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PubMed1996

An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology texts.

The biological literature presents a difficult challenge to information processing in its complexity, diversity, and in its sheer volume. Much of the diversity resides in its technical terminology, which has also become voluminous. In an effort to deal more effectively with this large vocabulary and improve information processing, a method of focus has been developed which allows one to classify terms based on a measure of their importance in describing the content of the documents in which they occur. The measurement is called the strength of a term and is a measure of how strongly the term's occurrences correlate with the subjects of documents in the database. If term occurrences are random then there will be no correlation and the strength will be zero, but if for any subject, the term is either always present or never present its strength will be one. We give here a new, information theoretical interpretation of term strength, review some of its uses in focusing the processing of documents for information retrieval and describe new results obtained in document categorization.

Abstracting and Indexing↗
PubMed2002

A note on the use of a single inequality index in testing the effect of income distribution on mortality.

A new literature has recently emerged which suggests that among the developed economies, at least in terms of health status, the distribution of income may be more important than its absolute level. In this literature, the effect of income inequality, in particular, relative inequality on health status is tested by examining the relationship between aggregate mortality and a single measure of inequality (such as the Atkinson Index). In this paper we look at whether a single measure of income inequality, even augmented by a measure of representative income can at the aggregate level, distinguish between the effects of relative as opposed to absolute income. An alternative approach that uses disaggregated income to distinguish between the effects of changes in relative and absolute income levels is applied to data from the 1990 US Census and mortality figures from the National Centre for Health Statistics. Our results indicate that the rate of mortality is sensitive to absolute, but not relative poverty and therefore suggest that to improve the health of the poor the focus must be on raising their absolute standard of living. The results also indicate that government supported programs may have important health enhancing effects and may therefore represent a key policy tool to improve the health of those at the bottom of the income distribution.

Abstracting and Indexing↗
PubMed1993

SRS--an indexing and retrieval tool for flat file data libraries.

SRS (Sequence Retrieval System) is an information indexing and retrieval system designed for libraries with a flat file format such as the EMBL nucleotide sequence databank, the SwissProt protein sequence databank or the Prosite library of protein subsequence consensus patterns. SRS supports the data structure of these libraries by providing special indices for implementing lists of subentities (e.g. feature tables) or hierarchically structured data-fields (e.g. taxonomic classification). A language (ODD) has been designed for the convenient specification of library format and organization, representation of individual data-fields within the system (design of indices) and structuring other data needed during retrieval. This ensures flexibility required for coping with different library formats, which are subject to continuous change. Queries and inspection of retrieved entries can be performed from a user interface with pull-down menus and windows. SRS supports various input and output formats but is particularly well adapted to the GCG programs.

Abstracting and Indexing↗
PubMed1992

Impact of HIV infection on mortality and accuracy of AIDS reporting on death certificates.

To assess the impact of HIV infection on mortality and the accuracy of AIDS reporting on death certificates, we analyzed data from 6704 homosexual and bisexual men in the San Francisco City Clinic cohort. Identification of AIDS cases and deaths in the cohort was determined through multiple sources, including the national AIDS surveillance registry and the National Death Index. Through 1990, 1518 deaths had been reported in the cohort and 1292 death certificates obtained. Of the 1292 death certificates, 1162 were for known AIDS cases, but 9% of the AIDS cases did not have HIV infection or AIDS noted on the death certificate. Only 0.7% of the decedents had AIDS listed as a cause of death and had not been reported to AIDS surveillance. AIDS and HIV infection was the leading cause of death in the cohort, with the highest proportionate mortality ratio (85%) and standardized mortality ratio (153 in 1987), and the largest number of years of potential life lost (32,008 years). The devastating impact of HIV infection on mortality is increasing and will require continued efforts to prevent and treat HIV infection.

Abstracting and Indexing↗
PubMed2003

Literature searching for clinical and cost-effectiveness studies used in health technology assessment reports carried out for the National Institute for Clinical Excellence appraisal system.

