WorldWideScience

Sample records for automated genome mining

  1. Automated genome mining for natural products

    Directory of Open Access Journals (Sweden)

    Zajkowski James

    2009-06-01

    Full Text Available Abstract Background Discovery of new medicinal agents from natural sources has largely been an adventitious process based on screening of plant and microbial extracts combined with bioassay-guided identification and natural product structure elucidation. Increasingly rapid and more cost-effective genome sequencing technologies coupled with advanced computational power have converged to transform this trend toward a more rational and predictive pursuit. Results We have developed a rapid method of scanning genome sequences for multiple polyketide, nonribosomal peptide, and mixed combination natural products with output in a text format that can be readily converted to two and three dimensional structures using conventional software. Our open-source and web-based program can assemble various small molecules composed of twenty standard amino acids and twenty two other chain-elongation intermediates used in nonribosomal peptide systems, and four acyl-CoA extender units incorporated into polyketides by reading a hidden Markov model of DNA. This process evaluates and selects the substrate specificities along the assembly line of nonribosomal synthetases and modular polyketide synthases. Conclusion Using this approach we have predicted the structures of natural products from a diverse range of bacteria based on a limited number of signature sequences. In accelerating direct DNA to metabolomic analysis, this method bridges the interface between chemists and biologists and enables rapid scanning for compounds with potential therapeutic value.

  2. Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products.

    Directory of Open Access Journals (Sweden)

    Marnix H Medema

    2014-09-01

    Full Text Available Nonribosomally and ribosomally synthesized bioactive peptides constitute a source of molecules of great biomedical importance, including antibiotics such as penicillin, immunosuppressants such as cyclosporine, and cytostatics such as bleomycin. Recently, an innovative mass-spectrometry-based strategy, peptidogenomics, has been pioneered to effectively mine microbial strains for novel peptidic metabolites. Even though mass-spectrometric peptide detection can be performed quite fast, true high-throughput natural product discovery approaches have still been limited by the inability to rapidly match the identified tandem mass spectra to the gene clusters responsible for the biosynthesis of the corresponding compounds. With Pep2Path, we introduce a software package to fully automate the peptidogenomics approach through the rapid Bayesian probabilistic matching of mass spectra to their corresponding biosynthetic gene clusters. Detailed benchmarking of the method shows that the approach is powerful enough to correctly identify gene clusters even in data sets that consist of hundreds of genomes, which also makes it possible to match compounds from unsequenced organisms to closely related biosynthetic gene clusters in other genomes. Applying Pep2Path to a data set of compounds without known biosynthesis routes, we were able to identify candidate gene clusters for the biosynthesis of five important compounds. Notably, one of these clusters was detected in a genome from a different subphylum of Proteobacteria than that in which the molecule had first been identified. All in all, our approach paves the way towards high-throughput discovery of novel peptidic natural products. Pep2Path is freely available from http://pep2path.sourceforge.net/, implemented in Python, licensed under the GNU General Public License v3 and supported on MS Windows, Linux and Mac OS X.

  3. Automation and robotics technology for intelligent mining systems

    Science.gov (United States)

    Welsh, Jeffrey H.

    1989-01-01

    The U.S. Bureau of Mines is approaching the problems of accidents and efficiency in the mining industry through the application of automation and robotics to mining systems. This technology can increase safety by removing workers from hazardous areas of the mines or from performing hazardous tasks. The short-term goal of the Automation and Robotics program is to develop technology that can be implemented in the form of an autonomous mining machine using current continuous mining machine equipment. In the longer term, the goal is to conduct research that will lead to new intelligent mining systems that capitalize on the capabilities of robotics. The Bureau of Mines Automation and Robotics program has been structured to produce the technology required for the short- and long-term goals. The short-term goal of application of automation and robotics to an existing mining machine, resulting in autonomous operation, is expected to be accomplished within five years. Key technology elements required for an autonomous continuous mining machine are well underway and include machine navigation systems, coal-rock interface detectors, machine condition monitoring, and intelligent computer systems. The Bureau of Mines program is described, including status of key technology elements for an autonomous continuous mining machine, the program schedule, and future work. Although the program is directed toward underground mining, much of the technology being developed may have applications for space systems or mining on the Moon or other planets.

  4. Comparative genomics using data mining tools

    Indian Academy of Sciences (India)

    Unknown

    1 | February 2002. Comparative genomics using data mining tools. 17 where L is the length of the concerned protein in amino acids and fi is the average frequency of occurrence of the ith amino acid in the set of proteins that are of high sequence complexity and are predicted to have globular fold within the same genome.

  5. Genomics Portals: integrative web-platform for mining genomics data.

    Science.gov (United States)

    Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

    2010-01-13

    A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  6. Genomics Portals: integrative web-platform for mining genomics data

    Science.gov (United States)

    2010-01-01

    Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org. PMID:20070909

  7. Comparative genomics using data mining tools

    Indian Academy of Sciences (India)

    We have analysed the genomes of representatives of three kingdoms of life, namely, archaea, eubacteria and eukaryota using data mining tools based on compositional analyses of the protein sequences. The representatives chosen in this analysis were Methanococcus jannaschii, Haemophilus influenzae and ...

  8. Comparative genomics using data mining tools

    Indian Academy of Sciences (India)

    Unknown

    We have analysed the genomes of representatives of three kingdoms of life, namely, archaea, eubacteria and eukaryota using data mining tools based on compositional analyses of the protein sequences. The repre- sentatives chosen in this analysis were Methanococcus jannaschii, Haemophilus influenzae and ...

  9. Text mining from ontology learning to automated text processing applications

    CERN Document Server

    Biemann, Chris

    2014-01-01

    This book comprises a set of articles that specify the methodology of text mining, describe the creation of lexical resources in the framework of text mining and use text mining for various tasks in natural language processing (NLP). The analysis of large amounts of textual data is a prerequisite to build lexical resources such as dictionaries and ontologies and also has direct applications in automated text processing in fields such as history, healthcare and mobile applications, just to name a few. This volume gives an update in terms of the recent gains in text mining methods and reflects

  10. Automation of mining machinery at RAG; Automation von Bergbaumaschinen bei der RAG Deutsche Steinkohle

    Energy Technology Data Exchange (ETDEWEB)

    Barabasch, Uwe [Zentralstab Kernbereich, RAG Deutsche Steinkohle AG, Herne (Germany); Weiss, Hans-Juergen [Bergwerk Prosper-Haniel, RAG Deutsche Steinkohle AG, Bottrop (Germany); Kotke, Frank [Elektrotechnik unter Tage, Zentralstab Kernbereich der RAG Deutsche Steinkohle AG, Herne (Germany)

    2009-11-05

    The improvement of processes specific to mining in the collieries of RAG and the improvement of the ergonomic conditions in the deep coal mining deposits of Germany require a higher degree of automation and control of the processes in progress. A higher degree of automation is also re-quired here for the machinery and systems used. RAG will be consolidating its engineering and research activities in these areas over the coming years. (orig.)

  11. Automated Coal-Mine Shuttle Car

    Science.gov (United States)

    Collins, E. R., Jr.

    1984-01-01

    Cable-guided car increases efficiency in underground coal mines. Unmanned vehicle contains storage batteries in side panels for driving traction motors located in wheels. Batteries recharged during inactive periods or slid out as unit and replaced by fresh battery bank. Onboard generator charges batteries as car operates.

  12. An automated annotation tool for genomic DNA sequences using ...

    Indian Academy of Sciences (India)

    Genomic sequence data are often available well before the annotated sequence is published. We present a method for analysis of genomic DNA to identify coding sequences using the GeneScan algorithm and characterize these resultant sequences by BLAST. The routines are used to develop a system for automated ...

  13. An automated annotation tool for genomic DNA sequences using

    Indian Academy of Sciences (India)

    Genomic sequence data are often available well before the annotated sequence is published. We present a method for analysis of genomic DNA to identify coding sequences using the GeneScan algorithm and characterize these resultant sequences by BLAST. The routines are used to develop a system for automated ...

  14. Automated tools to be used for ascertaining structural condition in South African hard rock mines

    CSIR Research Space (South Africa)

    Teleka, R

    2011-11-01

    Full Text Available The use of automation in deep level hard rock mines has over the years been overshadowed by mechanized mining. However, more and more readily, the industry is starting to recognize the validity of considering automation as an option both...

  15. DPMine Graphical Language for Automation of Experiments in Process Mining

    Directory of Open Access Journals (Sweden)

    S. A. Shershakov

    2014-01-01

    Full Text Available Process mining is a new direction in the field of modeling and analysis of processes, where the use of information from event logs describing the history of the system behavior plays an important role. Methods and approaches used in the process mining are often based on various heuristics, and experiments with large event logs are crucial for the study and comparison of the developed methods and algorithms. Such experiments are very time consuming, so automation of experiments is an important task in the field of process mining. This paper presents the language DPMine developed specifically to describe and carry out experiments on the discovery and analysis of process models. The basic concepts of the DPMine language as well as principles and mechanisms of its extension are described. Ways of integration of the DPMine language as dynamically loaded components into the VTMine modeling tool are considered. An illustrating example of an experiment for building a fuzzy model of the process discovered from the log data stored in a normalized database is given.

  16. Text Mining approaches for automated literature knowledge extraction and representation.

    Science.gov (United States)

    Nuzzo, Angelo; Mulas, Francesca; Gabetta, Matteo; Arbustini, Eloisa; Zupan, Blaz; Larizza, Cristiana; Bellazzi, Riccardo

    2010-01-01

    Due to the overwhelming volume of published scientific papers, information tools for automated literature analysis are essential to support current biomedical research. We have developed a knowledge extraction tool to help researcher in discovering useful information which can support their reasoning process. The tool is composed of a search engine based on Text Mining and Natural Language Processing techniques, and an analysis module which process the search results in order to build annotation similarity networks. We tested our approach on the available knowledge about the genetic mechanism of cardiac diseases, where the target is to find both known and possible hypothetical relations between specific candidate genes and the trait of interest. We show that the system i) is able to effectively retrieve medical concepts and genes and ii) plays a relevant role assisting researchers in the formulation and evaluation of novel literature-based hypotheses.

  17. BEACON: automated tool for Bacterial GEnome Annotation ComparisON

    KAUST Repository

    Kalkatawi, Manal M.

    2015-08-18

    Background Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON’s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/

  18. BEACON: automated tool for Bacterial GEnome Annotation ComparisON.

    Science.gov (United States)

    Kalkatawi, Manal; Alam, Intikhab; Bajic, Vladimir B

    2015-08-18

    Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON's utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27%, while the number of genes without any function assignment is reduced. We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/ .

  19. The evolution of genome mining in microbes – a review

    DEFF Research Database (Denmark)

    Ziemert, Nadine; Alanjary, Mohammad; Weber, Tilmann

    2016-01-01

    the development of these computational approaches during the last decade and shows how the revolution of next generation sequencing methods has led to an evolution of various genome mining approaches, techniques and tools. After a short introduction and brief overview of important milestones, this article...... clusters that await linkage to their encoded natural products. With the development of high-throughput sequencing methods and the wealth of DNA data available, a variety of genome mining methods and tools have been developed to guide discovery and characterisation of these compounds. This article reviews...

  20. Evaluation of Three Automated Genome Annotations for Halorhabdus utahensis

    DEFF Research Database (Denmark)

    Bakke, Peter; Carney, Nick; DeLoache, Will

    2009-01-01

    Genome annotations are accumulating rapidly and depend heavily on automated annotation systems. Many genome centers offer annotation systems but no one has compared their output in a systematic way to determine accuracy and inherent errors. Errors in the annotations are routinely deposited...... in databases such as NCBI and used to validate subsequent annotation errors. We submitted the genome sequence of halophilic archaeon Halorhabdus utahensis to be analyzed by three genome annotation services. We have examined the output from each service in a variety of ways in order to compare the methodology...... and effectiveness of the annotations, as well as to explore the genes, pathways, and physiology of the previously unannotated genome. The annotation services differ considerably in gene calls, features, and ease of use. We had to manually identify the origin of replication and the species-specific consensus...

  1. Highlights of recent articles on data mining in genomics & proteomics

    Science.gov (United States)

    This editorial elaborates on investigations consisting of different “OMICS” technologies and their application to biological sciences. In addition, advantages and recent development of the proteomic, genomic and data mining technologies are discussed. This information will be useful to scientists ...

  2. A new genome-mining tool redefines the lasso peptide biosynthetic landscape.

    Science.gov (United States)

    Tietz, Jonathan I; Schwalen, Christopher J; Patel, Parth S; Maxson, Tucker; Blair, Patricia M; Tai, Hua-Chia; Zakai, Uzma I; Mitchell, Douglas A

    2017-05-01

    Ribosomally synthesized and post-translationally modified peptide (RiPP) natural products are attractive for genome-driven discovery and re-engineering, but limitations in bioinformatic methods and exponentially increasing genomic data make large-scale mining of RiPP data difficult. We report RODEO (Rapid ORF Description and Evaluation Online), which combines hidden-Markov-model-based analysis, heuristic scoring, and machine learning to identify biosynthetic gene clusters and predict RiPP precursor peptides. We initially focused on lasso peptides, which display intriguing physicochemical properties and bioactivities, but their hypervariability renders them challenging prospects for automated mining. Our approach yielded the most comprehensive mapping to date of lasso peptide space, revealing >1,300 compounds. We characterized the structures and bioactivities of six lasso peptides, prioritized based on predicted structural novelty, including one with an unprecedented handcuff-like topology and another with a citrulline modification exceptionally rare among bacteria. These combined insights significantly expand the knowledge of lasso peptides and, more broadly, provide a framework for future genome-mining efforts.

  3. WGSSAT: A High-Throughput Computational Pipeline for Mining and Annotation of SSR Markers From Whole Genomes.

    Science.gov (United States)

    Pandey, Manmohan; Kumar, Ravindra; Srivastava, Prachi; Agarwal, Suyash; Srivastava, Shreya; Nagpure, Naresh S; Jena, Joy K; Kushwaha, Basdeo

    2018-03-16

    Mining and characterization of Simple Sequence Repeat (SSR) markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. Whole genome sequencing (WGS)-SSR Annotation Tool (WGSSAT) is a graphical user interface pipeline developed using Java Netbeans and Perl scripts which facilitates in simplifying the process of SSR mining and characterization. WGSSAT takes input in FASTA format and automates the prediction of genes, noncoding RNA (ncRNA), core genes, repeats and SSRs from whole genomes followed by mapping of the predicted SSRs onto a genome (classified according to genes, ncRNA, repeats, exonic, intronic, and core gene region) along with primer identification and mining of cross-species markers. The program also generates a detailed statistical report along with visualization of mapped SSRs, genes, core genes, and RNAs. The features of WGSSAT were demonstrated using Takifugu rubripes data. This yielded a total of 139 057 SSR, out of which 113 703 SSR primer pairs were uniquely amplified in silico onto a T. rubripes (fugu) genome. Out of 113 703 mined SSRs, 81 463 were from coding region (including 4286 exonic and 77 177 intronic), 7 from RNA, 267 from core genes of fugu, whereas 105 641 SSR and 601 SSR primer pairs were uniquely mapped onto the medaka genome. WGSSAT is tested under Ubuntu Linux. The source code, documentation, user manual, example dataset and scripts are available online at https://sourceforge.net/projects/wgssat-nbfgr.

  4. Whole-Genome Sequencing: Automated, Indexed Library Preparation.

    Science.gov (United States)

    Mardis, Elaine; McCombie, W Richard

    2017-03-01

    This protocol describes an automated procedure for constructing an indexed Illumina DNA library. With this method, genomic DNA fragments are produced by sonication, using high-frequency acoustic energy to shear DNA. Double-stranded DNA (dsDNA) will fragment when exposed to the energy of adaptive focused acoustic shearing (AFA). The resulting DNA fragments are ligated to adaptors, amplified by polymer chain reaction (PCR), and subjected to size selection using magnetic beads. The product is suitable for use as template in whole-genome sequencing. © 2017 Cold Spring Harbor Laboratory Press.

  5. Whole-Genome Sequencing: Automated, Nonindexed Library Preparation.

    Science.gov (United States)

    Mardis, Elaine; McCombie, W Richard

    2017-03-01

    This protocol describes an automated procedure for constructing a nonindexed Illumina DNA library and relies on the use of a CyBi-SELMA automated pipetting machine, the Covaris E210 shearing instrument, and the epMotion 5075. With this method, genomic DNA fragments are produced by sonication, using high-frequency acoustic energy to shear DNA. Here, double-stranded DNA is fragmented when exposed to the energy of adaptive focused acoustic shearing (AFA). The resulting DNA fragments are ligated to adaptors, amplified by polymerase chain reaction (PCR), and subjected to size selection using magnetic beads. The product is suitable for use as template in whole-genome sequencing. © 2017 Cold Spring Harbor Laboratory Press.

  6. Automated genome sequence analysis and annotation.

    Science.gov (United States)

    Andrade, M A; Brown, N P; Leroy, C; Hoersch, S; de Daruvar, A; Reich, C; Franchini, A; Tamames, J; Valencia, A; Ouzounis, C; Sander, C

    1999-05-01

    Large-scale genome projects generate a rapidly increasing number of sequences, most of them biochemically uncharacterized. Research in bioinformatics contributes to the development of methods for the computational characterization of these sequences. However, the installation and application of these methods require experience and are time consuming. We present here an automatic system for preliminary functional annotation of protein sequences that has been applied to the analysis of sets of sequences from complete genomes, both to refine overall performance and to make new discoveries comparable to those made by human experts. The GeneQuiz system includes a Web-based browser that allows examination of the evidence leading to an automatic annotation and offers additional information, views of the results, and links to biological databases that complement the automatic analysis. System structure and operating principles concerning the use of multiple sequence databases, underlying sequence analysis tools, lexical analyses of database annotations and decision criteria for functional assignments are detailed. The system makes automatic quality assessments of results based on prior experience with the underlying sequence analysis tools; overall error rates in functional assignment are estimated at 2.5-5% for cases annotated with highest reliability ('clear' cases). Sources of over-interpretation of results are discussed with proposals for improvement. A conservative definition for reporting 'new findings' that takes account of database maturity is presented along with examples of possible kinds of discoveries (new function, family and superfamily) made by the system. System performance in relation to sequence database coverage, database dynamics and database search methods is analysed, demonstrating the inherent advantages of an integrated automatic approach using multiple databases and search methods applied in an objective and repeatable manner. The GeneQuiz system

  7. Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology

    Science.gov (United States)

    Ping, Zheng; Siegal, Gene P.; Almeida, Jonas S.; Schnitt, Stuart J.; Shen, Dejun

    2014-01-01

    Background: Genetics and genomics have radically altered our understanding of breast cancer progression. However, the genomic basis of various histopathologic features of breast cancer is not yet well-defined. Materials and Methods: The Cancer Genome Atlas (TCGA) is an international database containing a large collection of human cancer genome sequencing data. cBioPortal is a web tool developed for mining these sequencing data. We performed mining of TCGA sequencing data in an attempt to characterize the genomic features correlated with breast cancer histopathology. We first assessed the quality of the TCGA data using a group of genes with known alterations in various cancers. Both genome-wide gene mutation and copy number changes as well as a group of genes with a high frequency of genetic changes were then correlated with various histopathologic features of invasive breast cancer. Results: Validation of TCGA data using a group of genes with known alterations in breast cancer suggests that the TCGA has accurately documented the genomic abnormalities of multiple malignancies. Further analysis of TCGA breast cancer sequencing data shows that accumulation of specific genomic defects is associated with higher tumor grade, larger tumor size and receptor negativity. Distinct groups of genomic changes were found to be associated with the different grades of invasive ductal carcinoma. The mutator role of the TP53 gene was validated by genomic sequencing data of invasive breast cancer and TP53 mutation was found to play a critical role in defining high tumor grade. Conclusions: Data mining of the TCGA genome sequencing data is an innovative and reliable method to help characterize the genomic abnormalities associated with histopathologic features of invasive breast cancer. PMID:24672738

  8. Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology

    Directory of Open Access Journals (Sweden)

    Zheng Ping

    2014-01-01

    Full Text Available Background: Genetics and genomics have radically altered our understanding of breast cancer progression. However, the genomic basis of various histopathologic features of breast cancer is not yet well-defined. Materials and Methods: The Cancer Genome Atlas (TCGA is an international database containing a large collection of human cancer genome sequencing data. cBioPortal is a web tool developed for mining these sequencing data. We performed mining of TCGA sequencing data in an attempt to characterize the genomic features correlated with breast cancer histopathology. We first assessed the quality of the TCGA data using a group of genes with known alterations in various cancers. Both genome-wide gene mutation and copy number changes as well as a group of genes with a high frequency of genetic changes were then correlated with various histopathologic features of invasive breast cancer. Results: Validation of TCGA data using a group of genes with known alterations in breast cancer suggests that the TCGA has accurately documented the genomic abnormalities of multiple malignancies. Further analysis of TCGA breast cancer sequencing data shows that accumulation of specific genomic defects is associated with higher tumor grade, larger tumor size and receptor negativity. Distinct groups of genomic changes were found to be associated with the different grades of invasive ductal carcinoma. The mutator role of the TP53 gene was validated by genomic sequencing data of invasive breast cancer and TP53 mutation was found to play a critical role in defining high tumor grade. Conclusions: Data mining of the TCGA genome sequencing data is an innovative and reliable method to help characterize the genomic abnormalities associated with histopathologic features of invasive breast cancer.

  9. Genome Mining for antibiotics biosynthesis pathways with antiSMASH 3

    DEFF Research Database (Denmark)

    Weber, Tilmann; Kim, Hyun Uk; Blin, Kai

    2014-01-01

    ://antismash.secondarymetabolites.org). antiSMASH3 currently is the most comprehensive automated genome mining platform for natural product biosynthetic pathways. It automatically screens genomic data of bacteria and fungi for the presence of 24 different types of secondary metabolite biosynthetic pathways. For different classes of secondary...... metabolites, detailed analyses on domain organization, enzyme active sites, and substrate specificities are integrated in the pipeline and allow the prediction of the biosynthetic core-­‐products of the pathways. In addition to tools focusing on the enzymes of the pathways, the identified gene clusters...... are searched compared against different integrated databases to identify homologous (often uncharacterized) gene clusters in other microorganisms, genes encoding the biosynthesis of conserved precursors or related experimentally validated gene clusters. A new module of antiSMASH3 now also provides a direct...

  10. Automated ensemble assembly and validation of microbial genomes

    Science.gov (United States)

    2014-01-01

    Background The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the majority of new genomes, it is important to establish best practices for genome assembly. However, recent evaluations such as GAGE and the Assemblathon have concluded that there is no single best approach to genome assembly. Instead, it is preferable to generate multiple assemblies and validate them to determine which is most useful for the desired analysis; this is a labor-intensive process that is often impossible or unfeasible. Results To encourage best practices supported by the community, we present iMetAMOS, an automated ensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. We demonstrate the utility of the ensemble process on 225 previously unassembled Mycobacterium tuberculosis genomes as well as a Rhodobacter sphaeroides benchmark dataset. On these real data, iMetAMOS reliably produces validated assemblies and identifies potential contamination without user intervention. In addition, intelligent parameter selection produces assemblies of R. sphaeroides comparable to or exceeding the quality of those from the GAGE-B evaluation, affecting the relative ranking of some assemblers. Conclusions Ensemble assembly with iMetAMOS provides users with multiple, validated assemblies for each genome. Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to

  11. Chapter 13: Mining electronic health records in the genomics era.

    Directory of Open Access Journals (Sweden)

    Joshua C Denny

    Full Text Available The combination of improved genomic analysis methods, decreasing genotyping costs, and increasing computing resources has led to an explosion of clinical genomic knowledge in the last decade. Similarly, healthcare systems are increasingly adopting robust electronic health record (EHR systems that not only can improve health care, but also contain a vast repository of disease and treatment data that could be mined for genomic research. Indeed, institutions are creating EHR-linked DNA biobanks to enable genomic and pharmacogenomic research, using EHR data for phenotypic information. However, EHRs are designed primarily for clinical care, not research, so reuse of clinical EHR data for research purposes can be challenging. Difficulties in use of EHR data include: data availability, missing data, incorrect data, and vast quantities of unstructured narrative text data. Structured information includes billing codes, most laboratory reports, and other variables such as physiologic measurements and demographic information. Significant information, however, remains locked within EHR narrative text documents, including clinical notes and certain categories of test results, such as pathology and radiology reports. For relatively rare observations, combinations of simple free-text searches and billing codes may prove adequate when followed by manual chart review. However, to extract the large cohorts necessary for genome-wide association studies, natural language processing methods to process narrative text data may be needed. Combinations of structured and unstructured textual data can be mined to generate high-validity collections of cases and controls for a given condition. Once high-quality cases and controls are identified, EHR-derived cases can be used for genomic discovery and validation. Since EHR data includes a broad sampling of clinically-relevant phenotypic information, it may enable multiple genomic investigations upon a single set of genotyped

  12. Data mining and the human genome

    Energy Technology Data Exchange (ETDEWEB)

    Abarbanel, Henry [The MITRE Corporation, McLean, VA (US). JASON Program Office; Callan, Curtis [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, William [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, Freeman [The MITRE Corporation, McLean, VA (US). JASON Program Office; Hwa, Terence [The MITRE Corporation, McLean, VA (US). JASON Program Office; Koonin, Steven [The MITRE Corporation, McLean, VA (US). JASON Program Office; Levine, Herbert [The MITRE Corporation, McLean, VA (US). JASON Program Office; Rothaus, Oscar [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, Roy [The MITRE Corporation, McLean, VA (US). JASON Program Office; Stubbs, Christopher [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, Peter [The MITRE Corporation, McLean, VA (US). JASON Program Office

    2000-01-07

    As genomics research moves from an era of data acquisition to one of both acquisition and interpretation, new methods are required for organizing and prioritizing the data. These methods would allow an initial level of data analysis to be carried out before committing resources to a particular genetic locus. This JASON study sought to delineate the main problems that must be faced in bioinformatics and to identify information technologies that can help to overcome those problems. While the current influx of data greatly exceeds what biologists have experienced in the past, other scientific disciplines and the commercial sector have been handling much larger datasets for many years. Powerful datamining techniques have been developed in other fields that, with appropriate modification, could be applied to the biological sciences.

  13. Mining of Microbial Genomes for the Novel Sources of Nitrilases

    Science.gov (United States)

    Sharma, Nikhil; Thakur, Neerja; Raj, Tilak; Savitri

    2017-01-01

    Next-generation DNA sequencing (NGS) has made it feasible to sequence large number of microbial genomes and advancements in computational biology have opened enormous opportunities to mine genome sequence data for novel genes and enzymes or their sources. In the present communication in silico mining of microbial genomes has been carried out to find novel sources of nitrilases. The sequences selected were analyzed for homology and considered for designing motifs. The manually designed motifs based on amino acid sequences of nitrilases were used to screen 2000 microbial genomes (translated to proteomes). This resulted in identification of one hundred thirty-eight putative/hypothetical sequences which could potentially code for nitrilase activity. In vitro validation of nine predicted sources of nitrilases was done for nitrile/cyanide hydrolyzing activity. Out of nine predicted nitrilases, Gluconacetobacter diazotrophicus, Sphingopyxis alaskensis, Saccharomonospora viridis, and Shimwellia blattae were specific for aliphatic nitriles, whereas nitrilases from Geodermatophilus obscurus, Nocardiopsis dassonvillei, Runella slithyformis, and Streptomyces albus possessed activity for aromatic nitriles. Flavobacterium indicum was specific towards potassium cyanide (KCN) which revealed the presence of nitrilase homolog, that is, cyanide dihydratase with no activity for either aliphatic, aromatic, or aryl nitriles. The present study reports the novel sources of nitrilases and cyanide dihydratase which were not reported hitherto by in silico or in vitro studies. PMID:28497061

  14. Mining of Microbial Genomes for the Novel Sources of Nitrilases

    Directory of Open Access Journals (Sweden)

    Nikhil Sharma

    2017-01-01

    Full Text Available Next-generation DNA sequencing (NGS has made it feasible to sequence large number of microbial genomes and advancements in computational biology have opened enormous opportunities to mine genome sequence data for novel genes and enzymes or their sources. In the present communication in silico mining of microbial genomes has been carried out to find novel sources of nitrilases. The sequences selected were analyzed for homology and considered for designing motifs. The manually designed motifs based on amino acid sequences of nitrilases were used to screen 2000 microbial genomes (translated to proteomes. This resulted in identification of one hundred thirty-eight putative/hypothetical sequences which could potentially code for nitrilase activity. In vitro validation of nine predicted sources of nitrilases was done for nitrile/cyanide hydrolyzing activity. Out of nine predicted nitrilases, Gluconacetobacter diazotrophicus, Sphingopyxis alaskensis, Saccharomonospora viridis, and Shimwellia blattae were specific for aliphatic nitriles, whereas nitrilases from Geodermatophilus obscurus, Nocardiopsis dassonvillei, Runella slithyformis, and Streptomyces albus possessed activity for aromatic nitriles. Flavobacterium indicum was specific towards potassium cyanide (KCN which revealed the presence of nitrilase homolog, that is, cyanide dihydratase with no activity for either aliphatic, aromatic, or aryl nitriles. The present study reports the novel sources of nitrilases and cyanide dihydratase which were not reported hitherto by in silico or in vitro studies.

  15. Mining the Genome for Therapeutic Targets.

    Science.gov (United States)

    Florez, Jose C

    2017-07-01

    Current pharmacological options for type 2 diabetes do not cure the disease. Despite the availability of multiple drug classes that modulate glycemia effectively and minimize long-term complications, these agents do not reverse pathogenesis, and in practice they are not selected to correct the molecular profile specific to the patient. Pharmaceutical companies find drug development programs increasingly costly and burdensome, and many promising compounds fail before launch to market. Human genetics can help advance the therapeutic enterprise. Genomic discovery that is agnostic to preexisting knowledge has uncovered dozens of loci that influence glycemic dysregulation. Physiological investigation has begun to define disease subtypes, clarifying heterogeneity and suggesting molecular pathways for intervention. Convincing genetic associations have paved the way for the identification of effector transcripts that underlie the phenotype, and genetic or experimental proof of gain or loss of function in select cases has clarified the direction of effect to guide therapeutic development. Genetic studies can also examine off-target effects and furnish causal inference. As this information is curated and made widely available to all stakeholders, it is hoped that it will enhance therapeutic development pipelines by accelerating efficiency, maximizing cost-effectiveness, and raising ultimate success rates. © 2017 by the American Diabetes Association.

  16. Automated system of monitoring and positioning of functional units of mining technological machines for coal-mining enterprises

    Directory of Open Access Journals (Sweden)

    Meshcheryakov Yaroslav

    2018-01-01

    Full Text Available This article is show to the development of an automated monitoring and positioning system for functional nodes of mining technological machines. It describes the structure, element base, algorithms for identifying the operating states of a walking excavator; various types of errors in the functioning of microelectromechanical gyroscopes and accelerometers, as well as methods for their correction based on the Madgwick fusion filter. The results of industrial tests of an automated monitoring and positioning system for functional units on one of the opencast coal mines of Kuzbass are presented. This work is addressed to specialists working in the fields of the development of embedded systems and control systems, radio electronics, mechatronics, and robotics.

