Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Data mining”

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 1,765 records · Page 98Linked to original sources
PubMed2006

SIGMA: a system for integrative genomic microarray analysis of cancer genomes.

BACKGROUND: The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes. RESULTS: We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types. CONCLUSION: In this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA) of cancer genomes, can be accessed at http://sigma.bccrc.ca.

Adenocarcinoma↗
PubMed2002

Geochemical evidence for atmospheric pollution derived from prehistoric copper mining at Copa Hill, Cwmystwyth, mid-Wales, UK.

This paper presents geochemical data from a blanket peat located close to a Bronze Age copper mine on the northern slopes of the Ystwyth valley, Ceredigion, mid-Wales, UK. The research objective was to explore the possibility that the peat contained a geochemical record of the pollution generateD by mining activity. Four peat monoliths were extracted from the blanket peat to reconstruct the pollution history of the prehistoric mine. Three different geochemical measurement techniques were employed and four copper profiles have been reconstructed, two of which are radiocarbon-dated. The radiocarbon dates at one profile located close to the mine confirm that copper enrichment occurs in the peat during the known period of prehistoric mining. Similar enrichment of copper concentrations is shown in one adjacent profile and a profile within 30 m away. In contrast, copper was not enriched in the other radiocarbon-dated monolith, collected approximately 1.35 km to the north of the mine. Whilst other possible explanations to explain the copper concentrations are discussed, it is argued that the high copper concentrations represent evidence of localised atmospheric pollution caused by Bronze Age copper mining in the British Isles. The results of this study suggest that copper may be immobile in blanket peat and such deposits can usefully be used to reconstruct atmospheric pollution histories in former copper mining areas.

Air Pollutants↗
PubMed2000

The risk of heat exhaustion at a deep underground metalliferous mine in relation to surface temperatures.

The risk of heat exhaustion at a deep underground metalliferous mine was assessed in relation to thermal conditions prevailing on the surface. For each day of a 1-year prospective case series of heat exhaustion, surface 24-h mean wet and dry bulb temperatures were recorded. From this data, 24-h mean wet bulb globe temperatures were derived using certain assumptions. The three surface temperature variables were significantly higher on those days on which heat exhaustion occurred, compared to those days on which it did not occur (P < 0.001). The relative risk of heat exhaustion on days when the 24-h mean wet bulb globe temperature was in the range 26.0-28.0 degrees C was 4.82 (95% confidence interval 2.12-10.96). Surface temperature data could be used at this mine to warn miners about the risk of heat exhaustion.

Acute Disease↗
PubMed1996

Respiratory health services reported by U.S. mining facilities in the National Occupational Health Survey of Mining (1984-1989).

This report describes the involvement of mine management personnel at U.S. mines in providing environmental and medical services related to respiratory health. The data were obtained by means of a questionnaire that was administered to mine management personnel at 491 mines and mills during May 1984 to August 1989. The data indicate that 62% of U.S. miners worked at facilities that provided at least a portion of workers with chest X-rays, and 41% worked at facilities that provided at least a portion of workers with pulmonary function tests. Eighty-five percent of miners worked at facilities in which the company required a medical examination of all new employees; the majority were required by company policy to have a medical examination before returning to work after an illness. However, only 2% of miners were required by company policy to have an exit medical examination when their employment ended. This report underscores the need for respiratory health to remain a primary concern of all persons who provide occupational health services to miners.

Environmental Monitoring↗
PubMed2005

CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences.

