Converting clinical data into information: mapping operational hospital data into a time-oriented clinical repository.
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Hospital Information Systems↗
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The beta- and delta-thalassemia repository (7th edition).
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Globins↗
Analysis of the candidate gene NRAMP1 in the first 61 ARC National Repository families for rheumatoid arthritis.
Maximum likelihood identity-by-descent (IBD) sib pair analysis using a 3 locus haplotype NRAMP1-IL8RB-VIL1, or NRAMP1 alone, provided preliminary evidence (maximum LOD score = 1.01, p = 0.024) for a gene in this region of human chromosome 2q35 contributing to susceptibility to rheumatoid arthritis (RA). Candidacy for NRAMP1 as the disease susceptibility gene was supported by a significant bias (p < 0.048) toward transmission of the NRAMP1 promoter region allele 3 in affected offspring.
Alleles↗
Internet access to a medical case repository for teaching and analysis.
The acute radiation syndrome is a rare disease. Teaching its treatment and the achievement of scientific progress require a sufficient number of accessible case histories. An information system for standardized recording of acute radiation syndrome case histories has been established in the framework of the World Health Organization Radiation Medical Emergency Preparedness and Assistance Network Centers. The information system has been realized in client/server architecture. The centers are able to access the database by easy to use graphical user interfaces via the Internet. Focusing on optimization of network traffic and flexible information retrieval the hypertext transfer protocol has not been applied. At the moment the system is tested on the campus of the University of Ulm before it will be installed at the other centers.
Acute Disease↗
Using computer modeling to help identify patient subgroups in clinical data repositories.
OBJECTIVE: The ability to accurately and efficiently identify patient cases of interest in a hospital information system has many important clinical, research, educational and administrative uses. The identification of cases of interest sometimes can be difficult. This paper describes a two-stage method for searching for cases of interest. DESIGN: First, a Boolean search is performed using coded database variables. The user classifies the retrieved cases as being of interest or not. Second, based on the user-classified cases, a computer model of the patient cases of interest is constructed. The model is then used to help locate additional cases. These cases provide an augmented training set for constructing a new computer model of the cases of interest. This cycle of modeling and user classification continues until halted by the user. MEASUREMENTS: This paper describes a pilot study in which this method is used to identify the records of patients who have venous thrombosis. RESULTS: The results indicate that computer modeling enhances the identification of patient cases of interest.
Bayes Theorem↗
Scaling an expert system data mart: more facilities in real-time.
Clinical Data Repositories are being rapidly adopted by large healthcare organizations as a method of centralizing and unifying clinical data currently stored in diverse and isolated information systems. Once stored in a clinical data repository, healthcare organizations seek to use this centralized data to store, analyze, interpret, and influence clinical care, quality and outcomes. A recent trend in the repository field has been the adoption of data marts--specialized subsets of enterprise-wide data taken from a larger repository designed specifically to answer highly focused questions. A data mart exploits the data stored in the repository, but can use unique structures or summary statistics generated specifically for an area of study. Thus, data marts benefit from the existence of a repository, are less general than a repository, but provide more effective and efficient support for an enterprise-wide data analysis task. In previous work, we described the use of batch processing for populating data marts directly from legacy systems. In this paper, we describe an architecture that uses both primary data sources and an evolving enterprise-wide clinical data repository to create real-time data sources for a clinical data mart to support highly specialized clinical expert systems.
Computer Systems↗
Microbiology in nuclear waste disposal: interfaces and reaction fronts.
It is now generally acknowledged that microbial populations will be present within nuclear waste repositories and that the consequences of such activity on repository performance must be assessed. Various modelling approaches--based either on mass balance/thermodynamics or on kinetics--have been developed to provide scoping estimates of the possible development of these populations. Past work has focused on particular areas of the repository which can be considered relatively homogeneous and hence can be represented by some kind of 'box' or 'mixing tank'. In reality, however, waste repositories include a range of engineering materials (steel, concrete, etc.) which are emplaced at depth in a rock formation. Strong chemical gradients--of the type which may be exploited by lithoautotrophic microbial populations--are likely to be found at the contacts between different materials and at the interface between the engineered structures and the host rock. Over the long timescales considered, solute transport processes will cause the locations of strong chemical gradients to move, forming reaction fronts. The high-pH plume resulting from the leaching of cement/concrete in some repository types is a particularly important example of such a reaction front. Redox fronts, which may occur in different areas of all kinds of repositories, also play an important role and would be locations where microbial activity is likely to be significant. In this paper, the key microbial processes expected at (or around) interfaces and fronts will be discussed, with particular emphasis on the development of quantitative models. The applicability of the models used wil be tested by considering similar fronts which can be found in natural systems.
