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PubMed1988

Interactions of 57Co, 85Sr and 137Cs with peat under acidic precipitation conditions.

Following the burial of low-level wastes in nuclear waste repositories, the interactions of radionuclides with surrounding soil infiltrated by acid precipitation could cause radionuclide migration and transport into nearby wells. To evaluate this migration through organically rich soil in the unsaturated zone, we measured sorption and desorption distribution ratios (Rd) of 57Co, 85Sr and 137Cs onto peat at pH 4. Peat samples rich in organic C showed relatively higher sorption Rd values for 57Co and 85Sr compared to soil samples with less organic C. The sorption and desorption Rd values for these radionuclides are similar, indicating the reversibility of the sorption process. The measurements suggest the importance of organic complexes for the retention of these radionuclides at the pH range (pH 4), where hydrolysis of the metals is not important and sorption is expected to be low. Cesium-137, on the other hand, appears to be associated more strongly with inorganic components of the soil samples, with its Rd value significantly higher in the peat material containing less organic C. The 137Cs desorption Rd on the same peat sample is also comparable to the sorption Rd indicating equilibrium. Both the organic and inorganic components of peat are thus able to retard the migration of radionuclides which may be found in nuclear waste repositories. The design of such a repository may be improved using a peat barrier to restrict radionuclide migration.

Cesium Radioisotopes↗
PubMed2004

The Pseudomonas aeruginosa PA01 gene collection.

Pseudomonas aeruginosa, a common inhabitant of soil and water, is an opportunistic pathogen of growing clinical relevance. Its genome, one of the largest among bacteria [5570 open reading frames (ORFs)] approaches that of simple eukaryotes. We have constructed a comprehensive gene collection for this organism utilizing the annotated genome of P. aeruginosa PA01 and a highly automated and laboratory information management system (LIMS)-supported production line. All the individual ORFs have been successfully PCR-amplified and cloned into a recombination-based cloning system. We have isolated and archived four independent isolates of each individual ORF. Full sequence analysis of the first isolate for one-third of the ORFs in the collection has been completed. We used two sets of genes from this repository for high-throughput expression and purification of recombinant proteins in different systems. The purified proteins have been used to set up biochemical and immunological assays directed towards characterization of histidine kinases and identification of bacterial proteins involved in the immune response of cystic fibrosis patients. This gene repository provides a powerful tool for proteome- and genome-scale research of this organism, and the strategies adopted to generate this repository serve as a model for building clone sets for other bacteria.

Bacterial Proteins↗
PubMed2006

Can the quality of care in family practice be measured using administrative data?

OBJECTIVE: To explore the feasibility of using administrative data to develop process indicators for measuring quality in primary care. DATA SOURCES/STUDY SETTING: The Population Health Research Data Repository (Repository) housed at the Manitoba Centre for Health Policy which includes physician claims, hospital discharge abstracts, pharmaceutical use (Drug Program Information Network (DPIN)), and the Manitoba Immunization Monitoring Program (MIMS) for all residents of Manitoba, Canada who used the health care system during the 2001/02 fiscal year. Family physicians were identified from the Physician Resource Database. Indicators were developed based on a literature review and focus group validation. DATA COLLECTION/EXTRACTION METHODS: Data files were extracted from administrative data available in the Repository. We extracted data based on the ICD-9-CM codes and ATC-class drugs prescribed and then linked them to the Physician Resource Database. Physician practices were defined by allocating patients to their most responsible physician. Every family physician in Manitoba that met the inclusion criteria (having either 5 or 10 eligible patients depending on the indicator) was 'scored' on each indicator. Physicians were then grouped according to the proportion of the patients allocated to their practice who received the recommended care for the specific indicator. PRINCIPAL FINDINGS: Using administrative health data we were able to develop and measure eight indicators of quality of care covering both preventive care services and chronic disease management. The number of eligible physicians and patients varied for each indicator as did the percent of patients with recommended care, per physician. For example, the childhood immunization indicator included 544 physicians who, on average, provided immunization for 65 percent of their patients. CONCLUSIONS: Quality of care provided by family physicians can be measured using administrative data. Despite the limitations addressed in this paper, this work establishes a practical methodology to measure quality of care provided by family physicians that can be used for quality improvement initiatives.

