Established computational methods developed in humanities disciplines and refined by humanities and social science scholars to interrogate large bodies of textual data are applicable and useful in environmental sciences but have not yet been widely applied. Two case studies provide evidence that digital tools can enhance insight. Two major conclusions emerge. First, digital tools enable scholars to engage large literatures rapidly and, in some cases, more comprehensively than is possible manually. Digital tools can confirm manually identified patterns or identify additional patterns visible only at a large scale. Second, digital tools allow for more replicable and transparent conclusions to be drawn from literature reviews and meta-analyses. The methodological subfields of digital humanities and computational social sciences will likely continue to create innovative tools for analyzing large bodies of text, providing opportunities for interdisciplinary collaboration with the environmental fields.

The Fate of Abstracts Presented at the 2013 and 2014 Annual Meetings of the Romanian Society of Gastroenterology and Hepatology.

PubMed

Trifan, Anca; Chihaia, Catalin-Alexandru; Tanase, Oana; Lungu, Cristina-Maria; Stanciu, Carol

2016-12-01

Oral and poster presentations at annual national meetings of the Romanian Society of Gastroenterology and Hepatology (RSGH) provide a forum for education, communication and discussion of new research. However, for the wide-spread dissemination of the new research work, each presentation should be subsequently published as a full-text article in peer-reviewed, indexed journals. to evaluate the publication rate of full-text articles in peer-reviewed journals after being first presented as abstracts at two consecutive RSGH annual meetings. A retrospective review of all abstracts presented at the annual meetings in 2013 and 2014 was performed. PubMed and Google Scholar were searched using abstract titles, first author's name and affiliation, and key words from the title to identify whether an abstract resulted in a peer-reviewed publication. Abstracts published in full-text were subsequently assessed for study type, study center, topics, publication year, journals and their impact factors (IFs). We chose the 2013 and 2014 meetings to ensure a minimum two-year follow-up period since the last meeting for the publication as full-length articles. A total of 562 abstracts were presented (275 in 2013, 287 in 2014). There were 150 oral presentations (93 in 2013, 57 in 2014) and 412 poster presentations (182 in 2013, 230 in 2014). Fifty seven of them (10.1%) were published as full-text articles, among them 26 (17.3%) after oral presentations and 31 (7.5%) after poster presentations (P=0.001). University affiliation and original research work were most likely to be published. The average IFs of the journals which published the articles were 2.42 in 2013 and 1.87 in 2014. The publication rate for the annual RSGH meetings abstracts as full-text articles in peer-reviewed journals is very low compared to the analyses performed in gastroenterology or other medical specialities from other countries. It is not clear yet what are the factors responsible for the failure of publication.

38 CFR 75.115 - Risk analysis.

Code of Federal Regulations, 2010 CFR

2010-07-01

... preparation of the risk analysis may include data mining if necessary for the development of relevant... degree of protection for the data, e.g., unencrypted, plain text; (6) Time the data has been out of VA...

How to locate and appraise qualitative research in complementary and alternative medicine

PubMed Central

2013-01-01

Background The aim of this publication is to present a case study of how to locate and appraise qualitative studies for the conduct of a meta-ethnography in the field of complementary and alternative medicine (CAM). CAM is commonly associated with individualized medicine. However, one established scientific approach to the individual, qualitative research, thus far has been explicitly used very rarely. This article demonstrates a case example of how qualitative research in the field of CAM studies was identified and critically appraised. Methods Several search terms and techniques were tested for the identification and appraisal of qualitative CAM research in the conduct of a meta-ethnography. Sixty-seven electronic databases were searched for the identification of qualitative CAM trials, including CAM databases, nursing, nutrition, psychological, social, medical databases, the Cochrane Library and DIMDI. Results 9578 citations were screened, 223 articles met the pre-specified inclusion criteria, 63 full text publications were reviewed, 38 articles were appraised qualitatively and 30 articles were included. The search began with PubMed, yielding 87% of the included publications of all databases with few additional relevant findings in the specific databases. CINHAL and DIMDI also revealed a high number of precise hits. Although CAMbase and CAM-QUEST® focus on CAM research only, almost no hits of qualitative trials were found there. Searching with broad text terms was the most effective search strategy in all databases. Conclusions This publication presents a case study on how to locate and appraise qualitative studies in the field of CAM. The example shows that the literature search for qualitative studies in the field of CAM is most effective when the search is begun in PubMed followed by CINHAL or DIMDI using broad text terms. Exclusive CAM databases delivered no additional findings to locate qualitative CAM studies. PMID:23731997

How to locate and appraise qualitative research in complementary and alternative medicine.