Biodegradation, Environmental↗
Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it.
BACKGROUND: The proliferation of data repositories in bioinformatics has resulted in the development of numerous interfaces that allow scientists to browse, search and analyse the data that they contain. Interfaces typically support repository access by means of web pages, but other means are also used, such as desktop applications and command line tools. Interfaces often duplicate functionality amongst each other, and this implies that associated development activities are repeated in different laboratories. Interfaces developed by public laboratories are often created with limited developer resources. In such environments, reducing the time spent on creating user interfaces allows for a better deployment of resources for specialised tasks, such as data integration or analysis. Laboratories maintaining data resources are challenged to reconcile requirements for software that is reliable, functional and flexible with limitations on software development resources. RESULTS: This paper proposes a model-driven approach for the partial generation of user interfaces for searching and browsing bioinformatics data repositories. Inspired by the Model Driven Architecture (MDA) of the Object Management Group (OMG), we have developed a system that generates interfaces designed for use with bioinformatics resources. This approach helps laboratory domain experts decrease the amount of time they have to spend dealing with the repetitive aspects of user interface development. As a result, the amount of time they can spend on gathering requirements and helping develop specialised features increases. The resulting system is known as Pierre, and has been validated through its application to use cases in the life sciences, including the PEDRoDB proteomics database and the e-Fungi data warehouse. CONCLUSION: MDAs focus on generating software from models that describe aspects of service capabilities, and can be applied to support rapid development of repository interfaces in bioinformatics. The Pierre MDA is capable of supporting common database access requirements with a variety of auto-generated interfaces and across a variety of repositories. With Pierre, four kinds of interfaces are generated: web, stand-alone application, text-menu, and command line. The kinds of repositories with which Pierre interfaces have been used are relational, XML and object databases.
Computational Biology↗
Modelling of geochemical reactions and experimental cation exchange in MX 80 bentonite.
Bentonites are widely used for waste repository systems because of their hydrodynamic, surface and chemical-retention properties. MX 80 bentonite (bentonite of Wyoming) contains approximately 85% Na/Ca-montmorillonite and 15% accessory minerals. The dominant presence of Na/Ca-montmorillonite in this clay mineral could cause it to perform exceptionally well as an engineered barrier for a radioactive waste repository because this buffer material is expected to fill up by swelling the void between canisters containing waste and the surrounding ground. However, the Na/Ca-montmorillonite could be transformed to other clay minerals as a function of time under repository conditions. Previous modelling studies based on the hydrolysis reactions have shown that the Na/Ca-montmorillonite-to-Ca-montmorillonite conversion is the most significant chemical transformation. In fact, this chemical process appears to be a simple cation exchange into the engineered barrier. The purpose of the present study was two-fold. Firstly, it was hoped to predict the newly formed products of bentonite-fluid reactions under repository conditions by applying a thermokinetic hydrochemical code (KIRMAT: Kinetic Reactions and Mass Transport). The system modelled herein was considered to consist of a 1-m thick zone of water-saturated engineered barrier. This non-equilibrated system was placed in contact with a geological fluid on one side, which was then allowed to diffuse into the barrier, while the other side was kept in contact with iron-charged water. Reducing initial conditions ( [P(O)2 approximately equals 0] ; Eh=-200 mV) and a constant reaction temperature (100 degrees C) were considered. Secondly, it was hoped to estimate the influence of inter-layer cations (Ca and Na) on the swelling behaviour of the MX 80 bentonite by using an isothermal system of water vapour adsorption and an environmental scanning electron microscope (ESEM) coupled with a digital image analysis (DIA) program. Here, the MX 80 bentonite was previously treated with concentrated solutions (1N) of calcium and sodium chlorides. The results confirmed that the Na/Ca-montmorillonite-to-Ca-montmorillonite conversion was the main chemical transformation in the bentonite barrier under repository conditions. A simplified method (based on volume balance) has shown that the swelling capacity of the engineered barrier would be slightly affected after 1000 years of diffusion-reaction because the volume of neo-formed swelling clays is almost directly proportional to the volume of transformed initial-montmorillonite. Minimal neo-formation of saponites, vermiculites and chlorites was also observed. In addition, an isothermal system of water adsorption and ESEM-DIA methods showed that in the raw-bentonite-to-Ca-bentonite exchange there is a small decrease in the amount of adsorbed water and the swelling potential.
