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Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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PubMed2004

Interpretation by modelling of observations in radon radiation carcinogenesis.

Biophysical models for radon-related induction of lung cancer are developed with the aim of reducing the uncertainties in current risk estimates at low doses by a better understanding of the relevant mechanisms. These models can make use of the full dosimetric information when extracting information on, say, age-at-exposure, protraction or fractionation effects. It is found that irradiation by radon and its progeny does act on the initiating event of carcinogenesis (e.g. mutation), but its dominating effect is via promoting the division of already initiated cells. Data show that the concept of a unit of exposure giving, in an additive way, a unit of lung cancer risk is too limited, while relatively simple mechanistic assumptions described in this article do yield an adequate description of observations. Exposures in epidemiological data sets are measured with error. For various error models it has been shown that likelihood-based techniques of correction work reliably; likewise for biologically based cancer models. When several parameters are allowed to be exposure dependent, for example, initiation and promotion, then their relative importance is influenced.

Air Pollutants, Radioactive↗

PubMed1999

Cystic fibrosis: molecular diagnosis, population screening, and public policy.

OBJECTIVE: To review the current status of scientific knowledge and opinion regarding molecular genetic testing of mutations in the CFTR gene for purposes of diagnosis and population carrier screening of cystic fibrosis (CF). DATA SOURCES: Published research findings on the nature of the CFTR gene, pilot population screening studies in the United States and Europe, and ongoing deliberations of professional and governmental agencies considering implementation of widespread testing. STUDY SELECTION: Findings relevant to the molecular heterogeneity of CFTR mutations and its implications for population carrier screening were considered. DATA EXTRACTION: Information was extracted from studies published by us and others, as made available to recent consensus panels and professional committees. DATA SYNTHESIS: These data were reevaluated in light of recent movements in professional and public policy regarding acceptability and desirability of widespread CF mutation testing. Effects to date of such testing on patient outcomes is reported. CONCLUSIONS: The ability to test for CFTR mutations at the molecular level has already improved the diagnosis of symptomatic patients and expanded the reproductive options of family members of CF patients. The same technology also holds promise of identifying asymptomatic carriers and at-risk couples without family history in the general population so that they too might be offered prenatal diagnosis or other options. However, a number of key questions remain to be worked out before a widespread national screening program can be put into practice. These include the target population to be offered testing (the entire population vs high-risk ethnic groups), the size and nature of the mutation test panel (universal vs ethnic specific), the inclusion or exclusion of CFTR variants that do not cause classical CF, the optimal testing technology, appropriate standards for laboratory quality assurance, and the development of sufficient educational materials and genetic counseling resources for test delivery, reporting, and interpretation. The answers to these questions will be relevant not only to CF testing but also to many other large-scale molecular genetic screening programs being considered in the future.

Cloning, Molecular↗

PubMed2004

MeSH and specialized terminologies: coverage in the field of molecular biology.

There is real need among researchers for data in molecular biology, due to the explosive development in this field. Information extraction techniques have been developed in this specific domain, to extract structured information from the literature. The National Library of Medicine provides access to 12 million MEDLINE citations, accessible via PubMed. Information retrieval techniques which are used to select documents that are relevant according to user request. As other domains in medicine, biomolecular scientific literature is indexed by MeSH terms. Automatic identification of protein and gene names in scientific articles is an important step in the indexing process, since proteins and genes are often associated with multiple names, and authors alternate between these synonyms. In this article we assess the contribution of specialized terminologies in the field of molecular biology compared to MeSH.

Abstracting and Indexing↗

PubMed2005

New approaches to health promotion and informatics education using Internet in the Czech Republic.

The paper describes nowadays information technology skills in the Czech Republic. It focuses on informatics education using Internet, ECDL concept and the links between computer literacy among health care professionals and quality of health care. Everyone understands that the main source of wealth of any nation is information management and the efficient transformation of information into knowledge. There appear completely new decisive factors for the economics of the near future based on circulation and exchange information. It is clear that modern health care cannot be built without information and communication technologies. We discuss several approaches how to contribute to some topics of information society in health care, namely the role of electronic health record, structured information, extraction of information from free medical texts and sharing knowledge stored in medical guidelines.