BACKGROUND: With the recent progress made in large-scale genome sequencing projects a vast amount of novel data is becoming available. A comparative sequence analysis, exploiting sequence information from various resources, can be used to uncover hidden information, such as genetic variation. Although there are enormous amounts of SNPs for a wide variety of organisms submitted to NCBI dbSNP and annotated in most genome assembly viewers like Ensembl and the UCSC Genome Browser, these platforms do not easily allow for extensive annotation and incorporation of experimental data supporting the polymorphism. However, such information is very important for selecting the most promising and useful candidate polymorphisms for use in experimental setups. DESCRIPTION: The CASCAD database is designed for presentation and query of candidate SNPs that are retrieved by in silico mining of high-throughput sequencing data. Currently, the database provides collections of laboratory rat (Rattus norvegicus) and zebrafish (Danio rerio) candidate SNPs. The database stores detailed information about raw data supporting the candidate, extensive annotation and links to external databases (e.g. GenBank, Ensembl, UniGene, and LocusLink), verification information, and predictions of a potential effect for non-synonymous polymorphisms in coding regions. The CASCAD website allows search based on an arbitrary combination of 27 different parameters related to characteristics like candidate SNP quality, genomic localization, and sequence data source or strain. In addition, the database can be queried with any custom nucleotide sequences of interest. The interface is crosslinked to other public databases and tightly coupled with primer design and local genome assembly interfaces in order to facilitate experimental verification of candidates. CONCLUSIONS: The CASCAD database discloses detailed information on rat and zebrafish candidate SNPs, including the raw data underlying its discovery. An advanced web-based search interface http://cascad.niob.knaw.nl allows universal access to the database content and allows various queries supporting many types of research utilizing single nucleotide polymorphisms.

Animals↗
PubMed2005

A methodology for the assessment of rehabilitation success of post mining landscapes--sediment and radionuclide transport at the former Nabarlek uranium mine, Northern Territory, Australia.

Protection of the environment post-mining is an important issue, especially where runoff and erosion can lead to undesirable material leaving post-mining landscapes and contaminating surrounding land and watercourses. Methods for assessment of the environmental impact and long-term behaviour of post-mining landforms based on scientific methodology are needed especially where field data are absent or poor. An appraisal of the former Nabarlek uranium mine was conducted to assess the site from a soil erosion perspective as part of an independent evaluation of overall rehabilitation success. Determination of the gross erosion occurring, sediment discharge to Cooper Creek and the resultant sediment associated radionuclide load in Cooper Creek were the primary objectives of the study. These objectives were achieved through the application of several models using parameter values collected from the site. The study found that the area containing the mill tailings repository is extremely stable and meets the guidelines established for long-term storage of uranium mill tailings. Most other areas on the site are stable; however there are some areas with a high sediment loss. Sediment concentration in Cooper Creek, which drains the site, was found to be within the Australian water quality guidelines for fresh water, however sediment concentrations in tributaries were found to exceed recommended levels. Radionuclide determinations on soil samples showed that the highest specific activities (Bq kg-1) were present on a small (0.44 ha) area with a relatively high erosion rate. This small area contributed the majority of the estimated flux to Cooper Creek of uranium-series radionuclides sorbed or structurally incorporated to eroded soil particles sourced from the mine site. This study provides a methodology for assessment of the erosional stability of such a landscape and consequent impact on water quality, using extensive field data and readily available and well known models and methodologies.

Environmental Monitoring↗
PubMed2006

Lineages of acidophilic archaea revealed by community genomic analysis.

Novel, low-abundance microbial species can be easily overlooked in standard polymerase chain reaction (PCR)-based surveys. We used community genomic data obtained without PCR or cultivation to reconstruct DNA fragments bearing unusual 16S ribosomal RNA (rRNA) and protein-coding genes from organisms belonging to novel archaeal lineages. The organisms are minor components of all biofilms growing in pH 0.5 to 1.5 solutions within the Richmond Mine, California. Probes specific for 16S rRNA showed that the fraction less than 0.45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of <0.006 cubic micrometer.

Amino Acid Sequence↗
PubMed2000

Interoperability of biodiversity databases: biodiversity information on every desktop.

Data about biodiversity are either scattered in many databases or reside on paper or other media not amenable to interactive searching. The Global Biodiversity Information Facility (GBIF) is a framework for facilitating the digitization of biodiversity data and for making interoperable an as-yet-unknown number of biodiversity databases that are distributed around the globe. In concert with other existing efforts, GBIF will catalyze the completion of a Catalog of the Names of Known Organisms and will develop search engines to mine the vast quantities of biodiversity data. It will be an outstanding tool for scientists, natural resource managers, and policy-makers.

Animals↗
PubMed1995

Exploration and exploitation of clinical databases.