Data Collection↗
PubMedDate not supplied

Upscaling of hydraulic conductivity and telescopic mesh refinement.

Performance assessments of repositories for the underground disposal of nuclear fuel and waste include models of ground water flow and transport in the host rocks. Estimates of hydraulic conductivity, K, based on field measurements may require adjustment (upscaling) for use in numerical models, but the choice of upscaling approach can be complicated by the use of nested modeling, large-scale fracture zones, and a high degree of heterogeneity. Four approaches to upscaling K are examined using a reference case based on exhaustive site data and an application of nested modeling to evaluate performance assessment of a waste repository. The upscaling approaches are evaluated for their effects on the flow balance between nested modeling domains and on simple measures of repository performance. Of the upscaling approaches examined in this study, the greatest consistency of boundary flows was achieved using the observed scale dependence for the rock domains, measured values from the large-scale interference test for the conductor domain, and a semivariogram regularization based on the Moye model for packer test interpretation. Making the assumption that large fracture zones are two-dimensional media results in the greatest changes to the median of travel time and improves the flow balance between the nested models. The uncertainty of upscaling methods apparently has a small impact on median performance measures, but a significant impact on the variances and earliest arrival times.

Models, Theoretical↗
PubMed2006

New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras.

A new computer program, called Mallard, is presented for screening entire 16S rRNA gene libraries of up to 1,000 sequences for chimeras and other artifacts. Written in the Java computer language and capable of running on all major operating systems, the program provides a novel graphical approach for visualizing phylogenetic relationships among 16S rRNA gene sequences. To illustrate its use, we analyzed most of the large libraries of cloned bacterial 16S rRNA gene sequences submitted to the public repository during 2005. Defining a large library as one containing 100 or more sequences of 1,200 bases or greater, we screened 25 of the 28 libraries and found that all but three contained substantial anomalies. Overall, 543 anomalous sequences were found. The average anomaly content per clone library was 9.0%, 4% higher than that previously estimated for the public repository overall. In addition, 90.8% of anomalies had characteristic chimeric patterns, a rise of 25.4% over that found previously. One library alone was found to contain 54 chimeras, representing 45.8% of its content. These figures far exceed previous estimates of artifacts within public repositories and further highlight the urgent need for all researchers to adequately screen their libraries prior to submission. Mallard is freely available from our website at http://www.cardiff.ac.uk/biosi/research/biosoft/.

Archaea↗
PubMed1988

Recommendations regarding handling of the necropsy in Rett syndrome.

In order to maximize biochemical, neurochemical, molecular, and pathologic information from patients with Rett syndrome, a uniform procedure has been developed for the conduct of the postmortem examination. Tissue should be prepared for freezing, for electron microscopy studies, and for standard histologic examination. For the purposes of uniformity, three central repositories for necropsy materials have been established and are available at all times. In the event of the death of a patient with Rett syndrome, parents who consent to necropsy should request that materials be handled according to the protocol and transported under appropriate conditions to the central repository. The National Neurological Research Bank (Los Angeles), the Brain Tissue Bank (Belmont, Mass), and the Department of Neuropathology at Johns Hopkins Hospital (Baltimore) have agreed to serve as repositories for tissues. A committee of the International Rett Syndrome Association medical advisory panel will monitor this process in cooperation with the directors of the respective tissue banks.

Ammonia↗
PubMed2006

A review of interventions triggered by hepatitis A infected food-handlers in Canada.