PubMed

Franzel, Brigitte; Schwiegershausen, Martina; Heusser, Peter; Berger, Bettina

2013-06-03

The aim of this publication is to present a case study of how to locate and appraise qualitative studies for the conduct of a meta-ethnography in the field of complementary and alternative medicine (CAM). CAM is commonly associated with individualized medicine. However, one established scientific approach to the individual, qualitative research, thus far has been explicitly used very rarely. This article demonstrates a case example of how qualitative research in the field of CAM studies was identified and critically appraised. Several search terms and techniques were tested for the identification and appraisal of qualitative CAM research in the conduct of a meta-ethnography. Sixty-seven electronic databases were searched for the identification of qualitative CAM trials, including CAM databases, nursing, nutrition, psychological, social, medical databases, the Cochrane Library and DIMDI. 9578 citations were screened, 223 articles met the pre-specified inclusion criteria, 63 full text publications were reviewed, 38 articles were appraised qualitatively and 30 articles were included. The search began with PubMed, yielding 87% of the included publications of all databases with few additional relevant findings in the specific databases. CINHAL and DIMDI also revealed a high number of precise hits. Although CAMbase and CAM-QUEST® focus on CAM research only, almost no hits of qualitative trials were found there. Searching with broad text terms was the most effective search strategy in all databases. This publication presents a case study on how to locate and appraise qualitative studies in the field of CAM. The example shows that the literature search for qualitative studies in the field of CAM is most effective when the search is begun in PubMed followed by CINHAL or DIMDI using broad text terms. Exclusive CAM databases delivered no additional findings to locate qualitative CAM studies.

Carers' Experiences, Needs, and Preferences During Inpatient Stroke Rehabilitation: A Systematic Review of Qualitative Studies.

PubMed

Luker, Julie; Murray, Carolyn; Lynch, Elizabeth; Bernhardsson, Susanne; Shannon, Michelle; Bernhardt, Julie

2017-09-01

To report and synthesize the experiences, needs, and preferences of carers of stroke survivors undergoing inpatient rehabilitation. MEDLINE, CINAHL, Embase, PsycINFO, and Web of Science were searched to March 2016. Reference lists of relevant publications were searched. No language restrictions were applied. Eligible qualitative studies reported the experiences of carers of stroke survivors who underwent inpatient rehabilitation. The search yielded 3532 records; 93 full-text publications were assessed for eligibility, and 34 documents (33 studies) were included. Comprehensiveness of reporting was assessed using the Consolidated Criteria for Reporting Qualitative Health Research framework. Data on the characteristics of included studies were independently extracted by 2 authors. Differences in data extraction between authors were resolved through discussion or by a third author. All text in studies' results and discussion sections were extracted for analysis. Extracted texts were analyzed inductively using thematic synthesis. Seven analytical themes were developed that related to the carers' experiences, needs, and preferences: (1) overwhelmed with emotions; (2) recognition as a stakeholder in recovery; (3) desire to be heard and informed; (4) persisting for action and outcomes; (5) being legitimate clients; (6) navigating an alien culture and environment; and (7) managing the transition home. This systematic review provides new insights into the experiences, needs, and preferences of carers of stroke survivors undergoing inpatient rehabilitation. Carers experienced distress as they navigated a foreign culture and environment without adequate communication and processes in place for their inclusion. We recommend deliberate efforts to provide a more inclusive environment that better supports and prepares carers for their new role. Copyright © 2017 American Congress of Rehabilitation Medicine. All rights reserved.

What Can Pictures Tell Us About Web Pages? Improving Document Search Using Images.

PubMed

Rodriguez-Vaamonde, Sergio; Torresani, Lorenzo; Fitzgibbon, Andrew W

2015-06-01

Traditional Web search engines do not use the images in the HTML pages to find relevant documents for a given query. Instead, they typically operate by computing a measure of agreement between the keywords provided by the user and only the text portion of each page. In this paper we study whether the content of the pictures appearing in a Web page can be used to enrich the semantic description of an HTML document and consequently boost the performance of a keyword-based search engine. We present a Web-scalable system that exploits a pure text-based search engine to find an initial set of candidate documents for a given query. Then, the candidate set is reranked using visual information extracted from the images contained in the pages. The resulting system retains the computational efficiency of traditional text-based search engines with only a small additional storage cost needed to encode the visual information. We test our approach on one of the TREC Million Query Track benchmarks where we show that the exploitation of visual content yields improvement in accuracies for two distinct text-based search engines, including the system with the best reported performance on this benchmark. We further validate our approach by collecting document relevance judgements on our search results using Amazon Mechanical Turk. The results of this experiment confirm the improvement in accuracy produced by our image-based reranker over a pure text-based system.

Ministry of Health Clinical Practice Guidelines: Prevention, Diagnosis and Management of Tuberculosis

PubMed Central

Wang, Yee Tang Sonny; Chee, Cynthia Bin Eng; Hsu, Li Yang; Jagadesan, Raghuram; Kaw, Gregory Jon Leng; Kong, Po Marn; Lew, Yii Jen; Lim, Choon Seng; Lim, Ting Ting Jayne; Lu, Kuo Fan Mark; Ooi, Peng Lim; Sng, Li-Hwei; Thoon, Koh Cheng

2016-01-01

The Ministry of Health (MOH) has developed the clinical practice guidelines on Prevention, Diagnosis and Management of Tuberculosis to provide doctors and patients in Singapore with evidence-based treatment for tuberculosis. This article reproduces the introduction and executive summary (with recommendations from the guidelines) from the MOH clinical practice guidelines on Prevention, Diagnosis and Management of Tuberculosis, for the information of SMJ readers. The chapters and page numbers mentioned in the reproduced extract refer to the full text of the guidelines, which are available from the Ministry of Health website: http://www.moh.gov.sg/content/moh_web/healthprofessionalsportal/doctors/guidelines/cpg_medical.html. The recommendations should be used with reference to the full text of the guidelines. Following this article are multiple choice questions based on the full text of the guidelines. PMID:26996216

Fitting Higgs data with nonlinear effective theory.