Clinical data repositories represent a potential gold mine of information and knowledge. Rapid access to such information can help bridge the gap between clinical care and research, support clinical and executive decision making, and improve the quality of care. A clinical database can be used in four ways: to display information about an individual patient (results reporting); to find data on a patient with similarities to one being seen (case finding); to describe a group of patients with at least one attribute in common (cohort description); and to analyze data patterns in terms of trends or relationships (predictive modeling). It seems unlikely that many important clinical questions will be subject to randomized clinical trials because of the ethics, logistics, and expense that would be involved. Evolving statistical and epidemiological methods allow us to approach these clinical data repositories with the purpose of building predictive models, but a clear understanding of the limitations of routinely collected clinical data and the inherent biases is necessary. The largest barrier to using routinely collected clinical data is not the limitations of the data themselves, but rather the lack of a data paradigm for the decision-maker. We present some of the problems and pitfalls in obtaining and using routinely collected data, based upon the use of ClinQuery at Boston's Beth Israel Hospital and the resources and traditions at the Mayo Clinic.

Databases, Factual↗
PubMed2006

Simulation of radiation damage to lung cells after exposure to radon decay products.

OBJECTIVES: Exposure to radon and radon decay products represents one of the greatest risks of ionizing radiation from natural sources in some residential and working areas. Recently increasing attention has been paid to accurate estimations of this health risk by using various models. METHODS: In the presented study, a bystander model was used to predict biological effects of radon products on lung tissue target cells. The model considers radiation response as a superposition of the direct alpha particles hit effect and the bystander (cells communication) effect. Energy deposition in the lung tissue and in the air gap was calculated using the Bethe-Bloch equation. The exponential distribution of radon progenies in the mucous layer of smokers and non-smokers was evaluated. RESULTS: The excess relative risk value of lung cancer occurrence per unit exposure obtained in our study was ERR/WLM=0.0047 for smokers and ERR/WLM=0.0171 (taking into account the environment in radioactive ore mines) for non-smokers. Other published results give the average excess relative risk values per unit exposure in the dwellings for smokers ERR=0.050 per 100 Bq.m(-3) and for non-smokers ERR=0.198 per 100 B.qm(-3). Results presented in this study are in good agreement with the published epidemiological data on lung cancer incidence for mines and residential areas. CONCLUSIONS: The bystander model is suitable for radon risk prediction in dwellings and at workplaces (residential and working areas).

Adult↗
PubMed1983

Thorium concentration in human tissues from two U.S. populations.

The concentrations of natural alpha-emitting isotopes of thorium (228Th, 230Th and 232Th) have been determined in 22 sets of human tissue samples obtained at autopsy from Grand Junction, CO and in 10 sets from Washington, DC. Tissues included lung, pulmonary lymph nodes, liver, kidney, bone, a few gonads, spleen and thyroid. Personal data on each individual's age, sex, smoking history and occupation were obtained whenever possible. The concentrations of 228Th, 230Th and 232Th were highest in lymph nodes for both populations with 2.6 and 5.1 pCi/kg of 228Th, 4.60 and 11.10 pCi/kg of 230Th, and 2.8 and 7.8 pCi/kg of 232Th in Washington, DC and Grand Junction, CO, respectively. The order of concentrations of all three isotopes in all other organs for both populations was as follows: (formula; see text) The data suggest that the non-mining residents who lived in the vicinity of uranium mine tailings do not have elevated 230Th concentrations in their lungs, when compared to the residents of Washington, DC who are not exposed to such tailings. However, 230Th concentration in bone of Grand Junction subjects was just significantly higher (at p less than 0.1) than that for Washington, DC subjects after suitable age adjustments. The data also suggest that 230Th is more available for accumulation in skeleton than would be supposed from its relative geochemical abundance.

Adolescent↗
PubMed2004

Gold concentrations in abiotic materials, plants, and animals: a synoptic review.