Adsorption↗
The saturated zone at Yucca Mountain: an overview of the characterization and assessment of the saturated zone as a barrier to potential radionuclide migration.
The US Department of Energy is pursuing Yucca Mountain, Nevada, for the development of a geologic repository for the disposal of spent nuclear fuel and high-level radioactive waste, if the repository is able to meet applicable radiation protection standards established by the US Nuclear Regulatory Commission and the US Environmental Protection Agency (EPA). Effective performance of such a repository would rely on a number of natural and engineered barriers to isolate radioactive waste from the accessible environment. Groundwater beneath Yucca Mountain is the primary medium through which most radionuclides might move away from the potential repository. The saturated zone (SZ) system is expected to act as a natural barrier to this possible movement of radionuclides both by delaying their transport and by reducing their concentration before they reach the accessible environment. Information obtained from Yucca Mountain Site Characterization Project activities is used to estimate groundwater flow rates through the site-scale SZ flow and transport model area and to constrain general conceptual models of groundwater flow in the site-scale area. The site-scale conceptual model is a synthesis of what is known about flow and transport processes at the scale required for total system performance assessment of the site. This knowledge builds on and is consistent with knowledge that has accumulated at the regional scale but is more detailed because more data are available at the site-scale level. The mathematical basis of the site-scale model and the associated numerical approaches are designed to assist in quantifying the uncertainty in the permeability of rocks in the geologic framework model and to represent accurately the flow and transport processes included in the site-scale conceptual model. Confidence in the results of the mathematical model was obtained by comparing calculated to observed hydraulic heads, estimated to measured permeabilities, and lateral flow rates calculated by the site-scale model to those calculated by the regional-scale flow model. In addition, it was confirmed that the flow paths leaving the region of the potential repository are consistent with those inferred from gradients of measured head and those independently inferred from water-chemistry data. The general approach of the site-scale SZ flow and transport model analysis is to calculate unit breakthrough curves for radionuclides at the interface between the SZ and the biosphere using the three-dimensional site-scale SZ flow and transport model. Uncertainties are explicitly incorporated into the site-scale SZ flow and transport abstractions through key parameters and conceptual models.
Forecasting↗
Experimental and numerical simulation of dissolution and precipitation: implications for fracture sealing at Yucca Mountain, Nevada.
Plugging of flow paths caused by mineral precipitation in fractures above the potential repository at Yucca Mountain, Nevada could reduce the probability of water seeping into the repository. As part of an ongoing effort to evaluate thermal-hydrological-chemical (THC) effects on flow in fractured media, we performed a laboratory experiment and numerical simulations to investigate mineral dissolution and precipitation under anticipated temperature and pressure conditions in the repository. To replicate mineral dissolution by vapor condensate in fractured tuff, water was flowed through crushed Yucca Mountain tuff at 94 degrees C. The resulting steady-state fluid composition had a total dissolved solids content of about 140 mg/l; silica was the dominant dissolved constituent. A portion of the steady-state mineralized water was flowed into a vertically oriented planar fracture in a block of welded Topopah Spring Tuff that was maintained at 80 degrees C at the top and 130 degrees C at the bottom. The fracture began to seal with amorphous silica within 5 days.A 1-D plug-flow numerical model was used to simulate mineral dissolution, and a similar model was developed to simulate the flow of mineralized water through a planar fracture, where boiling conditions led to mineral precipitation. Predicted concentrations of the major dissolved constituents for the tuff dissolution were within a factor of 2 of the measured average steady-state compositions. The mineral precipitation simulations predicted the precipitation of amorphous silica at the base of the boiling front, leading to a greater than 50-fold decrease in fracture permeability in 5 days, consistent with the laboratory experiment.These results help validate the use of a numerical model to simulate THC processes at Yucca Mountain. The experiment and simulations indicated that boiling and concomitant precipitation of amorphous silica could cause significant reductions in fracture porosity and permeability on a local scale. However, differences in fluid flow rates and thermal gradients between the experimental setup and anticipated conditions at Yucca Mountain need to be factored into scaling the results of the dissolution/precipitation experiments and associated simulations to THC models for the potential Yucca Mountain repository.
Chemical Precipitation↗
Near-surface disposal of concentrated NORM wastes.
