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At least 1,189 records · Page 66Linked to original sources
PubMed2006

Genomic comparison using data mining techniques based on a possibilistic fuzzy sets model.

Current copiousness of genomic information stored in biological databases [Mar Albà, M., Lee, M., Pearl, D., Shepherd, F.M.G., Martin, A.J., Orengo, N., Kellam, C.A., 2001. P. VIDA: a virus database system for the organisation of virus genome open reading frames. Nuleic Acids Res. 133-136] makes ultimately feasible the proposal for an application of knowledge management aimed to discover general rules in subcellular phenomena. The goal of this work is primarily to discover relationships between genes by microarray analysis. The tools exploited come from clustering techniques and are mainly based on Knowledge Discovery in Databases (KDD) concepts [Fayyad, U., Piatetsky-Shapiro, G., Smyth, P., 1996. From data mining to knowledge discovery in databases. AI Magazine 17(3), 37-54]. Starting from a data set, each element can be represented by a characteristic matrix, which sums up all data attributes. In this case data mining is oriented to perform a Pattern Recognition of related sequences, hidden in databases [Hand, D.J., Nicholas, A., 2005. Heard finding groups in gene expression data. J. Biomed. Biotechnol. 215-225]. Following a bottom up approach, the next refinement is to compare retrieved data to gather similar features, by dedicated clustering algorithms [Kaufman, L., Rousseeuw, P.J., 1990. Finding groups in data. An Introduction to Cluster Analysis. John Wiley & Sons, New York; Forman, G., Zhang, B., 2000. Distributed Data clustering can be efficient and exact HP. Laboratories Palo Alto HPL-2000, p. 158], driven by fuzzy logic, allowing us to perceive by intuition a common denominator for various genomic families and to anticipate likely future developments.

Algorithms↗
PubMed2005

Metal binding by bacteria from uranium mining waste piles and its technological applications.

Uranium mining waste piles, heavily polluted with radionuclides and other toxic metals, are a reservoir for bacteria that have evolved special strategies to survive in these extreme environments. Understanding the mechanisms of bacterial adaptation may enable the development of novel bioremediation strategies and other technological applications. Cell isolates of Bacillus sphaericus JG-A12 from a uranium mining waste pile in Germany are able to accumulate high amounts of toxic metals such as U, Cu, Pb, Al, and Cd as well as precious metals. Some of these metals, i.e. U, Cu, Pd(II), Pt(II) and Au(III), are also bound by the highly orderd paracrystalline proteinaceous surface layer (S-layer) that envelopes the cells of this strain. These special capabilities of the cells and the S-layer proteins of B. sphaericus JG-A12 are highly interesting for the clean-up of uranium contaminated waste waters, for the recovery of precious metals from electronic wastes, and for the production of metal nanoclusters. The fabricated nanoparticles are promising for the development of novel catalysts. This work reviews the molecular biology of the S-layer of the strain JG-A12 and the S-layer dependent interactions of the bacterial cells with metals. It presents future perspectives for their application in bioremediation and nanotechnology.

Bacillus↗
PubMed2006

Data mining and visualization for decision support and modeling of public health-care resources.

This paper proposes an innovative use of data mining and visualization techniques for decision support in planning and regional-level management of Slovenian public health-care. Data mining and statistical techniques were used to analyze databases collected by a regional Public Heath Institute. We also studied organizational aspects of public health resources in the selected Celje region with the objective to identify the areas that are atypical in terms of availability and accessibility of public health services for the population. The most important step was the detection of outliers and the analysis of availability and accessibility deviations. The results are applicable to health-care planning and support in decision making by local and regional health-care authorities. In addition to the practical results, which are directly useful for decision making in planning of the regional health-care system, the main methodological contribution of the paper are the developed visualization methods that can be used to facilitate knowledge management and decision making processes.

Database Management Systems↗
PubMed2026

In silico genome mining and characterization of putative horse feces-derived bacterial phytases as potential monogastric animal feed additive candidates.

