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PubMed2006

Using argumentation to extract key sentences from biomedical abstracts.

PROBLEM: key word assignment has been largely used in MEDLINE to provide an indicative "gist" of the content of articles and to help retrieving biomedical articles. Abstracts are also used for this purpose. However with usually more than 300 words, MEDLINE abstracts can still be regarded as long documents; therefore we design a system to select a unique key sentence. This key sentence must be indicative of the article's content and we assume that abstract's conclusions are good candidates. We design and assess the performance of an automatic key sentence selector, which classifies sentences into four argumentative moves: PURPOSE, METHODS, RESULTS and CONCLUSION METHODS: we rely on Bayesian classifiers trained on automatically acquired data. Features representation, selection and weighting are reported and classification effectiveness is evaluated on the four classes using confusion matrices. We also explore the use of simple heuristics to take the position of sentences into account. Recall, precision and F-scores are computed for the CONCLUSION class. For the CONCLUSION class, the F-score reaches 84%. Automatic argumentative classification using Bayesian learners is feasible on MEDLINE abstracts and should help user navigation in such repositories.

Abstracting and Indexing↗
PubMed2006

Healthcare practice ISOlation: articulating systems that drift toward higher quality.

Can higher quality healthcare practices emerge from the development and use of a loosely integrated set of intranets? This paper examines that question through a series of empirical examples that draw on data from one healthcare organization that was part of a multi-year, multi-industry study of intranets. Some of this organization's intranets link clinical practice guidelines to healthcare delivery, in ways that mimic manufacturing sector efforts to improve product quality and reliability. Others act as staging grounds and information repositories for coordinating responses to new rulings and changing interpretations of how to implement recently enacted healthcare legislation. This activity is reminiscent of coordinated responses, among firms and their legal counsel, to new legislation in other industries, like telecommunications; and to wide-reaching regulatory efforts, like environmental protection. Although the technologies have changed and the legislative objectives vary greatly, organizational approaches to such improvements are less varied. Ironically, these overarching similarities focus attention on the need for continued articulation of changes and local differences in information system use, and the ability of boundary-spanners to introduce ways of working that bridge these gaps and refine healthcare practices that drift toward higher quality.

Computer Communication Networks↗
PubMed2006

An e-consent-based shared EHR system architecture for integrated healthcare networks.

OBJECTIVES: Virtual integration of distributed patient data promises advantages over a consolidated health record, but raises questions mainly about practicability and authorization concepts. Our work aims on specification and development of a virtual shared health record architecture using a patient-centred integration and authorization model. METHODS: A literature survey summarizes considerations of current architectural approaches. Complemented by a methodical analysis in two regional settings, a formal architecture model was specified and implemented. RESULTS: Results presented in this paper are a survey of architectural approaches for shared health records and an architecture model for a virtual shared EHR, which combines a patient-centred integration policy with provider-oriented document management. An electronic consent system assures, that access to the shared record remains under control of the patient. A corresponding system prototype has been developed and is currently being introduced and evaluated in a regional setting. CONCLUSION: The proposed architecture is capable of partly replacing message-based communications. Operating highly available provider repositories for the virtual shared EHR requires advanced technology and probably means additional costs for care providers. Acceptance of the proposed architecture depends on transparently embedding document validation and digital signature into the work processes. The paradigm shift from paper-based messaging to a "pull model" needs further evaluation.

Computer Communication Networks↗
PubMed2004

A primer on gene expression and microarrays for machine learning researchers.

Data originating from biomedical experiments has provided machine learning researchers with an important source of motivation for developing and evaluating new algorithms. A new wave of algorithmic development has been initiated with the publication of gene expression data derived from microarrays. Microarray data analysis is particularly challenging given the large number of measurements (typically in the order of thousands) that are reported for relatively few samples (typically in the order of dozens). Many data sets are now available on the web. It is important that machine learning researchers understand how data are obtained and which assumptions are necessary in the analysis. Microarray data have the potential to cause significant impact in machine learning research, not just as a rich and realistic source of cases for testing new algorithms, as has been the UCI machine learning repository in the past decades, but also as a main motivation for their development. In this article, we briefly review the biology underlying microarrays, the process of obtaining gene expression measurements, and the rationale behind the common types of analyses involved in a microarray experiment. We outline the main challenges and reiterate critical considerations regarding the construction of supervised learning models that use this type of data. The goal of this article is to familiarize machine learning researchers with data originated from gene expression microarrays.