Health Promotion↗

PubMed1981

The perceptual domain: a taxonomy for allied health educators.

A taxonomy of the perceptual domain was proposed over a decade ago. It is hierarchical, as are the taxonomies in the cognitive, affective, and psychomotor domains. Perception involves extraction of information from presenting stimuli, and there is progression of information extraction as the hierarchy is ascended. Perceptual performance at the higher levels of the taxonomy assumes perceptual abilities at the lower levels. A modified version of the perceptual taxonomy applicable to allied health education is presented. Methods concerning application of the taxonomy are suggested. Use of the taxonomy of the perceptual domain would help allied health educators plan instruction and evaluate teaching.

Allied Health Personnel↗

PubMed1995

The impact of unemployment on health: a review of the evidence.

OBJECTIVE: To review the scientific evidence supporting an association between unemployment and adverse health outcomes and to assess the evidence on the basis of the epidemiologic criteria for causation. DATA SOURCES: MEDLINE was searched for all relevant articles with the use of the MeSH terms "unemployment," "employment," "job loss," "economy" and a range of mortality and morbidity outcomes. A secondary search was conducted for references from the primary search articles, review articles or published commentaries. Data and definitions of unemployment were drawn from Statistics Canada publications. STUDY SELECTION: Selection focused on articles published in the 1980s and 1990s. English-language reports of aggregate-level research (involving an entire population), such as time-series analyses, and studies of individual subjects, such as cross-sectional, case-control or cohort studies, were reviewed. In total, the authors reviewed 46 articles that described original studies. DATA EXTRACTION: Information was sought on the association (if any) between unemployment and health outcomes such as mortality rates, specific causes of death, incidence of physical and mental disorders and the use of health care services. Information was extracted on the nature of the association (positive or negative), measures of association (relative risk, odds ratio or standardized mortality ratio), and the direction of causation (whether unemployment caused ill health or vice versa). DATA SYNTHESIS: Most aggregate-level studies reported a positive association between national unemployment rates and rates of overall mortality and mortality due to cardiovascular disease and suicide. However, the relation between unemployment rates and motor-vehicle fatality rates may be inverse. Large, census-based cohort studies showed higher rates of overall mortality, death due to cardiovascular disease and suicide among unemployed men and women than among either employed people or the general population. Workers laid off because of factory closure have reported more symptoms and illnesses than employed people; some of these reports have been validated objectively. Unemployed people may be more likely than employed people to visit physicians, take medications or be admitted to general hospitals. A possible association between unemployment and rates of admission to psychiatric hospitals is complicated by other institutional and environmental factors. CONCLUSIONS: Evaluated on an epidemiologic basis, the evidence suggests a strong, positive association between unemployment and many adverse health outcomes. Whether unemployment causes these adverse outcomes is less straightforward, however, because there are likely many mediating and confounding factors, which may be social, economic or clinical. Many authors have suggested mechanisms of causation, but further research is needed to test these hypotheses.

Accidents, Traffic↗

PubMed1985

How much is an icon worth?

We report a new technique for assessing the amount of information extracted from the icon that follows a briefly presented picture. The problem of how to measure such information was formulated in terms of how much physical exposure of a picture an icon is worth. Consider two types of stimulus presentations, each with a base duration of d ms. The first is a d-ms picture followed by an icon, and the second is a d + a-ms picture not followed by an icon. How large does a have to be so that equivalent amounts of information are extracted in the two cases? To answer this question, we showed people pictures and later tested their memory for the pictures. We found that the physical exposure duration needed to reach a particular level of performance was approximately 100 ms longer when an icon was not permitted versus when the icon was permitted. This value was independent of the base duration and the luminance of the picture. Moreover, the same value was obtained using three different kinds of memory test and four different sets of pictures. We conclude that an icon is worth approximately 100 ms of additional physical exposure duration. A reasonable explanation for this robust equivalence between icon and stimulus is that the same encoding processes are responsible for extracting information from the icon and from the physical stimulus. Therefore, any variable that affects these encoding processes must affect extraction of information from the icon and the physical stimulus in an identical manner. This prediction was confirmed for one such variable, picture luminance.

Figural Aftereffect↗

PubMed2003

Extracting structured information from free text pathology reports.