PubMed

Buchalla, G; Catà, O; Celis, A; Krause, C

2016-01-01

In a recent paper we showed that the electroweak chiral Lagrangian at leading order is equivalent to the conventional [Formula: see text] formalism used by ATLAS and CMS to test Higgs anomalous couplings. Here we apply this fact to fit the latest Higgs data. The new aspect of our analysis is a systematic interpretation of the fit parameters within an EFT. Concentrating on the processes of Higgs production and decay that have been measured so far, six parameters turn out to be relevant: [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text]. A global Bayesian fit is then performed with the result [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text]. Additionally, we show how this leading-order parametrization can be generalized to next-to-leading order, thus improving the [Formula: see text] formalism systematically. The differences with a linear EFT analysis including operators of dimension six are also discussed. One of the main conclusions of our analysis is that since the conventional [Formula: see text] formalism can be properly justified within a QFT framework, it should continue to play a central role in analyzing and interpreting Higgs data.

The association between states' texting regulations and the prevalence of texting while driving among U.S. high school students.

PubMed

Rudisill, Toni M; Zhu, Motao

2015-12-01

To determine which distracted driving laws were associated with decreased texting while driving among U.S. teenage drivers. Data from the 2013 Youth Risk Behavior Surveillance System survey were merged with states' distracted driving legislation. The prevalence of texting while driving was assessed for different laws using log-binomial regression. Approximately 39.0% of students reported texting while driving at least once in the 30 days before survey. Compared to states with universal texting bans along with young driver all cellphone bans, the adjusted ratio of texting while driving was 0.94 (95% confidence interval [CI], 0.77-1.16) in states with no bans, 1.33 (95% CI, 1.11-1.58) for young driver bans only, 1.24 (95% CI, 1.00-1.52) in states with bans for young drivers but no young driver all cellphone bans, and 0.89 (95% CI, 0.66-1.19) in states with universal texting bans. The prevalence of texting was 28% less in states with delays of full licensure for texting offenses (prevalence ratio = 0.72; 95% CI, 0.59-0.88). Universal texting bans along with young driver all cellphone bans may be more effective in reducing texting while driving. Delays of full licensure may dissuade young drivers from texting and driving. Copyright © 2015 Elsevier Inc. All rights reserved.

The association between states’ texting regulations and the prevalence of texting while driving among U.S. high school students

PubMed Central

Rudisill, Toni M.; Zhu, Motao

2015-01-01

Purpose To determine which distracted driving laws were associated with decreased texting while driving among U.S. teenage drivers. Methods Data from the 2013 Youth Risk Behavior Surveillance System survey were merged with state’s distracted driving legislation. The prevalence of texting while driving was assessed for different laws using log-binomial regression. Results Approximately 39.0% of students reported texting while driving at least once in the 30 days before survey. Compared to states with universal texting bans along with young driver all cellphone bans, the adjusted ratio of texting while driving was 0.94 (95% confidence interval [CI], 0.77–1.16) in states with no bans, 1.33 (95% CI, 1.11–1.58) for young driver bans only, 1.24 (95% CI, 1.00–1.52) in states with bans for young drivers but no young driver all cellphone bans, and 0.89 (95% CI, 0.66–1.19) in states with universal texting bans. The prevalence of texting was 28% less in states with delays of full licensure for texting offenses (prevalence ratio = 0.72; 95% CI, 0.59–0.88). Conclusions Universal texting bans along with young driver all cellphone bans may be more effective in reducing texting while driving. Delays of full licensure may dissuade young drivers from texting and driving. PMID:26688117

Current Searching Methodology and Retrieval Issues: An Assessment

DTIC Science & Technology

2008-03-01

searching that are used by search engines are discussed. They are: full text searching, i.e., the searching of unstructured data, and metadata searching...also found among search engines ; however, it is the popularity of full text searching that has changed the road map to information access. The...other hand, information seekers’ willingness, or lack of, to learn the multiple search engines ’ capabilities may diminish their search results

Applied Actant Network Theory: Toward the Automated Detection of Technoscientific Emergence from Full Text Publications and Patents (Open Access)

DTIC Science & Technology

2012-11-02

Applied Actant-Network Theory: Toward the Automated Detection of Technoscientific Emergence from Full-Text Publications and Patents David C...Brock**, Olga Babko-Malaya*, James Pustejovsky***, Patrick Thomas****, *BAE Systems Advanced Information Technologies, ** David C. Brock Consulting... Wojick , D. 2008. Population modeling of the emergence and development of scientific fields. Scientometrics, 75(3):495–518. Cook, T. D. and

Family nurse practitioner student perception of journal abstract usefulness in clinical decision making: a randomized controlled trial.