  17. AGAPE (Automated Genome Analysis PipelinE for pan-genome analysis of Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Giltae Song

    Full Text Available The characterization and public release of genome sequences from thousands of organisms is expanding the scope for genetic variation studies. However, understanding the phenotypic consequences of genetic variation remains a challenge in eukaryotes due to the complexity of the genotype-phenotype map. One approach to this is the intensive study of model systems for which diverse sources of information can be accumulated and integrated. Saccharomyces cerevisiae is an extensively studied model organism, with well-known protein functions and thoroughly curated phenotype data. To develop and expand the available resources linking genomic variation with function in yeast, we aim to model the pan-genome of S. cerevisiae. To initiate the yeast pan-genome, we newly sequenced or re-sequenced the genomes of 25 strains that are commonly used in the yeast research community using advanced sequencing technology at high quality. We also developed a pipeline for automated pan-genome analysis, which integrates the steps of assembly, annotation, and variation calling. To assign strain-specific functional annotations, we identified genes that were not present in the reference genome. We classified these according to their presence or absence across strains and characterized each group of genes with known functional and phenotypic features. The functional roles of novel genes not found in the reference genome and associated with strains or groups of strains appear to be consistent with anticipated adaptations in specific lineages. As more S. cerevisiae strain genomes are released, our analysis can be used to collate genome data and relate it to lineage-specific patterns of genome evolution. Our new tool set will enhance our understanding of genomic and functional evolution in S. cerevisiae, and will be available to the yeast genetics and molecular biology community.

  18. Understanding social collaboration between actors and technology in an automated and digitised deep mining environment.

    Science.gov (United States)

    Sanda, M-A; Johansson, J; Johansson, B; Abrahamsson, L

    2011-10-01

    The purpose of this article is to develop knowledge and learning on the best way to automate organisational activities in deep mines that could lead to the creation of harmony between the human, technical and the social system, towards increased productivity. The findings showed that though the introduction of high-level technological tools in the work environment disrupted the social relations developed over time amongst the employees in most situations, the technological tools themselves became substitute social collaborative partners to the employees. It is concluded that, in developing a digitised mining production system, knowledge of the social collaboration between the humans (miners) and the technology they use for their work must be developed. By implication, knowledge of the human's subject-oriented and object-oriented activities should be considered as an important integral resource for developing a better technological, organisational and human interactive subsystem when designing the intelligent automation and digitisation systems for deep mines. STATEMENT OF RELEVANCE: This study focused on understanding the social collaboration between humans and the technologies they use to work in underground mines. The learning provides an added knowledge in designing technologies and work organisations that could better enhance the human-technology interactive and collaborative system in the automation and digitisation of underground mines.

  19. Automated training for algorithms that learn from genomic data.

    Science.gov (United States)

    Cilingir, Gokcen; Broschat, Shira L

    2015-01-01

    Supervised machine learning algorithms are used by life scientists for a variety of objectives. Expert-curated public gene and protein databases are major resources for gathering data to train these algorithms. While these data resources are continuously updated, generally, these updates are not incorporated into published machine learning algorithms which thereby can become outdated soon after their introduction. In this paper, we propose a new model of operation for supervised machine learning algorithms that learn from genomic data. By defining these algorithms in a pipeline in which the training data gathering procedure and the learning process are automated, one can create a system that generates a classifier or predictor using information available from public resources. The proposed model is explained using three case studies on SignalP, MemLoci, and ApicoAP in which existing machine learning models are utilized in pipelines. Given that the vast majority of the procedures described for gathering training data can easily be automated, it is possible to transform valuable machine learning algorithms into self-evolving learners that benefit from the ever-changing data available for gene products and to develop new machine learning algorithms that are similarly capable.

  20. Automated detection of hereditary syndromes using data mining.

    Science.gov (United States)

    Evans, S; Lemon, S J; Deters, C A; Fusaro, R M; Lynch, H T

    1997-10-01

    Computer-based data mining methodology applied to family history clinical data can algorithmically create highly accurate, clinically oriented hereditary disease pattern recognizers. For the example of hereditary colon cancer, the data mining's selection of relevant factors to assess for hereditary colon cancer was statistically significant (P recognizer-formulated patterns of hereditary colon cancer were independently confirmed by a clinical expert. Applied to previously analyzed family histories, the recognizer identified the definitive hereditary histories, correctly responded negatively to the putative hereditary histories, and correctly responded negatively to empirically elevated colon cancer risk situations. This capability facilitates patient selection for DNA studies in search of gene mutations. When genetic mutations are included as parameters in a patient database for a genetic disease, the process yields an expert system which characterizes variations in clinical disease presentations in terms of genetic mutations. Such information can greatly improve the efficiency of gene testing.

  1. Event-based text mining for biology and functional genomics.

    Science.gov (United States)

    Ananiadou, Sophia; Thompson, Paul; Nawaz, Raheel; McNaught, John; Kell, Douglas B

    2015-05-01

    The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of 'events', i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research. © The Author 2014. Published by Oxford University Press.

  2. Event-based text mining for biology and functional genomics

    Science.gov (United States)

    Thompson, Paul; Nawaz, Raheel; McNaught, John; Kell, Douglas B.

    2015-01-01

    The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of ‘events’, i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research. PMID:24907365

  3. Automated data mining: an innovative and efficient web-based approach to maintaining resident case logs.

    Science.gov (United States)

    Bhattacharya, Pratik; Van Stavern, Renee; Madhavan, Ramesh

    2010-12-01

    Use of resident case logs has been considered by the Residency Review Committee for Neurology of the Accreditation Council for Graduate Medical Education (ACGME). This study explores the effectiveness of a data-mining program for creating resident logs and compares the results to a manual data-entry system. Other potential applications of data mining to enhancing resident education are also explored. Patient notes dictated by residents were extracted from the Hospital Information System and analyzed using an unstructured mining program. History, examination and ICD codes were obtained and compared to the existing manual log. The automated data History, examination, and ICD codes were gathered for a 30-day period and compared to manual case logs. The automated method extracted all resident dictations with the dates of encounter and transcription. The automated data-miner processed information from all 19 residents, while only 4 residents logged manually. The manual method identified only broad categories of diseases; the major categories were stroke or vascular disorder 53 (27.6%), epilepsy 28 (14.7%), and pain syndromes 26 (13.5%). In the automated method, epilepsy 114 (21.1%), cerebral atherosclerosis 114 (21.1%), and headache 105 (19.4%) were the most frequent primary diagnoses, and headache 89 (16.5%), seizures 94 (17.4%), and low back pain 47 (9%) were the most common chief complaints. More detailed patient information such as tobacco use 227 (42%), alcohol use 205 (38%), and drug use 38 (7%) were extracted by the data-mining method. Manual case logs are time-consuming, provide limited information, and may be unpopular with residents. Data mining is a time-effective tool that may aid in the assessment of resident experience or the ACGME core competencies or in resident clinical research. More study of this method in larger numbers of residency programs is needed.

  4. TCGA4U: A Web-Based Genomic Analysis Platform To Explore And Mine TCGA Genomic Data For Translational Research.

    Science.gov (United States)

    Huang, Zhenzhen; Duan, Huilong; Li, Haomin

    2015-01-01

    Large-scale human cancer genomics projects, such as TCGA, generated large genomics data for further study. Exploring and mining these data to obtain meaningful analysis results can help researchers find potential genomics alterations that intervene the development and metastasis of tumors. We developed a web-based gene analysis platform, named TCGA4U, which used statistics methods and models to help translational investigators explore, mine and visualize human cancer genomic characteristic information from the TCGA datasets. Furthermore, through Gene Ontology (GO) annotation and clinical data integration, the genomic data were transformed into biological process, molecular function, cellular component and survival curves to help researchers identify potential driver genes. Clinical researchers without expertise in data analysis will benefit from such a user-friendly genomic analysis platform.

  5. Automated Comparative Auditing of NCIT Genomic Roles Using NCBI

    Science.gov (United States)

    Cohen, Barry; Oren, Marc; Min, Hua; Perl, Yehoshua; Halper, Michael

    2008-01-01

    Biomedical research has identified many human genes and various knowledge about them. The National Cancer Institute Thesaurus (NCIT) represents such knowledge as concepts and roles (relationships). Due to the rapid advances in this field, it is to be expected that the NCIT’s Gene hierarchy will contain role errors. A comparative methodology to audit the Gene hierarchy with the use of the National Center for Biotechnology Information’s (NCBI’s) Entrez Gene database is presented. The two knowledge sources are accessed via a pair of Web crawlers to ensure up-to-date data. Our algorithms then compare the knowledge gathered from each, identify discrepancies that represent probable errors, and suggest corrective actions. The primary focus is on two kinds of gene-roles: (1) the chromosomal locations of genes, and (2) the biological processes in which genes plays a role. Regarding chromosomal locations, the discrepancies revealed are striking and systematic, suggesting a structurally common origin. In regard to the biological processes, difficulties arise because genes frequently play roles in multiple processes, and processes may have many designations (such as synonymous terms). Our algorithms make use of the roles defined in the NCIT Biological Process hierarchy to uncover many probable gene-role errors in the NCIT. These results show that automated comparative auditing is a promising technique that can identify a large number of probable errors and corrections for them in a terminological genomic knowledge repository, thus facilitating its overall maintenance. PMID:18486558

  6. Automating slope monitoring in mines with terrestrial lidar scanners

    Science.gov (United States)

    Conforti, Dario

    2014-05-01

    Static terrestrial laser scanners (TLS) have been an important component of slope monitoring for some time, and many solutions for monitoring the progress of a slide have been devised over the years. However, all of these solutions have required users to operate the lidar equipment in the field, creating a high cost in time and resources, especially if the surveys must be performed very frequently. This paper presents a new solution for monitoring slides, developed using a TLS and an automated data acquisition, processing and analysis system. In this solution, a TLS is permanently mounted within sight of the target surface and connected to a control computer. The control software on the computer automatically triggers surveys according to a user-defined schedule, parses data into point clouds, and compares data against a baseline. The software can base the comparison against either the original survey of the site or the most recent survey, depending on whether the operator needs to measure the total or recent movement of the slide. If the displacement exceeds a user-defined safety threshold, the control computer transmits alerts via SMS text messaging and/or email, including graphs and tables describing the nature and size of the displacement. The solution can also be configured to trigger the external visual/audio alarm systems. If the survey areas contain high-traffic areas such as roads, the operator can mark them for exclusion in the comparison to prevent false alarms. To improve usability and safety, the control computer can connect to a local intranet and allow remote access through the software's web portal. This enables operators to perform most tasks with the TLS from their office, including reviewing displacement reports, downloading survey data, and adjusting the scan schedule. This solution has proved invaluable in automatically detecting and alerting users to potential danger within the monitored areas while lowering the cost and work required for

  7. Automating an integrated spatial data-mining model for landfill site selection

    Science.gov (United States)

    Abujayyab, Sohaib K. M.; Ahamad, Mohd Sanusi S.; Yahya, Ahmad Shukri; Ahmad, Siti Zubaidah; Aziz, Hamidi Abdul

    2017-10-01

    An integrated programming environment represents a robust approach to building a valid model for landfill site selection. One of the main challenges in the integrated model is the complicated processing and modelling due to the programming stages and several limitations. An automation process helps avoid the limitations and improve the interoperability between integrated programming environments. This work targets the automation of a spatial data-mining model for landfill site selection by integrating between spatial programming environment (Python-ArcGIS) and non-spatial environment (MATLAB). The model was constructed using neural networks and is divided into nine stages distributed between Matlab and Python-ArcGIS. A case study was taken from the north part of Peninsular Malaysia. 22 criteria were selected to utilise as input data and to build the training and testing datasets. The outcomes show a high-performance accuracy percentage of 98.2% in the testing dataset using 10-fold cross validation. The automated spatial data mining model provides a solid platform for decision makers to performing landfill site selection and planning operations on a regional scale.

  8. Automated information and control complex of hydro-gas endogenous mine processes

    Science.gov (United States)

    Davkaev, K. S.; Lyakhovets, M. V.; Gulevich, T. M.; Zolin, K. A.

    2017-09-01

    The automated information and control complex designed to prevent accidents, related to aerological situation in the underground workings, accounting of the received and handed over individual devices, transmission and display of measurement data, and the formation of preemptive solutions is considered. Examples for the automated workplace of an airgas control operator by individual means are given. The statistical characteristics of field data characterizing the aerological situation in the mine are obtained. The conducted studies of statistical characteristics confirm the feasibility of creating a subsystem of controlled gas distribution with an adaptive arrangement of points for gas control. The adaptive (multivariant) algorithm for processing measuring information of continuous multidimensional quantities and influencing factors has been developed.

  9. Mining olive genome through library sequencing and bioinformatics ...

    African Journals Online (AJOL)

    As one of the initial steps of olive (Olea europaea L.) genome analysis, a small insert genomic DNA library was constructed (digesting olive genomic DNA with SmaI and cloning the digestion products into pUC19 vector) and randomly picked 83 colonies were sequenced. Analysis of the insert sequences revealed 12 clones ...

  10. Prerequisites for the Establishment of the Automated Monitoring System and Accounting of the Displacement of the Roof of Underground Mines for the Improvement of Safety of Mining Work

    Science.gov (United States)

    Abramovich, Alexandr; Pudov, Evgeniy; Kuzin, Evgeny

    2017-11-01

    In the article the necessity of continuous control over the condition of the roof of mine workings is considered, to increase the safety in the conduct of mining operations. Provided the rationale for monitoring in complex mining and geological conditions, as well as in areas prone to rock blows and sudden coal emissions. The existing methods for controlling the displacement of the roof rocks are described, and their shortcomings are given. An idea is given of an automated system for monitoring the displacement of the workings. The stages of the system as a whole are considered, including the choice of a linear displacement sensor, a platform for software development, and a programming language. In order to ensure integration into other systems and subsequent analysis of the results, it is envisaged to output data to spreadsheets. Are shown the interfaces of the program and the output of the readings from the sensors to the monitors of the mining manager.

  11. Prerequisites for the Establishment of the Automated Monitoring System and Accounting of the Displacement of the Roof of Underground Mines for the Improvement of Safety of Mining Work

    Directory of Open Access Journals (Sweden)

    Abramovich Alexandr

    2017-01-01

    Full Text Available In the article the necessity of continuous control over the condition of the roof of mine workings is considered, to increase the safety in the conduct of mining operations. Provided the rationale for monitoring in complex mining and geological conditions, as well as in areas prone to rock blows and sudden coal emissions. The existing methods for controlling the displacement of the roof rocks are described, and their shortcomings are given. An idea is given of an automated system for monitoring the displacement of the workings. The stages of the system as a whole are considered, including the choice of a linear displacement sensor, a platform for software development, and a programming language. In order to ensure integration into other systems and subsequent analysis of the results, it is envisaged to output data to spreadsheets. Are shown the interfaces of the program and the output of the readings from the sensors to the monitors of the mining manager.

  12. Automating the Analysis of Spatial Grids A Practical Guide to Data Mining Geospatial Images for Human & Environmental Applications

    CERN Document Server

    Lakshmanan, Valliappa

    2012-01-01

    The ability to create automated algorithms to process gridded spatial data is increasingly important as remotely sensed datasets increase in volume and frequency. Whether in business, social science, ecology, meteorology or urban planning, the ability to create automated applications to analyze and detect patterns in geospatial data is increasingly important. This book provides students with a foundation in topics of digital image processing and data mining as applied to geospatial datasets. The aim is for readers to be able to devise and implement automated techniques to extract information from spatial grids such as radar, satellite or high-resolution survey imagery.

  13. Supplementary Material for: BEACON: automated tool for Bacterial GEnome Annotation ComparisON

    KAUST Repository

    Kalkatawi, Manal M.

    2015-01-01

    Abstract Background Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACONâ s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/ .

  14. An automated annotation tool for genomic DNA sequences using ...

    Indian Academy of Sciences (India)

    Unknown

    Introduction. DNA sequencing has evolved from a complicated labo- ratory process to an automated technique using high- throughput sequencers with fluorescent-dye-based chemistry. This technological advance coupled with the replacement of the traditional mapping and sequencing of clones in series to an integrated ...

  15. Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing.

    Science.gov (United States)

    Kong, Nguyet; Ng, Whitney; Thao, Kao; Agulto, Regina; Weis, Allison; Kim, Kristi Spittle; Korlach, Jonas; Hickey, Luke; Kelly, Lenore; Lappin, Stephen; Weimer, Bart C

    2017-01-01

    The PacBio RS II provides for single molecule, real-time DNA technology to sequence genomes and detect DNA modifications. The starting point for high-quality sequence production is high molecular weight genomic DNA. To automate the library preparation process, there must be high-throughput methods in place to assess the genomic DNA, to ensure the size and amounts of the sheared DNA fragments and final library. The library construction automation was accomplished using the Agilent NGS workstation with Bravo accessories for heating, shaking, cooling, and magnetic bead manipulations for template purification. The quality control methods from gDNA input to final library using the Agilent Bioanalyzer System and Agilent TapeStation System were evaluated. Automated protocols of PacBio 10 kb library preparation produced libraries with similar technical performance to those generated manually. The TapeStation System proved to be a reliable method that could be used in a 96-well plate format to QC the DNA equivalent to the standard Bioanalyzer System results. The DNA Integrity Number that is calculated in the TapeStation System software upon analysis of genomic DNA is quite helpful to assure that the starting genomic DNA is not degraded. In this respect, the gDNA assay on the TapeStation System is preferable to the DNA 12000 assay on the Bioanalyzer System, which cannot run genomic DNA, nor can the Bioanalyzer work directly from the 96-well plates.

  16. The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes.

    Science.gov (United States)

    Hamilton, John P; Neeno-Eckwall, Eric C; Adhikari, Bishwo N; Perna, Nicole T; Tisserat, Ned; Leach, Jan E; Lévesque, C André; Buell, C Robin

    2011-01-01

    The Comprehensive Phytopathogen Genomics Resource (CPGR) provides a web-based portal for plant pathologists and diagnosticians to view the genome and trancriptome sequence status of 806 bacterial, fungal, oomycete, nematode, viral and viroid plant pathogens. Tools are available to search and analyze annotated genome sequences of 74 bacterial, fungal and oomycete pathogens. Oomycete and fungal genomes are obtained directly from GenBank, whereas bacterial genome sequences are downloaded from the A Systematic Annotation Package (ASAP) database that provides curation of genomes using comparative approaches. Curated lists of bacterial genes relevant to pathogenicity and avirulence are also provided. The Plant Pathogen Transcript Assemblies Database provides annotated assemblies of the transcribed regions of 82 eukaryotic genomes from publicly available single pass Expressed Sequence Tags. Data-mining tools are provided along with tools to create candidate diagnostic markers, an emerging use for genomic sequence data in plant pathology. The Plant Pathogen Ribosomal DNA (rDNA) database is a resource for pathogens that lack genome or transcriptome data sets and contains 131 755 rDNA sequences from GenBank for 17 613 species identified as plant pathogens and related genera. Database URL: http://cpgr.plantbiology.msu.edu.

  17. Means to improve underground coal mine safety by automated control of methane drainage systems

    Directory of Open Access Journals (Sweden)

    Babut Gabriel Bujor

    2017-01-01

    Full Text Available Based on the critical analysis of the presently employed management of methane drainage systems operation in Jiu Valley collieries, the paper aims to assess the basic elements required to develop an automated monitoring and control system of these. The results obtained after studies and researches carried out also allowed formulating certain proposals regarding the modification of manual control procedures of methane drainage systems operation, in order to correlate them with the prescriptions of legislation requirements from countries having a well-developed mining industry. Putting in practice the mentioned proposals could have immediate and beneficial effects on increasing the methane drainage process efficiency, leading meanwhile to an improved working environment and, implicitly, to a higher level of occupational safety and health in Jiu Valley collieries.

  18. Digital combined instrument transformer for automated electric power supply control systems of mining companies

    Science.gov (United States)

    Topolsky, D. V.; Gonenko, T. V.; Khatsevskiy, V. F.

    2017-10-01

    The present paper discusses ways to solve the problem of enhancing operating efficiency of automated electric power supply control systems of mining companies. According to the authors, one of the ways to solve this problem is intellectualization of the electric power supply control system equipment. To enhance efficiency of electric power supply control and electricity metering, it is proposed to use specially designed digital combined instrument current and voltage transformers. This equipment conforms to IEC 61850 international standard and is adapted for integration into the digital substation structure. Tests were performed to check conformity of an experimental prototype of the digital combined instrument current and voltage transformer with IEC 61850 standard. The test results have shown that the considered equipment meets the requirements of the standard.

  19. Automation of route identification and optimisation based on data-mining and chemical intuition.

    Science.gov (United States)

    Lapkin, A A; Heer, P K; Jacob, P-M; Hutchby, M; Cunningham, W; Bull, S D; Davidson, M G

    2017-09-21

    Data-mining of Reaxys and network analysis of the combined literature and in-house reactions set were used to generate multiple possible reaction routes to convert a bio-waste feedstock, limonene, into a pharmaceutical API, paracetamol. The network analysis of data provides a rich knowledge-base for generation of the initial reaction screening and development programme. Based on the literature and the in-house data, an overall flowsheet for the conversion of limonene to paracetamol was proposed. Each individual reaction-separation step in the sequence was simulated as a combination of the continuous flow and batch steps. The linear model generation methodology allowed us to identify the reaction steps requiring further chemical optimisation. The generated model can be used for global optimisation and generation of environmental and other performance indicators, such as cost indicators. However, the identified further challenge is to automate model generation to evolve optimal multi-step chemical routes and optimal process configurations.

  20. PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results

    Directory of Open Access Journals (Sweden)

    Zhao Xuechun

    2007-02-01

    Full Text Available Abstract Background BLAST searches are widely used for sequence alignment. The search results are commonly adopted for various functional and comparative genomics tasks such as annotating unknown sequences, investigating gene models and comparing two sequence sets. Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data. A number of programs and hardware solutions exist for efficient BLAST searching, but there is a lack of generic software solutions for mining and personalized management of the results. Systematically reviewing the results and identifying information of interest remains tedious and time-consuming. Results Personal BLAST Navigator (PLAN is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1 query and target sequence database management, (2 automated high-throughput BLAST searching, (3 indexing and searching of results, (4 filtering results online, (5 managing results of personal interest in favorite categories, (6 automated sequence annotation (such as NCBI NR and ontology-based annotation. PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration. Conclusion PLAN has proved a valuable addition to the community for automated high-throughput BLAST searches, and, more importantly, for knowledge discovery, management and sharing based on sequence alignment results

  1. PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results.

    Science.gov (United States)

    He, Ji; Dai, Xinbin; Zhao, Xuechun

    2007-02-09

    BLAST searches are widely used for sequence alignment. The search results are commonly adopted for various functional and comparative genomics tasks such as annotating unknown sequences, investigating gene models and comparing two sequence sets. Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data. A number of programs and hardware solutions exist for efficient BLAST searching, but there is a lack of generic software solutions for mining and personalized management of the results. Systematically reviewing the results and identifying information of interest remains tedious and time-consuming. Personal BLAST Navigator (PLAN) is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1) query and target sequence database management, (2) automated high-throughput BLAST searching, (3) indexing and searching of results, (4) filtering results online, (5) managing results of personal interest in favorite categories, (6) automated sequence annotation (such as NCBI NR and ontology-based annotation). PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration. PLAN has proved a valuable addition to the community for automated high-throughput BLAST searches, and, more importantly, for knowledge discovery, management and sharing based on sequence alignment results. The PLAN web interface is platform

  2. Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria

    DEFF Research Database (Denmark)

    Machado, Henrique; Sonnenschein, Eva; Melchiorsen, Jette

    2015-01-01

    - and Gammaproteobacteria collected during the Galathea 3 expedition were sequenced and mined for natural product encoding gene clusters. Results: Independently of genome size, bacteria of all tested genera carried a large number of clusters encoding different potential bioactivities, especially within the Vibrionaceae...... that will facilitate natural product discovery in the future....

  3. antiSMASH 2.0-a versatile platform for genome mining of secondary metabolite producers

    NARCIS (Netherlands)

    Blin, Kai; Medema, Marnix H.; Kazempour, Daniyal; Fischbach, Michael A.; Breitling, Rainer; Takano, Eriko; Weber, Tilmann

    Microbial secondary metabolites are a potent source of antibiotics and other pharmaceuticals. Genome mining of their biosynthetic gene clusters has become a key method to accelerate their identification and characterization. In 2011, we developed antiSMASH, a web-based analysis platform that

  4. Discovery of novel phosphonate natural products and their biosynthetic pathways by large-scale genome mining

    Science.gov (United States)

    Genome mining has revolutionized the field of natural products, providing hope that new antibiotics can be discovered in time before all remainders are rendered useless against multidrug resistant pathogens. While this approach has been successful in academic settings focused on small collections or...

  5. Draft Genome Sequences of Two Novel Acidimicrobiaceae Members from an Acid Mine Drainage Biofilm Metagenome

    OpenAIRE

    Pinto, Ameet J.; Sharp, Jonathan O.; Yoder, Michael J.; Almstrand, Robert

    2016-01-01

    Bacteria belonging to the family Acidimicrobiaceae are frequently encountered in heavy metal-contaminated acidic environments. However, their phylogenetic and metabolic diversity is poorly resolved. We present draft genome sequences of two novel and phylogenetically distinct Acidimicrobiaceae members assembled from an acid mine drainage biofilm metagenome.

  6. Mining and characterization of microsatellites from a genome of Venturia carpophila

    Science.gov (United States)

    A total of 4,021 microsatellites were mined from a genome of Venturia carpophila and 192 were selected to screen 39 isolates of the fungus collected from peach and nectarine in the southeastern USA. Of the 192 selected, 32 primers consistently and reliably produced polymorphic amplicons. Subsequentl...

  7. An automated annotation tool for genomic DNA sequences using ...

    Indian Academy of Sciences (India)

    Unknown

    , New Delhi 110 067, India. Abstract ... analysis of genomic DNA to identify coding sequences using the GeneScan algorithm and characterize these resultant sequences by .... genes for the TCA cycle, while in mitochondria only a subset of the ...

  8. FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform

    Directory of Open Access Journals (Sweden)

    Pontarotti Pierre

    2005-08-01

    Full Text Available Abstract Background Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes. Structural and functional annotation both require the complex chaining of numerous different software, algorithms and methods under the supervision of a biologist. The automation of these pipelines is necessary to manage huge amounts of data released by sequencing projects. Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps. Results Here we propose an innovative automated platform, FIGENIX, which includes an expert system capable to substitute to human expertise at several key steps. FIGENIX currently automates complex pipelines of structural and functional annotation under the supervision of the expert system (which allows for example to make key decisions, check intermediate results or refine the dataset. The quality of the results produced by FIGENIX is comparable to those obtained by expert biologists with a drastic gain in terms of time costs and avoidance of errors due to the human manipulation of data. Conclusion The core engine and expert system of the FIGENIX platform currently handle complex annotation processes of broad interest for the genomic community. They could be easily adapted to new, or more specialized pipelines, such as for example the annotation of miRNAs, the classification of complex multigenic families, annotation of regulatory elements and other genomic features of interest.

  9. An Automated Approach for the Determination of the Seismic Moment Tensor in Mining Environments

    Science.gov (United States)

    Wamboldt, Lawrence R.

    A study was undertaken to evaluate an automated process to invert for seismic moment tensors from seismic data recorded in mining environments. The data for this study was recorded at Nickel Rim South mine, Sudbury, Ontario. The mine has a seismic monitoring system manufactured by ESG Solutions that performs continuous monitoring of seismicity. On average, approximately 400 seismic events are recorded each day. Currently, data are automatically processed by ESG Solution's software suite during acquisition. The automatic processors pick the P- and/or S-wave arrivals, locate the events and solve for certain source parameters, excluding the seismic moment tensor. In order to solve for the moment tensor, data must be manually processed, which is laborious and therefore seldom performed. This research evaluates an automatic seismic moment tensor inversion method and demonstrates some of the difficulties (through inversions of real and synthetic seismic data) of the inversion process. Results using the method are also compared to the inversion method currently available from ESG Solutions, which requires the manual picking of first-motion polarities for every event. As a result of the extensive synthetic testing of the automatic inversion program, as well as the inversion of real seismic data, it is apparent that there are key parameters requiring greater accuracy in order to increase the reliability of the automation. These parameters include the source time function definition, source location (in turn requiring more accurate and precise knowledge of the earth media), arrival time picks and an attenuation model to account for ray-path dependent filtering of the source time function. In order to improve the automatic method three key pieces of research are needed: (1) studying various location algorithms (and the effects of increasing earth model intricacy) and automatic time picking to improve source location methods, (2) studying how the source time pulse can be

  10. VirSorter: mining viral signal from microbial genomic data

    Directory of Open Access Journals (Sweden)

    Simon Roux

    2015-05-01

    Full Text Available Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome, new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter’s prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages. Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in “reverse” to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made

  11. The Functional Genomics Network in the evolution of biological text mining over the past decade.

    Science.gov (United States)

    Blaschke, Christian; Valencia, Alfonso

    2013-03-25

    Different programs of The European Science Foundation (ESF) have contributed significantly to connect researchers in Europe and beyond through several initiatives. This support was particularly relevant for the development of the areas related with extracting information from papers (text-mining) because it supported the field in its early phases long before it was recognized by the community. We review the historical development of text mining research and how it was introduced in bioinformatics. Specific applications in (functional) genomics are described like it's integration in genome annotation pipelines and the support to the analysis of high-throughput genomics experimental data, and we highlight the activities of evaluation of methods and benchmarking for which the ESF programme support was instrumental. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Strain Prioritization and Genome Mining for Enediyne Natural Products

    Science.gov (United States)

    Yan, Xiaohui; Ge, Huiming; Huang, Tingting; Hindra; Yang, Dong; Teng, Qihui; Crnovčić, Ivana; Li, Xiuling; Rudolf, Jeffrey D.; Lohman, Jeremy R.; Gansemans, Yannick; Zhu, Xiangcheng; Huang, Yong; Zhao, Li-Xing; Jiang, Yi; Van Nieuwerburgh, Filip; Rader, Christoph

    2016-01-01

    ABSTRACT The enediyne family of natural products has had a profound impact on modern chemistry, biology, and medicine, and yet only 11 enediynes have been structurally characterized to date. Here we report a genome survey of 3,400 actinomycetes, identifying 81 strains that harbor genes encoding the enediyne polyketide synthase cassettes that could be grouped into 28 distinct clades based on phylogenetic analysis. Genome sequencing of 31 representative strains confirmed that each clade harbors a distinct enediyne biosynthetic gene cluster. A genome neighborhood network allows prediction of new structural features and biosynthetic insights that could be exploited for enediyne discovery. We confirmed one clade as new C-1027 producers, with a significantly higher C-1027 titer than the original producer, and discovered a new family of enediyne natural products, the tiancimycins (TNMs), that exhibit potent cytotoxicity against a broad spectrum of cancer cell lines. Our results demonstrate the feasibility of rapid discovery of new enediynes from a large strain collection. PMID:27999165

  13. New advances in the automation of mining cartography and topography in coal exploitation. Nuevos avances en la automatizacion de la cartografia y topografia minera en explotaciones de carbon

    Energy Technology Data Exchange (ETDEWEB)

    Fuente Martin, P.; Gonzalez Marroquina, V.; Saez Garcia, E.; Perez Suarez, M.A. (HUNOSA, Madrid (Spain))

    1988-01-01

    In this entry are described some HUNOSA researches for automating the typographical information and any other technical information produced in the coal workings. Also recorded were some aspects about a basis of mining cartographic information. 3 tabs.