We have developed a method that extracts structured information about specimens and their related findings in free-text surgical pathology reports. Our method uses regular expressions that drive a state-automaton on top of XSLT and Java. Text fragments identified are coded against the UMLS. This paper describes the technical approach and reports on a preliminary evaluation study, designed to guide further development. We found that of 275 reviewed reports, 91% were coded at least so that all specimens and their critical pathologic findings were represented in codes.

Databases as Topic↗

PubMed2004

Extracting phenotypic information from the literature via natural language processing.

In recent years, the amount of biomedical knowledge has been increasing exponentially. Several Natural Language Processing (NLP) systems have been developed to help researchers extract, encode and organize new information automatically from textual literature or narrative reports. Some of these systems focus on extracting biological entities or molecular interactions while others retrieve and encode clinical information. To exploit gene functions in the post-genome era, it is necessary to extract phenotypic information automatically from the literature as well. However, few NLP projects have focused on this. We present the development of a system called BioMedLEE that extracts a broad variety of phenotypic information from the biomedical literature. The system was developed by adapting MedLEE, an existing clinical information extraction NLP engine. A feasibility evaluation study of BioMedLEE was performed using 300 randomly chosen journal titles. Results showed that experts achieved an average precision rate of 65.4%, (95%CI: [58.0%, 72.8%]) and a recall rate of 73.0%, (95%CI: [66.2%, 80.0%]). BioMedLEE had 64.0% precision and 77.1% recall respectively, according to expert agreements.

Databases as Topic↗

PubMed2003

Time-resolved polarization to extract coded information from early ballistic and snake signals through turbid media.

Time-resolved polarization is used to extract coded information buried within the multiple scattering profiles from the early ballistic and snake components as they pass through turbid media. By polarization analysis the depolarized diffusive component and the natural-light background are significantly reduced to enhance the signal-to-noise ratio of a coded pulse train. This procedure has the potential to improve optical wireless communication in cloudy environments.

Journal Article↗

PubMed2003

Potential for dramatic improvement in sequence alignment against structures of remote homologous proteins by extracting structural information from multiple structure alignment.

A novel method has been developed for acquiring the correct alignment of a query sequence against remotely homologous proteins by extracting structural information from profiles of multiple structure alignment. A systematic search algorithm combined with a group of score functions based on sequence information and structural information has been introduced in this procedure. A limited number of top solutions (15,000) with high scores were selected as candidates for further examination. On a test-set comprising 301 proteins from 75 protein families with sequence identity less than 30%, the proportion of proteins with completely correct alignment as first candidate was improved to 39.8% by our method, whereas the typical performance of existing sequence-based alignment methods was only between 16.1% and 22.7%. Furthermore, multiple candidates for possible alignment were provided in our approach, which dramatically increased the possibility of finding correct alignment, such that completely correct alignments were found amongst the top-ranked 1000 candidates in 88.3% of the proteins. With the assistance of a sequence database, completely correct alignment solutions were achieved amongst the top 1000 candidates in 94.3% of the proteins. From such a limited number of candidates, it would become possible to identify more correct alignment using a more time-consuming but more powerful method with more detailed structural information, such as side-chain packing and energy minimization, etc. The results indicate that the novel alignment strategy could be helpful for extending the application of highly reliable methods for fold identification and homology modeling to a huge number of homologous proteins of low sequence similarity. Details of the methods, together with the results and implications for future development are presented.

Algorithms↗

PubMed1996

Automating concept identification in the electronic medical record: an experiment in extracting dosage information.

We discuss the development and evaluation of an automated procedure for extracting drug-dosage information from clinical narratives. The process was developed rapidly using existing technology and resources, including categories of terms from UMLS96. Evaluations over a large training and smaller test set of medical records demonstrate an approximately 80% rate of exact and partial matches' on target phrases, with few false positives and a modest rate of false negatives. The results suggest a strategy for automating general concept identification in electronic medical records.

Classification↗

PubMed1984

Transsexual prostitution in New Zealand: predominance of persons of Maori extraction.