Phytic acid exerts a significant antinutritional effect in poultry, swine, and fish, which can be mitigated by supplementing monogastric feeds with efficient microbial phytases. Accordingly, mining bacterial genomes for novel phytases represents a strategic computational approach to identifying candidates for improving monogastric animal nutrition. In this study, 162 bacterial genomes associated with horse feces were systematically mined using an in silico pipeline to identify and characterize putative phytases.A total of 69 non-redundant sequences were identified and classified as histidine acid phytase (HAPhy) or protein tyrosine phosphatase-like phytase (PTPLPhy). HAPhys were detected in the genomes of Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Acinetobacter baumannii, and Cutibacterium equinum, whereas PTPLPhys were found in K. pneumoniae, Limosilactobacillus reuteri, Pediococcus acidilactici, Bifidobacterium pseudolongum, and Prescottella equi. Principal component analysis identified glucose-1-phosphatase (CAJ1242485.1) and bifunctional acid phosphatase (NHR17779.1) as the HAPhy candidates exhibiting the most favorable predicted physicochemical properties for potential feed applications. Similarly, among the PTPLPhys, protein tyrosine phosphatase (UNQ40438.1) and a hypothetical protein (CAJ1246072.1) showed the most favorable computational profiles. Biosafety analysis identified potential virulence factors, indicating that sources should be screened prior to feed application. High-quality AlphaFold2 models were obtained for these phytases (90.9-97.2). Molecular docking analysis showed that NHR17779.1 exhibited the strongest binding to phytic acid, whereas CAJ1246072.1 demonstrated the weakest interaction. Overall, this study identifies the horse fecal microbiota as a diverse source of putative phytases that may serve as promising targets for genetic and protein engineering; however, further in vitro and in vivo studies are essential to validate the enzymatic activity and industrial efficacy of these computational candidates.

Bacterial phytase↗
PubMed2006

A sediment quality triad assessment of the impact of copper mine tailings disposal on the littoral sedimentary environment in the Atacama region of northern Chile.

A sediment quality triad (SQT) assessment was made of the impact of copper mine tailings disposal on littoral meiofaunal assemblages in the Atacama region of northern Chile. This situation is unusual in that the disposal is direct into the high-energy coastal system and not via a river estuary or other low-energy environment. This situation also allows for the examination of the impact of copper mine tailings in the absence of confounding effects from other pollutants. The three components of the SQT were: 1. an analysis of the bioavailable metals in both the sedimentary porewater and the adjacent seawater, 2. a microcosm bioassay of both sediments and seawaters using meiofaunal assemblages, and 3. quantitative field samples of the meiofaunal assemblages. Twelve study sites with varying degrees of impact were used, including three reference sites. The study identified that both the meiofaunal assemblage densities and taxa diversities decrease with increasing levels of bioavailable copper, that the Foraminifera and Harpacticoida are sensitive to copper, and that otoplanid Turbellaria are often characteristic of impacted sites; tailings also have both chemical and physical impacts on the environment. In some cases the physical impact of tailings is more important in excluding some organisms e.g. the interstitial polychaete, Saccocirrus sonomacus, from a site than is their chemical impact.

Animals↗
PubMed2006

In silico mining in expressed sequences of Neurospora crassa for identification and abundance of microsatellites.

In the present study, 3217 UniGene sequences of Neurospora crassa downloaded from the National Center for Biotechnology Information (NCBI) were mined for the identification of microsatellites or simple sequence repeats (SSRs). A total of 287 SSRs detected gives density of 1SSR/14.6 kb of 4187.86 kb sequences mined suggests that only 250 (7.8%) of sequences contained SSRs. Depending on the repeat units, the length of SSRs ranged from 14 to 17 bp for mono-, 14 to 48 bp for di-, 18 to 90 bp for tri-, 24 to 48 bp for tetra-, 30 for penta- and 42 to 48 bp for hexa-nucleotide repeats. Tri-nucleotide repeats were the most frequent repeat type (88.8%) followed by di-nucleotide repeats (5.9%). An attempt was also made with the help of bioinformatics approach to find out primer pairs for identified SSRs and primers were found only for 239 sequences. But, this part needs experimental validation. Annotation of SSRs containing sequences was also carried out.

Computational Biology↗
PubMed2004

Data mining of Mycobacterium tuberculosis complex genotyping results using mycobacterial interspersed repetitive units validates the clonal structure of spoligotyping-defined families.

