Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “information extraction”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 235 records · Page 13Linked to original sources
PubMed1999

Guidelines for intensive care unit admission, discharge, and triage. Task Force of the American College of Critical Care Medicine, Society of Critical Care Medicine.

OBJECTIVE: To provide guidelines for admission, discharge, and triage of adult patients to the intensive care unit (ICU), based on expert opinion and the relevant literature. DATA SOURCES: Publications relevant to the admission, discharge, and triage of patients to the ICU were obtained from the medical literature. STUDY SELECTION: Not applicable. DATA EXTRACTION: Articles were reviewed and the relevant information extracted for analysis by an expert panel. DATA SYNTHESIS: The articles were reviewed and graded levels of recommendation made based on a rating system described in the text. CONCLUSIONS: Although little scientifically rigorous data exist validating the criteria for admission, discharge, and triage of adult patients to the ICU, current literature and expert opinion support guidelines to streamline the admission, discharge, and triage process.

Adult↗
PubMed2005

Supplier discretion over provision: theory and an application to medical care.

Suppliers who are better informed than purchasers, such as physicians treating insured patients, often have discretion over what to provide. I show how, when the purchaser observes what is supplied but neither the recipient type nor the actual cost incurred, optimal provision differs from what would be efficient if the purchaser had full information, weather or not the supplier can extract informational rent. The analysis is applied to, among other things, data on tests for coronary artery disease and to Medicare diagnosis-related groups defined by the treatment given, not just the diagnosis, illustrating the biases in provision that result.

Coronary Angiography↗
PubMed2005

An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.

BACKGROUND: The Gene Ontology Annotation (GOA) database http://www.ebi.ac.uk/GOA aims to provide high-quality supplementary GO annotation to proteins in the UniProt Knowledgebase. Like many other biological databases, GOA gathers much of its content from the careful manual curation of literature. However, as both the volume of literature and of proteins requiring characterization increases, the manual processing capability can become overloaded. Consequently, semi-automated aids are often employed to expedite the curation process. Traditionally, electronic techniques in GOA depend largely on exploiting the knowledge in existing resources such as InterPro. However, in recent years, text mining has been hailed as a potentially useful tool to aid the curation process. To encourage the development of such tools, the GOA team at EBI agreed to take part in the functional annotation task of the BioCreAtIvE (Critical Assessment of Information Extraction systems in Biology) challenge. BioCreAtIvE task 2 was an experiment to test if automatically derived classification using information retrieval and extraction could assist expert biologists in the annotation of the GO vocabulary to the proteins in the UniProt Knowledgebase. GOA provided the training corpus of over 9000 manual GO annotations extracted from the literature. For the test set, we provided a corpus of 200 new Journal of Biological Chemistry articles used to annotate 286 human proteins with GO terms. A team of experts manually evaluated the results of 9 participating groups, each of which provided highlighted sentences to support their GO and protein annotation predictions. Here, we give a biological perspective on the evaluation, explain how we annotate GO using literature and offer some suggestions to improve the precision of future text-retrieval and extraction techniques. Finally, we provide the results of the first inter-annotator agreement study for manual GO curation, as well as an assessment of our current electronic GO annotation strategies. RESULTS: The GOA database currently extracts GO annotation from the literature with 91 to 100% precision, and at least 72% recall. This creates a particularly high threshold for text mining systems which in BioCreAtIvE task 2 (GO annotation extraction and retrieval) initial results precisely predicted GO terms only 10 to 20% of the time. CONCLUSION: Improvements in the performance and accuracy of text mining for GO terms should be expected in the next BioCreAtIvE challenge. In the meantime the manual and electronic GO annotation strategies already employed by GOA will provide high quality annotations.

Animals↗
PubMed1989

Motion processing by chromatic and achromatic visual pathways.

We describe a family of stimuli consisting of colored bars of different orientations, which, when presented in rapid succession, may elicit unambiguous motion perception. These stimuli permitted the isolation of directional spatiotemporal information extracted from oriented luminance clues, from nonoriented chromatic-plus-luminance clues, or, when the stimuli were presented under equiluminant conditions, from pure chromatic clues. As a general rule, matching of orientation induces weaker motion-detection performances than does matching of color. When the orientation clues are in competition with the chromatic ones, motion perception based on the former is always overridden by motion perception based on the latter. We indirectly isolated an oriented chromatic mechanism that also contributes to motion perception. We finally showed that, under equiluminant conditions, matching of orientation across different colors is inefficient in eliciting motion perception, either because motion information is extracted poorly across different chromatic channels or because such channels show little orientational selectivity. Because motion strength determined by each of the manipulated attributes follows different functions with the displacement (or velocity) of the stimuli, we propose the existence of three underlying mechanisms, a luminance mechanism, a chromatic-plus-luminance mechanism, and a pure chromatic mechanism, each of which provides motion information.