Information concerning the racial distribution, family background, sexual history, education, and employment status of 27 New Zealand, male-to-female preoperative transsexual prostitutes was obtained by interview and questionnaire. Subjects lived in Wellington, New Zealand, and Sydney, Australia. Subjects recalled childhoods with maternal dominance, paternal absence, being youngest sons, and being dressed in girls' clothes by female relatives. Further, an early history of homosexual intercourse and cross-dressing behavior occurred significantly often. Moreover, it was apparent that the Maori race, which forms 9.0% of the total New Zealand population, was disproportionately represented; approximately 90% of the transsexual prostitute population in Wellington is Maori. Various explanations are offered for the racial inequality. It is concluded that cultural influences have an effect on the number of transsexual prostitutes in New Zealand. Further research is needed to assess whether these factors also influence the etiology and development of transsexualism.

Adolescent↗

PubMed1998

Extracting dynamic information from EXAFS: simultaneous analysis of multiple temperature-dependent data.

A new approach to the extraction of dynamic information from extended X-ray absorption fine-structure (EXAFS) spectra has been developed. With this method, a complete set of temperature-dependent spectra are fit simultaneously to one of a variety of pair-distribution functions. Distributions are calculated in r-space using the appropriate absorber-scatterer pair potential. The temperature-dependent EXAFS spectra are calculated by summing k-space models over a range of distances and angles weighted according to the relative contribution of each geometry to the distribution. This approach allows refinement of data using a full multiple-scattering analysis with only modest computational time.

Journal Article↗

PubMed1995

Cortical simple cells can extract achromatic information from the multiplexed chromatic and achromatic signals in the parvocellular pathway.

P cells, which carry both achromatic and chromatic information, are largely responsible for achromatic acuity and contrast sensitivity. The P cell achromatic information must be separated from the chromatic information to be useful. Cortical simple cells are well suited to the extraction of achromatic information by spatial bandpass filtering. Bandpass filtering of Type I P cells by cortical simple cells yields an achromatic signal with a residual chromatic response. The bandpass model makes predictions in accord with existing physiological data and explains the role of a heretofore puzzling class of cortical cells, which have bandpass tuning for both achromatic and chromatic modulations. The model is shown to be related to a previously postulated class of ideal detectors. Finally, the model is used to make a number of physiological and psychophysical predictions.

Color Perception↗

PubMed1996

Extracting quantitative information from digital electrogastrograms.

Cutaneous recordings of gastric electrical activity (electrogastrography (EGG)) could become a valuable non-invasive tool for recognising gastric electrical abnormalities. Although signals obtained with internally implanted electrodes deliver quantitative information, this technique cannot be used for diagnostic purposes because of its invasive nature. On the other hand, the objectivity of electrogastrography is still in question. The aims of this work are to develop computer techniques for extracting quantitative information from digital electrogastrograms, and to evaluate quantitatively EGG recordings from healthy volunteers. The dynamics of all four EGG parameters are studied: amplitude, frequency, time shift between different channels, and waveform. Four separate two-dimensional computer plots are developed using specially designed digital signal-processing procedures. Each parameter is evaluated in a study of 20 healthy volunteers. Frequency is found to be the only EGG parameter that shows quantitative consistency and merit.

Electrodiagnosis↗

PubMed1996

Algorithms for extracting motion information from navigator echoes.

Algorithms to reliably detect motion in navigator echoes are crucial to many MRI motion suppression techniques. The accuracy of these algorithms is affected by noise and deformation of navigator echo profile caused by physiologic motion. This study compared the performance of algorithms based on correlation and least squares for extracting displacement information from motion-monitoring navigator echoes, using computer simulation and in vivo imaging. The least squares algorithm was determined to be of higher accuracy than the correlation algorithm against errors caused by noise and profile deformation.

Algorithms↗

PubMed1995

Computer extraction of information on contractions and emergency conditions from the intrauterine pressure.

In this paper we describe the problems and solutions involved in getting the controlling computer in the system described in [1] to derive the necessary information about contractions and emergency conditions from the intrauterine pressure input. The required information in this case includes the detection and classification of contractions, the continuously-updated evaluation of the resting baseline tone, and the detection of emergency conditions such as excessively high intrauterine pressure, constant intrauterine pressure, the occurrence of series of contractions closely following each other whose amplitude are all exceedingly high or all exceedingly low. In extracting this information, the computer has to cope with problems of noise, both noise inherent in the monitoring system and that due to patient movement.

Algorithms↗