PubMed

Johnson, Heather L; Fontelo, Paul; Olsen, Cara H; Jones, Kenneth D; Gimbel, Ronald W

2013-11-01

To assess family nurse practitioner (FNP) student perception of research abstract usefulness in clinical decision making. A randomized controlled trial conducted in a simulated environment with graduate FNP students of the Graduate School of Nursing, Uniformed Services University of the Health Sciences. Given a clinical case study and modified MEDLINE search tool accessible via an iPad device, participants were asked to develop a treatment plan and complete a data collection form. The primary measure was perceived usefulness of the research abstracts in clinical decision making regarding a simulated obese patient seeking to prevent type 2 diabetes. Secondary measures related to participant demographics and accessibility and usefulness of full-text manuscripts. The majority of NP students identified readily available research abstracts as useful in shaping their clinical decision making. The presence or absence of full-text manuscripts associated with the abstracts did not appear to influence the perceived abstract usefulness. The majority of students with full-text manuscript access in the timed simulated clinical encounter read at least one paper, but cited insufficient time to read full-text as a constraint. Research abstracts at point of care may be valuable to FNPs if easily accessible and integrated into clinical workflow. ©2013 The Author(s) ©2013 American Association of Nurse Practitioners.

Runwien: a text-based interface for the WIEN package

NASA Astrophysics Data System (ADS)

Otero de la Roza, A.; Luaña, Víctor

2009-05-01

A new text-based interface for WIEN2k, the full-potential linearized augmented plane-waves (FPLAPW) program, is presented. This code provides an easy to use, yet powerful way of generating arbitrarily large sets of calculations. Thus, properties over a potential energy surface and WIEN2k parameter exploration can be calculated using a simple input text file. This interface also provides new capabilities to the WIEN2k package, such as the calculation of elastic constants on hexagonal systems or the automatic gathering of relevant information. Additionally, runwien is modular, flexible and intuitive. Program summaryProgram title: runwien Catalogue identifier: AECM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL version 3 No. of lines in distributed program, including test data, etc.: 62 567 No. of bytes in distributed program, including test data, etc.: 610 973 Distribution format: tar.gz Programming language: gawk (with locale POSIX or similar) Computer: All running Unix, Linux Operating system: Unix, GNU/Linux Classification: 7.3 External routines: WIEN2k ( http://www.wien2k.at/), GAWK ( http://www.gnu.org/software/gawk/), rename by L. Wall, a Perl script which renames files, modified by R. Barker to check for the existence of target files, gnuplot ( http://www.gnuplot.info/) Subprograms used:Cat Id: ADSY_v1_0/AECB_v1_0, Title: GIBBS/CRITIC, Reference: CPC 158 (2004) 57/CPC 999 (2009) 999 Nature of problem: Creation of a text-based, batch-oriented interface for the WIEN2k package. Solution method: WIEN2k solves the Kohn-Sham equations of a solid using the FPLAPW formalism. Runwien interprets an input file containing the description of the geometry and structure of the solid and drives the execution of the WIEN2k programs. The input is simplified thanks to the default values of the WIEN2k parameters known to runwien. Additional comments: Designed for WIEN2k versions 06.4, 07.2, 08.2, and 08.3. Running time: For the test case (TiC), a single geometry takes 5 to 10 minutes on a typical desktop PC (Intel Pentium 4, 3.4 GHz, 1 GB RAM). The full example including the calculation of the elastic constants and the equation of state, takes 9 hours and 32 minutes.

Methods for designing interventions to change healthcare professionals' behaviour: a systematic review.

PubMed

Colquhoun, Heather L; Squires, Janet E; Kolehmainen, Niina; Fraser, Cynthia; Grimshaw, Jeremy M

2017-03-04

Systematic reviews consistently indicate that interventions to change healthcare professional (HCP) behaviour are haphazardly designed and poorly specified. Clarity about methods for designing and specifying interventions is needed. The objective of this review was to identify published methods for designing interventions to change HCP behaviour. A search of MEDLINE, Embase, and PsycINFO was conducted from 1996 to April 2015. Using inclusion/exclusion criteria, a broad screen of abstracts by one rater was followed by a strict screen of full text for all potentially relevant papers by three raters. An inductive approach was first applied to the included studies to identify commonalities and differences between the descriptions of methods across the papers. Based on this process and knowledge of related literatures, we developed a data extraction framework that included, e.g. level of change (e.g. individual versus organization); context of development; a brief description of the method; tasks included in the method (e.g. barrier identification, component selection, use of theory). 3966 titles and abstracts and 64 full-text papers were screened to yield 15 papers included in the review, each outlining one design method. All of the papers reported methods developed within a specific context. Thirteen papers included barrier identification and 13 included linking barriers to intervention components; although not the same 13 papers. Thirteen papers targeted individual HCPs with only one paper targeting change across individual, organization, and system levels. The use of theory and user engagement were included in 13/15 and 13/15 papers, respectively. There is an agreement across methods of four tasks that need to be completed when designing individual-level interventions: identifying barriers, selecting intervention components, using theory, and engaging end-users. Methods also consist of further additional tasks. Examples of methods for designing the organisation and system-level interventions were limited. Further analysis of design tasks could facilitate the development of detailed guidelines for designing interventions.