  14. CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline.

    Science.gov (United States)

    Agrawal, Sonia; Arze, Cesar; Adkins, Ricky S; Crabtree, Jonathan; Riley, David; Vangala, Mahesh; Galens, Kevin; Fraser, Claire M; Tettelin, Hervé; White, Owen; Angiuoli, Samuel V; Mahurkar, Anup; Fricke, W Florian

    2017-04-27

    The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. CloVR-Comparative runs reference-free multiple whole-genome alignments to determine unique, shared and core coding sequences (CDSs) and single nucleotide polymorphisms (SNPs). Output includes short summary reports and detailed text-based results files, graphical visualizations (phylogenetic trees, circular figures), and a database file linked to the Sybil comparative genome browser. Data up- and download, pipeline configuration and monitoring, and access to Sybil are managed through CloVR-Comparative web interface. CloVR-Comparative and Sybil are distributed as part of the CloVR virtual appliance, which runs on local computers or the Amazon EC2 cloud. Representative datasets (e.g. 40 draft and complete Escherichia coli genomes) are processed in <36 h on a local desktop or at a cost of <$20 on EC2. CloVR-Comparative allows anybody with Internet access to run comparative genomics projects, while eliminating the need for on-site computational resources and expertise.

  15. SNP-RFLPing: restriction enzyme mining for SNPs in genomes

    OpenAIRE

    Chang, Hsueh-Wei; Yang, Cheng-Hong; Chang, Phei-Lang; Cheng, Yu-Huei; Chuang, Li-Yeh

    2006-01-01

    Abstract Background The restriction fragment length polymorphism (RFLP) is a common laboratory method for the genotyping of single nucleotide polymorphisms (SNPs). Here, we describe a web-based software, named SNP-RFLPing, which provides the restriction enzyme for RFLP assays on a batch of SNPs and genes from the human, rat, and mouse genomes. Results Three user-friendly inputs are included: 1) NCBI dbSNP "rs" or "ss" IDs; 2) NCBI Entrez gene ID and HUGO gene name; 3) any formats of SNP-in-se...

  16. Systematic association of genes to phenotypes by genome and literature mining.

    Directory of Open Access Journals (Sweden)

    Jan O Korbel

    2005-05-01

    Full Text Available One of the major challenges of functional genomics is to unravel the connection between genotype and phenotype. So far no global analysis has attempted to explore those connections in the light of the large phenotypic variability seen in nature. Here, we use an unsupervised, systematic approach for associating genes and phenotypic characteristics that combines literature mining with comparative genome analysis. We first mine the MEDLINE literature database for terms that reflect phenotypic similarities of species. Subsequently we predict the likely genomic determinants: genes specifically present in the respective genomes. In a global analysis involving 92 prokaryotic genomes we retrieve 323 clusters containing a total of 2,700 significant gene-phenotype associations. Some clusters contain mostly known relationships, such as genes involved in motility or plant degradation, often with additional hypothetical proteins associated with those phenotypes. Other clusters comprise unexpected associations; for example, a group of terms related to food and spoilage is linked to genes predicted to be involved in bacterial food poisoning. Among the clusters, we observe an enrichment of pathogenicity-related associations, suggesting that the approach reveals many novel genes likely to play a role in infectious diseases.

  17. Genome-wide mining, characterization, and development of microsatellite markers in gossypium species.

    Science.gov (United States)

    Wang, Qiong; Fang, Lei; Chen, Jiedan; Hu, Yan; Si, Zhanfeng; Wang, Sen; Chang, Lijing; Guo, Wangzhen; Zhang, Tianzhen

    2015-06-01

    Although much research has been conducted to characterize microsatellites and develop markers, the distribution of microsatellites remains ambiguous and the use of microsatellite markers in genomic studies and marker-assisted selection is limited. To identify microsatellites for cotton research, we mined 100,290, 83,160, and 56,937 microsatellites with frequencies of 41.2, 49.1, and 74.8 microsatellites per Mb in the recently sequenced Gossypium species: G. hirsutum, G. arboreum, and G. raimondii, respectively. The distributions of microsatellites in their genomes were non-random and were positively and negatively correlated with genes and transposable elements, respectively. Of the 77,996 developed microsatellite markers, 65,498 were physically anchored to the 26 chromosomes of G. hirsutum with an average marker density of 34 markers per Mb. We confirmed 67,880 (87%) universal and 7,705 (9.9%) new genic microsatellite markers. The polymorphism was estimated in above three species by in silico PCR and validated with 505 markers in G. hirsutum. We further predicted 8,825 polymorphic microsatellite markers within G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124. In our study, genome-wide mining and characterization of microsatellites, and marker development were very useful for the saturation of the allotetraploid genetic linkage map, genome evolution studies and comparative genome mapping.

  18. Use of industrial information, communication and control technologies in automated coal mines; Einsatz industrieller Informations-, Kommunikations- und Steuerungstechnologien im automatisierten Steinkohlenbergbau

    Energy Technology Data Exchange (ETDEWEB)

    Becker, F. [Becker Mining Systems GmbH, Friedrichsthal (Germany); Jakoby, W. [Fachhochschule Trier (Germany). Institut fuer Automatisierungstechnik

    2005-11-08

    The introduction of information technology is an important milestone in the development of automated mining. Highly integrated and practical mining PCs are paving the way for the use of innovative concepts of control, communication and machine operation underground. By using these systems the collieries will be able to develop new efficiency potentials. (orig.)

  19. Ask and Ye Shall Receive? Automated Text Mining of Michigan Capital Facility Finance Bond Election Proposals to Identify Which Topics Are Associated with Bond Passage and Voter Turnout

    Science.gov (United States)

    Bowers, Alex J.; Chen, Jingjing

    2015-01-01

    The purpose of this study is to bring together recent innovations in the research literature around school district capital facility finance, municipal bond elections, statistical models of conditional time-varying outcomes, and data mining algorithms for automated text mining of election ballot proposals to examine the factors that influence the…

  20. Correcting Inconsistencies and Errors in Bacterial Genome Metadata Using an Automated Curation Tool in Excel (AutoCurE).

    Science.gov (United States)

    Schmedes, Sarah E; King, Jonathan L; Budowle, Bruce

    2015-01-01

    Whole-genome data are invaluable for large-scale comparative genomic studies. Current sequencing technologies have made it feasible to sequence entire bacterial genomes with relative ease and time with a substantially reduced cost per nucleotide, hence cost per genome. More than 3,000 bacterial genomes have been sequenced and are available at the finished status. Publically available genomes can be readily downloaded; however, there are challenges to verify the specific supporting data contained within the download and to identify errors and inconsistencies that may be present within the organizational data content and metadata. AutoCurE, an automated tool for bacterial genome database curation in Excel, was developed to facilitate local database curation of supporting data that accompany downloaded genomes from the National Center for Biotechnology Information. AutoCurE provides an automated approach to curate local genomic databases by flagging inconsistencies or errors by comparing the downloaded supporting data to the genome reports to verify genome name, RefSeq accession numbers, the presence of archaea, BioProject/UIDs, and sequence file descriptions. Flags are generated for nine metadata fields if there are inconsistencies between the downloaded genomes and genomes reports and if erroneous or missing data are evident. AutoCurE is an easy-to-use tool for local database curation for large-scale genome data prior to downstream analyses.

  1. Chapter 10: Mining genome-wide genetic markers.

    Directory of Open Access Journals (Sweden)

    Xiang Zhang

    Full Text Available Genome-wide association study (GWAS aims to discover genetic factors underlying phenotypic traits. The large number of genetic factors poses both computational and statistical challenges. Various computational approaches have been developed for large scale GWAS. In this chapter, we will discuss several widely used computational approaches in GWAS. The following topics will be covered: (1 An introduction to the background of GWAS. (2 The existing computational approaches that are widely used in GWAS. This will cover single-locus, epistasis detection, and machine learning methods that have been recently developed in biology, statistic, and computer science communities. This part will be the main focus of this chapter. (3 The limitations of current approaches and future directions.

  2. metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research.

    Science.gov (United States)

    Lyne, Mike; Smith, Richard N; Lyne, Rachel; Aleksic, Jelena; Hu, Fengyuan; Kalderimis, Alex; Stepan, Radek; Micklem, Gos

    2013-01-01

    Common metabolic and endocrine diseases such as diabetes affect millions of people worldwide and have a major health impact, frequently leading to complications and mortality. In a search for better prevention and treatment, there is ongoing research into the underlying molecular and genetic bases of these complex human diseases, as well as into the links with risk factors such as obesity. Although an increasing number of relevant genomic and proteomic data sets have become available, the quantity and diversity of the data make their efficient exploitation challenging. Here, we present metabolicMine, a data warehouse with a specific focus on the genomics, genetics and proteomics of common metabolic diseases. Developed in collaboration with leading UK metabolic disease groups, metabolicMine integrates data sets from a range of experiments and model organisms alongside tools for exploring them. The current version brings together information covering genes, proteins, orthologues, interactions, gene expression, pathways, ontologies, diseases, genome-wide association studies and single nucleotide polymorphisms. Although the emphasis is on human data, key data sets from mouse and rat are included. These are complemented by interoperation with the RatMine rat genomics database, with a corresponding mouse version under development by the Mouse Genome Informatics (MGI) group. The web interface contains a number of features including keyword search, a library of Search Forms, the QueryBuilder and list analysis tools. This provides researchers with many different ways to analyse, view and flexibly export data. Programming interfaces and automatic code generation in several languages are supported, and many of the features of the web interface are available through web services. The combination of diverse data sets integrated with analysis tools and a powerful query system makes metabolicMine a valuable research resource. The web interface makes it accessible to first

  3. SNP-RFLPing: restriction enzyme mining for SNPs in genomes

    Directory of Open Access Journals (Sweden)

    Cheng Yu-Huei

    2006-02-01

    Full Text Available Abstract Background The restriction fragment length polymorphism (RFLP is a common laboratory method for the genotyping of single nucleotide polymorphisms (SNPs. Here, we describe a web-based software, named SNP-RFLPing, which provides the restriction enzyme for RFLP assays on a batch of SNPs and genes from the human, rat, and mouse genomes. Results Three user-friendly inputs are included: 1 NCBI dbSNP "rs" or "ss" IDs; 2 NCBI Entrez gene ID and HUGO gene name; 3 any formats of SNP-in-sequence, are allowed to perform the SNP-RFLPing assay. These inputs are auto-programmed to SNP-containing sequences and their complementary sequences for the selection of restriction enzymes. All SNPs with available RFLP restriction enzymes of each input genes are provided even if many SNPs exist. The SNP-RFLPing analysis provides the SNP contig position, heterozygosity, function, protein residue, and amino acid position for cSNPs, as well as commercial and non-commercial restriction enzymes. Conclusion This web-based software solves the input format problems in similar softwares and greatly simplifies the procedure for providing the RFLP enzyme. Mixed free forms of input data are friendly to users who perform the SNP-RFLPing assay. SNP-RFLPing offers a time-saving application for association studies in personalized medicine and is freely available at http://bio.kuas.edu.tw/snp-rflp/.

  4. SNP-RFLPing: restriction enzyme mining for SNPs in genomes.

    Science.gov (United States)

    Chang, Hsueh-Wei; Yang, Cheng-Hong; Chang, Phei-Lang; Cheng, Yu-Huei; Chuang, Li-Yeh

    2006-02-17

    The restriction fragment length polymorphism (RFLP) is a common laboratory method for the genotyping of single nucleotide polymorphisms (SNPs). Here, we describe a web-based software, named SNP-RFLPing, which provides the restriction enzyme for RFLP assays on a batch of SNPs and genes from the human, rat, and mouse genomes. Three user-friendly inputs are included: 1) NCBI dbSNP "rs" or "ss" IDs; 2) NCBI Entrez gene ID and HUGO gene name; 3) any formats of SNP-in-sequence, are allowed to perform the SNP-RFLPing assay. These inputs are auto-programmed to SNP-containing sequences and their complementary sequences for the selection of restriction enzymes. All SNPs with available RFLP restriction enzymes of each input genes are provided even if many SNPs exist. The SNP-RFLPing analysis provides the SNP contig position, heterozygosity, function, protein residue, and amino acid position for cSNPs, as well as commercial and non-commercial restriction enzymes. This web-based software solves the input format problems in similar softwares and greatly simplifies the procedure for providing the RFLP enzyme. Mixed free forms of input data are friendly to users who perform the SNP-RFLPing assay. SNP-RFLPing offers a time-saving application for association studies in personalized medicine and is freely available at http://bio.kuas.edu.tw/snp-rflp/.

  5. Genome Mining in Sorangium cellulosum So ce56

    Science.gov (United States)

    Ewen, Kerstin Maria; Hannemann, Frank; Khatri, Yogan; Perlova, Olena; Kappl, Reinhard; Krug, Daniel; Hüttermann, Jürgen; Müller, Rolf; Bernhardt, Rita

    2009-01-01

    Myxobacteria, especially members of the genus Sorangium, are known for their biotechnological potential as producers of pharmaceutically valuable secondary metabolites. The biosynthesis of several of those myxobacterial compounds includes cytochrome P450 activity. Although class I cytochrome P450 enzymes occur wide-spread in bacteria and rely on ferredoxins and ferredoxin reductases as essential electron mediators, the study of these proteins is often neglected. Therefore, we decided to search in the Sorangium cellulosum So ce56 genome for putative interaction partners of cytochromes P450. In this work we report the investigation of eight myxobacterial ferredoxins and two ferredoxin reductases with respect to their activity in cytochrome P450 systems. Intriguingly, we found not only one, but two ferredoxins whose ability to sustain an endogenous So ce56 cytochrome P450 was demonstrated by CYP260A1-dependent conversion of nootkatone. Moreover, we could demonstrate that the two ferredoxins were able to receive electrons from both ferredoxin reductases. These findings indicate that S. cellulosum can alternate between different electron transport pathways to sustain cytochrome P450 activity. PMID:19696019

  6. Genomic sovereignty and the African promise: mining the African genome for the benefit of Africa.

    Science.gov (United States)

    de Vries, Jantina; Pepper, Michael

    2012-08-01

    Scientific interest in genomics in Africa is on the rise with a number of funding initiatives aimed specifically at supporting research in this area. Genomics research on material of African origin raises a number of important ethical issues. A prominent concern relates to sample export, which is increasingly seen by researchers and ethics committees across the continent as being problematic. The concept of genomic sovereignty proposes that unique patterns of genomic variation can be found in human populations, and that these are commercially, scientifically or symbolically valuable and in need of protection against exploitation. Although it is appealing as a response to increasing concerns regarding sample export, there are a number of important conceptual problems relating to the term. It is not clear, for instance, whether it is appropriate that ownership over human genomic samples should rest with national governments. Furthermore, ethnic groups in Africa are frequently spread across multiple nation states, and protection offered in one state may not prevent researchers from accessing the same group elsewhere. Lastly, scientific evidence suggests that the assumption that genomic data is unique for population groups is false. Although the frequency with which particular variants are found can differ between groups, such genes or variants per se are not unique to any population group. In this paper, the authors describe these concerns in detail and argue that the concept of genomic sovereignty alone may not be adequate to protect the genetic resources of people of African descent.

  7. Mining genomes of cyanobacteria for elements of zinc homeostasis

    Directory of Open Access Journals (Sweden)

    James P Barnett

    2012-04-01

    Full Text Available Zinc is a recognised essential element for the majority of organisms, and is indispensable for the correct function of hundreds of enzymes and thousands of regulatory proteins. In aquatic photoautotrophs including cyanobacteria, zinc is thought to be required for carbonic anhydrase and alkaline phosphatase, although there is evidence that at least some carbonic anhydrases can be cambialistic, i.e. are able to acquire in vivo and function with different metal cofactors such as Co2+ and Cd2+. Given the global importance of marine phytoplankton, zinc availability in the oceans is likely to have an impact on both carbon and phosphorus cycles. Zinc concentrations in seawater vary over several orders of magnitude, and in the open oceans adopt a nutrient-like profile. Most studies on zinc handling by cyanobacteria have focused on freshwater strains and zinc toxicity; much less information is available on marine strains and zinc limitation. Several systems for zinc homeostasis have been characterised in the freshwater species Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803, but little is known about zinc requirements or zinc handling by marine species. Comparative metallo-genomics has begun to explore not only the putative zinc proteome, but also specific protein families predicted to have an involvement in zinc homeostasis, including sensors for excess and limitation (SmtB and its homologues as well as Zur, uptake systems (ZnuABC, putative intracellular zinc chaperones (COG0523 and metallothioneins (BmtA, and efflux pumps (ZiaA and its homologues. The present review will focus on possible mechanisms for coping with zinc limitation, with a particular emphasis on marine cyanobacteria.

  8. Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data.

    Science.gov (United States)

    Bolser, Dan; Staines, Daniel M; Pritchard, Emily; Kersey, Paul

    2016-01-01

    Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for a growing number of sequenced plant species (currently 33). Data provided includes genome sequence, gene models, functional annotation, and polymorphic loci. Various additional information are provided for variation data, including population structure, individual genotypes, linkage, and phenotype data. In each release, comparative analyses are performed on whole genome and protein sequences, and genome alignments and gene trees are made available that show the implied evolutionary history of each gene family. Access to the data is provided through a genome browser incorporating many specialist interfaces for different data types, and through a variety of additional methods for programmatic access and data mining. These access routes are consistent with those offered through the Ensembl interface for the genomes of non-plant species, including those of plant pathogens, pests, and pollinators.Ensembl Plants is updated 4-5 times a year and is developed in collaboration with our international partners in the Gramene ( http://www.gramene.org ) and transPLANT projects ( http://www.transplantdb.org ).

  9. Automated whole-genome multiple alignment of rat, mouse, and human

    Energy Technology Data Exchange (ETDEWEB)

    Brudno, Michael; Poliakov, Alexander; Salamov, Asaf; Cooper, Gregory M.; Sidow, Arend; Rubin, Edward M.; Solovyev, Victor; Batzoglou, Serafim; Dubchak, Inna

    2004-07-04

    We have built a whole genome multiple alignment of the three currently available mammalian genomes using a fully automated pipeline which combines the local/global approach of the Berkeley Genome Pipeline and the LAGAN program. The strategy is based on progressive alignment, and consists of two main steps: (1) alignment of the mouse and rat genomes; and (2) alignment of human to either the mouse-rat alignments from step 1, or the remaining unaligned mouse and rat sequences. The resulting alignments demonstrate high sensitivity, with 87% of all human gene-coding areas aligned in both mouse and rat. The specificity is also high: <7% of the rat contigs are aligned to multiple places in human and 97% of all alignments with human sequence > 100kb agree with a three-way synteny map built independently using predicted exons in the three genomes. At the nucleotide level <1% of the rat nucleotides are mapped to multiple places in the human sequence in the alignment; and 96.5% of human nucleotides within all alignments agree with the synteny map. The alignments are publicly available online, with visualization through the novel Multi-VISTA browser that we also present.

  10. BioCreative Workshops for DOE Genome Sciences: Text Mining for Metagenomics

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Cathy H. [Univ. of Delaware, Newark, DE (United States). Center for Bioinformatics and Computational Biology; Hirschman, Lynette [The MITRE Corporation, Bedford, MA (United States)

    2016-10-29

    The objective of this project was to host BioCreative workshops to define and develop text mining tasks to meet the needs of the Genome Sciences community, focusing on metadata information extraction in metagenomics. Following the successful introduction of metagenomics at the BioCreative IV workshop, members of the metagenomics community and BioCreative communities continued discussion to identify candidate topics for a BioCreative metagenomics track for BioCreative V. Of particular interest was the capture of environmental and isolation source information from text. The outcome was to form a “community of interest” around work on the interactive EXTRACT system, which supported interactive tagging of environmental and species data. This experiment is included in the BioCreative V virtual issue of Database. In addition, there was broad participation by members of the metagenomics community in the panels held at BioCreative V, leading to valuable exchanges between the text mining developers and members of the metagenomics research community. These exchanges are reflected in a number of the overview and perspective pieces also being captured in the BioCreative V virtual issue. Overall, this conversation has exposed the metagenomics researchers to the possibilities of text mining, and educated the text mining developers to the specific needs of the metagenomics community.

  11. Strategies for the discovery of new natural products by genome mining.

    Science.gov (United States)

    Zerikly, Malek; Challis, Gregory L

    2009-03-02

    Natural products have a very broad spectrum of applications. Many natural products are used clinically as antibacterial, antifungal, antiparasitic, anticancer and immunosuppressive agents and are therefore of utmost importance for our society. When in the 1940s the golden age of antibiotics was ushered in, a "gold rush fever" of natural product discovery in the pharmaceutical industry ensued for many decades. However, the traditional process of discovering new bioactive natural products is generally long and laborious, and known natural products are frequently rediscovered. A mass-withdrawal of pharmaceutical companies from new natural product discovery and natural products research has thus occurred in recent years. In this article, the concept of genome mining for novel natural product discovery, which promises to provide a myriad of new bioactive natural compounds, is summarized and discussed. Genome mining for new natural product discovery exploits the huge and constantly increasing quantity of DNA sequence data from a wide variety of organisms that is accumulating in publicly accessible databases. Genes encoding enzymes likely to be involved in natural product biosynthesis can be readily located in sequenced genomes by use of computational sequence comparison tools. This information can be exploited in a variety of ways in the search for new bioactive natural products.

  12. Automated Assessment of Patients' Self-Narratives for Posttraumatic Stress Disorder Screening Using Natural Language Processing and Text Mining.

    Science.gov (United States)

    He, Qiwei; Veldkamp, Bernard P; Glas, Cees A W; de Vries, Theo

    2017-03-01

    Patients' narratives about traumatic experiences and symptoms are useful in clinical screening and diagnostic procedures. In this study, we presented an automated assessment system to screen patients for posttraumatic stress disorder via a natural language processing and text-mining approach. Four machine-learning algorithms-including decision tree, naive Bayes, support vector machine, and an alternative classification approach called the product score model-were used in combination with n-gram representation models to identify patterns between verbal features in self-narratives and psychiatric diagnoses. With our sample, the product score model with unigrams attained the highest prediction accuracy when compared with practitioners' diagnoses. The addition of multigrams contributed most to balancing the metrics of sensitivity and specificity. This article also demonstrates that text mining is a promising approach for analyzing patients' self-expression behavior, thus helping clinicians identify potential patients from an early stage.

  13. Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data.

    Science.gov (United States)

    Bolser, Dan M; Staines, Daniel M; Perry, Emily; Kersey, Paul J

    2017-01-01

    Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for 39 sequenced plant species. Available data includes genome sequence, gene models, functional annotation, and polymorphic loci; for the latter, additional information including population structure, individual genotypes, linkage, and phenotype data is available for some species. Comparative data is also available, including genomic alignments and "gene trees," which show the inferred evolutionary history of each gene family represented in the resource. Access to the data is provided through a genome browser, which incorporates many specialist interfaces for different data types, through a variety of programmatic interfaces, and via a specialist data mining tool supporting rapid filtering and retrieval of bulk data. Genomic data from many non-plant species, including those of plant pathogens, pests, and pollinators, is also available via the same interfaces through other divisions of Ensembl.Ensembl Plants is updated 4-6 times a year and is developed in collaboration with our international partners in the Gramene ( http://www.gramene.org ) and transPLANT projects ( http://www.transplantdb.eu ).

  14. Development of an Underground Automated Thin-Seam Coal Mining Method

    OpenAIRE

    Holman, Darren Wayne

    1999-01-01

    It is predicted that coal mining in Southwest Virginia, and the economic stability that it brings to the area, will continue to decline over the next decade unless an environmentally sound, and economically viable means can be found to extract seams of high quality coal in the thickness range of 14 to 28 inches. Research into autonomous machine guidance, coupled with developments of thin-seam mining equipment, offer new opportunities for devising mining layouts suitable for extracting these t...

  15. Mining Plant Genomic and Genetic Data Using the GnpIS Information System.

    Science.gov (United States)

    Adam-Blondon, A-F; Alaux, M; Durand, S; Letellier, T; Merceron, G; Mohellibi, N; Pommier, C; Steinbach, D; Alfama, F; Amselem, J; Charruaud, D; Choisne, N; Flores, R; Guerche, C; Jamilloux, V; Kimmel, E; Lapalu, N; Loaec, M; Michotey, C; Quesneville, H

    2017-01-01

    GnpIS is an information system designed to help scientists working on plants and fungi to decipher the molecular and genetic architecture of trait variations by facilitating the navigation through genetic, genomic, and phenotypic information. The purpose of the present chapter is to illustrate how users can (1) explore datasets from phenotyping experiments in order to build new datasets for studying genotype × environment interactions in traits, (2) browse into the results of other genetic analysis data such as GWAS to generate or check working hypothesis about candidate genes or to identify important alleles and germplasms for breeding programs, and (3) explore the polymorphism in specific area of the genome using InterMine, JBrowse tools embedded in the GnpIS information system.

  16. A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation.

    Science.gov (United States)

    Aubrey, Wayne; Riley, Michael C; Young, Michael; King, Ross D; Oliver, Stephen G; Clare, Amanda

    2015-01-01

    Many advances in synthetic biology require the removal of a large number of genomic elements from a genome. Most existing deletion methods leave behind markers, and as there are a limited number of markers, such methods can only be applied a fixed number of times. Deletion methods that recycle markers generally are either imprecise (remove untargeted sequences), or leave scar sequences which can cause genome instability and rearrangements. No existing marker recycling method is automation-friendly. We have developed a novel openly available deletion tool that consists of: 1) a method for deleting genomic elements that can be repeatedly used without limit, is precise, scar-free, and suitable for automation; and 2) software to design the method's primers. Our tool is sequence agnostic and could be used to delete large numbers of coding sequences, promoter regions, transcription factor binding sites, terminators, etc in a single genome. We have validated our tool on the deletion of non-essential open reading frames (ORFs) from S. cerevisiae. The tool is applicable to arbitrary genomes, and we provide primer sequences for the deletion of: 90% of the ORFs from the S. cerevisiae genome, 88% of the ORFs from S. pombe genome, and 85% of the ORFs from the L. lactis genome.

  17. Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes.

    Science.gov (United States)

    Feschotte, Cédric; Keswani, Umeshkumar; Ranganathan, Nirmal; Guibotsy, Marcel L; Levine, David

    2009-07-23

    Eukaryotic genomes contain large amount of repetitive DNA, most of which is derived from transposable elements (TEs). Progress has been made to develop computational tools for ab initio identification of repeat families, but there is an urgent need to develop tools to automate the annotation of TEs in genome sequences. Here we introduce REPCLASS, a tool that automates the classification of TE sequences. Using control repeat libraries, we show that the program can classify accurately virtually any known TE types. Combining REPCLASS to ab initio repeat finding in the genomes of Caenorhabditis elegans and Drosophila melanogaster allowed us to recover the contrasting TE landscape characteristic of these species. Unexpectedly, REPCLASS also uncovered several novel TE families in both genomes, augmenting the TE repertoire of these model species. When applied to the genomes of distant Caenorhabditis and Drosophila species, the approach revealed a remarkable conservation of TE composition profile within each genus, despite substantial interspecific covariations in genome size and in the number of TEs and TE families. Lastly, we applied REPCLASS to analyze 10 fungal genomes from a wide taxonomic range, most of which have not been analyzed for TE content previously. The results showed that TE diversity varies widely across the fungi "kingdom" and appears to positively correlate with genome size, in particular for DNA transposons. Together, these data validate REPCLASS as a powerful tool to explore the repetitive DNA landscapes of eukaryotes and to shed light onto the evolutionary forces shaping TE diversity and genome architecture.

  18. Mining genomic patterns in Mycobacterium tuberculosis H37Rv using a web server Tuber-Gene.

    Science.gov (United States)

    Rishishwar, Lavanya; Pant, Bhasker; Pant, Kumud; Pardasani, Kamal R

    2011-10-01

    Mycobacterium tuberculosis (MTB), causative agent of tuberculosis, is one of the most dreaded diseases of the century. It has long been studied by researchers throughout the world using various wet-lab and dry-lab techniques. In this study, we focus on mining useful patterns at genomic level that can be applied for in silico functional characterization of genes from the MTB complex. The model developed on the basis of the patterns found in this study can correctly identify 99.77% of the input genes from the genome of MTB strain H37Rv. The model was tested against four other MTB strains and the homologue M. bovis to further evaluate its generalization capability. The mean prediction accuracy was 85.76%. It was also observed that the GC content remained fairly constant throughout the genome, implicating the absence of any pathogenicity island transferred from other organisms. This study reveals that dinucleotide composition is an efficient functional class discriminator for MTB complex. To facilitate the application of this model, a web server Tuber-Gene has been developed, which can be freely accessed at http://www.bifmanit.org/tb2/. Copyright © 2011 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.

  19. Mining, visualizing and comparing multidimensional biomolecular data using the Genomics Data Miner (GMine) Web-Server.

    Science.gov (United States)

    Proietti, Carla; Zakrzewski, Martha; Watkins, Thomas S; Berger, Bernard; Hasan, Shihab; Ratnatunga, Champa N; Brion, Marie-Jo; Crompton, Peter D; Miles, John J; Doolan, Denise L; Krause, Lutz

    2016-12-06

    Genomics Data Miner (GMine) is a user-friendly online software that allows non-experts to mine, cluster and compare multidimensional biomolecular datasets. Various powerful visualization techniques are provided, generating high quality figures that can be directly incorporated into scientific publications. Robust and comprehensive analyses are provided via a broad range of data-mining techniques, including univariate and multivariate statistical analysis, supervised learning, correlation networks, clustering and multivariable regression. The software has a focus on multivariate techniques, which can attribute variance in the measurements to multiple explanatory variables and confounders. Various normalization methods are provided. Extensive help pages and a tutorial are available via a wiki server. Using GMine we reanalyzed proteome microarray data of host antibody response against Plasmodium falciparum. Our results support the hypothesis that immunity to malaria is a higher-order phenomenon related to a pattern of responses and not attributable to any single antigen. We also analyzed gene expression across resting and activated T cells, identifying many immune-related genes with differential expression. This highlights both the plasticity of T cells and the operation of a hardwired activation program. These application examples demonstrate that GMine facilitates an accurate and in-depth analysis of complex molecular datasets, including genomics, transcriptomics and proteomics data.