BACKGROUND: In countries with low hepatitis A (HA) endemicity, infected food handlers are the source of most reported foodborne outbreaks. In Canada, accessible data repositories of infected food handler incidents are not available. We undertook a systematic review of such incidents to evaluate the extent of viral transmission through food contamination and the scope of post-exposure prophylaxis (PEP) interventions. METHODS: A systematic search of MEDLINE and EMBASE was conducted to identify published reports of incidents in Canada. An expanded search of a news repository (i.e., transcripts from newspapers and newscasts) was also conducted to identify the location and timing of an incident, which was used to retrieve the related report by contacting local public health departments. Data pertaining to case identification, public health risk, PEP interventions, and associated costs was independently abstracted by two reviewers and summarized according to incidents with and without large PEP interventions. RESULTS: A total of 16 incidents were identified from 1998-2004. There were approximately 3 incidents requiring public notification per year. Only 12.5% of incidents were described in published reports, indicating that published data significantly underestimated the number of incidents and PEP interventions. Data pertaining to the remaining incidents was unpublished, sparse and highly dispersed at the local public health level. Six of the 16 incidents required large PEP interventions to immunize on average 5000 potentially exposed individuals. Secondary transmission was low. Characteristics of incidents requiring large PEP interventions included potentially infectious food handlers working with uncooked food for a prolonged duration in high-volume grocery stores in high-density urban areas. CONCLUSION: Infected food handlers with hepatitis A virus (HAV) requiring public notification are not infrequent in Canada. Published data severely underestimated the burden of PEP intervention. Better and consistent reporting at the local and national level as well as a national data repository should be considered for the management of future incidents.

Canada↗
PubMed2005

Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.

BACKGROUND: The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of discovering additional genomic sequences beyond those originally sequenced. In particular, if the source DNA for a sequencing project came from a species that was colonized by another organism, then the project may yield substantial amounts of genomic DNA, including near-complete genomes, from the symbiotic or parasitic organism. RESULTS: By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis. We extracted all sequences with partial matches to a previously sequenced Wolbachia strain and assembled those sequences using customized software. For one of the three new species, the data recovered were sufficient to produce an assembly that covers more than 95% of the genome; for a second species the data produce the equivalent of a 'light shotgun' sampling of the genome, covering an estimated 75-80% of the genome; and for the third species the data cover approximately 6-7% of the genome. CONCLUSIONS: The results of this study reveal an unexpected benefit of depositing raw data in a central genome sequence repository: new species can be discovered within this data. The differences between these three new Wolbachia genomes and the previously sequenced strain revealed numerous rearrangements and insertions within each lineage and hundreds of novel genes. The three new genomes, with annotation, have been deposited in GenBank.

Animals↗
PubMed2026

MetaServe: a lightweight, metadata-aware governance and delivery layer for pre-publication research omics data.

BACKGROUND: Institutional research teams and core facilities routinely manage pre-publication omics datasets that span heterogeneous file types, nested project structures, and multiple downstream uses. Public repositories mainly support post-publication dissemination, while workflow systems and enterprise data platforms do not directly provide a lightweight governance and delivery layer for internal research assets. RESULTS: We present MetaServe, an open-source governance and delivery layer for pre-publication research assets in institutional multi-omics settings. MetaServe registers and delivers heterogeneous assets, including sequencing files, processed matrices, imaging data, analysis-ready objects, tabular files, and documents, without requiring repository-grade standardization. Its metadata-aware design combines file-type recognition, partial automatic extraction for selected formats, manually supplied project and biological annotations, and indexed faceted retrieval. MetaServe supports authenticated web download, viewer-oriented handoff for compatible services such as cellxgene, and path-manifest export for downstream workflows under shared-storage assumptions. The current implementation combines role-based controls, explicit file-level sharing, path-constrained delivery, and operational traceability to support controlled institutional access. MetaServe has been deployed at the Chinese Institutes for Medical Research (CIMR) as part of an institutional multi-omics data-management system. CONCLUSIONS: MetaServe provides a practical layer between institutional storage and downstream analytical platforms for pre-publication research data. Its contribution is the integration of lightweight metadata-aware registration, permission-aware retrieval, and controlled delivery for heterogeneous institutional omics assets. Rather than replacing workflow engines, public repositories, or enterprise-scale research data platforms, MetaServe offers a deployable governance layer for core facilities and collaborative teams that need structured discovery and traceable delivery before public deposition or manuscript release.

Metadata↗
PubMedDate not supplied

I2Cnet medical image annotation service.