High-heeled shoes and musculoskeletal injuries: a narrative systematic review

PubMed Central

Barnish, Maxwell S; Barnish, Jean

2016-01-01

Objectives To conduct the first systematic review from an epidemiological perspective regarding the association between high-heeled shoe wear and hallux valgus, musculoskeletal pain, osteoarthritis (OA) and both first-party and second-party injury in human participants without prior musculoskeletal conditions. Setting A systematic review of international peer-reviewed scientific literature across seven major languages. Data sources Searches were conducted on seven major bibliographic databases in July 2015 to initially identify all scholarly articles on high-heeled shoes. Supplementary manual searches were conducted. Titles, abstracts and full-text articles were sequentially screened to identify all articles assessing epidemiological evidence regarding the association between high-heeled shoe wear and hallux valgus, musculoskeletal pain, OA and both first-party and second-party injury in human participants without prior musculoskeletal conditions. Standardised data extraction and quality assessment (Threats to Validity tool) were conducted. Primary and secondary outcome measures Musculoskeletal pain or OA as assessed by clinical diagnosis or clinical assessment tool. First-party or second-party injury. Results 644 unique records were identified, 56 full-text articles were screened and 18 studies included in the review. Four studies assessed the relationship with hallux valgus and three found a significant association. Two studies assessed the association with OA and neither found a significant association. Five studies assessed the association with musculoskeletal pain and three found a significant association. Eight studies assessed first-party injury and seven found evidence of a significant injury toll associated with high-heeled shoes. One study provided data on second-party injury and the injury toll was low. Conclusions High-heeled shoes were shown to be associated with hallux valgus, musculoskeletal pain and first-party injury. No conclusive evidence regarding OA and second-party injury was found. Societal and clinical relevance of these findings is discussed. Concern is expressed about the expectation to wear high-heeled shoes in some work and social situations and access by children. PMID:26769789

Strategies to Prevent or Reduce Gender Bias in Peer Review of Research Grants: A Rapid Scoping Review.

PubMed

Tricco, Andrea C; Thomas, Sonia M; Antony, Jesmin; Rios, Patricia; Robson, Reid; Pattani, Reena; Ghassemi, Marco; Sullivan, Shannon; Selvaratnam, Inthuja; Tannenbaum, Cara; Straus, Sharon E

2017-01-01

To review the literature on strategies implemented or identified to prevent or reduce gender bias in peer review of research grants. Studies of any type of qualitative or quantitative design examining interventions to reduce or prevent gender bias during the peer review of health-related research grants were included. Electronic databases including MEDLINE, EMBASE, Education Resources Information Center (ERIC), PsycINFO, Joanna Briggs, the Cochrane Library, Evidence Based Medicine (EBM) Reviews, and the Campbell Library were searched from 2005 to April 2016. A search for grey (i.e., difficult to locate or unpublished) literature was conducted and experts in the field were consulted to identify additional potentially relevant articles. Two individuals screened titles and abstracts, full-text articles, and abstracted data with discrepancies resolved by a third person consistently. After screening 5524 citations and 170 full-text articles, one article evaluating gender-blinding of grant applications using an uncontrolled before-after study design was included. In this study, 891 applications for long-term fellowships in 2006 were included and 47% of the applicants were women. These were scored by 13 peer reviewers (38% were women). The intervention included eliminating references to gender from the applications, letters of recommendations, and interview reports that were sent to the committee members for evaluation. The proportion of successful applications led by women did not change with gender-blinding, although the number of successful applications that were led by men increased slightly. There is limited research on interventions to mitigate gender bias in the peer review of grants. Only one study was identified and no difference in the proportion of women who were successful in receiving grant funding was observed. Our results suggest that interventions to prevent gender bias should be adapted and tested in the context of grant peer review to determine if they will have an impact.

Clinical Outcomes of Comparing Soft Tissue Alternatives to Free Gingival Graft: A Systematic Review and Meta-Analysis
.

PubMed

Dragan, Irina F; Hotlzman, Lucrezia Paterno; Karimbux, Nadeem Y; Morin, Rebecca A; Bassir, Seyed Hossein

2017-12-01

This systematic review and meta-analysis aimed to compare clinical outcomes and width of keratinized tissue (KT) around teeth, following the soft tissue alter- natives and free gingival graft (FGG) procedures. The specific graft materials that were explored were extracellular matrix membrane, bilayer collagen membrane, living cellular construct, and acellular dermal matrix. Four different databases were queried to identify human controlled clinical trials and randomized controlled clinical trials that fulfilled the eligibility criteria. Relevant studies were identified by 3 independent reviewers, compiling the results of the electronic and handsearches. Studies identified through electronic and handsearches were reviewed by title, abstract, and full text using Covidence Software. Primary outcome in the present study was change in the width of KT. Results of the included studies were pooled to estimate the effect size, expressed as weighted mean differences and 95% confidence interval. A random-effects model was used to perform the meta-analyses. Six hundred thirty-eight articles were screened by title, 55 articles were screened by abstracts, and 34 full-text articles were reviewed. Data on quantitative changes in width of KT were provided in 7 studies. Quantitative analyses revealed a significant difference in changes in width of KT between patients treated with soft tissue alternatives and patients treated with FGGs (P < .001). The weighted mean difference of changes in the width of KT was 21.39 (95% confidence interval: 21.82 to 20.96; heterogeneity I 5 70.89%), indicating patients who were treated with soft tissue alternatives gained 1.39 mm less KT width compared with the patients who received free gingival graft. Based on the clinical outcomes, the results of this systematic review and meta-analysis showed that soft tissue alternatives result in an increased width of KT. Patients in the soft tissue alternatives group obtained 1.39 mm less KT compared with those in the FGGs group. Copyright © 2017 Elsevier Inc. All rights reserved.