Recently, a combination of spoligotyping and bioinformatics was proposed as a potential tool for defining major circulating clades of tuberculosis bacilli. In the present study, we attempted to validate the above mentioned classification using a new high-throughput marker, named mycobacterial interspersed repetitive units (MIRUs). Using 12 MIRU loci and spoligotyping, we performed data mining of results on clinical isolates of the Mycobacterium tuberculosis complex representative of global mycobacterial allelic diversity. Knowledge rules permitting automatic labeling of major M. tuberculosis families were defined. Using this strategy, MIRU 24 appeared to be most appropriate for classifying our dataset. The Bovis family was shown to be perfectly classified by a maximum of 3 MIRUs, followed by Africanum and East African Indian (EAI) families by 4 MIRUs, the Beijing family by 6 MIRUs, Haarlem and X families by 8 MIRUs, the T family by 9, and the Latin-American and Mediterranean (LAM) family by 10 MIRUs. Considering the hierarchy of family divergence, our results corroborate a recent suggestion that EAI is the ancestral family followed by Africanum and Bovis. On the other hand, T, X, LAM and Haarlem families appear to be of more recent evolution. These results indicate that data mining of MIRUs is a valuable new tool for analyzing the evolutionary dynamics of the M. tuberculosis complex, and for monitoring an infectious disease such as tuberculosis.

Bacterial Typing Techniques↗
PubMed2004

SEM-EDX analysis in the source apportionment of particulate matter on Hypogymnia physodes lichen transplants around the Cu smelter and former mining town of Karabash, South Urals, Russia.

Scanning electron microscopy with energy-dispersive X-ray analysis (SEM-EDX) of particulate matter on lichen transplant thalli (Hypogymnia physodes) was assessed as a complementary technique to wet chemical analysis for source apportionment of airborne contaminants. Transplants (2 month exposure) stationed in the Cu smelter and former mining town of Karabash were compared with those from a control site 30 km south. Particulate matter in Karabash samples (715 analyses) showed higher levels of S, Pb, Cu, Sn and Zn compared with the control (598 analyses). Complex element associations among the particles confounded detailed mineralogical identifications, and therefore a simplified particle classification scheme was devised for source apportionment. Karabash samples contained high levels of particles classified as mining-related (MRP), and these were also identified in control samples, indicating wide spatial dispersion from the smelter and highlighting the sensitivity of the method. It was noted that MRP <2.5-microm diameter were poorly represented on lichen surfaces suggesting this may limit the usefulness of Hypogymnia transplants as proxies when assessing human health impacts from airborne particulates. Analyses of the lichen thallus surface (away from surface particulates) revealed high levels of Cu, Zn, Fe and Pb associated with organics in the Karabash samples compared with the control, with a proportionate loss of K, interpreted as being due to a stress-related increase in cell membrane permeability. This type of analysis may provide a novel SEM-EDX-based method for assessing lichen vitality. The techniques developed are presented and further implications of the study are discussed.

Air Pollutants↗
PubMed2005

Release of toxic metals and metalloids from Los Rueldos mercury mine (Asturias, Spain).

The abandoned mercury mining works of "Los Rueldos" are located 20 km from Oviedo, along the northwestern border of the Asturian Central Coal Basin, in an area with intense tectonization. Hg mainly appears as cinnabar, but occasionally metacinnabar and native Hg are present; associated with Hg ore appear As-rich minerals (arsenopyrite, As-rich pyrite, realgar and scorodite). In the spoil heap, Hg content ranges from 14 to 2224 mg kg(-1), and As from 4746 to 62,196 mg kg(-1). Mine drainage and spoil heap leachates show acidic conditions (pH: 2.43-2.50), 2900-4600 mg l(-1) sulphate, 1.4-9.2 mg l(-1) As, 0.03-0.48 mg l(-1) Pb, and 3.6-14 microg l(-1) Hg. According to the analytical data and characteristics of the site, the application of corrective measurements to avoid the dispersion of contaminants in the environment must be considered.

Journal Article↗
PubMed2005

Modeling of geochemical processes related to uranium mobilization in the groundwater of a uranium mine.

This paper describes the processes leading to uranium distribution in the groundwater of five boreholes near a restored uranium mine (dug in granite), and the environmental impact of restoration work in the discharge area. The groundwater uranium content varied from <1 microg/L in reduced water far from the area of influence of the uranium ore-containing dyke, to 104 microg/L in a borehole hydraulically connected to the mine. These values, however, fail to reflect a chemical equilibrium between the water and the pure mineral phases. A model for the mobilization of uranium in this groundwater is therefore proposed. This involves the percolation of oxidized waters through the fractured granite, leading to the oxidation of pyrite and arsenopyrite and the precipitation of iron oxyhydroxides. This in turn leads to the dissolution of the primary pitchblende and, subsequently, the release of U(VI) species to the groundwater. These U(VI) species are retained by iron hydroxides. Secondary uranium species are eventually formed as reducing conditions are re-established due to water-rock interactions.