OBJECTIVE: To contribute to making searching for Technology Assessment Reports (TARs) more cost-effective by suggesting an optimum literature retrieval strategy. DATA SOURCES: A sample of 20 recent TARs. REVIEW METHODS: All sources used to search for clinical and cost-effectiveness studies were recorded. In addition, all studies that were included in the clinical and cost-effectiveness sections of the TARs were identified, and their characteristics recorded, including author, journal, year, study design, study size and quality score. Each was also classified by publication type, and then checked to see whether it was indexed in the following databases: MEDLINE, EMBASE, and then either the Cochrane Controlled Trials Register (CCTR) for clinical effectiveness studies or the NHS Economic Evaluation Database (NHS EED) for the cost-effectiveness studies. Any study not found in at least one of these databases was checked to see whether it was indexed in the Science Citation Index (SCI) and BIOSIS, and the American Society of Clinical Oncology (ASCO) Online if a cancer review. Any studies still not found were checked to see whether they were in a number of additional databases. RESULTS: The median number of sources searched per TAR was 20, and the range was from 13 to 33 sources. Six sources (CCTR, DARE, EMBASE, MEDLINE, NHS EED and sponsor/industry submissions to National Institute for Clinical Excellence) were used in all reviews. After searching the MEDLINE, EMBASE and NHS EED databases, 87.3% of the clinical effectiveness studies and 94.8% of the cost-effectiveness studies were found, rising to 98.2% when SCI, BIOSIS and ASCO Online and 97.9% when SCI and ASCO Online, respectively, were added. The median number of sources searched for the 14 TARs that included an economic model was 9.0 per TAR. A sensitive search filter for identifying non-randomised controlled trials (RCT), constructed for MEDLINE and using the search terms from the bibliographic records in the included studies, retrieved only 85% of the known sample. Therefore, it is recommended that when searching for non-RCT studies a search is done for the intervention alone, and records are then scanned manually for those that look relevant. CONCLUSIONS: Searching additional databases beyond the Cochrane Library (which includes CCTR, NHS EED and the HTA database), MEDLINE, EMBASE and SCI, plus BIOSIS limited to meeting abstracts only, was seldom found to be effective in retrieving additional studies for inclusion in the clinical and cost-effectiveness sections of TARs (apart from reviews of cancer therapies, where a search of the ASCO database is recommended). A more selective approach to database searching would suffice in most cases and would save resources, thereby making the TAR process more efficient. However, searching non-database sources (including submissions from manufacturers, recent meeting abstracts, contact with experts and checking reference lists) does appear to be a productive way of identifying further studies.

Abstracting and Indexing↗
PubMed1998

Medicare program; revisions to payment policies under the physician fee schedule for calendar year 1999--HCFA. Proposed rule.

This proposed rule would make several policy changes affecting Medicare Part B payment. The changes that relate to physician services include: resource-based practice expense relative value units, medical direction rules for anesthesia services, and payment for abnormal Pap smears. Also, we would rebase the Medicare Economic Index from a 1989 base year to a 1996 base year. Under the law, we are required to develop a resource-based system for determining practice expense relative value units. The Balanced Budget Act of 1997 (BBA 1997) delayed, for 1 year, implementation of the resource-based practice expense relative value units until January 1, 1999. Also, BBA 1997 revised our payment policy for nonphysician practitioners, for outpatient rehabilitation services, and for drugs and biologicals not paid on a cost or prospective payment basis. In addition, BBA 1997 permits certain physicians and practitioners to opt out of Medicare and furnish covered services to Medicare beneficiaries through private contracts. In addition, since we established the physician fee schedule on January 1, 1992, our experience indicates that some of our Part B payment policies need to be reconsidered. This proposed rule is intended to correct inequities in physician payment and solicits public comments on specific proposed policy changes.

Abstracting and Indexing↗
PubMedDate not supplied

A search tool based on 'encapsulated' MeSH thesaurus to retrieve quality health resources on the internet.

In the year 2001, the Internet has become a major source of health information for the health professional and the Netizen. The objective of Doc' CISMeF (D'C) was to create a powerful generic search tool based on a structured information model which 'encapsulates' the MeSH thesaurus to index and retrieve quality health resources on the Internet. To index resources, D'C uses four sections in its information model: 'meta-term', keyword, subheading, and resource type. Two search options are available: simple and advanced. The simple search requires the end-user to input a single term or expression. If this term belongs to the D'C information structure model, it will be exploded. If not, a full-text search is performed. In the advanced search, complex searches are possible combining Boolean operators with meta-terms, keywords, subheadings and resource types. D'C uses two standard tools for organising information: the MeSH thesaurus and the Dublin Core metadata format. Resources included in D'C are described according to the following elements: title, author or creator, subject and keywords, description, publishers, date, resource type, format, identifier, and language.