Attention↗
PubMed2004

Extraction of kinetic information from single-molecule experiments.

We discuss two possible approaches for extracting kinetic information from single-molecule experiments. The first approach is based on computing correlation functions from measured fluorescence signals, and the second on studying the statistics of on and off times of the same fluorescence signal. We show that in both cases it is possible to extract kinetic information about the nature of intramolecular fluctuations of the single molecule. We show that for single-molecule kinetics the intramolecular fluctuations produce stochastic memory effects which lead to new dynamic features that do not exist in traditional chemical kinetics. In particular, we investigate a new type of chemical oscillations in correlation functions observed experimentally by Edman and Rigler (Proc. Natl. Acad. Sci. USA 2000, 97, 8266).

Fluorescence↗
PubMed1993

Interactions between physicians and the pharmaceutical industry: what does the literature say?

OBJECTIVE: To determine the effect of three types of interaction between physicians and the pharmaceutical industry--company-funded clinical trials, company-sponsored continuing medical education (CME) and information for physicians supplied by pharmaceutical detailers--on orientation and quality of clinical trials, content of CME courses and physicians' prescribing behaviour. DATA SOURCES: MEDLINE and HEALTH searches for English-language articles published from 1978 to 1993, supplemented by material from the author's personal collection. STUDY SELECTION: A total of 227 papers from the MEDLINE and HEALTH searches and about 2000 items from the author's library were initially reviewed. The following selection criteria were used: studies conducted in Australia, Canada, New Zealand, Britain and the United States; studies conducted after 1977; quantitative surveys containing details of the survey methods; studies on the orientation and quality of company-funded clinical trials and on the content of CME courses giving explicit criteria used in the evaluation; and reports on the outcome of interactions stating how the outcomes were assessed. Thirty-six studies met these criteria. DATA EXTRACTION: Information was extracted on five topics: physicians' attitudes toward drug industry interactions, frequency with which physicians participate in the interactions, orientation and quality of company-funded clinical trials, content of company-sponsored CME courses and changes in physicians' prescribing behaviour as a result of an interaction. DATA SYNTHESIS: Although most physicians participate only occasionally in company-sponsored clinical trials, most see detailers and attend company-sponsored CME courses. However, physicians do not have a very high opinion of the information from detailers or of company-sponsored CME events. Many doctors regard pharmaceutical companies as an important source of funding for clinical trials, but they also have concerns about accepting money from this source. Company funding of clinical trials may affect the quality of the trials and the types of research that physicians undertake. Company-sponsored CME courses may have a commercial bias even if conducted under guidelines designed to ensure the independence of the event. All three types of interactions affect physicians' prescribing behaviour and, in the case of obtaining information from detailers, physicians' prescribing practices are less appropriate as a result of the interaction. CONCLUSIONS: Physicians are affected by their interactions with the pharmaceutical industry. Further research needs to be done in most cases to determine whether such interactions lead to more or less appropriate prescribing practices. The CMA's guidelines on this topic should be evaluated to see whether they are effective in controlling physician-industry interactions. Further measures may be necessary if the guidelines fail to prevent negative effects on prescribing practices.

Attitude of Health Personnel↗
PubMed2004

Experimental determination of compound action potential direction and propagation velocity from multi-electrode nerve cuffs.

Information extracted from whole-nerve electroneurograms, recorded using electrode cuffs, can provide signals to neuroprostheses. However, the amount of information that can be extracted from a single tripole is limited. This communication demonstrates how previously unavailable information about the direction of action potential propagation and velocity can be obtained using a multi-electrode cuff and that the arrangement acts as a velocity-selective filter. Results from in vitro experiments on frog nerves are presented.

Action Potentials↗
PubMed1998

Can raters consistently evaluate the content of focus groups?