Strategies to Prevent or Reduce Gender Bias in Peer Review of Research Grants: A Rapid Scoping Review

PubMed Central

Tricco, Andrea C.; Thomas, Sonia M.; Antony, Jesmin; Rios, Patricia; Robson, Reid; Pattani, Reena; Ghassemi, Marco; Sullivan, Shannon; Selvaratnam, Inthuja; Tannenbaum, Cara; Straus, Sharon E.

2017-01-01

Objective To review the literature on strategies implemented or identified to prevent or reduce gender bias in peer review of research grants. Methods Studies of any type of qualitative or quantitative design examining interventions to reduce or prevent gender bias during the peer review of health-related research grants were included. Electronic databases including MEDLINE, EMBASE, Education Resources Information Center (ERIC), PsycINFO, Joanna Briggs, the Cochrane Library, Evidence Based Medicine (EBM) Reviews, and the Campbell Library were searched from 2005 to April 2016. A search for grey (i.e., difficult to locate or unpublished) literature was conducted and experts in the field were consulted to identify additional potentially relevant articles. Two individuals screened titles and abstracts, full-text articles, and abstracted data with discrepancies resolved by a third person consistently. Results After screening 5524 citations and 170 full-text articles, one article evaluating gender-blinding of grant applications using an uncontrolled before-after study design was included. In this study, 891 applications for long-term fellowships in 2006 were included and 47% of the applicants were women. These were scored by 13 peer reviewers (38% were women). The intervention included eliminating references to gender from the applications, letters of recommendations, and interview reports that were sent to the committee members for evaluation. The proportion of successful applications led by women did not change with gender-blinding, although the number of successful applications that were led by men increased slightly. Conclusions There is limited research on interventions to mitigate gender bias in the peer review of grants. Only one study was identified and no difference in the proportion of women who were successful in receiving grant funding was observed. Our results suggest that interventions to prevent gender bias should be adapted and tested in the context of grant peer review to determine if they will have an impact. PMID:28061509

Cervical level IIb metastases in squamous cell carcinoma of the oral cavity: a systematic review and meta-analysis.

PubMed

Kou, Yurong; Zhao, Tengfei; Huang, Shaohui; Liu, Jie; Duan, Weiyi; Wang, Yunjing; Wang, Zechen; Li, Delong; Ning, Chunliu; Sun, Changfu

2017-01-01

The aim of this study was to clarify whether level IIb dissection should be performed or avoided in the treatment of oral squamous cell carcinoma by meta-analysis. Articles that were published before June 2017 were searched electronically in four databases (Web of Science, PubMed, Ovid and China National Knowledge Infrastructure) without any date or language restrictions by two independent reviewers. Abstracts and full-text papers which investigated the cervical metastases to level IIb from primary head and neck cancers and were deemed potentially relevant were screened. Data were analyzed using RevMan 5.3. Four hundred and fifty-five abstracts and 129 full-text papers were screened, and 22 studies were included in the analysis. Among the 2001 patients included, 112 patients had level IIb metastases, the pooled frequency of which was 6% (95% confidence interval [CI]: 4.0-7.0). Among the 400 patients with tongue squamous cell carcinoma from 12 studies, 37 patients had level IIb metastases, the pooled incidence of which was 7% (95% CI: 5.0-10.0). Metastases to level IIb always went together with level IIa, and only three patients were found to have isolated level IIb metastases without involving the other levels. Due to the low frequency of level IIb nodal metastases in oral squamous cell carcinoma patients and rare occurrence of isolated level IIb, level IIb dissection could be avoided when the primary lesions were in early stages (T1 and T2), with the exception of tongue cancer. It is recommended to dissect level IIb tongue cancers without considering the stages of primary lesions and the lymph nodes status. It is also suggested that level IIb dissection should be performed in patients preoperatively or intraoperatively found with multilevel neck metastasis, especially level IIa metastasis.

Cataloging the biomedical world of pain through semi-automated curation of molecular interactions

PubMed Central

Jamieson, Daniel G.; Roberts, Phoebe M.; Robertson, David L.; Sidders, Ben; Nenadic, Goran

2013-01-01

The vast collection of biomedical literature and its continued expansion has presented a number of challenges to researchers who require structured findings to stay abreast of and analyze molecular mechanisms relevant to their domain of interest. By structuring literature content into topic-specific machine-readable databases, the aggregate data from multiple articles can be used to infer trends that can be compared and contrasted with similar findings from topic-independent resources. Our study presents a generalized procedure for semi-automatically creating a custom topic-specific molecular interaction database through the use of text mining to assist manual curation. We apply the procedure to capture molecular events that underlie ‘pain’, a complex phenomenon with a large societal burden and unmet medical need. We describe how existing text mining solutions are used to build a pain-specific corpus, extract molecular events from it, add context to the extracted events and assess their relevance. The pain-specific corpus contains 765 692 documents from Medline and PubMed Central, from which we extracted 356 499 unique normalized molecular events, with 261 438 single protein events and 93 271 molecular interactions supplied by BioContext. Event chains are annotated with negation, speculation, anatomy, Gene Ontology terms, mutations, pain and disease relevance, which collectively provide detailed insight into how that event chain is associated with pain. The extracted relations are visualized in a wiki platform (wiki-pain.org) that enables efficient manual curation and exploration of the molecular mechanisms that underlie pain. Curation of 1500 grouped event chains ranked by pain relevance revealed 613 accurately extracted unique molecular interactions that in the future can be used to study the underlying mechanisms involved in pain. Our approach demonstrates that combining existing text mining tools with domain-specific terms and wiki-based visualization can facilitate rapid curation of molecular interactions to create a custom database. Database URL: ••• PMID:23707966

Cataloging the biomedical world of pain through semi-automated curation of molecular interactions.