Abstracting and Indexing↗
PubMed2001

Doc'CISMEF: a search tool based on "encapsulated" MeSH thesaurus.

In the year 2000, the Internet became a major source of health information for the health professional and the Netizen. The objective of Doc'CISMeF (D'C) was to create a powerful generic search tool based on an structured information model which â encapsulates' the MeSH thesaurus to index and retrieve quality health resources on the Internet. To index resources, D'C uses four sections in its information model: 'meta-term', keyword, subheading, and resource type. Two search options are available: simple and advanced. The simple search requires the end-user to input a single term or expression. If this term belongs to the D'C information structure model, it will be exploded. If not, a full-text search is performed. In the advanced search, complex searches are possible combining Boolean operators with meta-terms, keywords, subheadings and resource types. D'C uses two standard tools for organising information: the MeSH thesaurus and the Dublin Core metadata format. Resources included in D'C are described according to the following elements: title, author or creator, subject and keywords, description, publisher, date, resource type, format, identifier, and language.

Abstracting and Indexing↗
PubMed1988

A computerized approach to discipline-specific bibliographies in the allied health sciences.

The traditional subject headings in Index Medicus and other standard indexes have frequently proved too broad for researchers in the allied health sciences. Therefore, the Physician Assistant Program at the University of Florida has developed a computerized bibliography program designed to expedite research by using a selected list of keywords as subject headings and subheadings tailored to the interests and concerns of the physician assistant profession. Each subject heading and subheading is translated into a numerical coding system that permits efficient data entry and rapid identification of items in the professional literature as well as reducing the incidence of operator error in data entry. The program can be used for review of the literature, curriculum design, identification of supplementary reading material for education courses, and identification of appropriate resources to enhance the study of the physician assistant profession. Through the development of discipline-specific keywords, the program can be tailored to the educational and research interests of any discipline in the allied health sciences or other educational fields.

Abstracting and Indexing↗
PubMed1996

A comparison of authors publishing in two groups of U.S. medical journals.

This study compared the editorial peer review experiences of authors who published in two groups of indexed U.S. medical journals. The study tested the hypothesis that after one journal rejects a manuscript an author selects a less well-known journal for submission. Group One journals were defined as those indexed in 1992 MEDLINE that satisfied several additional qualitative measures; Group Two journals were indexed in the 1992 MEDLINE only. Surveys were sent to the first authors of 616 randomly selected articles, and 479 surveys were returned, for a response rate of 78.1%. A total of 20.8% of Group One and 15.7% of Group Two articles previously had been rejected. Group One authors were more likely to select a journal for its prestige and article quality, while Group Two authors were more likely to have been invited to submit the manuscript. More than 60% of both groups felt the peer review had offered constructive suggestions, but that it had changed article conclusions less than 3% of the time. Both groups thought the review process only marginally improved content, organization, or statistical analysis, or clarified conclusions. Between 3% and 15% of all authors received considerable conflicting advice from different reviewers. Authors from both groups differed as to their reasons for journal selection, their connections with the publishing journal, and patterns of resubmission after rejection.

Abstracting and Indexing↗
PubMed1993

Words or concepts: the features of indexing units and their optimal use in information retrieval.

Words or Concepts, which are a better choice for indexing the contents of documents? The answer depends on what method is used for retrieval. This paper studies the effects of using canonical concepts versus document words in different retrieval systems with a testing collection of MEDLINE documents. In our tests, for a retrieval system which does not use any human knowledge, using words yielded better retrieval results, while using concepts suffered from a vocabulary difference between canonical expressions of concepts and non-canonical words in queries or documents. For a system which depends on the UMLS synonym set for a mapping from queries or documents to canonical concepts, the retrieval results were slightly better than the case of not using the synonyms, but still worse than the systems using words. For the systems which automatically "learn" empirical connections between words and concepts from examples in the testing collection, the vocabulary problem was effectively solved, and the results of using concepts were competitive or better, compared to those using words.

Abstracting and Indexing↗
PubMed2002

Use of a MeSH-based index of faculty research interests to identify faculty publications: an IAIMSian study of precision, recall, and data reusability.