Gold (Au) is ubiquitous in the environment and mined commercially at numerous locations worldwide. It is also an allergen that induces dermatitis in sensitive individuals. Gold concentrations were comparatively elevated in samples collected near gold mining and processing facilities, although no data were found for birds and non-human mammals. Maximum gold concentrations reported in abiotic materials were 0.001 microg L(-1) in rainwater; 0.0015 microg L(-1) in seawater near hydrothermal vents vs. < 0.00004-0.0007 microg L(-1) elsewhere; 5.0 microg kg(-1) dry weight (DW) in the Earth's crust; 19.0 microg L(-1) in a freshwater stream near a gold mining site; 440 microg kg(-1) DW in atmospheric dust near a high traffic road; 843 microg kg(-1) DW in alluvial soil near a Nevada gold mine vs. < 29 microg kg(-1) DW premining; 2.53 mg kg(-1) DW in snow near a Russian smelter vs. < 0.35 mg kg(-1) DW at a reference site; 4.5 mg kg(-1) DW in sewage sludge; 28.7 mg kg(-1) DW in polymetallic sulfides from the ocean floor; and 256.0 mg kg(-1) DW in freshwater sediments near a gold mine tailings pile vs. < 5 microg kg(-1) DW prior to mining. In plants, elevated concentrations of 19 microg Au kg(-1) DW were reported in terrestrial vegetation near gold mining operations vs. < 4 microg kg(-1) DW at a reference site; 37 microg kg(-1) DW in aquatic bryophytes downstream from a gold mine; 150 microg Au kg(-1) DW in leaves of beans grown in soil containing 170 microg kg(-1) DW; up to 1.06 mg kg(-1) DW in algal mats of rivers receiving gold mine wastes; and 0.1-100 mg kg(-1) DW in selected gold accumulator plants. Fish and aquatic invertebrates contained 0.1-38.0 microg Au kg(-1) DW. In humans, gold concentrations up to 1.1 microg L(-1) were documented in urine of dental technicians vs. 0.002-0.85 microg L(-1) in reference populations; 2.1 microg L(-1) in breast milk, attributed to gold dental fillings and jewelry of mothers; 1.4 mg kg(-1) DW in hair of goldsmiths vs. a normal range of 6-880 microg kg(-1) DW; 2.39 mg L(-1) in whole blood of rheumatoid arthritis patients receiving gold thiol drugs to reduce inflammation (chrysotherapy) vs. a normal range of 0.2-2.0 microg L(-1); and 60.0 to 233.0 mg kg(-1) fresh weight (FW) in kidneys of rheumatoid arthritis patients undergoing active chrysotherapy vs. < 42.0 mg kg(-1) FW kidney 140 months posttreatment.

Animals↗
PubMed2004

Heat illness in the U.S. mining industry.

BACKGROUND: Heat illness is relatively common in the underground metalliferous mines of South Africa and Australia. Little is known about heat illness in other forms of mining and there have been no studies of heat illness in the US mining industry. METHODS: Mine Safety and Health Administration (MSHA) accident, injury, illness, and employment data were used to study heat illness reported by the US mining industry from January 1, 1983 to December 31, 2001. RESULTS: Five hundred thirty eight cases of heat illness were reported. None of these cases were fatal. Four hundred twenty seven cases (79.4%) occurred in the summer months of June, July, and August. Incidence rates of heat illness in underground mining ranged from 0.00275/10(6) person-hours for coal, to 0.168/10(6) person-hours for metal, rate-ratio = 61.1 (P < 0.001). Incidence rates in surface mining ranged from 0.0265/10(6) person-hours for coal, to 0.0644/10(6) person-hours for stone, rate-ratio = 2.43 (P < 0.001). Incidence rates in mills/preparation plants ranged from 0.0255/10(6) person-hours for coal, to 0.417/10(6) person-hours for stone, rate-ratio = 16.4 (P < 0.001). CONCLUSIONS: Heat illness occurs most frequently in stone mills, metal mills, and underground metal mines. Preventive measures should target the summer months of June, July, and August.

Adolescent↗
PubMed1998

Intercomparison of radon and decay product measurements in an underground mine and EPA Radon Laboratory: a study organized by the IAEA International Radon Metrology Programme. International Atomic Energy Agency.