Focus groups are increasingly being used to provide insights to researchers and policy makers. These data complement quantitative approaches to understanding the world. Unfortunately, quantitative and qualitative methodologies have often been viewed as antithetical, rather than complementary, strategies. While focus groups can clearly generate rich information that is unobtainable through other quantitative methods, it is important to determine the degree to which different raters can consistently extract information from transcripts. Thus, our goal was to quantify agreement in the interpretation of transcripts from patient and physician focus groups, using decision-making in ischemic heart disease as a model. We used data from focus groups with both patients and physicians that sought to identify factors affecting diagnostic and treatment decisions in ischemic heart disease. Three raters independently reviewed transcribed audiotapes from focus groups of patients with ischemic heart disease, as well as focus groups of physicians who care for these patients. We found that raters could not distinguish between major and minor factors reliably. More troubling, however, is that consistency regarding the apparently straightforward judgment as to the mere presence or absence of a factor was difficult to achieve. In particular, the three raters of each transcript failed to agree on between one third and one half of the factors. This reasonably high level of disagreement occurred despite the raters: (1) having generated the individual factors themselves based upon their reading a random sample of actual transcripts and (2) being trained in the use of rating forms (including standard definitions of themes). These data suggest that if a single rater evaluates focus group transcripts, as is commonly done, judgments may not be reproducible by other raters. Moreover, a single rater may not extract all important information contained in the transcripts.

Female↗
PubMed1994

Artificial neural networks within medical decision support systems.

Artificial neural networks offer a way to actively assimilate both past and present knowledge, to extract information, to map correlations and to produce inferences from available data; all tasks which have relevance to the clinical laboratory. In this paper, we describe one useful artificial neural network technique, backpropagation, and describe some of the practical considerations which need to be taken account of when using such methods. Examples are presented of the application of artificial neural networks in medicine and, particularly, in clinical chemistry. The paper goes on to describe the use of these methods within medical decision support. We conclude that artificial neural networks are useful multivariate techniques which are well able to play an important role in a decision support system. Further, that their properties as function approximators could be utilised in other areas of clinical chemistry. We conclude by pointing out that the pattern recognition ability of artificial neural networks holds out the promise of extracting useful information from currently available data which is at present seen as being of little diagnostic utility.

Chemistry, Clinical↗
PubMed2002

Cell analysis system based on compact disk technology.

BACKGROUND: A cell analysis system was developed to enumerate and differentiate magnetically aligned cells selected from whole blood. The cellular information extracted is similar to the readout of musical information from a compact disk (CD). Here we describe the optical design and data processing of the system. The performance of the system is demonstrated using fluorescent-labeled cells and beads. Materials and Methods System performance was demonstrated with 6-microm polystyrene beads labeled with magnetic nanoparticles and allophycocyanin (APC) and immunomagnetically aligned leukocytes, fluorescently labeled with Oxazine750 and CD4-APC, CD8-Cy5.5, and CD14-APC/Cy7 in whole blood. RESULTS: The sensitivity of the system was demonstrated using APC-labeled beads. With this system, beads containing 333 APC molecules could easily be resolved from the background. This level of sensitivity was not achievable with a commercial flow cytometer. A maximum of 20,000 immunomagnetically labeled cells could be aligned and analyzed in between 0.6 m of Ni lines, distributed over a surface area of 18 mm(2) and extracted from a blood volume that depended on the height of the chamber. The utility of the system was demonstrated by performing a three-color CD4-CD8-CD14 assay. CONCLUSIONS: We built a cell analysis system based on immunomagnetic cell selection and alignment and analysis of fluorescent signals employing CD-technology that is as good or better than current commercial analyzers. The cell analysis can be performed in whole blood or any other type of cell suspension without extensive sample preparation.

Animals↗
PubMed2004

Gridline: automatic grid alignment in DNA microarray scans.

We present a new automatic grid alignment algorithm for detecting two-dimensional (2-D) arrays of spots in DNA microarray images. Our motivation for this work is the lack of automation in high-throughput microarray data analysis that leads to a) spatial inaccuracy of located spots and hence inaccuracy of extracted information from a spot and b) inconsistency of extracted features due to manual selection of grid alignment parameters. The proposed grid alignment algorithm is novel in the sense that 1) it can detect irregularly row- and column-spaced spots in a 2-D array, 2) it is independent of spot color and size, 3) it is general to localize a grid of other primitive shapes than the spot shapes, 4) it can perform grid alignment on any number of input channels, 5) it reduces the number of free parameters to minimum by data driven optimization of most algorithmic parameters, and 6) it has a built-in speed versus accuracy tradeoff mechanism to accommodate user's requirements on performance time and accuracy of the results. The developed algorithm also automatically identifies multiple blocks of 2-D arrays, as it is the case in microarray images, and compensates for grid rotations in addition to grid translations.