Algorithms↗
PubMed2004

Discovering significant and interpretable patterns from multifactorial DNA microarray data with poor replication.

MOTIVATION: Multivariate analyses are advantageous for the simultaneous testing of the separate and combined effects of many variables and of their interactions. In factorial designs with many factors and/or levels, however, sufficient replication is often prohibitively costly. Furthermore, complicated statements are often required for the biological interpretation of the higher-order interactions determined by standard statistical techniques like analysis of variance. RESULTS: Because we are usually interested in finding factor-specific effects or their interactions, we assumed that the observed expression profile of a gene is a manifestation of an underlying factor-specific generative pattern (FSGP) combined with noise. Thus, a genetic algorithm was created to find the nearest FSGP for each expression profile. We then measured the distance between each profile and the corresponding nearest FSGP. Permutation testing for the distance measures successfully identified those genes with statistically significant profiles, thus yielding straightforward biological interpretations. Association networks of genes, drugs, and cell lines were created as tripartite graphs, representing significant and interpretable relations, by using a microarray experiment of gastric-cancer cell lines with a factorial design and no replication. The proposed method may benefit the combined analysis of heterogeneous expression data from the growing public repositories.

Algorithms↗
PubMed2005

Discrimination and calibration of mortality risk prediction models in interventional cardiology.

OBJECTIVES: Using a local percutaneous coronary intervention (PCI) data repository, we sought to compare the performance of a number of local and well-known mortality models with respect to discrimination and calibration. BACKGROUND: Accurate risk prediction is important for a number of reasons including physician decision support, quality of care assessment, and patient education. Current evidence on the value of applying PCI risk models to individual cases drawn from a different population is controversial. METHODS: Data were collected from January 01, 2002 to September 30, 2004 on 5216 consecutive percutaneous coronary interventions at Brigham and Women's Hospital (Boston, MA). Logistic regression was used to create a local risk model for in-hospital mortality in these procedures, and a number of statistical methods were used to compare the discrimination and calibration of this new and old local risk models, as well as the Northern New England Cooperative Group, New York State (1992 and 1997), University of Michigan consortium, American College of Cardiology-National Cardiovascular Data Registry, and The Cleveland Clinic Foundation risk prediction models. Areas under the ROC (AUC) curves were used to evaluate discrimination, and the Hosmer-Lemeshow (HL) goodness-of-fit test and calibration curves assessed applicability of the models to individual cases. RESULTS: Multivariate risk factors included in the newly constructed local model were: age, prior intervention, diabetes, unstable angina, salvage versus elective procedure, cardiogenic shock, acute myocardial infarction (AMI), and left anterior descending artery intervention. The area under the ROC curve (AUC) was 0.929 (SE=0.017), and the p value for the Hosmer-Lemeshow (HL) goodness-of-fit was 0.473. This indicates good discrimination and calibration. Bootstrap re-sampling indicated AUC stability. Evaluation of the external models showed an AUC range from 0.82 to 0.90 indicating good discrimination across all models, but poor calibration (HL p value < or = 0.0001). CONCLUSIONS: Validation of AUC values across all models suggests that certain risk factors have remained important over the last decade. However, the lack of calibration suggests that small changes in patient populations and data collection methods quickly reduce the accuracy of patient level estimations over time. Possible solutions to this problem involve either recalibration of models using local data or development of new local models.

Angioplasty, Balloon, Coronary↗
PubMed2005

Towards new information resources for public health--from WordNet to MedicalWordNet.

In the last two decades, WordNet has evolved as the most comprehensive computational lexicon of general English. In this article, we discuss its potential for supporting the creation of an entirely new kind of information resource for public health, viz. MedicalWordNet. This resource is not to be conceived merely as a lexical extension of the original WordNet to medical terminology; indeed, there is already a considerable degree of overlap between WordNet and the vocabulary of medicine. Instead, we propose a new type of repository, consisting of three large collections of (1) medically relevant word forms, structured along the lines of the existing Princeton WordNet; (2) medically validated propositions, referred to here as medical facts, which will constitute what we shall call MedicalFactNet; and (3) propositions reflecting laypersons' medical beliefs, which will constitute what we shall call the MedicalBeliefNet. We introduce a methodology for setting up the MedicalWordNet. We then turn to the discussion of research challenges that have to be met to build this new type of information resource. We build a database of sentences relevant to the medical domain. The sentences are generated from WordNet via its relations as well as from medical statements broken down into elementary propositions. Two subcorpora of sentences are distinguished, MedicalBeliefNet and MedicalFactNet. The former is rated for assent by laypersons; the latter for correctness by medical experts. The sentence corpora will be valuable for a variety of applications in information retrieval as well as in research in linguistics and psychology with respect to the study of expert and non-expert beliefs and their linguistic expressions. Our work has to meet several considerable challenges. These include accounting for the distinction between medical experts and laypersons, the social issues of expert-layperson communication in different media, the linguistic aspects of encoding medical knowledge, and the reliability, volume, and emergence of medical knowledge. The work described here has been tested in a small pilot experiment and awaits large-scale implementation.