Journal Article↗
PubMed2006

Text mining and its potential applications in systems biology.

With biomedical literature increasing at a rate of several thousand papers per week, it is impossible to keep abreast of all developments; therefore, automated means to manage the information overload are required. Text mining techniques, which involve the processes of information retrieval, information extraction and data mining, provide a means of solving this. By adding meaning to text, these techniques produce a more structured analysis of textual knowledge than simple word searches, and can provide powerful tools for the production and analysis of systems biology models.

Artificial Intelligence↗
PubMed2005

Multievidence microarray mining.

Microarray mining is a challenging task because of the superposition of several processes in the data. We believe that the combination of microarray data-based analyses (statistical significance analysis of gene expression) with array-independent analyses (literature-mining and promoter analysis) enables some of the problems of traditional array analysis to be overcome. As a proof-of-principle, we revisited publicly available microarray data derived from an experiment with platelet-derived growth factor (PDGF)-stimulated fibroblasts. Our strategy revealed results beyond the detection of the major metabolic pathway known to be linked to the PDGF response: we were able to identify the crosstalking regulatory networks underlying the metabolic pathway without using a priori knowledge about the experiment.

Computational Biology↗
PubMed2004

Effect of coal mine dust and clay extracts on the biological activity of the quartz surface.

Modification of the quartz surface by aluminium salts and metallic iron have been shown to reduce the biological activity of quartz. This study aimed to investigate the ability of water soluble extracts of coal mine dust (CMD), low aluminium clays (hectorite and montmorillonite) and high aluminium clays (attapulgite and kaolin) to inhibit the reactivity of the quartz surface. DQ12 induced significant haemolysis of sheep erythrocytes in vitro and inflammation in vivo as indicated by increases in the total cell numbers, neutrophil cell numbers, MIP-2 protein and albumin content of bronchoalveolar lavage (BAL) fluid. Treatment of DQ12 with CMD extract prevented both haemolysis and inflammation. Extracts of the high aluminium clays (kaolin and attapulgite) prevented inhibition of DQ12 induced haemolysis, and the kaolin extract inhibited quartz driven inflammation. DQ12 induced haemolysis by coal mine dust and kaolin extract could be prevented by pre-treatment of the extracts with a cation chellator. Extracts of the low aluminium clays (montmorillonite and hectorite) did not prevent DQ12 induced haemolysis, although the hectorite extract did prevent inflammation. These results suggest that CMD, and clays both low and rich in aluminium, all contain soluble components (possibly cations) capable of masking the reactivity of the quartz surface.

Administration, Inhalation↗
PubMed2004

Lead in residential soil and dust in a mining and smelting district in northern Armenia: a pilot study.

This pilot study of sources of lead exposure in residential settings was conducted in a mining and smelting district in northern Armenia. Samples of exterior soil and dust and interior house dust were collected in and around apartment buildings in Alaverdi where the country's largest polymetallic smelter is located, and in nearby mining towns of Aghtala and Shamlugh. The NITON XL-723 Multi-Element XRF analyzer was used for lead testing. Lead levels in samples from Alaverdi were higher than those in Shamlugh and Aghtala. In all three towns, the highest lead levels were found in loose exterior dust samples, and lead concentrations in yard soil were higher than those in garden soil. Many soil samples (34%) and the majority of loose dust samples (77%) in Alaverdi exceeded the US Environmental Protection Agency standard of 400 mg/kg for bare soil in children's play areas. In addition, 36% of floor dust samples from apartments in Alaverdi exceeded the US Environmental Protection Agency standard of 40 microg/ft(2) for lead loading in residential floor dust. The Armenian Ministry of Health and other interested agencies are being informed about the findings of the study so that they can consider and develop educational and preventive programs including blood lead screening among sensitive populations.

Armenia↗
PubMed2001

Reviewing mobile phases used on Chiralcel OD through an application of data mining tools to CHIRBASE database.