OBJECTIVE: To determine whether MEDLINE searches based on an existing automated faculty research interest index or on author name entities can be used to automate construction of accurate online lists of faculty publications. METHODS: Curricula vitae (CVs) for 36 faculty members were selected at random. Their lists of journal publications were used to determine recall and precision of two MEDLINE search strategies. OUTCOME: Most faculty publications in the CVs (86%) were indexed in MEDLINE. The research-interest-enhanced MEDLINE searches retrieved citations in the CVs that were also in MEDLINE with a recall of 0.53 and precision of 0.85. For every 10 citations in the research interest-enhanced search, on average 8.5 were in the CVs. The name entity searches retrieved a higher proportion of citations in the CVs (recall 0.94, precision 0.59) with a higher rate of citations not in the CVs: For every 10 citations in the faculty name searches, 7.3 citations were in the CVs. Name commonness or clinical or basic sciences appointment did not change these results. CONCLUSION: MEDLINE searches, especially those based on research interests, can be used to populate faculty publication lists with high rates of accuracy. Author based searches can also be used, but they retrieve a higher proportion of irrelevant citations. This study confirms a successful instance of data reusability and integration at a large health academic sciences institution.

Abstracting and Indexing↗
PubMed2006

Developing optimal search strategies for detecting clinically sound treatment studies in EMBASE.

OBJECTIVE: The ability to accurately identify articles about therapy in large bibliographic databases such as EMBASE is important for researchers and clinicians. Our study aimed to develop optimal search strategies for detecting sound treatment studies in EMBASE in the year 2000. METHODS: Hand searches of journals were compared with retrievals from EMBASE for candidate search strategies. Six trained research assistants reviewed fifty-five journals indexed in EMBASE and rated articles using purpose and quality indicators. Candidate search strategies were developed for identifying treatment articles and then tested, and the retrievals were compared with the hand-search data. The operating characteristics of the strategies were calculated. RESULTS: Three thousand eight hundred fifty articles were original studies on treatment, of which 1,256 (32.6%) were methodologically sound. Combining search terms revealed a top performing strategy (random:.tw. OR clinical trial:.mp. OR exp health care quality) with sensitivity of 98.9% and specificity of 72.0%. Maximizing specificity, a top performing strategy (double-blind:.mp. OR placebo:.tw. OR blind: .tw.) achieved a value over 96.0%, but with compromised sensitivity at 51.7%. A 3-term strategy achieved the best optimization of sensitivity and specificity (random:.tw. OR placebo:.mp. OR double-blind:.tw.), with both these values over 92.0%. CONCLUSION: Search strategies can achieve high performance for retrieving sound treatment studies in EMBASE.

Abstracting and Indexing↗
PubMed1998

The Merck Gene Index browser: an extensible data integration system for gene finding, gene characterization and EST data mining.

MOTIVATION: To make effective use of the vast amounts of expressed sequence tag (EST) sequence data generated by the Merck-sponsored EST project and other similar efforts, sequences must be organized into gene classes, and scientists must be able to 'mine' the gene class data in the context of related genomic data. RESULTS: This paper presents the Merck Gene Index browser, an easily extensible, World Wide Web-based system for mining the Merck Gene Index (MGI) and related genomic data. The MGI is a non-redundant set of clones and sequences, each representing a distinct gene, constructed from all high-quality 3' EST sequences generated by the Merck-sponsored EST project. The MGI browser integrates data from a variety of sources and storage formats, both local and remote, using an eclectic integration strategy, including a federation of relational databases, a local data warehouse and simple hypertext links. Data currently integrated include: LENS cDNA clone and EST data, dbEST protein and non-EST nucleic acid similarity data, WashU sequence chromatograms. Entrez sequence and Medline entries, and UniGene gene clusters. Flatfile sequence data are accessed using the Bioapps server, an internally developed client-server system that supports generic sequence analysis applications. Browser data are retrieved and formatted by means of the Bioinformatics Data Integration Toolkit (B-DIT), a new suite of Perl routines.

Abstracting and Indexing↗
PubMed2005

MorphoSaurus--design and evaluation of an interlingua-based, cross-language document retrieval engine for the medical domain.