  20. Automated Analysis of Renewable Energy Datasets ('EE/RE Data Mining')

    Energy Technology Data Exchange (ETDEWEB)

    Bush, Brian; Elmore, Ryan; Getman, Dan; Inman, Daniel; Kalendra, Eric

    2013-06-13

    This poster illustrates methods to substantially improve the understanding of renewable energy data sets and the depth and efficiency of their analysis through the application of statistical learning methods ('data mining') in the intelligent processing of these often large and messy information sources. The six examples apply methods for anomaly detection, data cleansing, and pattern mining to time-series data (measurements from metering points in buildings) and spatiotemporal data (renewable energy resource datasets).

  1. Genome mining: Prediction of lipopeptides and polyketides from Bacillus and related Firmicutes.

    Science.gov (United States)

    Aleti, Gajender; Sessitsch, Angela; Brader, Günter

    2015-01-01

    Bacillus and related genera in the Bacillales within the Firmicutes harbor a variety of secondary metabolite gene clusters encoding polyketide synthases and non-ribosomal peptide synthetases responsible for remarkable diverse number of polyketides (PKs) and lipopeptides (LPs). These compounds may be utilized for medical and agricultural applications. Here, we summarize the knowledge on structural diversity and underlying gene clusters of LPs and PKs in the Bacillales. Moreover, we evaluate by using published prediction tools the potential metabolic capacity of these bacteria to produce type I PKs or LPs. The huge sequence repository of bacterial genomes and metagenomes provides the basis for such genome-mining to reveal the potential for novel structurally diverse secondary metabolites. The otherwise cumbersome task to isolate often unstable PKs and deduce their structure can be streamlined. Using web based prediction tools, we identified here several novel clusters of PKs and LPs from genomes deposited in the database. Our analysis suggests that a substantial fraction of predicted LPs and type I PKs are uncharacterized, and their functions remain to be studied. Known and predicted LPs and PKs occurred in the majority of the plant associated genera, predominantly in Bacillus and Paenibacillus. Surprisingly, many genera from other environments contain no or few of such compounds indicating the role of these secondary metabolites in plant-associated niches.

  2. Genome mining: Prediction of lipopeptides and polyketides from Bacillus and related Firmicutes

    Directory of Open Access Journals (Sweden)

    Gajender Aleti

    2015-01-01

    Full Text Available Bacillus and related genera in the Bacillales within the Firmicutes harbor a variety of secondary metabolite gene clusters encoding polyketide synthases and non-ribosomal peptide synthetases responsible for remarkable diverse number of polyketides (PKs and lipopeptides (LPs. These compounds may be utilized for medical and agricultural applications. Here, we summarize the knowledge on structural diversity and underlying gene clusters of LPs and PKs in the Bacillales. Moreover, we evaluate by using published prediction tools the potential metabolic capacity of these bacteria to produce type I PKs or LPs. The huge sequence repository of bacterial genomes and metagenomes provides the basis for such genome-mining to reveal the potential for novel structurally diverse secondary metabolites. The otherwise cumbersome task to isolate often unstable PKs and deduce their structure can be streamlined. Using web based prediction tools, we identified here several novel clusters of PKs and LPs from genomes deposited in the database. Our analysis suggests that a substantial fraction of predicted LPs and type I PKs are uncharacterized, and their functions remain to be studied. Known and predicted LPs and PKs occurred in the majority of the plant associated genera, predominantly in Bacillus and Paenibacillus. Surprisingly, many genera from other environments contain no or few of such compounds indicating the role of these secondary metabolites in plant-associated niches.

  3. Automated detection of follow-up appointments using text mining of discharge records.

    Science.gov (United States)

    Ruud, Kari L; Johnson, Matthew G; Liesinger, Juliette T; Grafft, Carrie A; Naessens, James M

    2010-06-01

    To determine whether text mining can accurately detect specific follow-up appointment criteria in free-text hospital discharge records. Cross-sectional study. Mayo Clinic Rochester hospitals. Inpatients discharged from general medicine services in 2006 (n = 6481). Textual hospital dismissal summaries were manually reviewed to determine whether the records contained specific follow-up appointment arrangement elements: date, time and either physician or location for an appointment. The data set was evaluated for the same criteria using SAS Text Miner software. The two assessments were compared to determine the accuracy of text mining for detecting records containing follow-up appointment arrangements. Agreement of text-mined appointment findings with gold standard (manual abstraction) including sensitivity, specificity, positive predictive and negative predictive values (PPV and NPV). About 55.2% (3576) of discharge records contained all criteria for follow-up appointment arrangements according to the manual review, 3.2% (113) of which were missed through text mining. Text mining incorrectly identified 3.7% (107) follow-up appointments that were not considered valid through manual review. Therefore, the text mining analysis concurred with the manual review in 96.6% of the appointment findings. Overall sensitivity and specificity were 96.8 and 96.3%, respectively; and PPV and NPV were 97.0 and 96.1%, respectively. of individual appointment criteria resulted in accuracy rates of 93.5% for date, 97.4% for time, 97.5% for physician and 82.9% for location. Text mining of unstructured hospital dismissal summaries can accurately detect documentation of follow-up appointment arrangement elements, thus saving considerable resources for performance assessment and quality-related research.

  4. Automated genomic DNA purification options in agricultural applications using MagneSil paramagnetic particles

    Science.gov (United States)

    Bitner, Rex M.; Koller, Susan C.

    2002-06-01

    The automated high throughput purification of genomic DNA form plant materials can be performed using MagneSil paramagnetic particles on the Beckman-Coulter FX, BioMek 2000, and the Tecan Genesis robot. Similar automated methods are available for DNA purifications from animal blood. These methods eliminate organic extractions, lengthy incubations and cumbersome filter plates. The DNA is suitable for applications such as PCR and RAPD analysis. Methods are described for processing traditionally difficult samples such as those containing large amounts of polyphenolics or oils, while still maintaining a high level of DNA purity. The robotic protocols have ben optimized for agricultural applications such as marker assisted breeding, seed-quality testing, and SNP discovery and scoring. In addition to high yield purification of DNA from plant samples or animal blood, the use of Promega's DNA-IQ purification system is also described. This method allows for the purification of a narrow range of DNA regardless of the amount of additional DNA that is present in the initial sample. This simultaneous Isolation and Quantification of DNA allows the DNA to be used directly in applications such as PCR, SNP analysis, and RAPD, without the need for separate quantitation of the DNA.

  5. Automated Text Data Mining Analysis of Five Decades of Educational Leadership Research Literature: Probabilistic Topic Modeling of "EAQ" Articles From 1965 to 2014

    Science.gov (United States)

    Wang, Yinying; Bowers, Alex J.; Fikis, David J.

    2017-01-01

    Purpose: The purpose of this study is to describe the underlying topics and the topic evolution in the 50-year history of educational leadership research literature. Method: We used automated text data mining with probabilistic latent topic models to examine the full text of the entire publication history of all 1,539 articles published in…

  6. Mining

    Directory of Open Access Journals (Sweden)

    Khairullah Khan

    2014-09-01

    Full Text Available Opinion mining is an interesting area of research because of its applications in various fields. Collecting opinions of people about products and about social and political events and problems through the Web is becoming increasingly popular every day. The opinions of users are helpful for the public and for stakeholders when making certain decisions. Opinion mining is a way to retrieve information through search engines, Web blogs and social networks. Because of the huge number of reviews in the form of unstructured text, it is impossible to summarize the information manually. Accordingly, efficient computational methods are needed for mining and summarizing the reviews from corpuses and Web documents. This study presents a systematic literature survey regarding the computational techniques, models and algorithms for mining opinion components from unstructured reviews.

  7. Automated analysis for large amount gaseous fission product gamma-scanning spectra from nuclear power plant and its data mining

    International Nuclear Information System (INIS)

    Weihua Zhang; Kurt Ungar; Ian Hoffman; Ryan Lawrie; Jarmo Ala-Heikkila

    2010-01-01

    Based on the Linssi database and UniSampo/Shaman software, an automated analysis platform has been setup for the analysis of large amounts of gamma-spectra from the primary coolant monitoring systems of a CANDU reactor. Thus, a database inventory of gaseous and volatile fission products in the primary coolant of a CANDU reactor has been established. This database is comprised of 15,000 spectra of radioisotope analysis records. Records from the database inventory were retrieved by a specifically designed data-mining module and subjected to further analysis. Results from the analysis were subsequently used to identify the reactor coolant half-life of 135 Xe and 133 Xe, as well as the correlations of 135 Xe and 88 Kr activities. (author)

  8. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Yu-Wei [Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Simmons, Blake A. [Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Singer, Steven W. [Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2015-10-29

    The recovery of genomes from metagenomic datasets is a critical step to defining the functional roles of the underlying uncultivated populations. We previously developed MaxBin, an automated binning approach for high-throughput recovery of microbial genomes from metagenomes. Here, we present an expanded binning algorithm, MaxBin 2.0, which recovers genomes from co-assembly of a collection of metagenomic datasets. Tests on simulated datasets revealed that MaxBin 2.0 is highly accurate in recovering individual genomes, and the application of MaxBin 2.0 to several metagenomes from environmental samples demonstrated that it could achieve two complementary goals: recovering more bacterial genomes compared to binning a single sample as well as comparing the microbial community composition between different sampling environments. Availability and implementation: MaxBin 2.0 is freely available at http://sourceforge.net/projects/maxbin/ under BSD license. Supplementary information: Supplementary data are available at Bioinformatics online.

  9. Automation of the loading units employed in RWE Power AG's opencast mines; Vollautomatisierung der Beladewagen in den Tagebauen der RWE Power AG

    Energy Technology Data Exchange (ETDEWEB)

    Vestweber, Arne [RWE Power AG, Niederzier (DE). Elektrotechnik - Technische Unterstuetzung (PCH-EU); Winkel, Reik [indurad GmbH - The Industrial Radar Company, Aachen (Germany); Gau, Wilfried [RWE Power AG, Frechen (Germany). Technikzentrum Tagebaue/Hauptwerkstatt; Ressing, Hartwig [Cegelec Automatisierungstechnik GmbH und Co. KG, Koeln (Germany). Automatisierung Foerdergeraete

    2012-02-15

    Interlocking automation modules permit further cost-reduction potential to be exploited in RWE Power AG's opencast mines, with the automation of the loading units being an important core element. The complexity of the task and its high development share necessitated an intensive optimization process and interdisciplinary collaboration between electrical, mechanical and mining engineers. Radar sensor technology can open up new options in different fields of application. Simulation techniques permitting systems to commissioned virtually without time-consuming and cost-intensive tests on the real equipment have proven useful and will be increasingly used in future automation projects. Efficient tools for recording and analyzing in conjunction with remote access enable more economic and efficient working, thus supporting the efficient commissioning of complex automatic systems. (orig.)

  10. Automation of the loading units employed in RWE Power AG's opencast mines; Vollautomatisierung der Beladewagen in den Tagebauen der RWE Power AG

    Energy Technology Data Exchange (ETDEWEB)

    Vestweber, Arne [RWE Power AG, Frechen (Germany); Winkel, Reik [indurad GmbH - The Industrial Radar Company, Aachen (Germany); Gau, Wilfried [RWE Power AG, Eschweiler (Germany); Ressing, Hartwig [Cegelec Automatisierungstechnik GmbH und Co. KG, Koeln (Germany)

    2011-01-15

    Interlocking automation modules permit further cost-reduction potential to be exploited in RWE Power AG's opencast mines, with the automation of the loading units being an important core element. The complexity of the task and its high development share necessitated an intensive optimization process and interdisciplinary collaboration between electrical, mechanical and mining engineers. Radar sensor technology can open up new options in different fields of application. Simulation techniques permitting systems to commissioned virtually without time-consuming and cost-intensive tests on the real equipment have proven useful and will be increasingly used in future automation projects. Efficient tools for recording and analyzing in conjunction with remote access enable more economic and efficient working, thus supporting the efficient commissioning of complex automatic systems. (orig.)

  11. Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining

    Directory of Open Access Journals (Sweden)

    Iyer Vishwanath R

    2007-11-01

    Full Text Available Abstract Background Cis-acting transcriptional regulatory elements in mammalian genomes typically contain specific combinations of binding sites for various transcription factors. Although some cis-regulatory elements have been well studied, the combinations of transcription factors that regulate normal expression levels for the vast majority of the 20,000 genes in the human genome are unknown. We hypothesized that it should be possible to discover transcription factor combinations that regulate gene expression in concert by identifying over-represented combinations of sequence motifs that occur together in the genome. In order to detect combinations of transcription factor binding motifs, we developed a data mining approach based on the use of association rules, which are typically used in market basket analysis. We scored each segment of the genome for the presence or absence of each of 83 transcription factor binding motifs, then used association rule mining algorithms to mine this dataset, thus identifying frequently occurring pairs of distinct motifs within a segment. Results Support for most pairs of transcription factor binding motifs was highly correlated across different chromosomes although pair significance varied. Known true positive motif pairs showed higher association rule support, confidence, and significance than background. Our subsets of high-confidence, high-significance mined pairs of transcription factors showed enrichment for co-citation in PubMed abstracts relative to all pairs, and the predicted associations were often readily verifiable in the literature. Conclusion Functional elements in the genome where transcription factors bind to regulate expression in a combinatorial manner are more likely to be predicted by identifying statistically and biologically significant combinations of transcription factor binding motifs than by simply scanning the genome for the occurrence of binding sites for a single transcription

  12. Research into robotic automation of drilling equipment by the Institute of Mining, UB RAS

    Science.gov (United States)

    Regotunov, AS; Sukhov, RI

    2018-03-01

    The article discusses the issues connected with the development of instrumentation for the express-determination of strength characteristics of rocks during blasthole drilling in open pit mines. The trial results of the instrumentation are reported in terms of the drilling rate–energy content interrelation determined in the analyses of experimental drilling block data and by the digital model of rock distribution in depth versus drilling complexity index.

  13. An automated graphics tool for comparative genomics: the Coulson plot generator.

    Science.gov (United States)

    Field, Helen I; Coulson, Richard M R; Field, Mark C

    2013-04-27

    Comparative analysis is an essential component to biology. When applied to genomics for example, analysis may require comparisons between the predicted presence and absence of genes in a group of genomes under consideration. Frequently, genes can be grouped into small categories based on functional criteria, for example membership of a multimeric complex, participation in a metabolic or signaling pathway or shared sequence features and/or paralogy. These patterns of retention and loss are highly informative for the prediction of function, and hence possible biological context, and can provide great insights into the evolutionary history of cellular functions. However, representation of such information in a standard spreadsheet is a poor visual means from which to extract patterns within a dataset. We devised the Coulson Plot, a new graphical representation that exploits a matrix of pie charts to display comparative genomics data. Each pie is used to describe a complex or process from a separate taxon, and is divided into sectors corresponding to the number of proteins (subunits) in a complex/process. The predicted presence or absence of proteins in each complex are delineated by occupancy of a given sector; this format is visually highly accessible and makes pattern recognition rapid and reliable. A key to the identity of each subunit, plus hierarchical naming of taxa and coloring are included. A java-based application, the Coulson plot generator (CPG) automates graphic production, with a tab or comma-delineated text file as input and generating an editable portable document format or svg file. CPG software may be used to rapidly convert spreadsheet data to a graphical matrix pie chart format. The representation essentially retains all of the information from the spreadsheet but presents a graphically rich format making comparisons and identification of patterns significantly clearer. While the Coulson plot format is highly useful in comparative genomics, its

  14. RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome.

    Science.gov (United States)

    Thongjuea, Supat; Ruanjaichon, Vinitchan; Bruskiewich, Richard; Vanavichit, Apichart

    2009-01-01

    RiceGeneThresher is a public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, expressed sequence tags (ESTs), protein domains, gene ontology, plant stress-responsive genes, metabolic pathways and prediction of protein-protein interactions. RiceGeneThresher system integrates these diverse data sources and provides powerful web-based applications, and flexible tools for delivering customized set of biological data on rice. Its system supports whole-genome gene mining for QTL by querying using DNA marker intervals or genomic loci. RiceGeneThresher provides biologically supported evidences that are essential for targeting groups or networks of genes involved in controlling traits underlying QTL. Users can use it to discover and to assign the most promising candidate genes in preparation for the further gene function validation analysis. The web-based application is freely available at http://rice.kps.ku.ac.th.

  15. A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks.

    Science.gov (United States)

    Xiang, Zuoshuang; Qin, Tingting; Qin, Zhaohui S; He, Yongqun

    2013-10-16

    The large amount of literature in the post-genomics era enables the study of gene interactions and networks using all available articles published for a specific organism. MeSH is a controlled vocabulary of medical and scientific terms that is used by biomedical scientists to manually index articles in the PubMed literature database. We hypothesized that genome-wide gene-MeSH term associations from the PubMed literature database could be used to predict implicit gene-to-gene relationships and networks. While the gene-MeSH associations have been used to detect gene-gene interactions in some studies, different methods have not been well compared, and such a strategy has not been evaluated for a genome-wide literature analysis. Genome-wide literature mining of gene-to-gene interactions allows ranking of the best gene interactions and investigation of comprehensive biological networks at a genome level. The genome-wide GenoMesh literature mining algorithm was developed by sequentially generating a gene-article matrix, a normalized gene-MeSH term matrix, and a gene-gene matrix. The gene-gene matrix relies on the calculation of pairwise gene dissimilarities based on gene-MeSH relationships. An optimized dissimilarity score was identified from six well-studied functions based on a receiver operating characteristic (ROC) analysis. Based on the studies with well-studied Escherichia coli and less-studied Brucella spp., GenoMesh was found to accurately identify gene functions using weighted MeSH terms, predict gene-gene interactions not reported in the literature, and cluster all the genes studied from an organism using the MeSH-based gene-gene matrix. A web-based GenoMesh literature mining program is also available at: http://genomesh.hegroup.org. GenoMesh also predicts gene interactions and networks among genes associated with specific MeSH terms or user-selected gene lists. The GenoMesh algorithm and web program provide the first genome-wide, MeSH-based literature mining

  16. A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks

    Science.gov (United States)

    2013-01-01

    Background The large amount of literature in the post-genomics era enables the study of gene interactions and networks using all available articles published for a specific organism. MeSH is a controlled vocabulary of medical and scientific terms that is used by biomedical scientists to manually index articles in the PubMed literature database. We hypothesized that genome-wide gene-MeSH term associations from the PubMed literature database could be used to predict implicit gene-to-gene relationships and networks. While the gene-MeSH associations have been used to detect gene-gene interactions in some studies, different methods have not been well compared, and such a strategy has not been evaluated for a genome-wide literature analysis. Genome-wide literature mining of gene-to-gene interactions allows ranking of the best gene interactions and investigation of comprehensive biological networks at a genome level. Results The genome-wide GenoMesh literature mining algorithm was developed by sequentially generating a gene-article matrix, a normalized gene-MeSH term matrix, and a gene-gene matrix. The gene-gene matrix relies on the calculation of pairwise gene dissimilarities based on gene-MeSH relationships. An optimized dissimilarity score was identified from six well-studied functions based on a receiver operating characteristic (ROC) analysis. Based on the studies with well-studied Escherichia coli and less-studied Brucella spp., GenoMesh was found to accurately identify gene functions using weighted MeSH terms, predict gene-gene interactions not reported in the literature, and cluster all the genes studied from an organism using the MeSH-based gene-gene matrix. A web-based GenoMesh literature mining program is also available at: http://genomesh.hegroup.org. GenoMesh also predicts gene interactions and networks among genes associated with specific MeSH terms or user-selected gene lists. Conclusions The GenoMesh algorithm and web program provide the first genome

  17. antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

    DEFF Research Database (Denmark)

    Weber, Tilmann; Blin, Kai; Duddela, Srikanth

    2015-01-01

    Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we...... introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration...

  18. The Tripod for Bacterial Natural Product Discovery: Genome Mining, Silent Pathway Induction, and Mass Spectrometry-Based Molecular Networking.

    Science.gov (United States)

    Trivella, Daniela B B; de Felicio, Rafael

    2018-01-01

    Natural products are the richest source of chemical compounds for drug discovery. Particularly, bacterial secondary metabolites are in the spotlight due to advances in genome sequencing and mining, as well as for the potential of biosynthetic pathway manipulation to awake silent (cryptic) gene clusters under laboratory cultivation. Further progress in compound detection, such as the development of the tandem mass spectrometry (MS/MS) molecular networking approach, has contributed to the discovery of novel bacterial natural products. The latter can be applied directly to bacterial crude extracts for identifying and dereplicating known compounds, therefore assisting the prioritization of extracts containing novel natural products, for example. In our opinion, these three approaches-genome mining, silent pathway induction, and MS-based molecular networking-compose the tripod for modern bacterial natural product discovery and will be discussed in this perspective.

  19. Mining the genome of Rhodococcus fascians, a plant growth-promoting bacterium gone astray.

    Science.gov (United States)

    Francis, Isolde M; Stes, Elisabeth; Zhang, Yucheng; Rangel, Diana; Audenaert, Kris; Vereecke, Danny

    2016-09-25

    Rhodococcus fascians is a phytopathogenic Gram-positive Actinomycete with a very broad host range encompassing especially dicotyledonous herbaceous perennials, but also some monocots, such as the Liliaceae and, recently, the woody crop pistachio. The pathogenicity of R. fascians strain D188 is known to be encoded by the linear plasmid pFiD188 and to be dictated by its capacity to produce a mixture of cytokinins. Here, we show that D188-5, the nonpathogenic plasmid-free derivative of the wild-type strain D188 actually has a plant growth-promoting effect. With the availability of the genome sequence of R. fascians, the chromosome of strain D188 was mined for putative plant growth-promoting functions and the functionality of some of these activities was tested. This analysis together with previous results suggests that the plant growth-promoting activity of R. fascians is due to production of plant growth modulators, such as auxin and cytokinin, combined with degradation of ethylene through 1-amino-cyclopropane-1-carboxylic acid deaminase. Moreover, R. fascians has several functions that could contribute to efficient colonization and competitiveness, but there is little evidence for a strong impact on plant nutrition. Possibly, the plant growth promotion encoded by the D188 chromosome is imperative for the epiphytic phase of the life cycle of R. fascians and prepares the plant to host the bacteria, thus ensuring proper continuation into the pathogenic phase. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Mining Genome-Scale Growth Phenotype Data through Constant-Column Biclustering

    KAUST Repository

    Alzahrani, Majed A.

    2017-07-10

    Growth phenotype profiling of genome-wide gene-deletion strains over stress conditions can offer a clear picture that the essentiality of genes depends on environmental conditions. Systematically identifying groups of genes from such recently emerging high-throughput data that share similar patterns of conditional essentiality and dispensability under various environmental conditions can elucidate how genetic interactions of the growth phenotype are regulated in response to the environment. In this dissertation, we first demonstrate that detecting such “co-fit” gene groups can be cast as a less well-studied problem in biclustering, i.e., constant-column biclustering. Despite significant advances in biclustering techniques, very few were designed for mining in growth phenotype data. Here, we propose Gracob, a novel, efficient graph-based method that casts and solves the constant-column biclustering problem as a maximal clique finding problem in a multipartite graph. We compared Gracob with a large collection of widely used biclustering methods that cover different types of algorithms designed to detect different types of biclusters. Gracob showed superior performance on finding co-fit genes over all the existing methods on both a variety of synthetic data sets with a wide range of settings, and three real growth phenotype data sets for E. coli, proteobacteria, and yeast.

  1. An effective strategy for exploring unknown metabolic pathways by genome mining.

    Science.gov (United States)

    Castillo, Dorianne A; Kolesnikova, Mariya D; Matsuda, Seiichi P T

    2013-04-17

    Plants allocate an estimated 15-25% of their proteome to specialized metabolic pathways that remain largely uncharacterized. Here, we describe a genome mining strategy for exploring such unknown pathways and demonstrate this approach for triterpenoids by functionally characterizing three cytochrome P450s from Arabidopsis thaliana . Building on proven methods for characterizing oxidosqualene cyclases, we heterologously expressed in yeast known cyclases with candidate P450s chosen from gene clustering and microarray coexpression patterns. The yeast cultures produced mg/L amounts of plant metabolites in vivo without the complex phytochemical background of plant extracts. Despite this simplification, the product multiplicity and novelty overwhelmed analytical efforts by MS methods. HSQC analysis overcame this problem. Side-by-side HSQC comparisons of crude P450 extracts against a control resolved even minor P450 products among ~100 other yeast metabolites spanning a dynamic range of >10,000:1. HSQC and GC-MS then jointly guided purification and structure determination by classical NMR methods. Including our present results for P450 oxidation of thalianol, arabidiol, and marneral, the metabolic fate for most of the major triterpene synthase products in Arabidopsis is now at least partially known.

  2. High-frequency, long-duration water sampling in acid mine drainage studies: a short review of current methods and recent advances in automated water samplers

    Science.gov (United States)

    Chapin, Thomas

    2015-01-01

    Hand-collected grab samples are the most common water sampling method but using grab sampling to monitor temporally variable aquatic processes such as diel metal cycling or episodic events is rarely feasible or cost-effective. Currently available automated samplers are a proven, widely used technology and typically collect up to 24 samples during a deployment. However, these automated samplers are not well suited for long-term sampling in remote areas or in freezing conditions. There is a critical need for low-cost, long-duration, high-frequency water sampling technology to improve our understanding of the geochemical response to temporally variable processes. This review article will examine recent developments in automated water sampler technology and utilize selected field data from acid mine drainage studies to illustrate the utility of high-frequency, long-duration water sampling.

  3. Automated integration of genomic physical mapping data via parallel simulated annealing

    Energy Technology Data Exchange (ETDEWEB)

    Slezak, T.

    1994-06-01

    The Human Genome Center at the Lawrence Livermore National Laboratory (LLNL) is nearing closure on a high-resolution physical map of human chromosome 19. We have build automated tools to assemble 15,000 fingerprinted cosmid clones into 800 contigs with minimal spanning paths identified. These islands are being ordered, oriented, and spanned by a variety of other techniques including: Fluorescence Insitu Hybridization (FISH) at 3 levels of resolution, ECO restriction fragment mapping across all contigs, and a multitude of different hybridization and PCR techniques to link cosmid, YAC, AC, PAC, and Pl clones. The FISH data provide us with partial order and distance data as well as orientation. We made the observation that map builders need a much rougher presentation of data than do map readers; the former wish to see raw data since these can expose errors or interesting biology. We further noted that by ignoring our length and distance data we could simplify our problem into one that could be readily attacked with optimization techniques. The data integration problem could then be seen as an M x N ordering of our N cosmid clones which ``intersect`` M larger objects by defining ``intersection`` to mean either contig/map membership or hybridization results. Clearly, the goal of making an integrated map is now to rearrange the N cosmid clone ``columns`` such that the number of gaps on the object ``rows`` are minimized. Our FISH partially-ordered cosmid clones provide us with a set of constraints that cannot be violated by the rearrangement process. We solved the optimization problem via simulated annealing performed on a network of 40+ Unix machines in parallel, using a server/client model built on explicit socket calls. For current maps we can create a map in about 4 hours on the parallel net versus 4+ days on a single workstation. Our biologists are now using this software on a daily basis to guide their efforts toward final closure.

  4. Metro Maps of Plant Disease Dynamics—Automated Mining of Differences Using Hyperspectral Images

    Science.gov (United States)

    Wahabzada, Mirwaes; Mahlein, Anne-Katrin; Bauckhage, Christian; Steiner, Ulrike; Oerke, Erich-Christian; Kersting, Kristian

    2015-01-01

    Understanding the response dynamics of plants to biotic stress is essential to improve management practices and breeding strategies of crops and thus to proceed towards a more sustainable agriculture in the coming decades. In this context, hyperspectral imaging offers a particularly promising approach since it provides non-destructive measurements of plants correlated with internal structure and biochemical compounds. In this paper, we present a cascade of data mining techniques for fast and reliable data-driven sketching of complex hyperspectral dynamics in plant science and plant phenotyping. To achieve this, we build on top of a recent linear time matrix factorization technique, called Simplex Volume Maximization, in order to automatically discover archetypal hyperspectral signatures that are characteristic for particular diseases. The methods were applied on a data set of barley leaves (Hordeum vulgare) diseased with foliar plant pathogens Pyrenophora teres, Puccinia hordei and Blumeria graminis hordei. Towards more intuitive visualizations of plant disease dynamics, we use the archetypal signatures to create structured summaries that are inspired by metro maps, i.e. schematic diagrams of public transport networks. Metro maps of plant disease dynamics produced on several real-world data sets conform to plant physiological knowledge and explicitly illustrate the interaction between diseases and plants. Most importantly, they provide an abstract and interpretable view on plant disease progression. PMID:25621489

  5. Metro maps of plant disease dynamics--automated mining of differences using hyperspectral images.

    Directory of Open Access Journals (Sweden)

    Mirwaes Wahabzada

    Full Text Available Understanding the response dynamics of plants to biotic stress is essential to improve management practices and breeding strategies of crops and thus to proceed towards a more sustainable agriculture in the coming decades. In this context, hyperspectral imaging offers a particularly promising approach since it provides non-destructive measurements of plants correlated with internal structure and biochemical compounds. In this paper, we present a cascade of data mining techniques for fast and reliable data-driven sketching of complex hyperspectral dynamics in plant science and plant phenotyping. To achieve this, we build on top of a recent linear time matrix factorization technique, called Simplex Volume Maximization, in order to automatically discover archetypal hyperspectral signatures that are characteristic for particular diseases. The methods were applied on a data set of barley leaves (Hordeum vulgare diseased with foliar plant pathogens Pyrenophora teres, Puccinia hordei and Blumeria graminis hordei. Towards more intuitive visualizations of plant disease dynamics, we use the archetypal signatures to create structured summaries that are inspired by metro maps, i.e. schematic diagrams of public transport networks. Metro maps of plant disease dynamics produced on several real-world data sets conform to plant physiological knowledge and explicitly illustrate the interaction between diseases and plants. Most importantly, they provide an abstract and interpretable view on plant disease progression.

  6. Automated web usage data mining and recommendation system using K-Nearest Neighbor (KNN classification method

    Directory of Open Access Journals (Sweden)

    D.A. Adeniyi

    2016-01-01

    Full Text Available The major problem of many on-line web sites is the presentation of many choices to the client at a time; this usually results to strenuous and time consuming task in finding the right product or information on the site. In this work, we present a study of automatic web usage data mining and recommendation system based on current user behavior through his/her click stream data on the newly developed Really Simple Syndication (RSS reader website, in order to provide relevant information to the individual without explicitly asking for it. The K-Nearest-Neighbor (KNN classification method has been trained to be used on-line and in Real-Time to identify clients/visitors click stream data, matching it to a particular user group and recommend a tailored browsing option that meet the need of the specific user at a particular time. To achieve this, web users RSS address file was extracted, cleansed, formatted and grouped into meaningful session and data mart was developed. Our result shows that the K-Nearest Neighbor classifier is transparent, consistent, straightforward, simple to understand, high tendency to possess desirable qualities and easy to implement than most other machine learning techniques specifically when there is little or no prior knowledge about data distribution.