I2Cnet (Image Indexing by Content network) aims to provide services related to the content-based management of images in healthcare over the World-Wide Web. Each I2Cnet server maintains an autonomous repository of medical images and related information. The annotation service of I2Cnet allows specialists to interact with the contents of the repository, adding comments or illustrations to medical images of interest. I2Cnet annotations may be communicated to other users via e-mail or posted to I2Cnet for inclusion in its local repositories. This paper discusses the annotation service of I2Cnet and argues that such services pave the way towards the evolution of active digital medical image libraries.

Computer Communication Networks↗
PubMed2005

Effects of the osteopontin gene variants on milk production traits in dairy cattle.

Osteopontin (OPN) is a highly phosphorylated glycoprotein whose gene has been cloned and sequenced in different species. Several whole genome scans have identified quantitative trait loci (QTL) affecting milk production traits on bovine chromosome 6 close to the osteopontin gene (OPN) location. The presence of OPN in milk and its elevated expression in mammary gland epithelial cells together with previous QTL studies have prompted us to investigate the effects of OPN variants on milk production traits in the Holstein dairy cattle population. A single nucleotide polymorphism in intron 4 (C/T) was detected and primers were designed to amplify genomic DNA from 1362 bulls obtained from Cooperative Dairy DNA Repository and from 214 cows from the University of Wisconsin herd. For the Repository population, the C allele was associated with an increase in milk protein percentage and milk fat percentage. Correlation between milk protein percentage and milk fat percentage was about 0.57. For the University of Wisconsin herd, the estimates of the effects of allele C were in the same direction as for the Repository population, although these estimates did not reach statistical significance. Our results are consistent with other studies that showed a significant association of the microsatellite markers in the region of OPN with milk protein percentage and other correlated traits.

Alleles↗
PubMed2000

Characterization of subterranean bacteria in the Hungarian Upper Permian Siltstone (Aleurolite) Formation.

The main purpose of this work was to study the microbiology of the Hungarian Upper Permian Siltstone (Aleurolite) Formation, to assess the safety of future underground repositories for nuclear waste. Sixty-seven air, groundwater, technical water, rock, and surface samples were collected aseptically from different depths. The number of aerobic and anaerobic isolates was 277. The mesophilic minimum and maximum CFU counts of the air samples were 1.07-5.84 x 10(2).mL-1 (aerobic) and 0.22-1.04 x 10(2).mL-1 (anaerobic), respectively; those of the water samples were 0.39-1.25 x 10(5).mL-1 (aerobic) and 0.36-3.9 x 10(3).mL-1 (anaerobic); those of the technical water samples were 0.27-5.03 x 10(6).mL-1 (aerobic) and 4 x 10(5)-->10(6).mL-1 (anaerobic); and those of the aleurolite samples were 2.32 x 10(2)-2.47 x 10(5).g-1 (aerobic) and 0.45-9.5 x 10(2).g-1 (anaerobic). In the groundwater, the thermophilic aerobic bacteria count was 0-2.4 x 10(2).mL-1 and the thermophilic anaerobic bacteria count was 0.43-4.6 x 10(4).mL-1. The gases produced by the 16 gas-forming isolates were CO2 (aerobic isolates), and CO2 and H2 (anaerobic isolates). About 20% of the aerobic isolates produced siderophores. The proportions of organic acid producers were lowest in aerobic and anaerobic isolates from the aleurolite, 13% and 14%, respectively. The highest proportions of acid producers in the aerobic and anaerobic isolates from the air samples were 63% and 54%. Altogether 160 of the aerobic isolates and 52 of the anaerobic isolates were spore formers. The radiosensitivity of the aerobic isolates was also determined; the D10 values of the sporeformers ranged between 0.8-2.44 kGy. Our results indicate that the sulfate-reducing bacteria and the production of complexing agents (siderophores) may contribute to the mobilization of radionuclides from underground repositories. As well, microbial gas production can influence the environmental conditions. The variability in bacterial radiotolerance indicates the biodiversity at this potential disposal site. These facts must be considered during the planning of a nuclear waste repository.

Air Microbiology↗
PubMed2002

An XML-based system for the flexible classification and retrieval of clinical practice guidelines.