PubMed

Jamieson, Daniel G; Roberts, Phoebe M; Robertson, David L; Sidders, Ben; Nenadic, Goran

2013-01-01

The vast collection of biomedical literature and its continued expansion has presented a number of challenges to researchers who require structured findings to stay abreast of and analyze molecular mechanisms relevant to their domain of interest. By structuring literature content into topic-specific machine-readable databases, the aggregate data from multiple articles can be used to infer trends that can be compared and contrasted with similar findings from topic-independent resources. Our study presents a generalized procedure for semi-automatically creating a custom topic-specific molecular interaction database through the use of text mining to assist manual curation. We apply the procedure to capture molecular events that underlie 'pain', a complex phenomenon with a large societal burden and unmet medical need. We describe how existing text mining solutions are used to build a pain-specific corpus, extract molecular events from it, add context to the extracted events and assess their relevance. The pain-specific corpus contains 765 692 documents from Medline and PubMed Central, from which we extracted 356 499 unique normalized molecular events, with 261 438 single protein events and 93 271 molecular interactions supplied by BioContext. Event chains are annotated with negation, speculation, anatomy, Gene Ontology terms, mutations, pain and disease relevance, which collectively provide detailed insight into how that event chain is associated with pain. The extracted relations are visualized in a wiki platform (wiki-pain.org) that enables efficient manual curation and exploration of the molecular mechanisms that underlie pain. Curation of 1500 grouped event chains ranked by pain relevance revealed 613 accurately extracted unique molecular interactions that in the future can be used to study the underlying mechanisms involved in pain. Our approach demonstrates that combining existing text mining tools with domain-specific terms and wiki-based visualization can facilitate rapid curation of molecular interactions to create a custom database. Database URL: •••

What Chemistry To Teach Engineers?

ERIC Educational Resources Information Center

Hawkes, Stephen J.

2000-01-01

Examines possible general chemistry topics that would be most relevant and practical for engineering majors. Consults the Accreditation Board for Engineering and Technology (ABET), engineering textbooks, texts from other required subjects, and practicing engineers for recommendations. (Contains 24 references.) (WRM)

Documenting research with transgender and gender diverse people: protocol for an evidence map and thematic analysis.

PubMed

Marshall, Zack; Welch, Vivian; Thomas, James; Brunger, Fern; Swab, Michelle; Shemilt, Ian; Kaposy, Chris

2017-02-20

There is limited information about how transgender, gender diverse, and Two-Spirit (trans) people have been represented and studied by researchers. The objectives of this study are to (1) map and describe trans research in the social sciences, sciences, humanities, health, education, and business, (2) identify evidence gaps and opportunities for more responsible research with trans people, (3) assess the use of text mining for study identification, and (4) increase access to trans research for key stakeholders through the creation of a web-based evidence map. Study design was informed by community consultations and pilot searches. Eligibility criteria were established to include all original research of any design, including trans people or their health information, and published in English in peer-reviewed journals. A complex electronic search strategy based on relevant concepts in 15 databases was developed to obtain a broad range of results linked to transgender, gender diverse, and Two-Spirit individuals and communities. Searches conducted in early 2015 resulted in 25,242 references after removal of duplicates. Based on the number of references, resources, and an objective to capture upwards of 90% of the existing literature, this study is a good candidate for text mining using Latent Dirichlet Allocation to improve efficiency of the screening process. The following information will be collected for evidence mapping: study topic, study design, methods and data sources, recruitment strategies, sample size, sample demographics, researcher name and affiliation, country where research was conducted, funding source, and year of publication. The proposed research incorporates an extensive search strategy, text mining, and evidence map; it therefore has the potential to build on knowledge in several fields. Review results will increase awareness of existing trans research, identify evidence gaps, and inform strategic research prioritization. Publishing the map online will improve access to research for key stakeholders including community members, policy makers, and healthcare providers. This study will also contribute to knowledge in the area of text mining for study identification by providing an example of how semi-automation performs for screening on title and abstract and on full text.