The International Atomic Energy Agency (IAEA) in Vienna and the European Union (EU) in Bruxelles formed the "International Radon Metrology Programme" (IRMP, scientific secretary: F. Steinhäusler, University of Salzburg, Austria). The IRMP is designed to assess and foster the improvement of radon and decay product measurements that are made around the world. Within the framework of the IRMP, the U.S. Environmental Protection Agency Radiation and Indoor Environments National Laboratory (EPA) in Las Vegas, Nevada, organized jointly with the U.S. Bureau of Mines an international intercomparison exercise at a former uranium mine (Twilight Mine, Colorado) and the EPA Radon Laboratory. The main objective of this exercise was to compare radon and radon decay product instruments under both well-controlled as well as widely fluctuating exposure conditions. The laboratory exposures occurred under relatively steady radon and decay product conditions, with a moderate equilibrium ratio, while the conditions in the mine fluctuated greatly and the equilibrium ratio was low. An additional purpose of the exercise was to provide a forum for manufacturers and measurement organizations worldwide to exchange information and plan improvements in their operations and calibration programs. Altogether 19 organizations from seven countries intercomparing 32 different radon and radon decay product instruments participated in this exercise. This paper summarizes the results from the analysis of the experimental data obtained in the Bureau of Mines Twilight Mine in July of 1994, as well as the results from the EPA Radon laboratory in August of 1994.

Calibration↗
PubMed2006

Soil risk assessment of As and Zn contamination in a coal mining region using geostatistics [corrected].

The present paper aims to map As and Zn contamination and assess the risk for agricultural soils in a wider disposal site containing wastes derived from coal beneficiation. Geochemical data related to environmental studies show that the waste characteristics favor solubilisation and mobilization of inorganic contaminants and in some cases the generation of acidic leachates. 135 soil samples were collected from a 34 km(2) area and analysed by using geostatistics under the maximum entropy principle in order to produce risk assessment maps and estimate the probability of soil contamination. In addition, the present paper discusses the main issues related to risk assessment in wider mining and waste disposal sites in order to assist decision makers in selecting feasible rehabilitation schemes.

Arsenic↗
PubMed2004

Translocation of transposition-deficient (TndPKLH2-like) transposons in the natural environment: mechanistic insights from the study of adjacent DNA sequences.

A family of plasmid-borne DNA fragments of different length, apparently inherited from an ancient plasmid, has been identified in the world population of environmental Acinetobacter strains. These fragments, named PPFs (parental plasmid DNA fragments), were >/=99.8 % identical to each other in the common regions, and contained in their central region a variant of an aberrant mercury-resistance transposon (Tn(d)PKLH2) that has lost its transposition genes. As a rule, recombinogenic elements were found at the breakpoints of identity between the different PPFs. Of these recombinogenic elements, a newly identified IS6 family element, a transposon, or a resolvase gene interrupted one end of the PPFs. At the opposite end, the breakpoint of some PPFs was mapped to the recombination point within, in each case, a different variant of a res site (RS2), whilst in other PPFs, this end was eroded by insertion of a newly identified IS6 family element. On the basis of DNA sequence data, possible mechanisms of translocation of defective Tn(d)PKLH2-like elements via recombination events implicating the nearby res (resolution) site and IS element are proposed.

Acinetobacter↗
PubMed2006

Diesel exhaust and coal mine dust: lung cancer risk in occupational settings.

Conflicting evidence on the carcinogenicity of diesel exhaust (DE) and coal mine dust in occupational settings exist. Exposure measurement in most studies is inferred on the basis of job classifications and may lead to misclassification. Confounding behavioral factors (i.e., smoking) and occupational risk factors (exposure to asbestos, arsenic, radon) need to be considered. We evaluated the epidemiological evidence and current findings of the carcinogenicity of DE and coal mine dust in occupational settings. Pertaining literature was identified through Medline search and recent review articles. Strengths and limitations of recent approaches are discussed. Many epidemiological studies have addressed the question of carcinogenicity in workers exposed to DE, and most showed a low-to-medium increase in the risk of bronchial carcinoma. The pooled relative risk (RR) estimates lie between 1.33 and 1.47, and a consistent rise in risk across various job categories and study designs point to a causal relationship. Data on the carcinogenicity of coal mine dust are less consistent and the potential for confounding by unmeasured risk factors (arsenic, radon, DE) are higher. While silica as one of its components has been evaluated as carcinogenic, there is inadequate evidence for the carcinogenicity of pure coal dust according to the International Agency for Research on Cancer (IARC). There is sufficient evidence for a causal relationship between DE and lung cancer in occupational settings. The evidence for coal mine dust is less convincing, but individual studies show an increase in risk of lung cancer in exposed workers.

Animals↗