Beneficial effects of clinical practice guidelines (CPGs) have not yet reached expectations due to limited routine adoption. Electronic distribution and reminder systems have the potential to overcome implementation barriers. Existing electronic CPG repositories like the National Guideline Clearinghouse (NGC) provide individual access but lack standardized computer-readable interfaces necessary for automated guideline retrieval. The aim of this paper was to facilitate automated context-based selection and presentation of CPGs. Using attributes from the NGC classification scheme, an XML-based metadata repository was successfully implemented, providing document storage, classification and retrieval functionality. Semi-automated extraction of attributes was implemented for the import of XML guideline documents using XPath. A hospital information system interface was exemplarily implemented for diagnosis-based guideline invocation. Limitations of the implemented system are discussed and possible future work is outlined. Integration of standardized computer-readable search interfaces into existing CPG repositories is proposed.

Information Systems↗
PubMed2005

Security and confidentiality approach for the Clinical E-Science Framework (CLEF).

OBJECTIVES: CLEF is an MRC sponsored project in the E-Science programme that aims to establish methodologies and a technical infrastructure for the next generation of integrated clinical and bioscience research. METHODS: The heart of the CLEF approach to this challenge is to design and develop a pseudonymised repository of histories of cancer patients that can be accessed by researchers. Robust mechanisms and policies have been developed to ensure that patient privacy and confidentiality are preserved while delivering a repository of such medically rich information for the purposes of scientific research. RESULTS: This paper summarises the overall approach adopted by CLEF to meet data protection requirements, including the data flows, pseudonymisation measures and additional monitoring policies that are currently being developed. CONCLUSION: Once evaluated, it is hoped that the CLEF approach can serve as a model for other distributed electronic health record repositories to be accessed for research.

Access to Information↗
PubMed2006

[Radioactive waste due to electric power and mineral fertiliser production].

Radiation Protection Unit of the Institute for Medical Research and Occupational Health in Zagreb has been conducting systematic investigations of radioactive contamination of the Croatian environment by anthropogenic fission products as well as by naturally occurring radioactive material (NORM) since 1963. Several critical sites in Croatia were identified for NORM, that is, for slag and ash repositories from coal-fired power plants and phosphogypsum repository from a mineral fertilizer production plant. As the coals and phosphate ores contain naturally occurring radionuclides, especially the members of the uranium and thorium radioactive chains, utilising these materials in various industries only enhances their natural radioactivity in residual waste. Consequently, the resulting activity concentrations of natural radionuclides in waste material could be several times higher than in the adjacent soil. These deposited materials pose permanent risk of radiation exposure due to the long physical half-life of natural radionuclides (e.g., T 1/2 = 1600 years for 226Ra). Results of scientific investigations related to natural radioactivity are used in the recovery of slag and ash repositories and landfills, as well as in establishing regulatory criteria targeting import of coal and phosphate ores. In consequence, recently measured activity concentrations of natural radioactivity in imported materials used nowadays in coal-fired power plants are significantly lower than in previously used raw materials. Therefore, slag and ash can be used as additive materials in cement production.

Croatia↗
PubMed1995

Re-engineering care delivery to improve the health outcome of asthmatics in Campbelltown, New South Wales.