Naturally occurring radioactive material (NORM) in concentrated forms arises in nature and in industry where natural radioisotopes become mobile and then accumulate at particular sites. In industry this often occurs in an acidic environment, where precipitates containing radionuclides plate out onto pipe walls, filters, tank linings, etc. As the radionuclides are selectively deposited, they build up and there is a multiplying effect in terms of the radioactivity concentration. Conditions often tend to favour the build-up of radium, particularly when barium is present and can cause the co-precipitation of radium compounds. As radium is highly radiotoxic, the handling and disposal of such material requires careful management. The state of Western Australia currently has the only low level waste repository in Australia, located at Mt Walton East. To date this repository has been used predominantly to dispose of packaged radioactive waste containing artificial radioisotopes, but there is an increasing demand for the repository to accept bulk concentrated NORM wastes from mining and related industries. Already steelwork from a dismantled phosphoric acid plant and other items contaminated with NORM have been disposed of. The Mt Walton East repository is now proposed as the disposal site for 6000 tonnes per annum of gangue residue from the processing of monazite. The residue contains thorium and a small amount of radium. This paper looks at the technical and related considerations of these disposal operations.
Environmental Exposure↗
Regional mapping panels for human chromosomes 1, 2, and 7.
The NIGMS Human Genetic Cell Repository has assembled regional mapping panels for human chromosomes 1, 2, and 7 from human rodent somatic cell hybrids submitted to the collection by researchers from 14 different laboratories. All hybrids were characterized initially by the submitters and verified by the Repository. Each hybrid carries a stable defined human segment as a derivative or deletion chromosome. These panels define 8-10 intervals for each chromosome. The panel for chromosome 2 is a new resource. The panels for chromosomes 1 and 7 complement previously published panels. The Repository distributes these regional mapping panels as cell cultures or as DNA. Information about these panels as well as for panels for chromosomes 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 22, and X may be viewed in the NIGMS Repository electronic catalog (http://locus.umdnj.edu/nigms).
Animals↗
Environmental protection problems in the vicinity of the Zelazny most flotation wastes depository in Poland.
The Zelazny Most depository of wastes from copper-ore processing, located in southwest Poland, is the largest mineral wastes repository in Europe. Moreover, it is located in a seismically active area. The seismicity is induced and is connected with mining works in the nearby underground copper mines. Any release of the contents of the repository to the environment could have devastating and even catastrophic consequences. For this reason, geophysical methods are used for continuous monitoring the state of the repository containment dams. The article presents examples of the application of geoelectric methods for detecting sites of leakage of contaminated water and a sketch of the seismic hazard analysis, which was used to predict future seismic vibrations of the repository dams.
Copper↗
Computational knowledge integration in biopharmaceutical research.
An initiative to increase biopharmaceutical research productivity by capturing, sharing and computationally integrating proprietary scientific discoveries with public knowledge is described. This initiative involves both organisational process change and multiple interoperating software systems. The software components rely on mutually supporting integration techniques. These include a richly structured ontology, statistical analysis of experimental data against stored conclusions, natural language processing of public literature, secure document repositories with lightweight metadata, web services integration, enterprise web portals and relational databases. This approach has already begun to increase scientific productivity in our enterprise by creating an organisational memory (OM) of internal research findings, accessible on the web. Through bringing together these components it has also been possible to construct a very large and expanding repository of biological pathway information linked to this repository of findings which is extremely useful in analysis of DNA microarray data. This repository, in turn, enables our research paradigm to be shifted towards more comprehensive systems-based understandings of drug action.
Algorithms↗
Evidence-based neurosurgery.
OBJECTIVE: The evidence-based medicine movement is gaining influence in many medical specialties. Although many think that clinical medicine always has been based on evidence, the discipline of evidence-based medicine places particular emphasis on a defined set of principles of critical analysis of individual research reports, methodologically rigorous synthesis of multiple reports, and the collection and dissemination of evidence repositories that allow rapid application of evidence in practice. This article provides a selective introduction to the discipline of evidence-based medicine as it applies to neurological surgery. METHODS: The vast literature on evidence-based medicine has been reviewed selectively to identify resources that are readable, accessible, and relevant to neurosurgery. RESULTS: The history, concepts, and techniques of evidence-based medicine are presented in brief, and educational and methodological resources, as well as evidence repositories, are introduced. CONCLUSION: The techniques of evidence-based medicine are relevant to neurological surgery. There is a relatively large repository of critically analyzed and summarized evidence that is useful to the neurosurgical practitioner. Familiarity with these techniques and repositories can help the neurosurgeon bring the best available evidence to bear on the care of individual patients.