Computational Biology↗
PubMed2006

Inter-patient distance metrics using SNOMED CT defining relationships.

BACKGROUND: Patient-based similarity metrics are important case-based reasoning tools which may assist with research and patient care applications. Ontology and information content principles may be potentially helpful tools for similarity metric development. METHODS: Patient cases from 1989 through 2003 from the Columbia University Medical Center data repository were converted to SNOMED CT concepts. Five metrics were implemented: (1) percent disagreement with data as an unstructured "bag of findings," (2) average links between concepts, (3) links weighted by information content with descendants, (4) links weighted by information content with term prevalence, and (5) path distance using descendants weighted by information content with descendants. Three physicians served as gold standard for 30 cases. RESULTS: Expert inter-rater reliability was 0.91, with rank correlations between 0.61 and 0.81, representing upper-bound performance. Expert performance compared to metrics resulted in correlations of 0.27, 0.29, 0.30, 0.30, and 0.30, respectively. Using SNOMED axis Clinical Findings alone increased correlation to 0.37. CONCLUSION: Ontology principles and information content provide useful information for similarity metrics but currently fall short of expert performance.

Algorithms↗
PubMed2003

Treatment of radioactive wastes: an X-ray absorption spectroscopy study of the reaction of technetium with green rust.

Technetium is a long-lived product of nuclear fission that readily forms the soluble pertechnetate anion [TcO(4)](-). Green rusts (layered hydrous oxides containing both Fe(II) and Fe(III) and with interlayer sulfate or carbonate anions) concentrate >99.8% of 99Tc, present as [TcO(4)](-), from aqueous solution, even in the presence of high concentrations of NaNO(3), a common constituent of radioactive waste streams. The mechanism of removal from solution is apparently reduction and formation of strong Tc(IV) surface complexes. X-ray absorption spectroscopy shows that [TcO(4)](-) is indeed reduced by reaction with both sulfate- and carbonate-form green rusts and is found in a TcO(2)-like environment. On contact with air, the green rusts oxidize to poorly crystalline goethite but the Tc environment is unchanged. There is no increase in Tc solubility associated with oxidation of the host green rust. This behavior suggests that green rusts may be useful in the treatment of Tc-containing waste streams, in groundwater cleanup, and in restricting Tc migration from repositories.

Journal Article↗
PubMed2004

A triple-continuum approach for modeling flow and transport processes in fractured rock.

This paper presents a triple-continuum conceptual model for simulating flow and transport processes in fractured rock. Field data collected from the unsaturated zone of Yucca Mountain, a repository site of high-level nuclear waste, show a large number of small-scale fractures. The effect of these small fractures has not been considered in previous modeling investigations within the context of a continuum approach. A new triple-continuum model (consisting of matrix, small-fracture, and large-fracture continua) has been developed to investigate the effect of these small fractures. This paper derives the model formulation and discusses the basic triple-continuum behavior of flow and transport processes under different conditions, using both analytical solutions and numerical approaches. The simulation results from the site-scale model of the unsaturated zone of Yucca Mountain indicate that these small fractures may have an important effect on radionuclide transport within the mountain.

Geological Phenomena↗
PubMed2006

A temperature-profile method for estimating flow in geologic heat pipes.

Above-boiling temperature conditions, as encountered, for example, in geothermal reservoirs and in geologic repositories for the storage of heat-producing radioactive wastes, may induce strong liquid and gas flow processes in porous subsurface environments. The magnitude of these flow processes is extremely hard to measure in the field. We therefore propose a simple temperature-profile method that uses high-resolution temperature data for deriving such information. The energy that is transmitted with the vapor and water flow creates a nearly isothermal zone maintained at about the boiling temperature, referred to as a heat pipe. Characteristic features of measured temperature profiles, such as the differences in the gradients inside and outside of the heat-pipe regions, are used to derive the approximate magnitude of the liquid and gas fluxes in the subsurface.