  7. O-miner: an integrative platform for automated analysis and mining of -omics data.

    Science.gov (United States)

    Cutts, Rosalind J; Dayem Ullah, Abu Z; Sangaralingam, Ajanthah; Gadaleta, Emanuela; Lemoine, Nicholas R; Chelala, Claude

    2012-07-01

    High-throughput profiling has generated massive amounts of data across basic, clinical and translational research fields. However, open source comprehensive web tools for analysing data obtained from different platforms and technologies are still lacking. To fill this gap and the unmet computational needs of ongoing research projects, we developed O-miner, a rapid, comprehensive, efficient web tool that covers all the steps required for the analysis of both transcriptomic and genomic data starting from raw image files through in-depth bioinformatics analysis and annotation to biological knowledge extraction. O-miner was developed from a biologist end-user perspective. Hence, it is as simple to use as possible within the confines of the complexity of the data being analysed. It provides a strong analytical suite able to overlay and harness large, complicated, raw and heterogeneous sets of profiles with biological/clinical data. Biologists can use O-miner to analyse and integrate different types of data and annotations to build knowledge of relevant altered mechanisms and pathways in order to identify and prioritize novel targets for further biological validation. Here we describe the analytical workflows currently available using O-miner and present examples of use. O-miner is freely available at www.o-miner.org.

  8. Data Mining Approaches for Genomic Biomarker Development: Applications Using Drug Screening Data from the Cancer Genome Project and the Cancer Cell Line Encyclopedia.

    Directory of Open Access Journals (Sweden)

    David G Covell

    Full Text Available Developing reliable biomarkers of tumor cell drug sensitivity and resistance can guide hypothesis-driven basic science research and influence pre-therapy clinical decisions. A popular strategy for developing biomarkers uses characterizations of human tumor samples against a range of cancer drug responses that correlate with genomic change; developed largely from the efforts of the Cancer Cell Line Encyclopedia (CCLE and Sanger Cancer Genome Project (CGP. The purpose of this study is to provide an independent analysis of this data that aims to vet existing and add novel perspectives to biomarker discoveries and applications. Existing and alternative data mining and statistical methods will be used to a evaluate drug responses of compounds with similar mechanism of action (MOA, b examine measures of gene expression (GE, copy number (CN and mutation status (MUT biomarkers, combined with gene set enrichment analysis (GSEA, for hypothesizing biological processes important for drug response, c conduct global comparisons of GE, CN and MUT as biomarkers across all drugs screened in the CGP dataset, and d assess the positive predictive power of CGP-derived GE biomarkers as predictors of drug response in CCLE tumor cells. The perspectives derived from individual and global examinations of GEs, MUTs and CNs confirm existing and reveal unique and shared roles for these biomarkers in tumor cell drug sensitivity and resistance. Applications of CGP-derived genomic biomarkers to predict the drug response of CCLE tumor cells finds a highly significant ROC, with a positive predictive power of 0.78. The results of this study expand the available data mining and analysis methods for genomic biomarker development and provide additional support for using biomarkers to guide hypothesis-driven basic science research and pre-therapy clinical decisions.

  9. Data Mining Approaches for Genomic Biomarker Development: Applications Using Drug Screening Data from the Cancer Genome Project and the Cancer Cell Line Encyclopedia.

    Science.gov (United States)

    Covell, David G

    2015-01-01

    Developing reliable biomarkers of tumor cell drug sensitivity and resistance can guide hypothesis-driven basic science research and influence pre-therapy clinical decisions. A popular strategy for developing biomarkers uses characterizations of human tumor samples against a range of cancer drug responses that correlate with genomic change; developed largely from the efforts of the Cancer Cell Line Encyclopedia (CCLE) and Sanger Cancer Genome Project (CGP). The purpose of this study is to provide an independent analysis of this data that aims to vet existing and add novel perspectives to biomarker discoveries and applications. Existing and alternative data mining and statistical methods will be used to a) evaluate drug responses of compounds with similar mechanism of action (MOA), b) examine measures of gene expression (GE), copy number (CN) and mutation status (MUT) biomarkers, combined with gene set enrichment analysis (GSEA), for hypothesizing biological processes important for drug response, c) conduct global comparisons of GE, CN and MUT as biomarkers across all drugs screened in the CGP dataset, and d) assess the positive predictive power of CGP-derived GE biomarkers as predictors of drug response in CCLE tumor cells. The perspectives derived from individual and global examinations of GEs, MUTs and CNs confirm existing and reveal unique and shared roles for these biomarkers in tumor cell drug sensitivity and resistance. Applications of CGP-derived genomic biomarkers to predict the drug response of CCLE tumor cells finds a highly significant ROC, with a positive predictive power of 0.78. The results of this study expand the available data mining and analysis methods for genomic biomarker development and provide additional support for using biomarkers to guide hypothesis-driven basic science research and pre-therapy clinical decisions.

  10. Manipulation of metabolic pathways controlled by signaling molecules, inducers of antibiotic production, for genome mining in Streptomyces spp.

    Science.gov (United States)

    Arakawa, Kenji

    2018-02-23

    Streptomyces is well characterized by an ability to produce a wide variety of secondary metabolites including antibiotics, whose expression is strictly controlled by small diffusible signaling molecules at nano-molar concentrations. The signaling molecules identified to date are classified into three skeletons; γ-butyrolactones, furans, and γ-butenolides. Accumulated data suggest the structural diversity of the signaling molecules in Streptomyces species and their potential in activating cryptic secondary metabolite biosynthetic pathways. Several genome mining approaches to activate silent biosynthetic gene clusters have been reported for natural product discovery. This review updates recent examples on genetic manipulation including blockage of metabolic pathways together with inactivation of transcriptional repressor genes.

  11. Automation of the Design of the Anchorage System Taking into Account the Geomechanical State of the Massif and Mining Development Schemes

    Directory of Open Access Journals (Sweden)

    Demin Vladimir

    2018-01-01

    Full Text Available The article presents the system for the automation of the design of the anchorage, which regulates the calculation of the required parameters of the fasteners for the fastening of the fastening system. The main factors affecting the operation of the anchor support are grouped in the following way: mining and geological conditions, technical characteristics of the anchor support, geomechanical conditions for conducting and operating the mine workings. Mining and geological conditions for carrying out excavations include: physical and mechanical properties of rocks, the category of roof stability, fracturing, etc. Technical characteristics of the anchor support: material of the rod, filler, filling completeness, etc. Conditions (geomechanical of carrying out and exploitation of the mine workings: the depth of the conduct, the location relative to the zone of influence of the cleaning works, the location relative to the waste zone, etc. As a result of calculations the program gives out the basic parameters of the anchor support, which coincide with the parameters adopted by the passport.

  12. Producing genome structure populations with the dynamic and automated PGS software.

    Science.gov (United States)

    Hua, Nan; Tjong, Harianto; Shin, Hanjun; Gong, Ke; Zhou, Xianghong Jasmine; Alber, Frank

    2018-05-01

    Chromosome conformation capture technologies such as Hi-C are widely used to investigate the spatial organization of genomes. Because genome structures can vary considerably between individual cells of a population, interpreting ensemble-averaged Hi-C data can be challenging, in particular for long-range and interchromosomal interactions. We pioneered a probabilistic approach for the generation of a population of distinct diploid 3D genome structures consistent with all the chromatin-chromatin interaction probabilities from Hi-C experiments. Each structure in the population is a physical model of the genome in 3D. Analysis of these models yields new insights into the causes and the functional properties of the genome's organization in space and time. We provide a user-friendly software package, called PGS, which runs on local machines (for practice runs) and high-performance computing platforms. PGS takes a genome-wide Hi-C contact frequency matrix, along with information about genome segmentation, and produces an ensemble of 3D genome structures entirely consistent with the input. The software automatically generates an analysis report, and provides tools to extract and analyze the 3D coordinates of specific domains. Basic Linux command-line knowledge is sufficient for using this software. A typical running time of the pipeline is ∼3 d with 300 cores on a computer cluster to generate a population of 1,000 diploid genome structures at topological-associated domain (TAD)-level resolution.

  13. Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources.

    Science.gov (United States)

    Wang, Xiaobo; Wu, Jian; Liang, Jianli; Cheng, Feng; Wang, Xiaowu

    2015-01-01

    The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/. © The Author(s) 2015. Published by Oxford University Press.

  14. Genome-wide data-mining of candidate human splice translational efficiency polymorphisms (STEPs and an online database.

    Directory of Open Access Journals (Sweden)

    Christopher A Raistrick

    2010-10-01

    Full Text Available Variation in pre-mRNA splicing is common and in some cases caused by genetic variants in intronic splicing motifs. Recent studies into the insulin gene (INS discovered a polymorphism in a 5' non-coding intron that influences the likelihood of intron retention in the final mRNA, extending the 5' untranslated region and maintaining protein quality. Retention was also associated with increased insulin levels, suggesting that such variants--splice translational efficiency polymorphisms (STEPs--may relate to disease phenotypes through differential protein expression. We set out to explore the prevalence of STEPs in the human genome and validate this new category of protein quantitative trait loci (pQTL using publicly available data.Gene transcript and variant data were collected and mined for candidate STEPs in motif regions. Sequences from transcripts containing potential STEPs were analysed for evidence of splice site recognition and an effect in expressed sequence tags (ESTs. 16 publicly released genome-wide association data sets of common diseases were searched for association to candidate polymorphisms with HapMap frequency data. Our study found 3324 candidate STEPs lying in motif sequences of 5' non-coding introns and further mining revealed 170 with transcript evidence of intron retention. 21 potential STEPs had EST evidence of intron retention or exon extension, as well as population frequency data for comparison.Results suggest that the insulin STEP was not a unique example and that many STEPs may occur genome-wide with potentially causal effects in complex disease. An online database of STEPs is freely accessible at http://dbstep.genes.org.uk/.

  15. Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes

    Science.gov (United States)

    Although natural products have been a particularly rich source of human medicines, the rate at which new molecules are being discovered is declining precipitously. Based on the large number of natural product biosynthetic genes in microbial genomes, many have suggested “genome mining” as an approach...

  16. Mining Xanthomonas and Streptomyces genomes for new pectinase-encoding sequences and their heterologous expression in Escherichia coli.

    Science.gov (United States)

    Xiao, Zhizhuang; Boyd, Jason; Grosse, Stephan; Beauchemin, Manon; Coupe, Elizabeth; Lau, Peter C K

    2008-04-01

    Microbial genome sequencing has left a legacy of annotated yet uncharacterized genes or open reading frames, activities that may have useful applications in health and/or the environment. We are interested in the discovery and characterization of potentially new pectinolytic activities for the enzymatic retting of natural bast fibers such as hemp and flax. A highlight in this study is the discovery of a cold-active pectate lyase among five pectate-lyase-encoding sequences and two polygalacturonase-encoding sequences that we have cloned from the genomes of Xanthomonas campestris pv. campestris and Streptomyces coelicolor A3(2). Heterologous expression of these sequences as active pectate lyases and polygalacturonases required their subcloning in Escherichia coli Rosetta cells. The most active recombinant pectate lyase (XcPL NP_638163), a cold-active pectate lyase (XcPL NP_636037), and a polygalacturonase (XcPG NP_638805) were purified to near homogeneity and their kinetic parameters were determined. A significant amount of pectin degradation products was shown to be released by the two pectate lyases but not the polygalacturonase when hemp fiber pectin was used as substrate. Results of this study showed that genome data mining, besides an economical approach to new gene acquisition, may uncover new findings such as the discovery of a cold-active pectate-lyase-encoding sequence from X. campestris, a mesophilic microorganism.

  17. Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments.

    Science.gov (United States)

    Nunoura, Takuro; Hirayama, Hisako; Takami, Hideto; Oida, Hanako; Nishi, Shinro; Shimamura, Shigeru; Suzuki, Yohey; Inagaki, Fumio; Takai, Ken; Nealson, Kenneth H; Horikoshi, Koki

    2005-12-01

    Within a phylum Crenarchaeota, only some members of the hyperthermophilic class Thermoprotei, have been cultivated and characterized. In this study, we have constructed a metagenomic library from a microbial mat formation in a subsurface hot water stream of the Hishikari gold mine, Japan, and sequenced genome fragments of two different phylogroups of uncultivated thermophilic Crenarchaeota: (i) hot water crenarchaeotic group (HWCG) I (41.2 kb), and (ii) HWCG III (49.3 kb). The genome fragment of HWCG I contained a 16S rRNA gene, two tRNA genes and 35 genes encoding proteins but no 23S rRNA gene. Among the genes encoding proteins, several genes for putative aerobic-type carbon monoxide dehydrogenase represented a potential clue with regard to the yet unknown metabolism of HWCG I Archaea. The genome fragment of HWCG III contained a 16S/23S rRNA operon and 44 genes encoding proteins. In the 23S rRNA gene, we detected a homing-endonuclease encoding a group I intron similar to those detected in hyperthermophilic Crenarchaeota and Bacteria, as well as eukaryotic organelles. The reconstructed phylogenetic tree based on the 23S rRNA gene sequence reinforced the intermediate phylogenetic affiliation of HWCG III bridging the hyperthermophilic and non-thermophilic uncultivated Crenarchaeota.

  18. Genome mining reveals high incidence of putative lipopeptide biosynthesis NRPS/PKS clusters containing fatty acyl-AMP ligase genes inbiofilm-forming cyanobacteria

    Czech Academy of Sciences Publication Activity Database

    Galica, Tomáš; Hrouzek, P.; Mareš, Jan

    2017-01-01

    Roč. 53, č. 5 (2017), s. 985-998 ISSN 0022-3646 R&D Projects: GA ČR(CZ) GA16-09381S Institutional support: RVO:60077344 Keywords : cyanobacteria * fatty-acyl AMP ligase * genome mining * lipopeptides * microbial biofilm Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 2.608, year: 2016

  19. Genome sequence of the acid-tolerant Desulfovibrio sp. DV isolated from the sediments of a Pb-Zn mine tailings dam in the Chita region, Russia

    Directory of Open Access Journals (Sweden)

    Anastasiia Kovaliova

    2017-03-01

    Full Text Available Here we report the draft genome sequence of the acid-tolerant Desulfovibrio sp. DV isolated from the sediments of a Pb-Zn mine tailings dam in the Chita region, Russia. The draft genome has a size of 4.9 Mb and encodes multiple K+-transporters and proton-consuming decarboxylases. The phylogenetic analysis based on concatenated ribosomal proteins revealed that strain DV clusters together with the acid-tolerant Desulfovibrio sp. TomC and Desulfovibrio magneticus. The draft genome sequence and annotation have been deposited at GenBank under the accession number MLBG00000000.

  20. BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters

    Directory of Open Access Journals (Sweden)

    Gong Cheng

    2017-11-01

    Full Text Available Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker. The present workflow enables analysis and visualization of pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various publicly available biological databases. The present step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily.

  1. Process mining

    DEFF Research Database (Denmark)

    van der Aalst, W.M.P.; Rubin, V.; Verbeek, H.M.W.

    2010-01-01

    Process mining includes the automated discovery of processes from event logs. Based on observed events (e.g., activities being executed or messages being exchanged) a process model is constructed. One of the essential problems in process mining is that one cannot assume to have seen all possible...... behavior. At best, one has seen a representative subset. Therefore, classical synthesis techniques are not suitable as they aim at finding a model that is able to exactly reproduce the log. Existing process mining techniques try to avoid such “overfitting” by generalizing the model to allow for more...

  2. REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

    Directory of Open Access Journals (Sweden)

    Guy Leonard

    2009-01-01

    Full Text Available The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment fi le, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree fi les (with a user-defined combination of species name and/or database accession number. Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file and generation of species and accession number lists for use in supplementary materials or figure legends.

  3. MutaNET: a tool for automated analysis of genomic mutations in gene regulatory networks.

    Science.gov (United States)

    Hollander, Markus; Hamed, Mohamed; Helms, Volkhard; Neininger, Kerstin

    2018-03-01

    Mutations in genomic key elements can influence gene expression and function in various ways, and hence greatly contribute to the phenotype. We developed MutaNET to score the impact of individual mutations on gene regulation and function of a given genome. MutaNET performs statistical analyses of mutations in different genomic regions. The tool also incorporates the mutations in a provided gene regulatory network to estimate their global impact. The integration of a next-generation sequencing pipeline enables calling mutations prior to the analyses. As application example, we used MutaNET to analyze the impact of mutations in antibiotic resistance (AR) genes and their potential effect on AR of bacterial strains. MutaNET is freely available at https://sourceforge.net/projects/mutanet/. It is implemented in Python and supported on Mac OS X, Linux and MS Windows. Step-by-step instructions are available at http://service.bioinformatik.uni-saarland.de/mutanet/. volkhard.helms@bioinformatik.uni-saarland.de. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  4. REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

    Directory of Open Access Journals (Sweden)

    Guy Leonard

    2009-05-01

    Full Text Available The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment fi le, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree fi les (with a user-defined combination of species name and/or database accession number. Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file and generation of species and accession number lists for use in supplementary materials or figure legends.

  5. Genomic analyses of metal resistance genes in three plant growth promoting bacteria of legume plants in Northwest mine tailings, China.

    Science.gov (United States)

    Xie, Pin; Hao, Xiuli; Herzberg, Martin; Luo, Yantao; Nies, Dietrich H; Wei, Gehong

    2015-01-01

    To better understand the diversity of metal resistance genetic determinant from microbes that survived at metal tailings in northwest of China, a highly elevated level of heavy metal containing region, genomic analyses was conducted using genome sequence of three native metal-resistant plant growth promoting bacteria (PGPB). It shows that: Mesorhizobium amorphae CCNWGS0123 contains metal transporters from P-type ATPase, CDF (Cation Diffusion Facilitator), HupE/UreJ and CHR (chromate ion transporter) family involved in copper, zinc, nickel as well as chromate resistance and homeostasis. Meanwhile, the putative CopA/CueO system is expected to mediate copper resistance in Sinorhizobium meliloti CCNWSX0020 while ZntA transporter, assisted with putative CzcD, determines zinc tolerance in Agrobacterium tumefaciens CCNWGS0286. The greenhouse experiment provides the consistent evidence of the plant growth promoting effects of these microbes on their hosts by nitrogen fixation and/or indoleacetic acid (IAA) secretion, indicating a potential in-site phytoremediation usage in the mining tailing regions of China. Copyright © 2014. Published by Elsevier B.V.

  6. From DNA Sequences to Chemical Structures – Methods for Mining Microbial Genomic and Metagenomic Data Sets for New Natural Products

    Directory of Open Access Journals (Sweden)

    Jurica Zucko

    2010-01-01

    Full Text Available Rapid mining of large genomic and metagenomic data sets for modular polyketide synthases, non-ribosomal peptide synthetases and hybrid polyketide synthase/non-ribosomal peptide synthetase biosynthetic gene clusters has been achieved using the generic computer program packages ClustScan and CompGen. These program packages perform the annotation with the hierarchical structuring into polypeptides, modules and domains, as well as storage and graphical presentations of the data. This aims to achieve the most accurate predictions of the activities and specificities of catalytically active domains that can be made with present knowledge, leading to a prediction of the most likely chemical structures produced by these enzymes. The program packages also allow generation of novel clusters by homologous recombination of the annotated genes in silico. ClustScan and CompGen were used to construct a custom database of known compounds (CSDB and of predicted entirely novel recombinant products (r-CSDB that can be used for in silico screening with computer aided drug design technology. The use of these programs has been exemplified by analysing genomic sequences from terrestrial prokaryotes and eukaryotic microorganisms, a marine metagenomic data set and a newly discovered example of a 'shared metabolic pathway' in marine-microbial endosymbiosis.

  7. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.

    Science.gov (United States)

    Weber, Tilmann; Blin, Kai; Duddela, Srikanth; Krug, Daniel; Kim, Hyun Uk; Bruccoleri, Robert; Lee, Sang Yup; Fischbach, Michael A; Müller, Rolf; Wohlleben, Wolfgang; Breitling, Rainer; Takano, Eriko; Medema, Marnix H

    2015-07-01

    Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. AHCODA-DB: a data repository with web-based mining tools for the analysis of automated high-content mouse phenomics data.

    Science.gov (United States)

    Koopmans, Bastijn; Smit, August B; Verhage, Matthijs; Loos, Maarten

    2017-04-04

    Systematic, standardized and in-depth phenotyping and data analyses of rodent behaviour empowers gene-function studies, drug testing and therapy design. However, no data repositories are currently available for standardized quality control, data analysis and mining at the resolution of individual mice. Here, we present AHCODA-DB, a public data repository with standardized quality control and exclusion criteria aimed to enhance robustness of data, enabled with web-based mining tools for the analysis of individually and group-wise collected mouse phenotypic data. AHCODA-DB allows monitoring in vivo effects of compounds collected from conventional behavioural tests and from automated home-cage experiments assessing spontaneous behaviour, anxiety and cognition without human interference. AHCODA-DB includes such data from mutant mice (transgenics, knock-out, knock-in), (recombinant) inbred strains, and compound effects in wildtype mice and disease models. AHCODA-DB provides real time statistical analyses with single mouse resolution and versatile suite of data presentation tools. On March 9th, 2017 AHCODA-DB contained 650 k data points on 2419 parameters from 1563 mice. AHCODA-DB provides users with tools to systematically explore mouse behavioural data, both with positive and negative outcome, published and unpublished, across time and experiments with single mouse resolution. The standardized (automated) experimental settings and the large current dataset (1563 mice) in AHCODA-DB provide a unique framework for the interpretation of behavioural data and drug effects. The use of common ontologies allows data export to other databases such as the Mouse Phenome Database. Unbiased presentation of positive and negative data obtained under the highly standardized screening conditions increase cost efficiency of publicly funded mouse screening projects and help to reach consensus conclusions on drug responses and mouse behavioural phenotypes. The website is publicly

  9. Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining.

    Science.gov (United States)

    Skinnider, Michael A; Johnston, Chad W; Edgar, Robyn E; Dejong, Chris A; Merwin, Nishanth J; Rees, Philip N; Magarvey, Nathan A

    2016-10-18

    Microbial natural products are an evolved resource of bioactive small molecules, which form the foundation of many modern therapeutic regimes. Ribosomally synthesized and posttranslationally modified peptides (RiPPs) represent a class of natural products which have attracted extensive interest for their diverse chemical structures and potent biological activities. Genome sequencing has revealed that the vast majority of genetically encoded natural products remain unknown. Many bioinformatic resources have therefore been developed to predict the chemical structures of natural products, particularly nonribosomal peptides and polyketides, from sequence data. However, the diversity and complexity of RiPPs have challenged systematic investigation of RiPP diversity, and consequently the vast majority of genetically encoded RiPPs remain chemical "dark matter." Here, we introduce an algorithm to catalog RiPP biosynthetic gene clusters and chart genetically encoded RiPP chemical space. A global analysis of 65,421 prokaryotic genomes revealed 30,261 RiPP clusters, encoding 2,231 unique products. We further leverage the structure predictions generated by our algorithm to facilitate the genome-guided discovery of a molecule from a rare family of RiPPs. Our results provide the systematic investigation of RiPP genetic and chemical space, revealing the widespread distribution of RiPP biosynthesis throughout the prokaryotic tree of life, and provide a platform for the targeted discovery of RiPPs based on genome sequencing.

  10. Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation.

    Directory of Open Access Journals (Sweden)

    Sheri L Simmons

    2008-07-01

    Full Text Available Deeply sampled community genomic (metagenomic datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth approximately 20x. The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types ( approximately 94% sequence identity have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the

  11. Mining in the Future: Autonomous Robotics for Safer Mines

    CSIR Research Space (South Africa)

    Shahdi, A

    2012-10-01

    Full Text Available include ? Security patrols ? Transportation of cargo ? Mining ? CSIR 2012 Slide 7 Mine Safety Platform ? Joint project with CSIR Centre for Mining Innovation and Material Science and Manufacturing ? Focuses on performing pre-entry safety... Project outcome can be adopted for automating haul trucks in opencast mines ? Mine Safety Platform is a joint project with CMI and MSM targeting the task of post-blast inspection in deep hard rock mines ? CSIR 2012 Slide 14 Thank you ...

  12. Novel Tn4371-ICE like element in Ralstonia pickettii and genome mining for comparative elements.

    Science.gov (United States)

    Ryan, Michael P; Pembroke, J Tony; Adley, Catherine C

    2009-11-26

    Integrative Conjugative Elements (ICEs) are important factors in the plasticity of microbial genomes. An element related to the ICE Tn4371 was discovered during a bioinformatic search of the Ralstonia pickettii 12J genome. This element was analysed and further searches carried out for additional elements.A PCR method was designed to detect and characterise new elements of this type based on this scaffold and a culture collection of fifty-eight Ralstonia pickettii and Ralstonia insidiosa strains were analysed for the presence of the element. Comparative sequence analysis of bacterial genomes has revealed the presence of a number of uncharacterised Tn4371-like ICEs in the genomes of several beta and gamma- Proteobacteria. These elements vary in size, GC content, putative function and have a mosaic-like structure of plasmid- and phage-like sequences which is typical of Tn4371-like ICEs. These elements were found after a through search of the GenBank database. The elements, which are found in Ralstonia, Delftia, Acidovorax, Bordetella, Comamonas, Acidovorax, Congregibacter, Shewanella, Pseudomonas Stenotrophomonas, Thioalkalivibrio sp. HL-EbGR7, Polaromonas, Burkholderia and Diaphorobacter sp. share a common scaffold. A PCR method was designed (based on the Tn4371- like element detected in the Ralstonia pickettii 12J genome) to detect and characterise new elements of this type. All elements found in this study possess a common scaffold of core genes but contain different accessory genes. A new uniform nomenclature is suggested for ICEs of the Tn4371 family. Two novel Tn4371-like ICE were discovered and characterised, using the novel PCR method described in two different isolates of Ralstonia pickettii from laboratory purified water.

  13. Genomic insights into a new acidophilic, copper-resistant Desulfosporosinus isolate from the oxidized tailings area of an abandoned gold mine.

    Science.gov (United States)

    Mardanov, Andrey V; Panova, Inna A; Beletsky, Alexey V; Avakyan, Marat R; Kadnikov, Vitaly V; Antsiferov, Dmitry V; Banks, David; Frank, Yulia A; Pimenov, Nikolay V; Ravin, Nikolai V; Karnachuk, Olga V

    2016-08-01

    Microbial sulfate reduction in acid mine drainage is still considered to be confined to anoxic conditions, although several reports have shown that sulfate-reducing bacteria occur under microaerophilic or aerobic conditions. We have measured sulfate reduction rates of up to 60 nmol S cm(-3) day(-1) in oxidized layers of gold mine tailings in Kuzbass (SW Siberia). A novel, acidophilic, copper-tolerant Desulfosporosinus sp. I2 was isolated from the same sample and its genome was sequenced. The genomic analysis and physiological data indicate the involvement of transporters and additional mechanisms to tolerate metals, such as sequestration by polyphosphates. Desulfosporinus sp. I2 encodes systems for a metabolically versatile life style. The genome possessed a complete Embden-Meyerhof pathway for glycolysis and gluconeogenesis. Complete oxidation of organic substrates could be enabled by the complete TCA cycle. Genomic analysis found all major components of the electron transfer chain necessary for energy generation via oxidative phosphorylation. Autotrophic CO2 fixation could be performed through the Wood-Ljungdahl pathway. Multiple oxygen detoxification systems were identified in the genome. Taking into account the metabolic activity and genomic analysis, the traits of the novel isolate broaden our understanding of active sulfate reduction and associated metabolism beyond strictly anaerobic niches. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. High-throughput automated microfluidic sample preparation for accurate microbial genomics.

    Science.gov (United States)

    Kim, Soohong; De Jonghe, Joachim; Kulesa, Anthony B; Feldman, David; Vatanen, Tommi; Bhattacharyya, Roby P; Berdy, Brittany; Gomez, James; Nolan, Jill; Epstein, Slava; Blainey, Paul C

    2017-01-27

    Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (∼10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence ∼400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications.

  15. Omics-based natural product discovery and the lexicon of genome mining.

    Science.gov (United States)

    Machado, Henrique; Tuttle, Robert N; Jensen, Paul R

    2017-10-01

    Genome sequencing and the application of omic techniques are driving many important advances in the field of microbial natural products research. Despite these gains, there remain aspects of the natural product discovery pipeline where our knowledge remains poor. These include the extent to which biosynthetic gene clusters are transcriptionally active in native microbes, the temporal dynamics of transcription, translation, and natural product assembly, as well as the relationships between small molecule production and detection. Here we touch on a number of these concepts in the context of continuing efforts to unlock the natural product potential revealed in genome sequence data and discuss nomenclatural issues that warrant consideration as the field moves forward. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Genome mining unveils widespread natural product biosynthetic capacity in human oral microbe Streptococcus mutans.

    Science.gov (United States)

    Liu, Liwei; Hao, Tingting; Xie, Zhoujie; Horsman, Geoff P; Chen, Yihua

    2016-11-21

    Streptococcus mutans is a major pathogen causing human dental caries. As a Gram-positive bacterium with a small genome (about 2 Mb) it is considered a poor source of natural products. Due to a recent explosion in genomic data available for S. mutans strains, we were motivated to explore the natural product production potential of this organism. Bioinformatic characterization of 169 publically available genomes of S. mutans from human dental caries revealed a surprisingly rich source of natural product biosynthetic gene clusters. Anti-SMASH analysis identified one nonribosomal peptide synthetase (NRPS) gene cluster, seven polyketide synthase (PKS) gene clusters and 136 hybrid PKS/NRPS gene clusters. In addition, 211 ribosomally synthesized and post-translationally modified peptides (RiPPs) clusters and 615 bacteriocin precursors were identified by a combined analysis using BAGEL and anti-SMASH. S. mutans harbors a rich and diverse natural product genetic capacity, which underscores the importance of probing the human microbiome and revisiting species that have traditionally been overlooked as "poor" sources of natural products.