Critical Pathways↗
Viability and recovery of peripheral blood mononuclear cells cryopreserved for up to 12 years in a multicenter study.
The Multicenter AIDS Cohort Study (MACS), an ongoing prospective study of the natural history of human immunodeficiency virus (HIV), has stored biologic specimens, including peripheral blood mononuclear cells (PBMC), from 5,622 participants for up to 12 years. The purpose of the present analysis was to evaluate the quality of the PBMC in the MACS repository in order to test the validity and feasibility of nested retrospective studies and to guide the planning of future repositories. PBMC were collected from MACS participants at four centers at 6-month intervals from 1984 to 1995, cryopreserved, and transported to a central repository for storage. A total of 596 of these specimens were subsequently tested for viability and used to evaluate cell function, to conduct immunophenotype analysis, or to isolate HIV. Simple linear regression models were applied to evaluate trends in recovery and viability over time and by center. Results indicated that from a nominal 10(7) cells cryopreserved per vial at all four centers, the median number of viable cells recovered was at least 5 x 10(6) (50% of the number stored) and the median viability was at least 90%. Results suggested that cryopreserved cells can be stored for at least 12 years with no general tendency toward cell loss over time. Furthermore, there were no statistically significant changes in the percent cell viability according to the length of time frozen, regardless of HIV serostatus or the level of CD4(+) lymphocytes. Storing 10(7) PBMC per vial yields sufficient viable cells for phenotypic and/or functional analysis. Results from the MACS provide the basis for the planning of future repositories for use by investigators with similar research goals.
Blood Preservation↗
Radiation protection recommendations as applied to the disposal of long-lived solid radioactive waste. A report of The International Commission on Radiological Protection.
(79) Waste, by definition, has no benefit. It should be viewed as one aspect of the beneficial practice that gave rise to it. Furthermore, radioactive waste management should be placed in the context of the management of society's waste in general. (80) A major issue in evaluating the acceptability of a disposal system for long-lived solid radioactive waste is that doses or risks may arise from exposures in the distant future. There is uncertainty surrounding any estimate of these doses or risks due to lack of knowledge about future conditions. Such exposures are treated as potential exposures as their magnitude depends on future processes and conditions that have probabilities associated with them. (81) Nevertheless, the Commission recognises a basic principle that individuals and populations in the future should be afforded at least the same level of protection from the action of disposing of radioactive waste today as is the current generation. This implies use of the current quantitative dose and risk criteria derived from considering associated health detriment. Therefore, protection of future generations should be achieved by applying these dose or risk criteria to the estimated future doses or risks in appropriately defined critical groups. These estimates should not be regarded as measures of health detriment beyond times of around several hundreds of years into the future. In the case of these longer time periods, they represent indicators of the protection afforded by the disposal system. (82 Constrained optimisation is the central approach to evaluating the radiological acceptability of a waste disposal system; dose or risk constraints are used rather than dose or risk limits. By this transition from limitation to optimisation, the needs of practical application of the radiological protection system to the disposal of long-lived solid waste disposal are met: determination of acceptability now for exposures that may occur in the distant future. Optimisation should be applied in an iterative manner during the disposal system development process and should particularly cover both site selection and repository design. (83) Two broad categories of exposure situations should be considered: natural processes and human intrusion. The latter only refers to intrusion that is inadvertent. The radiological implications of deliberate intrusion into a repository are the responsibility of the intruder. Assessed doses or risks arising from natural processes should be compared with a dose constraint of 0.3 mSv per year or its risk equivalent of around 10(-5) per year. With regard to human intrusion, the consequences from one or more plausible stylized scenarios should be considered in order to evaluate the resilience of the repository to such events. (84) The Commission considers that in circumstances where human intrusion could lead to doses to those living around the site sufficiently high that intervention on current criteria would almost always be justified, reasonable efforts should be made at the repository development stage to reduce the probability of human intrusion or to limit its consequences. In this respect, the Commission has previously advised that an existing annual dose of around 10 mSv per year may be used as a generic reference level below which intervention is not likely to be justifiable. Conversely, an existing annual dose of around 100 mSv per year may be used as a generic reference level above which intervention should be considered almost always justifiable. Similar considerations apply in situations where the thresholds for deterministic effects in relevant organs are exceeded. (85) Compliance with the constraints can be assessed by utilising either an aggregated risk-oriented approach, with a risk constraint, or a disaggregated dose/probability approach, with a dose constraint, or a combination of both. A similar level of protection can be achieved by any of these approaches; however, more information may
Hazardous Waste↗