Algorithms↗
PubMed2003

Narrative electronic patient records as source of discharge diagnoses.

OBJECTIVE: To evaluate the consistency of diagnostic data extracted from narrative electronic patient record (EPR) notes compared with the data from a patient administrative system (PAS). To assess potential benefit of using EPR notes as source of diagnosis data and as basis for case identification. DESIGN: Construction of a computer algorithm to extract ICD-9 codes from narrative EPR notes. Assessment of consistency and reliability of the diagnostic codes retrieved from EPR notes and PAS. Estimation of efficiency of case identification based on data from PAS and EPR. RESULTS: Diagnosis codes were retrieved from PAS with sensitivity of 0.989 and the positive predictive value (PPV) was 0.993. Codes were retrieved from EPR with sensitivity of 0.908 and PPV of 0.990. Combining these two sources increased sensitivity to 0.999. CONCLUSION: Discharge diagnoses were easily extracted from narrative EPR notes by automatic methods. Information extracted from record notes was not significantly different from the corresponding data in PAS, but EPR was incomplete as compared with PAS. Utilizing data extracted from EPR improved case identification significantly.

Algorithms↗
PubMed2006

Combination of text-mining algorithms increases the performance.

MOTIVATION: Recently, several information extraction systems have been developed to retrieve relevant information out of biomedical text. However, these methods represent individual efforts. In this paper, we show that by combining different algorithms and their outcome, the results improve significantly. For this reason, CONAN has been created, a system which combines different programs and their outcome. Its methods include tagging of gene/protein names, finding interaction and mutation data, tagging of biological concepts and linking to MeSH and Gene Ontology terms. RESULTS: In this paper, we will present data that show that combining different text-mining algorithms significantly improves the results. Not only is CONAN a full-scale approach that will ultimately cover all of PubMed/MEDLINE, we also show that this universality has no effect on quality: our system performs as well as or better than existing systems. AVAILABILITY: The LDD corpus presented is available by request to the author. The system will be available shortly. For information and updates on CONAN please visit http://www.cs.uu.nl/people/rainer/conan.html.

Abstracting and Indexing↗
PubMed2002

E-cadherin mutations and hereditary gastric cancer: prevention by resection?

BACKGROUND: A small percentage of gastric cancers (1-3%) arise as a result of clearly identified inherited gastric cancer predisposition syndromes. Recently, linkage analysis has implicated E-cadherin (CDH1) mutations in a subset of dominantly inherited gastric cancers termed hereditary diffuse gastric cancer (HDGC). Heterozygotes with the CDH1 mutation have a 70-80% chance of developing gastric cancer and once patients have invasive, symptomatic disease there is a high associated morbidity and mortality. As a result prophylactic gastrectomy has been advocated for affected family members identified by genetic screening. There are many issues to be considered in order to determine whether prophylactic gastrectomy is the optimal management strategy for these patients. METHODS: A MEDLINE literature search was performed and combined with our own experience in order to identify relevant background information on hereditary gastric cancer. In particular we extracted information about prophylactic gastrectomy in HDGC patients. RESULTS: Once the decision has been undertaken to perform genetic testing, the therapeutic options are either endoscopic screening with the aim of identifying an early, curable lesion or prophylactic surgery. Two groups have published their data on prophylactically resected stomachs in asymptomatic patients from affected families. In these series all of the post-gastrectomy specimens had microscopic evidence of diffuse gastric cancer confined within the mucosal layer. These early cancers had not been identified by endoscopic surveillance. Technical issues surrounding the age at which to operate, the best operation to reduce the risk of post-operative complications and the risk of other cancers developing in other organs in these patients are still controversial. Long-term follow-up studies in specialist centres are required to resolve these issues. CONCLUSIONS: From the limited experience so far the estimated risk reduction of gastric cancer by gastrectomy is significant.

Cadherins↗
PubMed1994

Cisapride: a gastrointestinal prokinetic drug.