An Operational Definition of Learning Disabilities (Cognitive Domain) Using WISC Full Scale IQ and Peabody Individual Achievement Test Scores

ERIC Educational Resources Information Center

Brenton, Beatrice White; Gilmore, Doug

1976-01-01

An operational index of discrepancy to assist in identifying learning disabilities was derived using the Full Scale IQ, Wechsler Intelligence Scale for Children, and relevant subtest scores on the Peabody Individual Achievement Test. Considerable caution should be exercised when classifying children, especially females, as learning disabled.…

Leveraging Text Messaging and Mobile Technology to Support Pediatric Obesity-Related Behavior Change: A Qualitative Study Using Parent Focus Groups and Interviews

PubMed Central

Dryden, Eileen M; Horan, Christine M; Price, Sarah; Marshall, Richard; Hacker, Karen; Finkelstein, Jonathan A; Taveras, Elsie M

2013-01-01

Background Text messaging (short message service, SMS) is a widely accessible and potentially cost-effective medium for encouraging behavior change. Few studies have examined text messaging interventions to influence child health behaviors or explored parental perceptions of mobile technologies to support behavior change among children. Objective Our aim was to examine parental acceptability and preferences for text messaging to support pediatric obesity-related behavior change. Methods We conducted focus groups and follow-up interviews with parents of overweight and obese children, aged 6-12 years, seen for “well-child” care in eastern Massachusetts. A professional moderator used a semistructured discussion guide and sample text messages to catalyze group discussions. Seven participants then received 3 weeks of text messages before a follow-up one-on-one telephone interview. All focus groups and interviews were recorded and transcribed verbatim. Using a framework analysis approach, we systematically coded and analyzed group and interview data to identify salient and convergent themes. Results We reached thematic saturation after five focus groups and seven follow-up interviews with a total of 31 parents of diverse race/ethnicity and education levels. Parents were generally enthusiastic about receiving text messages to support healthy behaviors for their children and preferred them to paper or email communication because they are brief and difficult to ignore. Participants anticipated high responsiveness to messaging endorsed by their child’s doctor and indicated they would appreciate messages 2-3 times/week or more as long as content remains relevant. Suggestions for maintaining message relevance included providing specific strategies for implementation and personalizing information. Most felt the negative features of text messaging (eg, limited message size) could be overcome by providing links within messages to other media including email or websites. Conclusions Text messaging is a promising medium for supporting pediatric obesity-related behavior change. Parent perspectives could assist in the design of text-based interventions. Trial Registration Clinicaltrials.gov NCT01565161; http://clinicaltrials.gov/show/NCT01565161 (Archived by WebCite at http://www.webcitation.org/6LSaqFyPP). PMID:24317406

Leveraging text messaging and mobile technology to support pediatric obesity-related behavior change: a qualitative study using parent focus groups and interviews.

PubMed

Sharifi, Mona; Dryden, Eileen M; Horan, Christine M; Price, Sarah; Marshall, Richard; Hacker, Karen; Finkelstein, Jonathan A; Taveras, Elsie M

2013-12-06

Text messaging (short message service, SMS) is a widely accessible and potentially cost-effective medium for encouraging behavior change. Few studies have examined text messaging interventions to influence child health behaviors or explored parental perceptions of mobile technologies to support behavior change among children. Our aim was to examine parental acceptability and preferences for text messaging to support pediatric obesity-related behavior change. We conducted focus groups and follow-up interviews with parents of overweight and obese children, aged 6-12 years, seen for "well-child" care in eastern Massachusetts. A professional moderator used a semistructured discussion guide and sample text messages to catalyze group discussions. Seven participants then received 3 weeks of text messages before a follow-up one-on-one telephone interview. All focus groups and interviews were recorded and transcribed verbatim. Using a framework analysis approach, we systematically coded and analyzed group and interview data to identify salient and convergent themes. We reached thematic saturation after five focus groups and seven follow-up interviews with a total of 31 parents of diverse race/ethnicity and education levels. Parents were generally enthusiastic about receiving text messages to support healthy behaviors for their children and preferred them to paper or email communication because they are brief and difficult to ignore. Participants anticipated high responsiveness to messaging endorsed by their child's doctor and indicated they would appreciate messages 2-3 times/week or more as long as content remains relevant. Suggestions for maintaining message relevance included providing specific strategies for implementation and personalizing information. Most felt the negative features of text messaging (eg, limited message size) could be overcome by providing links within messages to other media including email or websites. Text messaging is a promising medium for supporting pediatric obesity-related behavior change. Parent perspectives could assist in the design of text-based interventions. Clinicaltrials.gov NCT01565161; http://clinicaltrials.gov/show/NCT01565161 (Archived by WebCite at http://www.webcitation.org/6LSaqFyPP).

Differences between multimedia and text-based assessments of emotion management: An exploration with the multimedia emotion management assessment (MEMA).

PubMed

MacCann, Carolyn; Lievens, Filip; Libbrecht, Nele; Roberts, Richard D

2016-11-01

People process emotional information using visual, vocal, and verbal cues. However, emotion management is typically assessed with text based rather than multimedia stimuli. This study (N = 427) presents the new multimedia emotion management assessment (MEMA) and compares it to the text-based assessment of emotion management used in the MSCEIT. The text-based and multimedia assessment showed similar levels of cognitive saturation and similar prediction of relevant criteria. Results demonstrate that the MEMA scores have equivalent evidence of validity to the text-based MSCEIT test scores, demonstrating that multimedia assessment of emotion management is viable. Furthermore, our results inform the debate as to whether cognitive saturation in emotional intelligence (EI) measures represents "noise" or "substance". We find that cognitive ability associations with EI represent substantive variance rather than construct-irrelevant shared variance due to reading comprehension ability required for text-based items.