Air Movements↗
PubMed2005

Growth factor deposition in anterior subcapsular cataract.

PURPOSE: To characterize immunohistochemically the distribution of growth factors and extracellular matrix (ECM) components in an anterior subcapsular cataract (ASC) and to determine the role of growth factors in the development of ASC. SETTING: Department of Ophthalmology, Wakayama Medical University, Wakayama, Japan. METHODS: During cataract surgery in 22 patients, anterior capsules with an ASC were obtained. Sections of each specimen were immunostained with a panel of antibodies against ECM components, growth factors, cytoskeletal components, and signal transduction-related molecules. RESULTS: Collagen types I, V, and VI; fibronectin; fibrillin-1; and latent transforming growth factor beta binding protein-1 (LTBP-1) were localized to the ECM in ASC tissues. Collagen IV was localized to the ECM and the capsule. Lens epithelial cells (LECs) were positive for alpha-smooth muscle actin (alphaSMA). Lens epithelial cells and ECM stained for transforming growth factor beta2 (TGFbeta2) and TGFbeta3 in all samples, but TGFbeta1 latency-associated peptide (TGFbeta1-LAP) were detected in some samples. Fibroblast growth factor-2 (FGF-2) and hepatocyte growth factor-alpha (HGF-alpha) were localized to the ECM. Lens epithelial cells with nuclear staining for Erk-1, the mitogen-activated protein kinase (MAP kinase) cascade-related molecule, and Smad3, 1 of the Smad family members involving TGFbeta signaling, were detected. CONCLUSIONS: Matrix components (ie, collagen types, fibronectin, fibrillin-1), as well as growth factors such as TGFbeta1-LAP, TGFbeta2, TGFbeta3, FGF-2, and HGF-alpha, were detected in ASC. Fibrillin-1 might serve as a repository for TGFbetas. These growth factors may modulate the phenotypic alteration and behavior of LECs. The MAP kinase cascade and TGFbeta signaling are both activated in LECs in ASC.

Adult↗
PubMed2006

Quantitative analysis of HBsAg, IgM anti-HBc and anti-HBc avidity in acute and chronic hepatitis B.

BACKGROUND AND OBJECTIVES: We evaluated hepatitis B virus (HBV) serological markers by novel, quantitative immunoassays in order to study their behaviours and possible role in the various phases of HBV infection. STUDY DESIGN: The quantitative determination of HBsAg and anti-HBc/IgM by chemiluminescent immunoassays (Abbott Architect) and the calculation of anti-HBc avidity index have been carried out on repository specimens from patients with acute or chronic hepatitis B. RESULTS: In acute hepatitis the levels of HBsAg were generally >10,000 UI/mL and decreased sharply in the recovery phase. In 35 anti-HBe-positive chronic hepatitis cases HBsAg levels were generally lower than 10,000 UI/mL (mean: 2655), whereas in five HBeAg-positive chronic hepatitis patients the mean value was 78,756 UI/mL and 90% of specimens exceeded 10,000 UI/mL. The lowest values (mean: 1029 IU/mL) were found in the seven patients with minimal hepatic damage. IgM anti-HBc antibodies were positive in all acute cases and in 68/207 samples (32.85%) from patients with chronic hepatitis, with significantly lower levels (average sample/cutoff (S/CO) ratio: 2.95 in chronic cases versus 25.96 in acute cases; p<0.005). A S/CO value of 10 for anti-HBc IgM had a 100% negative predictive value and a 99.13% positive predictive value for acute hepatitis B. The study of anti-HBc avidity by an experimental procedure showed that an avidity index (AI) threshold of 0.7 had a good efficacy to discriminate the cases of chronic hepatitis, among whom only 2 specimens out of 193 (1.04%) had an AI<0.7. CONCLUSION: The quantitative determination of HBsAg, anti-HBc/IgM and anti-HBc avidity provides additional information and may be useful in the differential diagnosis of acute and chronic HBV infections and in the follow-up of chronically infected patients.

Acute Disease↗
PubMed2005

Interdisciplinary resources optimize Evidence-Based Dental Practice.