During the past decade, thousands of compounds have been resolved on Chiralcel OD (a cellulose-based chiral stationary phase) under diverse eluting conditions. Many researches have documented the effects of mobile phase on enantioselectivity for a given family of samples but today no comprehensive study aimed at identifying the associations between the structural features present on solute and appropriate mobile phase conditions has yet been proposed. In this review of mobile phases used on Chiralcel OD, we try to go far beyond a simple enumeration of eluting conditions and an effort is made to explore the utility of data mining tools for assessing the knowledge contained in CHIRBASE database. We have extracted from CHIRBASE the chemical features of 2363 chiral compounds separated on Chiralcel OD and their corresponding mobile phases. This data set was submitted to data mining programs for molecular pattern recognition and mobile phase predictions for new cases. Some substructural characteristics of solutes were related to the efficient use of some specific mobile phases. For example, the application of CH3CN/salt buffer at pH 6-7 was found convenient for reversed-phase separation of compounds bearing a tertiary amine functional group. Furthermore, a cluster analysis allowed the arrangement of the mobile phases according to similarity found in molecular patterns of solutes. A decision tree, which may lead to a more rational choice of the mobile phase under reversed-phase conditions, is also proposed.

Carbamates↗
PubMed2002

Selenium and its redox speciation in rainwater from sites of Valparaiso region in Chile, impacted by mining activities of copper ores.

The determination of the total concentration of selenium does not provide sufficient information about its toxicity and its bioavailability. The determination of its chemical forms is the basis for understanding the biogeochemical cycle in terrestrial and aquatic ecosystems and for detecting the species which might be toxic to biota. In this work we describe an analytical procedure to carry out the redox speciation of selenium present at ultratrace levels in rainwater from sites of Valparaiso region in Chile, impacted by mining activities of copper ores. A simple preconcentration step of the rainwater sample on a rotavapor system, in vacuum at low temperature permits the concentration of the different redox selenium species until levels quantifiable by sensitive techniques such as differential pulse cathodic stripping voltammetry or by spectrometric techniques, based on the hydride generation and detection by atomic absorption or atomic fluorescence spectrometry. These techniques coupled to redox chemical reactions allow the redox speciation of selenium. The results show that the open evaporation system can be used to concentrate water samples when the aim of the analysis is the determination of the total selenium concentration. On the contrary, to carry out its redox speciation only the preconcentration performed on rotavapor system, in vacuum can be used. When synthetic solutions containing different redox species of selenium, at ultratrace levels, were slowly evaporated on open system, Se(II) and Se(IV) were oxidized. The optimized procedure was then applied to the selenium determination and its redox speciation in rainwater samples collected in sites impacted by mining activities of copper ores. It was found that the amounts of total selenium in rainwater, as copper, from Puchuncavi valley decrease exponentially with the distance from the source, indicating that these elements in this region arise from the industrial complex Las Ventanas. In the redox speciation of selenium, Se(IV) and Se(VI) were the species found in all rainwater samples analyzed, providing selenium in species which are most favorable for their uptake by the vegetation grown in these soils.

Biological Availability↗
PubMed2001

10-year experience of injuries sustained during clearance of anti-personnel mines.

Clearance of anti-personnel mines and unexploded ordnance in countries recovering from war usually continues long after conflict has ceased. We prospectively recorded 92 traumatic injuries sustained by 73 mineclearers working in seven countries over a period of 10 years. 15% of injuries were fatal, with an incidence of 116 injuries per 100000 workers per year. Limb injury occurred in 59% of cases, with an overall amputation rate of 30%. 44% of injuries were sustained by workers handling a mine, resulting in severe upper limb and facial injuries. The incidence of facial injuries fell after the introduction of visors.

Adult↗
PubMed2000

Marine macroalgal community structure, metal content and reproductive function near an acid mine drainage outflow.

Marine macroalgal communities were examined near the outflow of acid mine drainage (AMD) from the Britannia Mine, British Columbia, Canada. No marine algae were present within 100 m of the mouth of Britannia Creek, which carries the AMD into the marine environment. At greater distances (300-700 m) from this Creek, mean summer cover of filamentous green algae, mostly Enteromorpha intestinalis, was >60%, which was significantly higher than at nearby reference stations. At still greater distances (600-1000 m) from Britannia Creek, Fucus gardneri dominated algal communities that were similar to those at reference stations. No consistent differences were detected in mean plant length, mean per cent cover or mean oocyte production between F. gardneri near Britannia Creek and those at reference stations. Cu body burden in F. gardneri near Britannia Creek was five to 17 times higher than in reference plants.

Journal Article↗