  17. Novel transcripts discovered by mining genomic DNA from defined regions of bovine chromosome 6

    Directory of Open Access Journals (Sweden)

    Eberlein Annett

    2009-04-01

    Full Text Available Abstract Background Linkage analyses strongly suggest a number of QTL for production, health and conformation traits in the middle part of bovine chromosome 6 (BTA6. The identification of the molecular background underlying the genetic variation at the QTL and subsequent functional studies require a well-annotated gene sequence map of the critical QTL intervals. To complete the sequence map of the defined subchromosomal regions on BTA6 poorly covered with comparative gene information, we focused on targeted isolation of transcribed sequences from bovine bacterial artificial chromosome (BAC clones mapped to the QTL intervals. Results Using the method of exon trapping, 92 unique exon trapping sequences (ETS were discovered in a chromosomal region of poor gene coverage. Sequence identity to the current NCBI sequence assembly for BTA6 was detected for 91% of unique ETS. Comparative sequence similarity search revealed that 11% of the isolated ETS displayed high similarity to genomic sequences located on the syntenic chromosomes of the human and mouse reference genome assemblies. Nearly a third of the ETS identified similar equivalent sequences in genomic sequence scaffolds from the alternative Celera-based sequence assembly of the human genome. Screening gene, EST, and protein databases detected 17% of ETS with identity to known transcribed sequences. Expression analysis of a subset of the ETS showed that most ETS (84% displayed a distinctive expression pattern in a multi-tissue panel of a lactating cow verifying their existence in the bovine transcriptome. Conclusion The results of our study demonstrate that the exon trapping method based on region-specific BAC clones is very useful for targeted screening for novel transcripts located within a defined chromosomal region being deficiently endowed with annotated gene information. The majority of identified ETS represents unknown noncoding sequences in intergenic regions on BTA6 displaying a

  18. Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern citrus varieties.

    Directory of Open Access Journals (Sweden)

    Franck Curk

    Full Text Available Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105 were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species

  19. MOST-visualization: software for producing automated textbook-style maps of genome-scale metabolic networks.

    Science.gov (United States)

    Kelley, James J; Maor, Shay; Kim, Min Kyung; Lane, Anatoliy; Lun, Desmond S

    2017-08-15

    Visualization of metabolites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding cellular metabolism. Three attributes are desirable in software used for visualizing GEMs: (i) automation, since GEMs can be quite large; (ii) production of understandable maps that provide ease in identification of pathways, reactions and metabolites; and (iii) visualization of the entire network to show how pathways are interconnected. No software currently exists for visualizing GEMs that satisfies all three characteristics, but MOST-Visualization, an extension of the software package MOST (Metabolic Optimization and Simulation Tool), satisfies (i), and by using a pre-drawn overview map of metabolism based on the Roche map satisfies (ii) and comes close to satisfying (iii). MOST is distributed for free on the GNU General Public License. The software and full documentation are available at http://most.ccib.rutgers.edu/. dslun@rutgers.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  20. EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration.

    Science.gov (United States)

    Forment, Javier; Gilabert, Francisco; Robles, Antonio; Conejero, Vicente; Nuez, Fernando; Blanca, Jose M

    2008-01-07

    Expressed sequence tag (EST) collections are composed of a high number of single-pass, redundant, partial sequences, which need to be processed, clustered, and annotated to remove low-quality and vector regions, eliminate redundancy and sequencing errors, and provide biologically relevant information. In order to provide a suitable way of performing the different steps in the analysis of the ESTs, flexible computation pipelines adapted to the local needs of specific EST projects have to be developed. Furthermore, EST collections must be stored in highly structured relational databases available to researchers through user-friendly interfaces which allow efficient and complex data mining, thus offering maximum capabilities for their full exploitation. We have created EST2uni, an integrated, highly-configurable EST analysis pipeline and data mining software package that automates the pre-processing, clustering, annotation, database creation, and data mining of EST collections. The pipeline uses standard EST analysis tools and the software has a modular design to facilitate the addition of new analytical methods and their configuration. Currently implemented analyses include functional and structural annotation, SNP and microsatellite discovery, integration of previously known genetic marker data and gene expression results, and assistance in cDNA microarray design. It can be run in parallel in a PC cluster in order to reduce the time necessary for the analysis. It also creates a web site linked to the database, showing collection statistics, with complex query capabilities and tools for data mining and retrieval. The software package presented here provides an efficient and complete bioinformatics tool for the management of EST collections which is very easy to adapt to the local needs of different EST projects. The code is freely available under the GPL license and can be obtained at http://bioinf.comav.upv.es/est2uni. This site also provides detailed instructions

  1. EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration

    Directory of Open Access Journals (Sweden)

    Nuez Fernando

    2008-01-01

    Full Text Available Abstract Background Expressed sequence tag (EST collections are composed of a high number of single-pass, redundant, partial sequences, which need to be processed, clustered, and annotated to remove low-quality and vector regions, eliminate redundancy and sequencing errors, and provide biologically relevant information. In order to provide a suitable way of performing the different steps in the analysis of the ESTs, flexible computation pipelines adapted to the local needs of specific EST projects have to be developed. Furthermore, EST collections must be stored in highly structured relational databases available to researchers through user-friendly interfaces which allow efficient and complex data mining, thus offering maximum capabilities for their full exploitation. Results We have created EST2uni, an integrated, highly-configurable EST analysis pipeline and data mining software package that automates the pre-processing, clustering, annotation, database creation, and data mining of EST collections. The pipeline uses standard EST analysis tools and the software has a modular design to facilitate the addition of new analytical methods and their configuration. Currently implemented analyses include functional and structural annotation, SNP and microsatellite discovery, integration of previously known genetic marker data and gene expression results, and assistance in cDNA microarray design. It can be run in parallel in a PC cluster in order to reduce the time necessary for the analysis. It also creates a web site linked to the database, showing collection statistics, with complex query capabilities and tools for data mining and retrieval. Conclusion The software package presented here provides an efficient and complete bioinformatics tool for the management of EST collections which is very easy to adapt to the local needs of different EST projects. The code is freely available under the GPL license and can be obtained at http

  2. Transcriptome analysis in Concholepas concholepas (Gastropoda, Muricidae): mining and characterization of new genomic and molecular markers.

    Science.gov (United States)

    Cárdenas, Leyla; Sánchez, Roland; Gomez, Daniela; Fuenzalida, Gonzalo; Gallardo-Escárate, Cristián; Tanguy, Arnaud

    2011-09-01

    The marine gastropod Concholepas concholepas, locally known as the "loco", is the main target species of the benthonic Chilean fisheries. Genetic and genomic tools are necessary to study the genome of this species in order to understand the molecular basis of its development, growth, and other key traits to improve the management strategies and to identify local adaptation to prevent loss of biodiversity. Here, we use pyrosequencing technologies to generate the first transcriptomic database from adult specimens of the loco. After trimming, a total of 140,756 Expressed Sequence Tag sequences were achieved. Clustering and assembly analysis identified 19,219 contigs and 105,435 singleton sequences. BlastN analysis showed a significant identity with Expressed Sequence Tags of different gastropod species available in public databases. Similarly, BlastX results showed that only 895 out of the total 124,654 had significant hits and may represent novel genes for marine gastropods. From this database, simple sequence repeat motifs were also identified and a total of 38 primer pairs were designed and tested to assess their potential as informative markers and to investigate their cross-species amplification in different related gastropod species. This dataset represents the first publicly available 454 data for a marine gastropod endemic to the southeastern Pacific coast, providing a valuable transcriptomic resource for future efforts of gene discovery and development of functional markers in other marine gastropods. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. Genome mining reveals high incidence of putative lipopeptide biosynthesis NRPS/PKS clusters containing fatty acyl-AMP ligase genes inbiofilm-forming cyanobacteria

    Czech Academy of Sciences Publication Activity Database

    Galica, Tomáš; Hrouzek, Pavel; Mareš, Jan

    2017-01-01

    Roč. 53, č. 5 (2017), s. 985-998 ISSN 0022-3646 R&D Projects: GA ČR(CZ) GA16-09381S; GA MŠk(CZ) LO1416; GA MŠk(CZ) ED2.1.00/19.0392 Institutional support: RVO:61388971 Keywords : cyanobacteria * fatty-acyl AMP ligase * genome mining Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 2.608, year: 2016

  4. The Raising Influence of Information Technologies on Professional Training in the Sphere of Automated Driving When Transporting Mined Rock

    Directory of Open Access Journals (Sweden)

    Kosolapov Andrey

    2017-01-01

    Full Text Available Revolutionary changes in the area of production, holding and exploitation of the automobile as a transport vehicle are analyzed in the article. Current state of the issue is described and the development stages of new approach to driving without human participation are predicted, taking into consideration the usage of automobiles for transportation of mined rock in Kuzbass. The influence of modern information technologies on the development of new sector of automobile industry and on the process of professional and further training of the specialists in the sphere of automobile driving is considered.

  5. The Raising Influence of Information Technologies on Professional Training in the Sphere of Automated Driving When Transporting Mined Rock

    Science.gov (United States)

    Kosolapov, Andrey; Krysin, Sergey

    2017-11-01

    Revolutionary changes in the area of production, holding and exploitation of the automobile as a transport vehicle are analyzed in the article. Current state of the issue is described and the development stages of new approach to driving without human participation are predicted, taking into consideration the usage of automobiles for transportation of mined rock in Kuzbass. The influence of modern information technologies on the development of new sector of automobile industry and on the process of professional and further training of the specialists in the sphere of automobile driving is considered.

  6. Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes.

    Science.gov (United States)

    Adu-Oppong, Boahemaa; Gasparrini, Andrew J; Dantas, Gautam

    2017-01-01

    Microbial communities contain diverse bacteria that play important roles in every environment. Advances in sequencing and computational methodologies over the past decades have illuminated the phylogenetic and functional diversity of microbial communities from diverse habitats. Among the activities encoded in microbiomes are the abilities to synthesize and resist small molecules, yielding antimicrobial activity. These functions are of particular interest when viewed in light of the public health emergency posed by the increase in clinical antimicrobial resistance and the dwindling antimicrobial discovery and approval pipeline, and given the intimate ecological and evolutionary relationship between antimicrobial biosynthesis and resistance. Here, we review genomic and functional methods that have been developed for accessing the antimicrobial biosynthesis and resistance capacity of microbiomes and highlight outstanding examples of their applications. © 2016 New York Academy of Sciences.

  7. Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters

    DEFF Research Database (Denmark)

    Blin, Kai; Kim, Hyun Uk; Medema, Marnix H.

    2017-01-01

    are no longer possible and require the use of automated genome mining pipelines, such as the antiSMASH software. In this review, we discuss the principles underlying the predictions of antiSMASH and other tools and provide practical advice for their application. Furthermore, we discuss important caveats...

  8. Genomic mining for novel FADH₂-dependent halogenases in marine sponge-associated microbial consortia.

    Science.gov (United States)

    Bayer, Kristina; Scheuermayer, Matthias; Fieseler, Lars; Hentschel, Ute

    2013-02-01

    Many marine sponges (Porifera) are known to contain large amounts of phylogenetically diverse microorganisms. Sponges are also known for their large arsenal of natural products, many of which are halogenated. In this study, 36 different FADH₂-dependent halogenase gene fragments were amplified from various Caribbean and Mediterranean sponges using newly designed degenerate PCR primers. Four unique halogenase-positive fosmid clones, all containing the highly conserved amino acid motif "GxGxxG", were identified in the microbial metagenome of Aplysina aerophoba. Sequence analysis of one halogenase-bearing fosmid revealed notably two open reading frames with high homologies to efflux and multidrug resistance proteins. Single cell genomic analysis allowed for a taxonomic assignment of the halogenase genes to specific symbiotic lineages. Specifically, the halogenase cluster S1 is predicted to be produced by a deltaproteobacterial symbiont and halogenase cluster S2 by a poribacterial sponge symbiont. An additional halogenase gene is possibly produced by an actinobacterial symbiont of marine sponges. The identification of three novel, phylogenetically, and possibly also functionally distinct halogenase gene clusters indicates that the microbial consortia of sponges are a valuable resource for novel enzymes involved in halogenation reactions.

  9. Interactive knowledge discovery and data mining on genomic expression data with numeric formal concept analysis.

    Science.gov (United States)

    González-Calabozo, Jose M; Valverde-Albacete, Francisco J; Peláez-Moreno, Carmen

    2016-09-15

    Gene Expression Data (GED) analysis poses a great challenge to the scientific community that can be framed into the Knowledge Discovery in Databases (KDD) and Data Mining (DM) paradigm. Biclustering has emerged as the machine learning method of choice to solve this task, but its unsupervised nature makes result assessment problematic. This is often addressed by means of Gene Set Enrichment Analysis (GSEA). We put forward a framework in which GED analysis is understood as an Exploratory Data Analysis (EDA) process where we provide support for continuous human interaction with data aiming at improving the step of hypothesis abduction and assessment. We focus on the adaptation to human cognition of data interpretation and visualization of the output of EDA. First, we give a proper theoretical background to bi-clustering using Lattice Theory and provide a set of analysis tools revolving around [Formula: see text]-Formal Concept Analysis ([Formula: see text]-FCA), a lattice-theoretic unsupervised learning technique for real-valued matrices. By using different kinds of cost structures to quantify expression we obtain different sequences of hierarchical bi-clusterings for gene under- and over-expression using thresholds. Consequently, we provide a method with interleaved analysis steps and visualization devices so that the sequences of lattices for a particular experiment summarize the researcher's vision of the data. This also allows us to define measures of persistence and robustness of biclusters to assess them. Second, the resulting biclusters are used to index external omics databases-for instance, Gene Ontology (GO)-thus offering a new way of accessing publicly available resources. This provides different flavors of gene set enrichment against which to assess the biclusters, by obtaining their p-values according to the terminology of those resources. We illustrate the exploration procedure on a real data example confirming results previously published. The GED

  10. In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalus bubalis and development of first BuffSatDB

    Directory of Open Access Journals (Sweden)

    Sarika

    2013-01-01

    Full Text Available Abstract Background Though India has sequenced water buffalo genome but its draft assembly is based on cattle genome BTau 4.0, thus de novo chromosome wise assembly is a major pending issue for global community. The existing radiation hybrid of buffalo and these reported STR can be used further in final gap plugging and “finishing” expected in de novo genome assembly. QTL and gene mapping needs mining of putative STR from buffalo genome at equal interval on each and every chromosome. Such markers have potential role in improvement of desirable characteristics, such as high milk yields, resistance to diseases, high growth rate. The STR mining from whole genome and development of user friendly database is yet to be done to reap the benefit of whole genome sequence. Description By in silico microsatellite mining of whole genome, we have developed first STR database of water buffalo, BuffSatDb (Buffalo MicroSatellite Database (http://cabindb.iasri.res.in/buffsatdb/ which is a web based relational database of 910529 microsatellite markers, developed using PHP and MySQL database. Microsatellite markers have been generated using MIcroSAtellite tool. It is simple and systematic web based search for customised retrieval of chromosome wise and genome-wide microsatellites. Search has been enabled based on chromosomes, motif type (mono-hexa, repeat motif and repeat kind (simple and composite. The search may be customised by limiting location of STR on chromosome as well as number of markers in that range. This is a novel approach and not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of the selected markers enabling researcher to select markers of choice at desired interval over the chromosome. The unique add-on of degenerate bases further helps in resolving presence of degenerate bases in current buffalo assembly. Conclusion Being first buffalo STR database in the world

  11. CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM to identify genetically-associated cancers and candidate genes

    Directory of Open Access Journals (Sweden)

    Jones Steven

    2005-03-01

    Full Text Available Abstract Background Online Mendelian Inheritance in Man (OMIM is a computerized database of information about genes and heritable traits in human populations, based on information reported in the scientific literature. Our objective was to establish an automated text-mining system for OMIM that will identify genetically-related cancers and cancer-related genes. We developed the computer program CGMIM to search for entries in OMIM that are related to one or more cancer types. We performed manual searches of OMIM to verify the program results. Results In the OMIM database on September 30, 2004, CGMIM identified 1943 genes related to cancer. BRCA2 (OMIM *164757, BRAF (OMIM *164757 and CDKN2A (OMIM *600160 were each related to 14 types of cancer. There were 45 genes related to cancer of the esophagus, 121 genes related to cancer of the stomach, and 21 genes related to both. Analysis of CGMIM results indicate that fewer than three gene entries in OMIM should mention both, and the more than seven-fold discrepancy suggests cancers of the esophagus and stomach are more genetically related than current literature suggests. Conclusion CGMIM identifies genetically-related cancers and cancer-related genes. In several ways, cancers with shared genetic etiology are anticipated to lead to further etiologic hypotheses and advances regarding environmental agents. CGMIM results are posted monthly and the source code can be obtained free of charge from the BC Cancer Research Centre website http://www.bccrc.ca/ccr/CGMIM.

  12. A novel data mining method to identify assay-specific signatures in functional genomic studies

    Directory of Open Access Journals (Sweden)

    Guidarelli Jack W

    2006-08-01

    Full Text Available Abstract Background: The highly dimensional data produced by functional genomic (FG studies makes it difficult to visualize relationships between gene products and experimental conditions (i.e., assays. Although dimensionality reduction methods such as principal component analysis (PCA have been very useful, their application to identify assay-specific signatures has been limited by the lack of appropriate methodologies. This article proposes a new and powerful PCA-based method for the identification of assay-specific gene signatures in FG studies. Results: The proposed method (PM is unique for several reasons. First, it is the only one, to our knowledge, that uses gene contribution, a product of the loading and expression level, to obtain assay signatures. The PM develops and exploits two types of assay-specific contribution plots, which are new to the application of PCA in the FG area. The first type plots the assay-specific gene contribution against the given order of the genes and reveals variations in distribution between assay-specific gene signatures as well as outliers within assay groups indicating the degree of importance of the most dominant genes. The second type plots the contribution of each gene in ascending or descending order against a constantly increasing index. This type of plots reveals assay-specific gene signatures defined by the inflection points in the curve. In addition, sharp regions within the signature define the genes that contribute the most to the signature. We proposed and used the curvature as an appropriate metric to characterize these sharp regions, thus identifying the subset of genes contributing the most to the signature. Finally, the PM uses the full dataset to determine the final gene signature, thus eliminating the chance of gene exclusion by poor screening in earlier steps. The strengths of the PM are demonstrated using a simulation study, and two studies of real DNA microarray data – a study of

  13. Evaluation of a new automated homogeneous PCR assay, GenomEra C. difficile, for rapid detection of Toxigenic Clostridium difficile in fecal specimens.

    Science.gov (United States)

    Hirvonen, Jari J; Mentula, Silja; Kaukoranta, Suvi-Sirkku

    2013-09-01

    We evaluated a new automated homogeneous PCR assay to detect toxigenic Clostridium difficile, the GenomEra C. difficile assay (Abacus Diagnostica, Finland), with 310 diarrheal stool specimens and with a collection of 33 known clostridial and nonclostridial isolates. Results were compared with toxigenic culture results, with discrepancies being resolved by the GeneXpert C. difficile PCR assay (Cepheid). Among the 80 toxigenic culture-positive or GeneXpert C. difficile assay-positive fecal specimens, 79 were also positive with the GenomEra C. difficile assay. Additionally, one specimen was positive with the GenomEra assay but negative with the confirmatory methods. Thus, the sensitivity and specificity were 98.8% and 99.6%, respectively. With the culture collection, no false-positive or -negative results were observed. The analytical sensitivity of the GenomEra C. difficile assay was approximately 5 CFU per PCR test. The short hands-on (<5 min for 1 to 4 samples) and total turnaround (<1 h) times, together with the high positive and negative predictive values (98.8% and 99.6%, respectively), make the GenomEra C. difficile assay an excellent option for toxigenic C. difficile detection in fecal specimens.

  14. Exposing exposure: enhancing patient safety through automated data mining of nuclear medicine reports for quality assurance and organ dose monitoring.

    Science.gov (United States)

    Ikuta, Ichiro; Sodickson, Aaron; Wasser, Elliot J; Warden, Graham I; Gerbaudo, Victor H; Khorasani, Ramin

    2012-08-01

    To develop and validate an open-source informatics toolkit capable of creating a radiation exposure data repository from existing nuclear medicine report archives and to demonstrate potential applications of such data for quality assurance and longitudinal patient-specific radiation dose monitoring. This study was institutional review board approved and HIPAA compliant. Informed consent was waived. An open-source toolkit designed to automate the extraction of data on radiopharmaceuticals and administered activities from nuclear medicine reports was developed. After iterative code training, manual validation was performed on 2359 nuclear medicine reports randomly selected from September 17, 1985, to February 28, 2011. Recall (sensitivity) and precision (positive predictive value) were calculated with 95% binomial confidence intervals. From the resultant institutional data repository, examples of usage in quality assurance efforts and patient-specific longitudinal radiation dose monitoring obtained by calculating organ doses from the administered activity and radiopharmaceutical of each examination were provided. Validation statistics yielded a combined recall of 97.6% ± 0.7 (95% confidence interval) and precision of 98.7% ± 0.5. Histograms of administered activity for fluorine 18 fluorodeoxyglucose and iodine 131 sodium iodide were generated. An organ dose heatmap which displays a sample patient's dose accumulation from multiple nuclear medicine examinations was created. Large-scale repositories of radiation exposure data can be extracted from institutional nuclear medicine report archives with high recall and precision. Such repositories enable new approaches in radiation exposure patient safety initiatives and patient-specific radiation dose monitoring.

  15. Exposing Exposure: Enhancing Patient Safety through Automated Data Mining of Nuclear Medicine Reports for Quality Assurance and Organ Dose Monitoring

    Science.gov (United States)

    Ikuta, Ichiro; Wasser, Elliot J.; Warden, Graham I.; Gerbaudo, Victor H.; Khorasani, Ramin

    2012-01-01

    Purpose: To develop and validate an open-source informatics toolkit capable of creating a radiation exposure data repository from existing nuclear medicine report archives and to demonstrate potential applications of such data for quality assurance and longitudinal patient-specific radiation dose monitoring. Materials and Methods: This study was institutional review board approved and HIPAA compliant. Informed consent was waived. An open-source toolkit designed to automate the extraction of data on radiopharmaceuticals and administered activities from nuclear medicine reports was developed. After iterative code training, manual validation was performed on 2359 nuclear medicine reports randomly selected from September 17, 1985, to February 28, 2011. Recall (sensitivity) and precision (positive predictive value) were calculated with 95% binomial confidence intervals. From the resultant institutional data repository, examples of usage in quality assurance efforts and patient-specific longitudinal radiation dose monitoring obtained by calculating organ doses from the administered activity and radiopharmaceutical of each examination were provided. Results: Validation statistics yielded a combined recall of 97.6% ± 0.7 (95% confidence interval) and precision of 98.7% ± 0.5. Histograms of administered activity for fluorine 18 fluorodeoxyglucose and iodine 131 sodium iodide were generated. An organ dose heatmap which displays a sample patient’s dose accumulation from multiple nuclear medicine examinations was created. Conclusion: Large-scale repositories of radiation exposure data can be extracted from institutional nuclear medicine report archives with high recall and precision. Such repositories enable new approaches in radiation exposure patient safety initiatives and patient-specific radiation dose monitoring. © RSNA, 2012 PMID:22627599

  16. GenomEra MRSA/SA, a fully automated homogeneous PCR assay for rapid detection of Staphylococcus aureus and the marker of methicillin resistance in various sample matrixes.

    Science.gov (United States)

    Hirvonen, Jari J; Kaukoranta, Suvi-Sirkku

    2013-09-01

    The GenomEra MRSA/SA assay (Abacus Diagnostica, Turku, Finland) is the first commercial homogeneous PCR assay using thermally stable, intrinsically fluorescent time-resolved fluorometric (TRF) labels resistant to autofluorescence and other background effects. This fully automated closed tube PCR assay simultaneously detects Staphylococcus aureus specific DNA and the mecA gene within 50 min. It can be used for both screening and confirmation of methicillin-resistant and -sensitive S. aureus (MRSA and MSSA) directly in different specimen types or from preceding cultures. The assay has shown excellent performance in comparisons with other diagnostic methods in all the sample types tested. The GenomEra MRSA/SA assay provides rapid assistance for the detection of MRSA as well as invasive staphylococcal infections and helps the early targeting of antimicrobial therapy to patients with potential MRSA infection.

  17. Quantification of Operational Risk Using A Data Mining

    Science.gov (United States)

    Perera, J. Sebastian

    1999-01-01

    What is Data Mining? - Data Mining is the process of finding actionable information hidden in raw data. - Data Mining helps find hidden patterns, trends, and important relationships often buried in a sea of data - Typically, automated software tools based on advanced statistical analysis and data modeling technology can be utilized to automate the data mining process

  18. Characterization of the alkaline laccase Ssl1 from Streptomyces sviceus with unusual properties discovered by genome mining.

    Directory of Open Access Journals (Sweden)

    Matthias Gunne

    Full Text Available Fungal laccases are well investigated enzymes with high potential in diverse applications like bleaching of waste waters and textiles, cellulose delignification, and organic synthesis. However, they are limited to acidic reaction conditions and require eukaryotic expression systems. This raises a demand for novel laccases without these constraints. We have taken advantage of the laccase engineering database LccED derived from genome mining to identify and clone the laccase Ssl1 from Streptomyces sviceus which can circumvent the limitations of fungal laccases. Ssl1 belongs to the family of small laccases that contains only few characterized enzymes. After removal of the twin-arginine signal peptide Ssl1 was readily expressed in E. coli. Ssl1 is a small laccase with 32.5 kDa, consists of only two cupredoxin-like domains, and forms trimers in solution. Ssl1 oxidizes 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid (ABTS and phenolic substrates like 2,6-dimethoxy phenol, guaiacol, and syringaldazine. The k(cat value for ABTS oxidation was at least 20 times higher than for other substrates. The optimal pH for oxidation reactions is substrate dependent: for phenolic substrates the highest activities were detected at alkaline conditions (pH 9.0 for 2,6-dimethoxy phenol and guaiacol and pH 8.0 for syringaldazine, while the highest reaction rates with ABTS were observed at pH 4.0. Though originating from a mesophilic organism, Ssl demonstrates remarkable stability at elevated temperatures (T(1/2,60°C = 88 min and in a wide pH range (pH 5.0 to 11.0. Notably, the enzyme retained 80% residual activity after 5 days of incubation at pH 11. Detergents and organic co-solvents do not affect Ssl1 stability. The described robustness makes Ssl1 a potential candidate for industrial applications, preferably in processes that require alkaline reaction conditions.

  19. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  20. Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining

    OpenAIRE

    Morgan, Xochitl C; Ni, Shulin; Miranker, Daniel P; Iyer, Vishwanath R

    2007-01-01

    Abstract Background Cis-acting transcriptional regulatory elements in mammalian genomes typically contain specific combinations of binding sites for various transcription factors. Although some cis-regulatory elements have been well studied, the combinations of transcription factors that regulate normal expression levels for the vast majority of the 20,000 genes in the human genome are unknown. We hypothesized that it should be possible to discover transcription factor combinations that regul...

  1. Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining.

    Directory of Open Access Journals (Sweden)

    Etienne G J Danchin

    2013-10-01

    Full Text Available Root-knot nematodes are globally the most aggressive and damaging plant-parasitic nematodes. Chemical nematicides have so far constituted the most efficient control measures against these agricultural pests. Because of their toxicity for the environment and danger for human health, these nematicides have now been banned from use. Consequently, new and more specific control means, safe for the environment and human health, are urgently needed to avoid worldwide proliferation of these devastating plant-parasites. Mining the genomes of root-knot nematodes through an evolutionary and comparative genomics approach, we identified and analyzed 15,952 nematode genes conserved in genomes of plant-damaging species but absent from non target genomes of chordates, plants, annelids, insect pollinators and mollusks. Functional annotation of the corresponding proteins revealed a relative abundance of putative transcription factors in this parasite-specific set compared to whole proteomes of root-knot nematodes. This may point to important and specific regulators of genes involved in parasitism. Because these nematodes are known to secrete effector proteins in planta, essential for parasitism, we searched and identified 993 such effector-like proteins absent from non-target species. Aiming at identifying novel targets for the development of future control methods, we biologically tested the effect of inactivation of the corresponding genes through RNA interference. A total of 15 novel effector-like proteins and one putative transcription factor compatible with the design of siRNAs were present as non-redundant genes and had transcriptional support in the model root-knot nematode Meloidogyne incognita. Infestation assays with siRNA-treated M. incognita on tomato plants showed significant and reproducible reduction of the infestation for 12 of the 16 tested genes compared to control nematodes. These 12 novel genes, showing efficient reduction of parasitism when

  2. Mining robotics sensors

    CSIR Research Space (South Africa)

    Green, JJ

    2012-04-01

    Full Text Available sources, and techniques such as surfel modeling and synthetic view generation are explored towards creating visualizations of the data that could be used by miners to monitor areas of risk in the stope. Further work will determine this potential.... Index Terms?underground mining robotics, perception sensors, sensor fusion, infrared camera, 3D laser scan. I. INTRODUCTION To date, robotics in the mining industry has seen much advancement in automation for above-ground applications where...

  3. -Genomic data mining of the marine actinobacteriaStreptomycessp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis.

    Science.gov (United States)

    Undabarrena, Agustina; Ugalde, Juan A; Seeger, Michael; Cámara, Beatriz

    2017-01-01

    Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria ( S. aureus and L. monocytogenes ). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces  sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces . In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.

  4. Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes

    Science.gov (United States)

    Gallus, Susanne; Janke, Axel

    2017-01-01

    Abstract Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation. PMID:28985298

  5. Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data

    Directory of Open Access Journals (Sweden)

    Minucci Saverio

    2011-10-01

    Full Text Available Abstract Background High-throughput sequencing is generating massive amounts of data at a pace that largely exceeds the throughput of data analysis routines. Here we introduce Fish the ChIPs (FC, a computational pipeline aimed at a broad public of users and designed to perform complete ChIP-Seq data analysis of an unlimited number of samples, thus increasing throughput, reproducibility and saving time. Results Starting from short read sequences, FC performs the following steps: 1 quality controls, 2 alignment to a reference genome, 3 peak calling, 4 genomic annotation, 5 generation of raw signal tracks for visualization on the UCSC and IGV genome browsers. FC exploits some of the fastest and most effective tools today available. Installation on a Mac platform requires very basic computational skills while configuration and usage are supported by a user-friendly graphic user interface. Alternatively, FC can be compiled from the source code on any Unix machine and then run with the possibility of customizing each single parameter through a simple configuration text file that can be generated using a dedicated user-friendly web-form. Considering the execution time, FC can be run on a desktop machine, even though the use of a computer cluster is recommended for analyses of large batches of data. FC is perfectly suited to work with data coming from Illumina Solexa Genome Analyzers or ABI SOLiD and its usage can potentially be extended to any sequencing platform. Conclusions Compared to existing tools, FC has two main advantages that make it suitable for a broad range of users. First of all, it can be installed and run by wet biologists on a Mac machine. Besides it can handle an unlimited number of samples, being convenient for large analyses. In this context, computational biologists can increase reproducibility of their ChIP-Seq data analyses while saving time for downstream analyses. Reviewers This article was reviewed by Gavin Huttley, George

  6. Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes.

    Science.gov (United States)

    Lammers, Fritjof; Gallus, Susanne; Janke, Axel; Nilsson, Maria A

    2017-10-01

    Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  7. Text Mining Applications and Theory

    CERN Document Server

    Berry, Michael W

    2010-01-01

    Text Mining: Applications and Theory presents the state-of-the-art algorithms for text mining from both the academic and industrial perspectives.  The contributors span several countries and scientific domains: universities, industrial corporations, and government laboratories, and demonstrate the use of techniques from machine learning, knowledge discovery, natural language processing and information retrieval to design computational models for automated text analysis and mining. This volume demonstrates how advancements in the fields of applied mathematics, computer science, machine learning

  8. In silico mining of microsatellites in coding sequences of the date palm (Arecaceae) genome, characterization, and transferability.