OBJECTIVE: To summarize the pharmacology, pharmacokinetics, efficacy, and safety of cisapride, and to evaluate its potential therapeutic role. DATA SOURCES: A computerized search of the MEDLINE database was used to identify English-language publications of cisapride data in humans. The MEDLINE search was supplemented by review article bibliographies. There was no attempt to limit the search to a specific gastrointestinal motility disorder. STUDY SELECTION: The MEDLINE search alone identified 165 citations. Because of the volume of available human cisapride data, the focus of the efficacy section is on complete published reports of controlled clinical studies. Abstracts and uncontrolled data are discussed only when other information is unavailable to address important aspects. DATA EXTRACTION: Information regarding study design, study population, results, and safety was recorded from each publication. The placebo response to gastrointestinal complaints in patients with motility disorders is high. Therefore, objective evidence of improvement was emphasized when documentation was available. DATA SYNTHESIS: Cisapride stimulates the motility of smooth muscle lining the esophagus, stomach, small intestine, and colon, and increases the tone of gut sphincters in vitro and in vivo. In controlled investigations, cisapride was superior to placebo in relieving symptoms associated with reflux esophagitis, nonulcer dyspepsia, and gastroparesis. Similar symptom and healing effects were observed with cisapride and histamine (H)2-antagonists in reflux esophagitis. Cisapride was either equal to or superior to metoclopramide in relieving reflux symptoms. However, metoclopramide was associated with significantly more central nervous system adverse effects. Cisapride was well tolerated, with adverse effects limited primarily to the gastrointestinal tract. CONCLUSIONS: Cisapride represents an attractive alternative to metoclopramide for the treatment of a variety of motility disorders. Because it addresses a primary underlying cause of reflux esophagitis, cisapride may also prove to be an effective alternative to acid suppressants in the management of this disorder.

Adult↗
PubMed2004

Identification of diesel front sound source based on continuous wavelet transform.

Acoustic signals from diesel engines contain useful information but also include considerable noise components. To extract information for condition monitoring purposes, continuous wavelet transform (CWT) is used for the characterization of engine acoustics. This paper first reviews CWT characteristics represented by short duration transient signals. Wavelet selection and CWT are then implemented and wavelet transform is used to analyze the major sources of the engine front's exterior radiation sound. The research provides a reliable basis for engineering practice to reduce vehicle sound level. Comparison of the identification results of the measured acoustic signals with the identification results of the measured surface vibration showed good agreement.

Algorithms↗
PubMed2004

Biomedical literature mining: challenges and solutions in the 'omics' era.

It is now obvious that the rate-limiting step in high throughput experimentation is neither data acquisition nor analysis, but rather our ability to interpret data on a genome-wide scale. Indeed, the explosion of data sampling capacity combined with increasing publication rates greatly impairs our ability to find meaning in vast collections of data. In order to support data interpretation, bioinformatic tools are needed to identify critical information contained in large bodies of literature. However, extracting knowledge embedded in free text is an arduous task, compounded in the biomedical field by an inconsistent gene nomenclature, domain-specific language and restricted access to full text articles. This paper presents a selection of currently available biomedical literature mining software. These tools rely on statistic and, more recently, semantic analyses (Natural Language Processing) to automatically extract information from the literature. In addition, a literature mining strategy has been developed to explore patterns of term occurrences in abstracts. This method automatically identifies relevant keywords in collections of abstracts, and uses a pattern discovery algorithm to generate a visual interface for exploring functional associations among genes. Term occurrence heatmaps can also be combined with gene expression profiles to provide valuable functional annotations. Furthermore, as demonstrated with tumor cell line literature profiling results, this approach can be applied to a variety of themes beyond genomic data analysis. Altogether, these examples illustrate how literature analysis can be employed to support knowledge discovery in biomedical research.

Algorithms↗
PubMed1998

Can the patient's memory of the timing of pain events replace chart notes?

The reliability of the patient's memory as to when pain remitted and relapsed was studied ten years after knee replacement. Pain was chosen because it is the most frequent spontaneous patient complaint, and the remission and relapse points in time are clinically important. The standard for the comparison was information extracted from the medical records. The patient's information on the time of remission of pain could not be trusted. For relapse there was a fair but insufficient association (Spearman's correlation coefficient + 0.51).

Adult↗