OBJECTIVES: We propose an interlingua-based indexing approach to account for the particular challenges that arise in the design and implementation of cross-language document retrieval systems for the medical domain. METHODS: Documents, as well as queries, are mapped to a language-independent conceptual layer on which retrieval operations are performed. We contrast this approach with the direct translation of German queries to English ones which, subsequently, are matched against English documents. RESULTS: We evaluate both approaches, interlingua-based and direct translation, on a large medical document collection, the OHSUMED corpus. A substantial benefit for interlingua-based document retrieval using German queries on English texts is found, which amounts to 93% of the (monolingual) English baseline. CONCLUSIONS: Most state-of-the-art cross-language information retrieval systems translate user queries to the language(s) of the target documents. In contra-distinction to this approach, translating both documents and user queries into a language-independent, concept-like representation format is more beneficial to enhance cross-language retrieval performance.

Abstracting and Indexing↗
PubMed2006

Advancing biomedical image retrieval: development and analysis of a test collection.

OBJECTIVE: Develop and analyze results from an image retrieval test collection. METHODS: After participating research groups obtained and assessed results from their systems in the image retrieval task of Cross-Language Evaluation Forum, we assessed the results for common themes and trends. In addition to overall performance, results were analyzed on the basis of topic categories (those most amenable to visual, textual, or mixed approaches) and run categories (those employing queries entered by automated or manual means as well as those using visual, textual, or mixed indexing and retrieval methods). We also assessed results on the different topics and compared the impact of duplicate relevance judgments. RESULTS: A total of 13 research groups participated. Analysis was limited to the best run submitted by each group in each run category. The best results were obtained by systems that combined visual and textual methods. There was substantial variation in performance across topics. Systems employing textual methods were more resilient to visually oriented topics than those using visual methods were to textually oriented topics. The primary performance measure of mean average precision (MAP) was not necessarily associated with other measures, including those possibly more pertinent to real users, such as precision at 10 or 30 images. CONCLUSIONS: We developed a test collection amenable to assessing visual and textual methods for image retrieval. Future work must focus on how varying topic and run types affect retrieval performance. Users' studies also are necessary to determine the best measures for evaluating the efficacy of image retrieval systems.

Abstracting and Indexing↗
PubMed2007

Improvements to the Red List Index.

The Red List Index uses information from the IUCN Red List to track trends in the projected overall extinction risk of sets of species. It has been widely recognised as an important component of the suite of indicators needed to measure progress towards the international target of significantly reducing the rate of biodiversity loss by 2010. However, further application of the RLI (to non-avian taxa in particular) has revealed some shortcomings in the original formula and approach: It performs inappropriately when a value of zero is reached; RLI values are affected by the frequency of assessments; and newly evaluated species may introduce bias. Here we propose a revision to the formula, and recommend how it should be applied in order to overcome these shortcomings. Two additional advantages of the revisions are that assessment errors are not propagated through time, and the overall level extinction risk can be determined as well as trends in this over time.

Abstracting and Indexing↗
PubMed2003

Weight change after an atypical antipsychotic switch.

BACKGROUND: Atypical antipsychotics successfully treat schizophrenia and other conditions, with a lower incidence of extrapyramidal side effects than other agents used in treatment of these disorders. However, some atypical antipsychotics are associated with weight gain. OBJECTIVE: To quantify the impact on weight and identify atypical antipsychotics causing the least amount of weight gain among patients switched from risperidone to olanzapine and olanzapine to risperidone. METHODS: Patients included in the study (n = 86) were > or =18 years and had received > or =2 prescriptions for risperidone or olanzapine for > or =60 days, switched to the other atypical antipsychotic, and were dispensed > or =2 prescriptions for at least 60 days after the index date. Age, weight, and body mass index (BMI) were retrospectively abstracted from automated databases containing patient-specific prescription and vital sign information. RESULTS: At the time of their switch, the average patient age was 53.2 years (range 25-83). The average weight change in patients switched to olanzapine (n = 47) was +2.3 kg (p = 0.01) and the BMI change was +0.8 kg/m(2) (p = 0.02). The average percent body weight change was +2.8% and the BMI change was +3.0%. The average weight change after patients switched to risperidone (n = 39) was -0.45 kg (p = 0.69) and BMI change was -0.2 kg/m2 (p = 0.64). The average percentage weight change was -0.4% and BMI change was -0.5%. CONCLUSIONS: Practitioners' concern regarding weight changes after switching atypical antipsychotics seems warranted and patients should be provided consistent, ongoing weight monitoring. Further investigations should examine whether weight changes associated with atypical antipsychotic treatment further jeopardize this already at-risk population for severe comorbid conditions such as hypertension, coronary artery disease, and type 2 diabetes.

Adult↗