Evidence-Based Dental Practice (EBDP) is the most appropriate and best patient-centered care because it uses the evidence derived from interdisciplinary resources. These resources include the integration of the clinical and basic science researcher, clinician, and patient in the clinical decision-making process. Best evidence has different meanings to each of the interdisciplinary decision makers and, thus, defines their individual roles accordingly. Implementing EBDP requires an organizational structure and process that involve evidence-based dentistry databases in centralized repositories that are shared nationally and internationally. Facilitating the inclusive and reciprocal transfer of information from all resources requires use of information technology and computerized decision-making support programs. However, the potential lack of financial resources and incentives will diminish the universal adoption of EBDP.

Journal Article↗
PubMed2003

State of the art techniques for preservation and reuse of hard copy electrocardiograms.

Baseline examinations and periodic reexaminations in longitudinal population studies, together with ongoing surveillance for morbidity and mortality, provide unique opportunities for seeking ways to enhance the value of electrocardiography (ECG) as an inexpensive and noninvasive tool for prognosis and diagnosis. We used newly developed optical ECG waveform recognition (OEWR) technique capable of extracting raw waveform data from legacy hard copy ECG recording. Hardcopy ECG recordings were scanned and processed by the OEWR algorithm. The extracted ECG datasets were formatted into a newly proposed, vendor-neutral, ECG XML data format. Oracle database was used as a repository for ECG records in XML format. The proposed technique for XML encapsulation of OEWR processed hard copy records resulted in an efficient method for inclusion of paper ECG records into research databases, thus providing their preservation, reuse and accession.

Algorithms↗
PubMed2005

"Reference Biospheres" for solid radioactive waste disposal: the BIOMASS methodology.

The BIOMASS Theme 1 project has developed a methodology for the logical and defensible construction of 'assessment biospheres': mathematical representations of biospheres used in the total system performance assessment of radioactive waste disposal. The BIOMASS Methodology provides a systematic approach to decision making, including decisions on how to address biosphere change. The BIOMASS Methodology was developed through consultation and collaboration with many relevant organisations, including regulators, operators and a variety of independent experts. It has been developed to be practical and to be consistent with recommendations from ICRP and IAEA on radiation protection in the context of the disposal of long-lived solid radioactive wastes. The five main steps in the methodology are described in this paper. The importance of a clear assessment context, to clarify intentions and to support a coherent biosphere assessment process within an overall repository performance assessment, is strongly emphasised. A well described assessment context is an important tool for ensuring consistency across the performance assessment as a whole. The use of interaction matrices has been found to be helpful in clarifying the interactions between different habitats within the biosphere system and the significant radionuclide transfer pathways within the biosphere system. Matrices also provide a useful means of checking for consistency.

Program Development↗
PubMed2005

Consideration of environmental change in performance assessments.

Depending on the particular circumstances in which a post-closure performance assessment of a radioactive waste repository is made, it may be appropriate to follow simple or more complex approaches in characterising the biosphere. Several different Example Reference Biospheres were explored in BIOMASS Theme 1 to address a range of issues that arise. Here, consideration is given to Example Reference Biospheres relevant to representing the implications of changes that may occur within the biosphere system during the period over which releases of radionuclides from a disposal facility might take place. Mechanisms of change considered include those extrinsic and intrinsic to the system of interest. An overall methodology for incorporating environmental change into assessments is proposed. This includes screening of primary mechanisms of change; identification of possible time sequences of change; development of a coherent description of the regional landscape response for each time sequence; integration of source term and geosphere-biosphere interface information; identification and description of one or more time series of assessment biospheres; and evaluation of the advantages and disadvantages of simulating the effects of sequences of biosphere systems and the transitions between them, or of defining a set of biosphere systems to be represented individually in a non-sequential analysis. The usefulness of the methodology is explored in two site-specific examples and one generic example.

Climate↗
PubMed2004

The effect of sulfate-reducing bacteria on adsorption of 137Cs by soils from arid and tropical regions.

Soils from different climatic regions of Australia were studied to determine their adsorption of (137)Cs, and the effect of microbial sulfate reduction on this adsorption. The soils consisted of a surface and regolith samples from the site of a proposed low and intermediate level radioactive waste repository in arid South Australia, and two red earth loam soils from an experimental plot in the tropical Northern Territory. The process of bacterial sulfate reduction substantially decreased the adsorption of (137)Cs to the arid and tropical soils, although extended incubation resulted in greater adsorption to the regolith sample. This could have implications for the mobility of radionuclides entering these soil ecosystems.

Adsorption↗