    Science.gov (United States)

    Aberlenc-Bertossi, Frédérique; Castillo, Karina; Tranchant-Dubreuil, Christine; Chérif, Emira; Ballardini, Marco; Abdoulkader, Sabira; Gros-Balthazard, Muriel; Chabrillange, Nathalie; Santoni, Sylvain; Mercuri, Antonio; Pintaud, Jean-Christophe

    2014-01-01

    To complement existing sets of primarily dinucleotide microsatellite loci from noncoding sequences of date palm, we developed primers for tri- and hexanucleotide microsatellite loci identified within genes. Due to their conserved genomic locations, the primers should be useful in other palm taxa, and their utility was tested in seven other Phoenix species and in Chamaerops, Livistona, and Hyphaene. • Tandem repeat motifs of 3-6 bp were searched using a simple sequence repeat (SSR)-pipeline package in coding portions of the date palm draft genome sequence. Fifteen loci produced highly consistent amplification, intraspecific polymorphisms, and stepwise mutation patterns. • These microsatellite loci showed sufficient levels of variability and transferability to make them useful for population genetic, selection signature, and interspecific gene flow studies in Phoenix and other Coryphoideae genera.

  9. In Silico Mining of Microsatellites in Coding Sequences of the Date Palm (Arecaceae Genome, Characterization, and Transferability

    Directory of Open Access Journals (Sweden)

    Frédérique Aberlenc-Bertossi

    2014-01-01

    Full Text Available Premise of the study: To complement existing sets of primarily dinucleotide microsatellite loci from noncoding sequences of date palm, we developed primers for tri- and hexanucleotide microsatellite loci identified within genes. Due to their conserved genomic locations, the primers should be useful in other palm taxa, and their utility was tested in seven other Phoenix species and in Chamaerops, Livistona, and Hyphaene. Methods and Results: Tandem repeat motifs of 3–6 bp were searched using a simple sequence repeat (SSR–pipeline package in coding portions of the date palm draft genome sequence. Fifteen loci produced highly consistent amplification, intraspecific polymorphisms, and stepwise mutation patterns. Conclusions: These microsatellite loci showed sufficient levels of variability and transferability to make them useful for population genetic, selection signature, and interspecific gene flow studies in Phoenix and other Coryphoideae genera.

  10. High-quality draft genome sequence of Kocuria marina SO9-6, an actinobacterium isolated from a copper mine.

    Science.gov (United States)

    Castro, Daniel B A; Pereira, Letícia Bianca; Silva, Marcus Vinícius M E; Silva, Bárbara P da; Palermo, Bruna Rafaella Z; Carlos, Camila; Belgini, Daiane R B; Limache, Elmer Erasmo G; Lacerda, Gileno V Jr; Nery, Mariana B P; Gomes, Milene B; Souza, Salatiel S de; Silva, Thiago M da; Rodrigues, Viviane D; Paulino, Luciana C; Vicentini, Renato; Ferraz, Lúcio F C; Ottoboni, Laura M M

    2015-09-01

    An actinobacterial strain, designated SO9-6, was isolated from a copper iron sulfide mineral. The organism is Gram-positive, facultatively anaerobic, and coccoid. Chemotaxonomic and phylogenetic properties were consistent with its classification in the genus Kocuria. Here, we report the first draft genome sequence of Kocuria marina SO9-6 under accession JROM00000000 (http://www.ncbi.nlm.nih.gov/nuccore/725823918), which provides insights for heavy metal bioremediation and production of compounds of biotechnological interest.

  11. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems.

    Directory of Open Access Journals (Sweden)

    Sophie S Abby

    Full Text Available Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose.Macromolecular System Finder (MacSyFinder provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include functional analogs, and the multiple uses of a same component by different systems. Models are used to search for molecular systems in complete genomes or in unstructured data like metagenomes. The components of the systems are searched by sequence similarity using Hidden Markov model (HMM protein profiles. The assignment of hits to a given system is decided based on compliance with the content and organization of the system model. A graphical interface, MacSyView, facilitates the analysis of the results by showing overviews of component content and genomic context. To exemplify the use of MacSyFinder we built models to detect and class CRISPR-Cas systems following a previously established classification. We show that MacSyFinder allows to easily define an accurate "Cas-finder" using publicly available protein profiles.MacSyFinder is a standalone application implemented in Python. It requires Python 2.7, Hmmer and makeblastdb (version 2.2.28 or higher. It is freely available with its source code under a GPLv3 license at https://github.com/gem-pasteur/macsyfinder. It is compatible with all platforms supporting Python and Hmmer/makeblastdb. The "Cas-finder" (models and HMM profiles is distributed as a compressed tarball archive as Supporting Information.

  12. High-recovery visual identification and single-cell retrieval of circulating tumor cells for genomic analysis using a dual-technology platform integrated with automated immunofluorescence staining

    International Nuclear Information System (INIS)

    Campton, Daniel E; Ramirez, Arturo B; Nordberg, Joshua J; Drovetto, Nick; Clein, Alisa C; Varshavskaya, Paulina; Friemel, Barry H; Quarre, Steve; Breman, Amy; Dorschner, Michael; Blau, Sibel; Blau, C Anthony; Sabath, Daniel E; Stilwell, Jackie L; Kaldjian, Eric P

    2015-01-01

    Circulating tumor cells (CTCs) are malignant cells that have migrated from solid cancers into the blood, where they are typically present in rare numbers. There is great interest in using CTCs to monitor response to therapies, to identify clinically actionable biomarkers, and to provide a non-invasive window on the molecular state of a tumor. Here we characterize the performance of the AccuCyte® – CyteFinder® system, a comprehensive, reproducible and highly sensitive platform for collecting, identifying and retrieving individual CTCs from microscopic slides for molecular analysis after automated immunofluorescence staining for epithelial markers. All experiments employed a density-based cell separation apparatus (AccuCyte) to separate nucleated cells from the blood and transfer them to microscopic slides. After staining, the slides were imaged using a digital scanning microscope (CyteFinder). Precisely counted model CTCs (mCTCs) from four cancer cell lines were spiked into whole blood to determine recovery rates. Individual mCTCs were removed from slides using a single-cell retrieval device (CytePicker™) for whole genome amplification and subsequent analysis by PCR and Sanger sequencing, whole exome sequencing, or array-based comparative genomic hybridization. Clinical CTCs were evaluated in blood samples from patients with different cancers in comparison with the CellSearch® system. AccuCyte – CyteFinder presented high-resolution images that allowed identification of mCTCs by morphologic and phenotypic features. Spike-in mCTC recoveries were between 90 and 91%. More than 80% of single-digit spike-in mCTCs were identified and even a single cell in 7.5 mL could be found. Analysis of single SKBR3 mCTCs identified presence of a known TP53 mutation by both PCR and whole exome sequencing, and confirmed the reported karyotype of this cell line. Patient sample CTC counts matched or exceeded CellSearch CTC counts in a small feasibility cohort. The AccuCyte

  13. Whole genome sequencing of group A Streptococcus: development and evaluation of an automated pipeline for emmgene typing

    Directory of Open Access Journals (Sweden)

    Georgia Kapatai

    2017-04-01

    Full Text Available Streptococcus pyogenes group A Streptococcus (GAS is the most common cause of bacterial throat infections, and can cause mild to severe skin and soft tissue infections, including impetigo, erysipelas, necrotizing fasciitis, as well as systemic and fatal infections including septicaemia and meningitis. Estimated annual incidence for invasive group A streptococcal infection (iGAS in industrialised countries is approximately three per 100,000 per year. Typing is currently used in England and Wales to monitor bacterial strains of S. pyogenes causing invasive infections and those isolated from patients and healthcare/care workers in cluster and outbreak situations. Sequence analysis of the emm gene is the currently accepted gold standard methodology for GAS typing. A comprehensive database of emm types observed from superficial and invasive GAS strains from England and Wales informs outbreak control teams during investigations. Each year the Bacterial Reference Department, Public Health England (PHE receives approximately 3,000 GAS isolates from England and Wales. In April 2014 the Bacterial Reference Department, PHE began genomic sequencing of referred S. pyogenes isolates and those pertaining to selected elderly/nursing care or maternity clusters from 2010 to inform future reference services and outbreak analysis (n = 3, 047. In line with the modernizing strategy of PHE, we developed a novel bioinformatics pipeline that can predict emmtypes using whole genome sequence (WGS data. The efficiency of this method was measured by comparing the emmtype assigned by this method against the result from the current gold standard methodology; concordance to emmsubtype level was observed in 93.8% (2,852/3,040 of our cases, whereas in 2.4% (n = 72 of our cases concordance was observed to emm type level. The remaining 3.8% (n = 117 of our cases corresponded to novel types/subtypes, contamination, laboratory sample transcription errors or problems arising

  14. Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds

    Directory of Open Access Journals (Sweden)

    Menno evan der Voort

    2015-07-01

    Full Text Available The plant microbiome represents an enormous untapped resource for discovering novel genes and bioactive compounds. Previously, we isolated Pseudomonas sp. SH-C52 from the rhizosphere of sugar beet plants grown in a soil suppressive to the fungal pathogen Rhizoctonia solani and showed that its antifungal activity is, in part, attributed to the production of the chlorinated 9-amino-acid lipopeptide thanamycin (Mendes et al. 2011. Science. To get more insight into its biosynthetic repertoire, the genome of Pseudomonas sp. SH-C52 was sequenced and subjected to in silico, mutational and functional analyses. The sequencing revealed a genome size of 6.3 Mb and 5,579 predicted ORFs. Phylogenetic analysis placed strain SH-C52 within the Pseudomonas corrugata clade. In silico analysis for secondary metabolites revealed a total of six nonribosomal peptide synthetase (NRPS gene clusters, including the two previously described NRPS clusters for thanamycin and the 2-amino acid antibacterial lipopeptide brabantamide. Here we show that thanamycin also has activity against an array of other fungi and that brabantamide A exhibits anti-oomycete activity and affects phospholipases of the late blight pathogen Phytophthora infestans. Most notably, mass spectrometry led to the discovery of a third LP, designated thanapeptin, with a 22-amino-acid peptide moiety. Seven structural variants of thanapeptin were found with varying degrees of activity against P. infestans. Of the remaining four NRPS clusters, one was predicted to encode for yet another and unknown lipopeptide with a predicted peptide moiety of 8-amino acids. Collectively, these results show an enormous metabolic potential for Pseudomonas sp. SH-C52, with at least three structurally diverse lipopeptides, each with a different antimicrobial activity spectrum.

  15. Automation of plasma-process fultext bibliography databases. An on-line data-collection, data-mining and data-input system

    International Nuclear Information System (INIS)

    Suzuki, Manabu; Pichl, Lukas; Murakami, Izumi; Kato, Takako; Sasaki, Akira

    2006-01-01

    Searching for relevant data, information retrieval, data extraction and data input are time- and resource-consuming activities in most data centers. Here we develop a Linux system automating the process in case of bibliography, abstract and fulltext databases. The present system is an open-source free-software low-cost solution that connects the target and provider databases in cyberspace through various web publishing formats. The abstract/fulltext relevance assessment is interfaced to external software modules. (author)

  16. iSubgraph: integrative genomics for subgroup discovery in hepatocellular carcinoma using graph mining and mixture models.

    Directory of Open Access Journals (Sweden)

    Bahadir Ozdemir

    Full Text Available The high tumor heterogeneity makes it very challenging to identify key tumorigenic pathways as therapeutic targets. The integration of multiple omics data is a promising approach to identify driving regulatory networks in patient subgroups. Here, we propose a novel conceptual framework to discover patterns of miRNA-gene networks, observed frequently up- or down-regulated in a group of patients and to use such networks for patient stratification in hepatocellular carcinoma (HCC. We developed an integrative subgraph mining approach, called iSubgraph, and identified altered regulatory networks frequently observed in HCC patients. The miRNA and gene expression profiles were jointly analyzed in a graph structure. We defined a method to transform microarray data into graph representation that encodes miRNA and gene expression levels and the interactions between them as well. The iSubgraph algorithm was capable to detect cooperative regulation of miRNAs and genes even if it occurred only in some patients. Next, the miRNA-mRNA modules were used in an unsupervised class prediction model to discover HCC subgroups via patient clustering by mixture models. The robustness analysis of the mixture model showed that the class predictions are highly stable. Moreover, the Kaplan-Meier survival analysis revealed that the HCC subgroups identified by the algorithm have different survival characteristics. The pathway analyses of the miRNA-mRNA co-modules identified by the algorithm demonstrate key roles of Myc, E2F1, let-7, TGFB1, TNF and EGFR in HCC subgroups. Thus, our method can integrate various omics data derived from different platforms and with different dynamic scales to better define molecular tumor subtypes. iSubgraph is available as MATLAB code at http://www.cs.umd.edu/~ozdemir/isubgraph/.

  17. Establishing a new methodology for genome mining and biosynthesis of polyketides and peptides through yeast molecular genetics.

    Science.gov (United States)

    Ishiuchi, Kan'ichiro; Nakazawa, Takehito; Ookuma, Takashi; Sugimoto, Satoru; Sato, Michio; Tsunematsu, Yuta; Ishikawa, Noriyasu; Noguchi, Hiroshi; Hotta, Kinya; Moriya, Hisao; Watanabe, Kenji

    2012-04-16

    Fungal genome sequencing has revealed many genes coding for biosynthetic enzymes, including polyketide synthases and nonribosomal peptide synthetases. However, characterizing these enzymes and identifying the compounds they synthesize remains a challenge, whether the genes are expressed in their original hosts or in more tractable heterologous hosts, such as yeast. Here, we developed a streamlined method for isolating biosynthetic genes from fungal sources and producing bioactive molecules in an engineered Saccharomyces cerevisiae host strain. We used overlap extension PCR and yeast homologous recombination to clone desired fungal polyketide synthase or a nonribosomal peptide synthetase genes (5-20 kb) into a yeast expression vector quickly and efficiently. This approach was used successfully to clone five polyketide synthases and one nonribosomal peptide synthetase, from various fungal species. Subsequent detailed chemical characterizations of the resulting natural products identified six polyketide and two nonribosomal peptide products, one of which was a new compound. Our system should facilitate investigating uncharacterized fungal biosynthetic genes, identifying novel natural products, and rationally engineering biosynthetic pathways for the production of enzyme analogues possessing modified bioactivity. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Carotenoid metabolic profiling and transcriptome-genome mining reveal functional equivalence among blue-pigmented copepods and appendicularia

    KAUST Repository

    Mojib, Nazia

    2014-06-01

    The tropical oligotrophic oceanic areas are characterized by high water transparency and annual solar radiation. Under these conditions, a large number of phylogenetically diverse mesozooplankton species living in the surface waters (neuston) are found to be blue pigmented. In the present study, we focused on understanding the metabolic and genetic basis of the observed blue phenotype functional equivalence between the blue-pigmented organisms from the phylum Arthropoda, subclass Copepoda (Acartia fossae) and the phylum Chordata, class Appendicularia (Oikopleura dioica) in the Red Sea. Previous studies have shown that carotenoid–protein complexes are responsible for blue coloration in crustaceans. Therefore, we performed carotenoid metabolic profiling using both targeted and nontargeted (high-resolution mass spectrometry) approaches in four different blue-pigmented genera of copepods and one blue-pigmented species of appendicularia. Astaxanthin was found to be the principal carotenoid in all the species. The pathway analysis showed that all the species can synthesize astaxanthin from β-carotene, ingested from dietary sources, via 3-hydroxyechinenone, canthaxanthin, zeaxanthin, adonirubin or adonixanthin. Further, using de novo assembled transcriptome of blue A. fossae (subclass Copepoda), we identified highly expressed homologous β-carotene hydroxylase enzymes and putative carotenoid-binding proteins responsible for astaxanthin formation and the blue phenotype. In blue O. dioica (class Appendicularia), corresponding putative genes were identified from the reference genome. Collectively, our data provide molecular evidences for the bioconversion and accumulation of blue astaxanthin–protein complexes underpinning the observed ecological functional equivalence and adaptive convergence among neustonic mesozooplankton.

  19. Genome Sequence and Mutational Analysis of Plant-Growth-Promoting Bacterium Agrobacterium tumefaciens CCNWGS0286 Isolated from a Zinc-Lead Mine Tailing

    Science.gov (United States)

    Hao, Xiuli; Xie, Pin; Johnstone, Laurel; Miller, Susan J.

    2012-01-01

    The plant-growth-promoting bacterium Agrobacterium tumefaciens CCNWGS0286, isolated from the nodules of Robinia pseudoacacia growing in zinc-lead mine tailings, both displayed high metal resistance and enhanced the growth of Robinia plants in a metal-contaminated environment. Our goal was to determine whether bacterial metal resistance or the capacity to produce phytohormones had a larger impact on the growth of host plants under zinc stress. Eight zinc-sensitive mutants and one zinc-sensitive mutant with reduced indole-3-acetic acid (IAA) production were obtained by transposon mutagenesis. Analysis of the genome sequence and of transcription via reverse transcriptase PCR (RT-PCR) combined with transposon gene disruptions revealed that ZntA-4200 and the transcriptional regulator ZntR1 played important roles in the zinc homeostasis of A. tumefaciens CCNWGS0286. In addition, interruption of a putative oligoketide cyclase/lipid transport protein reduced IAA synthesis and also showed reduced zinc and cadmium resistance but had no influence on copper resistance. In greenhouse studies, R. pseudoacacia inoculated with A. tumefaciens CCNWGS0286 displayed a significant increase in biomass production over that without inoculation, even in a zinc-contaminated environment. Interestingly, the differences in plant biomass improvement among A. tumefaciens CCNWGS0286, A. tumefaciens C58, and zinc-sensitive mutants 12-2 (zntA::Tn5) and 15-6 (low IAA production) revealed that phytohormones, rather than genes encoding zinc resistance determinants, were the dominant factor in enhancing plant growth in contaminated soil. PMID:22636006

  20. Two non-synonymous markers in PTPN21, identified by genome-wide association study data-mining and replication, are associated with schizophrenia.

    LENUS (Irish Health Repository)

    Chen, Jingchun

    2011-09-01

    We conducted data-mining analyses of genome wide association (GWA) studies of the CATIE and MGS-GAIN datasets, and found 13 markers in the two physically linked genes, PTPN21 and EML5, showing nominally significant association with schizophrenia. Linkage disequilibrium (LD) analysis indicated that all 7 markers from PTPN21 shared high LD (r(2)>0.8), including rs2274736 and rs2401751, the two non-synonymous markers with the most significant association signals (rs2401751, P=1.10 × 10(-3) and rs2274736, P=1.21 × 10(-3)). In a meta-analysis of all 13 replication datasets with a total of 13,940 subjects, we found that the two non-synonymous markers are significantly associated with schizophrenia (rs2274736, OR=0.92, 95% CI: 0.86-0.97, P=5.45 × 10(-3) and rs2401751, OR=0.92, 95% CI: 0.86-0.97, P=5.29 × 10(-3)). One SNP (rs7147796) in EML5 is also significantly associated with the disease (OR=1.08, 95% CI: 1.02-1.14, P=6.43 × 10(-3)). These 3 markers remain significant after Bonferroni correction. Furthermore, haplotype conditioned analyses indicated that the association signals observed between rs2274736\\/rs2401751 and rs7147796 are statistically independent. Given the results that 2 non-synonymous markers in PTPN21 are associated with schizophrenia, further investigation of this locus is warranted.

  1. The Aspergillus Mine - publishing bioinformatics

    DEFF Research Database (Denmark)

    Vesth, Tammi Camilla; Rasmussen, Jane Lind Nybo; Theobald, Sebastian

    with the Joint Genome Institute. The Aspergillus Mine is not intended as a genomic data sharing service but instead focuses on creating an environment where the results of bioinformatic analysis is made available for inspection. The data and code is public upon request and figures can be obtained directly from...

  2. Unmanned Mine of the 21st Centuries

    Science.gov (United States)

    Semykina, Irina; Grigoryev, Aleksandr; Gargayev, Andrey; Zavyalov, Valeriy

    2017-11-01

    The article is analytical. It considers the construction principles of the automation system structure which realize the concept of «unmanned mine». All of these principles intend to deal with problems caused by a continuous complication of mining-and-geological conditions at coalmine such as the labor safety and health protection, the weak integration of different mining automation subsystems and the deficiency of optimal balance between a quantity of resource and energy consumed by mining machines and their throughput. The authors describe the main problems and neck stage of mining machines autonomation and automation subsystem. The article makes a general survey of the applied «unmanned technology» in the field of mining such as the remotely operated autonomous complexes, the underground positioning systems of mining machines using infrared radiation in mine workings etc. The concept of «unmanned mine» is considered with an example of the robotic road heading machine. In the final, the authors analyze the techniques and methods that could solve the task of underground mining without human labor.

  3. Text Mining of the Electronic Health Record: An Information Extraction Approach for Automated Identification and Subphenotyping of HFpEF Patients for Clinical Trials.

    Science.gov (United States)

    Jonnalagadda, Siddhartha R; Adupa, Abhishek K; Garg, Ravi P; Corona-Cox, Jessica; Shah, Sanjiv J

    2017-06-01

    Precision medicine requires clinical trials that are able to efficiently enroll subtypes of patients in whom targeted therapies can be tested. To reduce the large amount of time spent screening, identifying, and recruiting patients with specific subtypes of heterogeneous clinical syndromes (such as heart failure with preserved ejection fraction [HFpEF]), we need prescreening systems that are able to automate data extraction and decision-making tasks. However, a major obstacle is the vast amount of unstructured free-form text in medical records. Here we describe an information extraction-based approach that automatically converts unstructured text into structured data, which is cross-referenced against eligibility criteria using a rule-based system to determine which patients qualify for a major HFpEF clinical trial (PARAGON). We show that we can achieve a sensitivity and positive predictive value of 0.95 and 0.86, respectively. Our open-source algorithm could be used to efficiently identify and subphenotype patients with HFpEF and other disorders.

  4. Longwall mining

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-03-14

    As part of EIA`s program to provide information on coal, this report, Longwall-Mining, describes longwall mining and compares it with other underground mining methods. Using data from EIA and private sector surveys, the report describes major changes in the geologic, technological, and operating characteristics of longwall mining over the past decade. Most important, the report shows how these changes led to dramatic improvements in longwall mining productivity. For readers interested in the history of longwall mining and greater detail on recent developments affecting longwall mining, the report includes a bibliography.

  5. Genome mining for new α-amylase and glucoamylase encoding sequences and high level expression of a glucoamylase from Talaromyces stipitatus for potential raw starch hydrolysis.

    Science.gov (United States)

    Xiao, Zhizhuang; Wu, Meiqun; Grosse, Stephan; Beauchemin, Manon; Lévesque, Michelle; Lau, Peter C K

    2014-01-01

    Mining fungal genomes for glucoamylase and α-amylase encoding sequences led to the selection of 23 candidates, two of which (designated TSgam-2 and NFamy-2) were advanced to testing for cooked or raw starch hydrolysis. TSgam-2 is a 66-kDa glucoamylase recombinantly produced in Pichia pastoris and originally derived for Talaromyces stipitatus. When harvested in a 20-L bioreactor at high cell density (OD600 > 200), the secreted TSgam-2 enzyme activity from P. pastoris strain GS115 reached 800 U/mL. In a 6-L working volume of a 10-L fermentation, the TSgam-2 protein yield was estimated to be ∼8 g with a specific activity of 360 U/mg. In contrast, the highest activity of NFamy-2, a 70-kDa α-amylase originally derived from Neosartorya fischeri, and expressed in P. pastoris KM71 only reached 8 U/mL. Both proteins were purified and characterized in terms of pH and temperature optima, kinetic parameters, and thermostability. TSgam-2 was more thermostable than NFamy-2 with a respective half-life (t1/2) of >300 min at 55 °C and >200 min at 40 °C. The kinetic parameters for raw starch adsorption of TSgam-2 and NFamy-2 were also determined. A combination of NFamy-2 and TSgam-2 hydrolyzed cooked potato and triticale starch into glucose with yields, 71-87 %, that are competitive with commercially available α-amylases. In the hydrolysis of raw starch, the best hydrolysis condition was seen with a sequential addition of 40 U of a thermostable Bacillus globigii amylase (BgAmy)/g starch at 80 °C for 16 h, and 40 U TSgam-2/g starch at 45 °C for 24 h. The glucose released was 8.7 g/10 g of triticale starch and 7.9 g/10 g of potato starch, representing 95 and 86 % of starch degradation rate, respectively.

  6. Real world data mining applications

    CERN Document Server

    Abou-Nasr, Mahmoud; Stahlbock, Robert; Weiss, Gary M

    2014-01-01

    Data mining applications range from commercial to social domains, with novel applications appearing swiftly; for example, within the context of social networks. The expanding application sphere and social reach of advanced data mining raise pertinent issues of privacy and security. Present-day data mining is a progressive multidisciplinary endeavor. This inter- and multidisciplinary approach is well reflected within the field of information systems. The information systems research addresses software and hardware requirements for supporting computationally and data-intensive applications. Furthermore, it encompasses analyzing system and data aspects, and all manual or automated activities. In that respect, research at the interface of information systems and data mining has significant potential to produce actionable knowledge vital for corporate decision-making. The aim of the proposed volume is to provide a balanced treatment of the latest advances and developments in data mining; in particular, exploring s...

  7. Introduction to Space Resource Mining

    Science.gov (United States)

    Mueller, Robert P.

    2013-01-01

    There are vast amounts of resources in the solar system that will be useful to humans in space and possibly on Earth. None of these resources can be exploited without the first necessary step of extra-terrestrial mining. The necessary technologies for tele-robotic and autonomous mining have not matured sufficiently yet. The current state of technology was assessed for terrestrial and extraterrestrial mining and a taxonomy of robotic space mining mechanisms was presented which was based on current existing prototypes. Terrestrial and extra-terrestrial mining methods and technologies are on the cusp of massive changes towards automation and autonomy for economic and safety reasons. It is highly likely that these industries will benefit from mutual cooperation and technology transfer.

  8. Use of a Pan-Genomic DNA Microarray in Determination of the Phylogenetic Relatedness among Cronobacter spp. and Its Use as a Data Mining Tool to Understand Cronobacter Biology.

    Science.gov (United States)

    Tall, Ben D; Gangiredla, Jayanthi; Grim, Christopher J; Patel, Isha R; Jackson, Scott A; Mammel, Mark K; Kothary, Mahendra H; Sathyamoorthy, Venugopal; Carter, Laurenda; Fanning, Séamus; Iversen, Carol; Pagotto, Franco; Stephan, Roger; Lehner, Angelika; Farber, Jeffery; Yan, Qiong Q; Gopinath, Gopal R

    2017-03-04

    Cronobacter (previously known as Enterobacter sakazakii ) is a genus of Gram-negative, facultatively anaerobic, oxidase-negative, catalase-positive, rod-shaped bacteria of the family Enterobacteriaceae . These organisms cause a variety of illnesses such as meningitis, necrotizing enterocolitis, and septicemia in neonates and infants, and urinary tract, wound, abscesses or surgical site infections, septicemia, and pneumonia in adults. The total gene content of 379 strains of Cronobacter spp. and taxonomically-related isolates was determined using a recently reported DNA microarray. The Cronobacter microarray as a genotyping tool gives the global food safety community a rapid method to identify and capture the total genomic content of outbreak isolates for food safety, environmental, and clinical surveillance purposes. It was able to differentiate the seven Cronobacter species from one another and from non- Cronobacter species. The microarray was also able to cluster strains within each species into well-defined subgroups. These results also support previous studies on the phylogenic separation of species members of the genus and clearly highlight the evolutionary sequence divergence among each species of the genus compared to phylogenetically-related species. This review extends these studies and illustrates how the microarray can also be used as an investigational tool to mine genomic data sets from strains. Three case studies describing the use of the microarray are shown and include: (1) the determination of allelic differences among Cronobacter sakazakii strains possessing the virulence plasmid pESA3; (2) mining of malonate and myo-inositol alleles among subspecies of Cronobacter dublinensis strains to determine subspecies identity; and (3) lastly using the microarray to demonstrate sequence divergence and phylogenetic relatedness trends for 13 outer-membrane protein alleles among 240 Cronobacter and phylogenetically-related strains. The goal of this review is

  9. Web Mining

    Science.gov (United States)

    Fürnkranz, Johannes

    The World-Wide Web provides every internet citizen with access to an abundance of information, but it becomes increasingly difficult to identify the relevant pieces of information. Research in web mining tries to address this problem by applying techniques from data mining and machine learning to Web data and documents. This chapter provides a brief overview of web mining techniques and research areas, most notably hypertext classification, wrapper induction, recommender systems and web usage mining.

  10. Text Mining.

    Science.gov (United States)

    Trybula, Walter J.

    1999-01-01

    Reviews the state of research in text mining, focusing on newer developments. The intent is to describe the disparate investigations currently included under the term text mining and provide a cohesive structure for these efforts. A summary of research identifies key organizations responsible for pushing the development of text mining. A section…

  11. Section of Cybernetics in Mining of Mining Committee of Polish Academy of Sciences - Pro Memoria

    Science.gov (United States)

    Wojaczek, Antoni; Miśkiewicz, Kazimierz

    2017-09-01

    Section of Cybernetics in Mining of Mining Committee of Polish Academy of Science (PAN) has been created by PAN Mining Committee in 1969. It was a section in Mining Committee of PAN, whose operation range included widely understood issues of automation, telecommunication and informatics in mining industry. The main operation method of the Section was to organize the periodic conferences dedicated to issues of control systems in mining. The first conference took place in 1971 in Katowice. Together with new (the current one) term of office of Mining Committee of PAN this Section ceased to exist. The paper presents (pro memoria) over 40 year long conference output of this Section that functioned within the scope of operation of Mining Committee of PAN up to 12th January 2016.

  12. Development of a real-time PCR for detection of Staphylococcus pseudintermedius using a novel automated comparison of whole-genome sequences.

    Directory of Open Access Journals (Sweden)

    Koen M Verstappen

    Full Text Available Staphylococcus pseudintermedius is an opportunistic pathogen in dogs and cats and occasionally causes infections in humans. S. pseudintermedius is often resistant to multiple classes of antimicrobials. It requires a reliable detection so that it is not misidentified as S. aureus. Phenotypic and currently-used molecular-based diagnostic assays lack specificity or are labour-intensive using multiplex PCR or nucleic acid sequencing. The aim of this study was to identify a specific target for real-time PCR by comparing whole genome sequences of S. pseudintermedius and non-pseudintermedius.Genome sequences were downloaded from public repositories and supplemented by isolates that were sequenced in this study. A Perl-script was written that analysed 300-nt fragments from a reference genome sequence of S. pseudintermedius and checked if this sequence was present in other S. pseudintermedius genomes (n = 74 and non-pseudintermedius genomes (n = 138. Six sequences specific for S. pseudintermedius were identified (sequence length between 300-500 nt. One sequence, which was located in the spsJ gene, was used to develop primers and a probe. The real-time PCR showed 100% specificity when testing for S. pseudintermedius isolates (n = 54, and eight other staphylococcal species (n = 43. In conclusion, a novel approach by comparing whole genome sequences identified a sequence that is specific for S. pseudintermedius and provided a real-time PCR target for rapid and reliable detection of S. pseudintermedius.