The pilot study for this project was established in February 1993 under a Health Communications Network initiative to improve the treatment results for asthmatics in Campbelltown, New South Wales. A user specific, standardized information environment was implemented across the community and hospital sectors linking General Practitioners, Specialist Consultants, and hospital doctors and nurses. The pilot included 20 General Practitioners, four pediatricians and respiratory physicians, and the nurses and doctors of a district hospital. ¿A multi-disciplinary team implemented the pilot, consisting of men and women from Campbelltown Health Service, Ernst & Young Health Services Consulting, and a major systems vendor. The team used process modeling tools to document the required changes to the roles and responsibilities of the individual practitioners and the impact of these changes on the cost of providing services and patient flow. Significant cost savings were anticipated from moving care out of the hospital and into the community. In the re-engineered environment, the General Practitioner became the case manager, responsible for guiding and coordinating the management of the patient's asthma, in consultation with the appropriate specialist consultants. The hospital continued to provide acute/emergency care. The level of sophistication of the information systems solutions was determined by the level of technical awareness of the users. Fax based communications were chosen to support the flow of timely and relevant information between the practitioners. A VAX based system was used as a data repository for the information collected by hospital staff and General Practitioners. The data repository acted as a clinical record for asthmatics who participated in the pilot. The clinical history of an asthmatic could then be viewed when a patient sought treatment from Campbelltown's Emergency Department during periods when the General Practitioner was not available. If a patient did seek emergency treatment, a record of the patient's visit was faxed immediately to the General Practitioner upon discharge from the hospital. Specialist consultants are independent practitioners in Australia. They were provided with a custom built application for their own personal computers. A key feature of this application was the automatic generation of letters to the General Practitioner to assist them in the management of asthmatics. The Specialist Consultants also identified a sub-group of high risk patients for whom additional clinical information was stored in the data repository at Campbelltown Hospital. Analysis of the patient information formed a core component of the project. Clinical outcomes for individual patients were forwarded to the General Practitioners regularly to assist them in their case management duties. System implementation in this re-engineered environment yielded the following: Strategies for managing the responses of clinicians and patients to the use of technology and a standardized information sharing environment. A means of assessing the system's impact on both the clinician-patient relationship and the professionals' relationship with other clinicians; The evolution of clinical use of information regarding individual patient's health outcome for the management of asthma; The integration of the information systems with policy and planning cycles for the Area Health Service; and The establishment of effective links with vendors of health service applications.

Asthma↗
PubMedDate not supplied

Large-scale protein modelling and integration with the SWISS-PROT and SWISS-2DPAGE databases: the example of Escherichia coli.

Knowledge-based molecular modelling of proteins has proven useful in many instances, including the rational design of mutagenesis experiments, but it has generally been limited by the availability of expensive computer hardware and software. To overcome these limitations, we developed the SWISS-MODEL server for automated knowledge-based protein modelling. The SWISS-MODEL server uses the Brookhaven Protein Data Bank as a source of structural information and automatically generates protein models for sequences which share significant similarities with at least one protein of known three-dimensional structure. We have now used the software framework of the server to generate large collections of protein models, and established the SWISS-MODEL Repository, a new database for automatically generated and theoretical protein models. This repository is directly integrated with the SWISS-PROT and SWISS-2DPAGE databases through the ExPASy World Wide Web server (URL is http://expasy.hcuge.ch). Here we present an illustration of this process by an application to the Escherichia coli sequences.

Bacterial Proteins↗
PubMed2006

Jaw tremor: prevalence and clinical correlates in three essential tremor case samples.

The spectrum of involuntary movements seen in essential tremor (ET) is limited. Jaw tremor is one such movement. The prevalence and clinical correlates of jaw tremor have not been studied in detail. The objective of this study was to estimate the prevalence and examine the clinical correlates of jaw tremor in ET using ET cases from three distinct settings (population, tertiary-referral center, brain repository). All ET cases underwent a videotaped tremor examination in which tremors (including limb, head, voice, and jaw) were assessed. The prevalence [95% confidence interval (CI)] of jaw tremor was lowest in the population sample (7.5%; 3.9%-14.2%), intermediate in the tertiary-referral center (10.1%; 6.8%-14.7%), and highest in the brain repository (18.0%; 12.3%-25.5%; P = 0.03). Jaw tremor was associated with older age (P < 0.001), more severe action tremor of the arms (P < 0.001), and presence of head and voice tremor (P < 0.001). Jaw tremor was present in 4/14 (28.6%) ET cases with consistent rest tremor vs. 15/193 (7.8%) cases without rest tremor (odds ratio = 4.8; 95% CI = 1.3-7.0; P = 0.009). The prevalence of jaw tremor was 7.5% to 18.0% and was dependent on the mode of ascertainment, being least prevalent in a population-based sample. ET cases with jaw tremor had a more clinically severe and more topographically widespread disorder. The association in our study between jaw tremor and rest tremor, along with the published observation that jaw tremor can occur in Parkinson's disease (PD), raises the question whether jaw tremor in ET is a marker for subsequent conversion to PD.

Age Factors↗