  13. FASER Rescue Equipment and Mining Lamp Factory

    Energy Technology Data Exchange (ETDEWEB)

    Kubala, L.

    1984-12-01

    The history of the FASER Rescue Equipment and Mining Lamp Factory founded in 1924 is discussed. Plant development from 1924 to 1939 and from 1947 to 1984 is evaluated. The FASER Plant has been subordinated to the EMAG Center for Research and Production of Electrical Engineering and Mine Automation since 1980. Equipment manufactured by the plant is discussed: oxygen respirators, canisters, protective clothing, control systems and measuring instruments used in mine rescue, medical equipment, lighting systems and light bulbs for underground mines. Some problems associated with manufacturing processes are evaluated: manufacturing equipment, manufacturing technologies, quality of rescue equipment, innovation and its economic significance, etc.

  14. Library Automation

    OpenAIRE

    Dhakne, B. N.; Giri, V. V; Waghmode, S. S.

    2010-01-01

    New technologies library provides several new materials, media and mode of storing and communicating the information. Library Automation reduces the drudgery of repeated manual efforts in library routine. By use of library automation collection, Storage, Administration, Processing, Preservation and communication etc.

  15. An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database.

    Science.gov (United States)

    Kobayashi, Naohiro; Harano, Yoko; Tochio, Naoya; Nakatani, Eiichi; Kigawa, Takanori; Yokoyama, Shigeyuki; Mading, Steve; Ulrich, Eldon L; Markley, John L; Akutsu, Hideo; Fujiwara, Toshimichi

    2012-08-01

    Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including (1)H, (13)C and (15)N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001-2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies.

  16. Automated Extraction of Genomic DNA from Medically Important Yeast Species and Filamentous Fungi by Using the MagNA Pure LC System

    OpenAIRE

    Loeffler, Juergen; Schmidt, Kathrin; Hebart, Holger; Schumacher, Ulrike; Einsele, Hermann

    2002-01-01

    A fully automated assay was established for the extraction of DNA from clinically important fungi by using the MagNA Pure LC instrument. The test was evaluated by DNA isolation from 23 species of yeast and filamentous fungi and by extractions (n = 28) of serially diluted Aspergillus fumigatus conidia (105 to 0 CFU/ml). Additionally, DNA from 67 clinical specimens was extracted and compared to the manual protocol. The detection limit of the MagNA Pure LC assay of 10 CFU corresponded to the sen...

  17. Process automation

    International Nuclear Information System (INIS)

    Moser, D.R.

    1986-01-01

    Process automation technology has been pursued in the chemical processing industries and to a very limited extent in nuclear fuel reprocessing. Its effective use has been restricted in the past by the lack of diverse and reliable process instrumentation and the unavailability of sophisticated software designed for process control. The Integrated Equipment Test (IET) facility was developed by the Consolidated Fuel Reprocessing Program (CFRP) in part to demonstrate new concepts for control of advanced nuclear fuel reprocessing plants. A demonstration of fuel reprocessing equipment automation using advanced instrumentation and a modern, microprocessor-based control system is nearing completion in the facility. This facility provides for the synergistic testing of all chemical process features of a prototypical fuel reprocessing plant that can be attained with unirradiated uranium-bearing feed materials. The unique equipment and mission of the IET facility make it an ideal test bed for automation studies. This effort will provide for the demonstration of the plant automation concept and for the development of techniques for similar applications in a full-scale plant. A set of preliminary recommendations for implementing process automation has been compiled. Some of these concepts are not generally recognized or accepted. The automation work now under way in the IET facility should be useful to others in helping avoid costly mistakes because of the underutilization or misapplication of process automation. 6 figs

  18. Automated extraction of genomic DNA from medically important yeast species and filamentous fungi by using the MagNA Pure LC system.

    Science.gov (United States)

    Loeffler, Juergen; Schmidt, Kathrin; Hebart, Holger; Schumacher, Ulrike; Einsele, Hermann

    2002-06-01

    A fully automated assay was established for the extraction of DNA from clinically important fungi by using the MagNA Pure LC instrument. The test was evaluated by DNA isolation from 23 species of yeast and filamentous fungi and by extractions (n = 28) of serially diluted Aspergillus fumigatus conidia (10(5) to 0 CFU/ml). Additionally, DNA from 67 clinical specimens was extracted and compared to the manual protocol. The detection limit of the MagNA Pure LC assay of 10 CFU corresponded to the sensitivity when DNA was extracted manually; in 9 of 28 runs, we could achieve a higher sensitivity of 1 CFU/ml blood, which was found to be significant (p DNA from all fungal species analyzed could be extracted and amplified by real-time PCR. Negative controls from all MagNA Pure isolations remained negative. Sixty-three clinical samples showed identical results by both methods, whereas in 4 of 67 samples, discordant results were obtained. Thus, the MagNA Pure LC technique offers a fast protocol for automated DNA isolation from numerous fungi, revealing high sensitivity and purity.

  19. Use of a Pan–Genomic DNA Microarray in Determination of the Phylogenetic Relatedness among Cronobacter spp. and Its Use as a Data Mining Tool to Understand Cronobacter Biology

    Directory of Open Access Journals (Sweden)

    Ben D. Tall

    2017-03-01

    Full Text Available Cronobacter (previously known as Enterobacter sakazakii is a genus of Gram-negative, facultatively anaerobic, oxidase-negative, catalase-positive, rod-shaped bacteria of the family Enterobacteriaceae. These organisms cause a variety of illnesses such as meningitis, necrotizing enterocolitis, and septicemia in neonates and infants, and urinary tract, wound, abscesses or surgical site infections, septicemia, and pneumonia in adults. The total gene content of 379 strains of Cronobacter spp. and taxonomically-related isolates was determined using a recently reported DNA microarray. The Cronobacter microarray as a genotyping tool gives the global food safety community a rapid method to identify and capture the total genomic content of outbreak isolates for food safety, environmental, and clinical surveillance purposes. It was able to differentiate the seven Cronobacter species from one another and from non-Cronobacter species. The microarray was also able to cluster strains within each species into well-defined subgroups. These results also support previous studies on the phylogenic separation of species members of the genus and clearly highlight the evolutionary sequence divergence among each species of the genus compared to phylogenetically-related species. This review extends these studies and illustrates how the microarray can also be used as an investigational tool to mine genomic data sets from strains. Three case studies describing the use of the microarray are shown and include: (1 the determination of allelic differences among Cronobacter sakazakii strains possessing the virulence plasmid pESA3; (2 mining of malonate and myo-inositol alleles among subspecies of Cronobacter dublinensis strains to determine subspecies identity; and (3 lastly using the microarray to demonstrate sequence divergence and phylogenetic relatedness trends for 13 outer-membrane protein alleles among 240 Cronobacter and phylogenetically-related strains. The goal of

  20. TONO MINE

    OpenAIRE

    齊藤 宏; 湯佐 泰久; 小出 馨; 松井 裕哉; 太田 久仁雄; 濱 克宏; 川瀬 啓一

    1999-01-01

    This technical report provides a comprehensive presentation the "Geoscientific Studies" performed since 1986, and new work for the "Earthquake Frontier Research for Terrestrial Subsurface" programme performed since 1995 in and around the Tono Mine, Gifu Prefecture. This technical report also provides fieldstop descriptions for visits to the Tono Mine. The descriptions are attached at the end of this report.

  1. Mine Water Treatment in Hongai Coal Mines

    OpenAIRE

    Dang Phuong Thao; Dang Vu Chi

    2018-01-01

    Acid mine drainage (AMD) is recognized as one of the most serious environmental problem associated with mining industry. Acid water, also known as acid mine drainage forms when iron sulfide minerals found in the rock of coal seams are exposed to oxidizing conditions in coal mining. Until 2009, mine drainage in Hongai coal mines was not treated, leading to harmful effects on humans, animals and aquatic ecosystem. This report has examined acid mine drainage problem and techniques for acid mine ...

  2. Genome mining of the genetic diversity in the Aspergillus genus - from a collection of more than 30 Aspergillus species

    DEFF Research Database (Denmark)

    Rasmussen, Jane Lind Nybo; Vesth, Tammi Camilla; Theobald, Sebastian

    , this project uses BLAST on the amino acid level to discover orthologs. With a potential of 300 Aspergillus species each having ~12,000 annotated genes, traditional clustering will demand supercomputing. Instead, our approach reduces the search space by identifying isoenzymes within each genome creating...

  3. Investigation of the Cross-talk Mechanism in Caco-2 Cells duringClostridium difficileInfection through Genetic-and-Epigenetic Interspecies Networks: Big Data Mining and Genome-Wide Identification.

    Science.gov (United States)

    Li, Cheng-Wei; Su, Ming-He; Chen, Bor-Sen

    2017-01-01

    Clostridium difficile is the leading cause of nosocomial antibiotic-associated diarrhea and the major etiologic agent of pseudomembranous colitis. In severe cases, C. difficile infection (CDI) can cause toxic megacolon, intestinal perforation, and death. The intestinal epithelium is the first tissue encountered in the adhesion and colonization of C. difficile , and serves as a physical defense barrier against infection. Despite the well-characterized cytotoxicity, few studies have investigated the genome-wide interplay between host cells and C. difficile . The aim of this study is to investigate the genetic-and-epigenetic molecular mechanisms between human colorectal epithelial Caco-2 cells and C. difficile during the early (0-60 min) and late stages (30-120 min) of infection. To investigate the cross-talk mechanisms during the progression of infection, we introduced a systems biology approach using big data mining, dynamic network modeling, a genome-wide data identification method, system order detection scheme, and principal network projection method (PNP). We focused on the construction of genome-wide genetic-and-epigenetic interspecies networks (GEINs) and subsequent extraction of host-pathogen core networks (HPNs) to investigate the progression of underlying host/pathogen genetic-and-epigenetic mechanisms from the early to late stages of CDI. Based on our results, we suggest that the cell-wall proteins CD2787 and CD0237, which both play an important role in cell adhesion and pathogen defense mechanisms, can be considered as potential drug targets. In addition, the crucial proteins employed by C. difficile for sporulation, including CD1214, CD2629, and CD2643, can also be considered as potential drug targets since spore-mediated re-infection is a critical issue.

  4. The modernisation of mining

    CSIR Research Space (South Africa)

    Ritchken, E

    2017-10-01

    Full Text Available This presentation discusses the modernisation of mining. The presentation focuses on the mining clusters, Mining Challenges, Compliance versus Collaboration, The Phakisa, The Mining Precinct & the Mining Hub also Win-Win Beneficiation: Iron...

  5. Extending mine life

    International Nuclear Information System (INIS)

    Anon.

    1984-01-01

    Mine layouts, new machines and techniques, research into problem areas of ground control and so on, are highlighted in this report on extending mine life. The main resources taken into account are coal mining, uranium mining, molybdenum and gold mining

  6. Uranium mining

    International Nuclear Information System (INIS)

    2008-01-01

    Full text: The economic and environmental sustainability of uranium mining has been analysed by Monash University researcher Dr Gavin Mudd in a paper that challenges the perception that uranium mining is an 'infinite quality source' that provides solutions to the world's demand for energy. Dr Mudd says information on the uranium industry touted by politicians and mining companies is not necessarily inaccurate, but it does not tell the whole story, being often just an average snapshot of the costs of uranium mining today without reflecting the escalating costs associated with the process in years to come. 'From a sustainability perspective, it is critical to evaluate accurately the true lifecycle costs of all forms of electricity production, especially with respect to greenhouse emissions, ' he says. 'For nuclear power, a significant proportion of greenhouse emissions are derived from the fuel supply, including uranium mining, milling, enrichment and fuel manufacture.' Dr Mudd found that financial and environmental costs escalate dramatically as the uranium ore is used. The deeper the mining process required to extract the ore, the higher the cost for mining companies, the greater the impact on the environment and the more resources needed to obtain the product. I t is clear that there is a strong sensitivity of energy and water consumption and greenhouse emissions to ore grade, and that ore grades are likely to continue to decline gradually in the medium to long term. These issues are critical to the current debate over nuclear power and greenhouse emissions, especially with respect to ascribing sustainability to such activities as uranium mining and milling. For example, mining at Roxby Downs is responsible for the emission of over one million tonnes of greenhouse gases per year and this could increase to four million tonnes if the mine is expanded.'

  7. Antimicrobials of Bacillus species: mining and engineering

    NARCIS (Netherlands)

    Zhao, Xin

    2016-01-01

    Bacillus sp. have been successfully used to suppress various bacterial and fungal pathogens. Due to the wide availability of whole genome sequence data and the development of genome mining tools, novel antimicrobials are being discovered and updated,;not only bacteriocins, but also NRPs and PKs. A

  8. Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA).

    KAUST Repository

    Grötzinger, Stefan W.

    2014-04-07

    Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs) and poor homology of novel extremophile\\'s genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the Integrated Data Warehouse of Microbial Genomes (INDIGO) data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes) may translate into false positives when searching for specific functions. The Profile and Pattern Matching (PPM) strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO)-terms (which represent enzyme function profiles) and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern). The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2577 enzyme commission (E.C.) numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from six different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter) and PROSITE IDs (pattern filter). Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits) are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns) are present. Scripts for annotation, as well as for the PPM algorithm, are available

  9. Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26.

    Science.gov (United States)

    Andres, Jérémy; Arsène-Ploetze, Florence; Barbe, Valérie; Brochier-Armanet, Céline; Cleiss-Arnold, Jessica; Coppée, Jean-Yves; Dillies, Marie-Agnès; Geist, Lucie; Joublin, Aurélie; Koechler, Sandrine; Lassalle, Florent; Marchal, Marie; Médigue, Claudine; Muller, Daniel; Nesme, Xavier; Plewniak, Frédéric; Proux, Caroline; Ramírez-Bahena, Martha Helena; Schenowitz, Chantal; Sismeiro, Odile; Vallenet, David; Santini, Joanne M; Bertin, Philippe N

    2013-01-01

    Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolize the compound. Here, we present the first reference set of genomic, transcriptomic and proteomic data of an Alphaproteobacterium isolated from an arsenic-containing goldmine: Rhizobium sp. NT-26. Although phylogenetically related to the plant-associated bacteria, this organism has lost the major colonizing capabilities needed for symbiosis with legumes. In contrast, the genome of Rhizobium sp. NT-26 comprises a megaplasmid containing the various genes, which enable it to metabolize arsenite. Remarkably, although the genes required for arsenite oxidation and flagellar motility/biofilm formation are carried by the megaplasmid and the chromosome, respectively, a coordinate regulation of these two mechanisms was observed. Taken together, these processes illustrate the impact environmental pressure can have on the evolution of bacterial genomes, improving the fitness of bacterial strains by the acquisition of novel functions.

  10. 30 CFR 75.209 - Automated Temporary Roof Support (ATRS) systems.

    Science.gov (United States)

    2010-07-01

    ... of temporary support shall be used, as specified in the roof control plan, when— (1) Mining... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Automated Temporary Roof Support (ATRS) systems... COAL MINE SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Roof Support § 75.209...

  11. Accident rates in mine transport

    Energy Technology Data Exchange (ETDEWEB)

    Skurka, V.

    1987-11-01

    Describes accident trends for mine transport which now, due to increased automation, makes up 60-80% of all mining activities. Gives figures in tabular form for fatalities and serious injuries in organizations under control of State Mining Authority, showing that transport accidents are the most numerous (38% for period 1976-1986), followed by rock bursts (22%) and machinery accidents (10%). Analysis shows that both surface and underground transport are equally involved and that conveyors are the worst offenders, causing 31% of transport accidents during 1976-1986, followed by rail transport with 26% and automobile transport with 16%. Gives further details of precise causes of accidents involving these 3 types of transport and stresses that accidents can be prevented by using transport systems correctly, organizing them correctly, proper maintenance, use of safety devices and good working discipline. 5 refs.

  12. Text mining for systems biology.

    Science.gov (United States)

    Fluck, Juliane; Hofmann-Apitius, Martin

    2014-02-01

    Scientific communication in biomedicine is, by and large, still text based. Text mining technologies for the automated extraction of useful biomedical information from unstructured text that can be directly used for systems biology modelling have been substantially improved over the past few years. In this review, we underline the importance of named entity recognition and relationship extraction as fundamental approaches that are relevant to systems biology. Furthermore, we emphasize the role of publicly organized scientific benchmarking challenges that reflect the current status of text-mining technology and are important in moving the entire field forward. Given further interdisciplinary development of systems biology-orientated ontologies and training corpora, we expect a steadily increasing impact of text-mining technology on systems biology in the future. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Mining online genomic resources in Anolis carolinensis facilitates rapid and inexpensive development of cross-species microsatellite markers for the Anolis lizard genus.

    Science.gov (United States)

    Wordley, Claire; Slate, Jon; Stapley, Jessica

    2011-01-01

    Online sequence databases can provide valuable resources for the development of cross-species genetic markers. In particular, mining expressed tag sequences (EST) for microsatellites and developing conserved cross-species microsatellite markers can provide a rapid and relatively inexpensive method to develop new markers for a range of species. Here, we adopt this approach to develop cross-species microsatellite markers in Anolis lizards, which is a model genus in evolutionary biology and ecology. Using EST sequences from Anolis carolinensis, we identified 127 microsatellites that satisfied our criteria, and tested 49 of these in five species of Anolis (carolinensis, distichus, apletophallus, porcatus and sagrei). We identified between 8 and 25 new variable genetic markers for five Anolis species. These markers will be a valuable resource for studies of population genetics, comparative mapping, mating systems, behavioural ecology and adaptive radiations in this diverse lineage. © 2010 Blackwell Publishing Ltd.

  14. INTEGRATING DATA MINING INTO BUSINESS INTELLIGENCE

    Directory of Open Access Journals (Sweden)

    Maria Cristina ENACHE

    2006-01-01

    Full Text Available Data Mining is a broad term often used to describe the process of using database technology, modeling techniques, statistical analysis, and machine learning to analyze large amounts of data in an automated fashion to discover hidden patterns and predictive information in the data. By building highly complex and sophisticated statistical and mathematical models, organizations can gain new insight into their activities. The purpose of this document is to provide users with a background of a few key data mining concepts and business intelligence and about benefits of integrating business intelligence and data mining.

  15. Social big data mining

    CERN Document Server

    Ishikawa, Hiroshi

    2015-01-01

    Social Media. Big Data and Social Data. Hypotheses in the Era of Big Data. Social Big Data Applications. Basic Concepts in Data Mining. Association Rule Mining. Clustering. Classification. Prediction. Web Structure Mining. Web Content Mining. Web Access Log Mining, Information Extraction and Deep Web Mining. Media Mining. Scalability and Outlier Detection.

  16. Mining a database of single amplified genomes from Red Sea brine pool extremophiles – Improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA

    Directory of Open Access Journals (Sweden)

    Stefan Wolfgang Grötzinger

    2014-04-01

    Full Text Available Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs and poor homology of novel extremophile’s genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the INDIGO data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes may translate into false positives when searching for specific functions. The Profile & Pattern Matching (PPM strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO-terms (which represent enzyme function profiles and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern. The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2,577 E.C. numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from 6 different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter and PROSITE IDs (pattern filter. Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns are present. Scripts for annotation, as well as for the PPM algorithm, are available through the INDIGO website.

  17. Automated External Defibrillator

    Science.gov (United States)

    ... To Health Topics / Automated External Defibrillator Automated External Defibrillator Also known as What Is An automated external ... in survival. Training To Use an Automated External Defibrillator Learning how to use an AED and taking ...

  18. Mine Water Treatment in Hongai Coal Mines

    Science.gov (United States)

    Dang, Phuong Thao; Dang, Vu Chi

    2018-03-01

    Acid mine drainage (AMD) is recognized as one of the most serious environmental problem associated with mining industry. Acid water, also known as acid mine drainage forms when iron sulfide minerals found in the rock of coal seams are exposed to oxidizing conditions in coal mining. Until 2009, mine drainage in Hongai coal mines was not treated, leading to harmful effects on humans, animals and aquatic ecosystem. This report has examined acid mine drainage problem and techniques for acid mine drainage treatment in Hongai coal mines. In addition, selection and criteria for the design of the treatment systems have been presented.

  19. Mine Water Treatment in Hongai Coal Mines

    Directory of Open Access Journals (Sweden)

    Dang Phuong Thao

    2018-01-01

    Full Text Available Acid mine drainage (AMD is recognized as one of the most serious environmental problem associated with mining industry. Acid water, also known as acid mine drainage forms when iron sulfide minerals found in the rock of coal seams are exposed to oxidizing conditions in coal mining. Until 2009, mine drainage in Hongai coal mines was not treated, leading to harmful effects on humans, animals and aquatic ecosystem. This report has examined acid mine drainage problem and techniques for acid mine drainage treatment in Hongai coal mines. In addition, selection and criteria for the design of the treatment systems have been presented.

  20. ­Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis

    Directory of Open Access Journals (Sweden)

    Agustina Undabarrena

    2017-02-01

    Full Text Available Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes. Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes, oxidative stress (69 genes and antibiotic resistance (97 genes. This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2. Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.

  1. Mining whole genomes and transcriptomes of Jatropha (Jatropha curcas) and Castor bean (Ricinus communis) for NBS-LRR genes and defense response associated transcription factors.

    Science.gov (United States)

    Sood, Archit; Jaiswal, Varun; Chanumolu, Sree Krishna; Malhotra, Nikhil; Pal, Tarun; Chauhan, Rajinder Singh

    2014-11-01

    Jatropha (Jatropha curcas L.) and Castor bean (Ricinus communis) are oilseed crops of family Euphorbiaceae with the potential of producing high quality biodiesel and having industrial value. Both the bioenergy plants are becoming susceptible to various biotic stresses directly affecting the oil quality and content. No report exists as of today on analysis of Nucleotide Binding Site-Leucine Rich Repeat (NBS-LRR) gene repertoire and defense response transcription factors in both the plant species. In silico analysis of whole genomes and transcriptomes identified 47 new NBS-LRR genes in both the species and 122 and 318 defense response related transcription factors in Jatropha and Castor bean, respectively. The identified NBS-LRR genes and defense response transcription factors were mapped onto the respective genomes. Common and unique NBS-LRR genes and defense related transcription factors were identified in both the plant species. All NBS-LRR genes in both the species were characterized into Toll/interleukin-1 receptor NBS-LRRs (TNLs) and coiled-coil NBS-LRRs (CNLs), position on contigs, gene clusters and motifs and domains distribution. Transcript abundance or expression values were measured for all NBS-LRR genes and defense response transcription factors, suggesting their functional role. The current study provides a repertoire of NBS-LRR genes and transcription factors which can be used in not only dissecting the molecular basis of disease resistance phenotype but also in developing disease resistant genotypes in Jatropha and Castor bean through transgenic or molecular breeding approaches.

  2. Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species.

    Science.gov (United States)

    Dettori, Maria Teresa; Micali, Sabrina; Giovinazzi, Jessica; Scalabrin, Simone; Verde, Ignazio; Cipriani, Guido

    2015-01-01

    A wide inventory of molecular markers is nowadays available for individual fingerprinting. Microsatellites, or simple sequence repeats (SSRs), play a relevant role due to their relatively ease of use, their abundance in the plant genomes, and their co-dominant nature, together with the availability of primer sequences in many important agricultural crops. Microsatellites with long-core motifs are more easily scored and were adopted long ago in human genetics but they were developed only in few crops, and Prunus species are not among them. In the present work the peach whole-genome sequence was used to select 216 SSRs containing long-core motifs with tri-, tetra- and penta-nucleotide repeats. Microsatellite primer pairs were designed and tested for polymorphism in the five diploid Prunus species of economic relevance (almond, apricot, Japanese plum, peach and sweet cherry). A set of 26 microsatellite markers covering all the eight chromosomes, was also selected and used in the molecular characterization, population genetics and structure analyses of a representative sample of the five diploid Prunus species, assessing their transportability and effectiveness. The combined probability of identity between two random individuals for the whole set of 26 SSRs was quite low, ranging from 2.30 × 10(-7) in peach to 9.48 × 10(-10) in almond, confirming the usefulness of the proposed set for fingerprinting analyses in Prunus species.

  3. Library Automation.

    Science.gov (United States)

    Husby, Ole

    1990-01-01

    The challenges and potential benefits of automating university libraries are reviewed, with special attention given to cooperative systems. Aspects discussed include database size, the role of the university computer center, storage modes, multi-institutional systems, resource sharing, cooperative system management, networking, and intelligent…

  4. Bovine Genome Database: new tools for gleaning function from the Bos taurus genome.

    Science.gov (United States)

    Elsik, Christine G; Unni, Deepak R; Diesh, Colin M; Tayal, Aditi; Emery, Marianne L; Nguyen, Hung N; Hagen, Darren E

    2016-01-04

    We report an update of the Bovine Genome Database (BGD) (http://BovineGenome.org). The goal of BGD is to support bovine genomics research by providing genome annotation and data mining tools. We have developed new genome and annotation browsers using JBrowse and WebApollo for two Bos taurus genome assemblies, the reference genome assembly (UMD3.1.1) and the alternate genome assembly (Btau_4.6.1). Annotation tools have been customized to highlight priority genes for annotation, and to aid annotators in selecting gene evidence tracks from 91 tissue specific RNAseq datasets. We have also developed BovineMine, based on the InterMine data warehousing system, to integrate the bovine genome, annotation, QTL, SNP and expression data with external sources of orthology, gene ontology, gene interaction and pathway information. BovineMine provides powerful query building tools, as well as customized query templates, and allows users to analyze and download genome-wide datasets. With BovineMine, bovine researchers can use orthology to leverage the curated gene pathways of model organisms, such as human, mouse and rat. BovineMine will be especially useful for gene ontology and pathway analyses in conjunction with GWAS and QTL studies. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Surface Mines, Other - Longwall Mining Panels

    Data.gov (United States)

    NSGIC Education | GIS Inventory — Coal mining has occurred in Pennsylvania for over a century. A method of coal mining known as Longwall Mining has become more prevalent in recent decades. Longwall...

  6. Mining Review

    Science.gov (United States)

    ,

    2013-01-01

    In 2012, the estimated value of mineral production increased in the United States for the third consecutive year. Production and prices increased for most industrial mineral commodities mined in the United States. While production for most metals remained relatively unchanged, with the notable exception of gold, the prices for most metals declined. Minerals remained fundamental to the U.S. economy, contributing to the real gross domestic product (GDP) at several levels, including mining, processing and manufacturing finished products. Minerals’ contribution to the GDP increased for the second consecutive year.

  7. Data mining

    CERN Document Server

    Gorunescu, Florin

    2011-01-01

    The knowledge discovery process is as old as Homo sapiens. Until some time ago, this process was solely based on the 'natural personal' computer provided by Mother Nature. Fortunately, in recent decades the problem has begun to be solved based on the development of the Data mining technology, aided by the huge computational power of the 'artificial' computers. Digging intelligently in different large databases, data mining aims to extract implicit, previously unknown and potentially useful information from data, since 'knowledge is power'. The goal of this book is to provide, in a friendly way

  8. Genome mining in Sorangium cellulosum So ce56: identification and characterization of the homologous electron transfer proteins of a myxobacterial cytochrome P450.

    Science.gov (United States)

    Ewen, Kerstin Maria; Hannemann, Frank; Khatri, Yogan; Perlova, Olena; Kappl, Reinhard; Krug, Daniel; Hüttermann, Jürgen; Müller, Rolf; Bernhardt, Rita

    2009-10-16

    Myxobacteria, especially members of the genus Sorangium, are known for their biotechnological potential as producers of pharmaceutically valuable secondary metabolites. The biosynthesis of several of those myxobacterial compounds includes cytochrome P450 activity. Although class I cytochrome P450 enzymes occur wide-spread in bacteria and rely on ferredoxins and ferredoxin reductases as essential electron mediators, the study of these proteins is often neglected. Therefore, we decided to search in the Sorangium cellulosum So ce56 genome for putative interaction partners of cytochromes P450. In this work we report the investigation of eight myxobacterial ferredoxins and two ferredoxin reductases with respect to their activity in cytochrome P450 systems. Intriguingly, we found not only one, but two ferredoxins whose ability to sustain an endogenous So ce56 cytochrome P450 was demonstrated by CYP260A1-dependent conversion of nootkatone. Moreover, we could demonstrate that the two ferredoxins were able to receive electrons from both ferredoxin reductases. These findings indicate that S. cellulosum can alternate between different electron transport pathways to sustain cytochrome P450 activity.

  9. Text Mining in Biomedical Domain with Emphasis on Document Clustering.

    Science.gov (United States)

    Renganathan, Vinaitheerthan

    2017-07-01

    With the exponential increase in the number of articles published every year in the biomedical domain, there is a need to build automated systems to extract unknown information from the articles published. Text mining techniques enable the extraction of unknown knowledge from unstructured documents. This paper reviews text mining processes in detail and the software tools available to carry out text mining. It also reviews the roles and applications of text mining in the biomedical domain. Text mining processes, such as search and retrieval of documents, pre-processing of documents, natural language processing, methods for text clustering, and methods for text classification are described in detail. Text mining techniques can facilitate the mining of vast amounts of knowledge on a given topic from published biomedical research articles and draw meaningful conclusions that are not possible otherwise.

  10. Determining Underground Mining Work Postures Using Motion Capture and Digital Human Modeling

    OpenAIRE

    Lutz, Timothy J.; DuCarme, Joseph P.; Smith, Adam K.; Ambrose, Dean

    2016-01-01

    According to Mine Safety and Health Administration (MSHA) data, during 2008���2012 in the U.S., there were, on average, 65 lost-time accidents per year during routine mining and maintenance activities involving remote-controlled continuous mining machines (CMMs). To address this problem, the National Institute for Occupational Safety and Health (NIOSH) is currently investigating the implementation and integration of existing and emerging technologies in underground mines to provide automated,...

  11. A methodology for direct and indirect discrimination prevention in data mining

    OpenAIRE

    Domingo-Ferrer, J.; Hajian, S.

    2013-01-01

    10.1109/TKDE.2012.72 Data mining is an increasingly important technology for extracting useful knowledge hidden in large collections of data. There are, however, negative social perceptions about data mining, among which potential privacy invasion and potential discrimination. The latter consists of unfairly treating people on the basis of their belonging to a specific group. Automated data collection and data mining techniques such as classification rule mining have paved the way to maki...

  12. Protective and control relays as coal-mine power-supply ACS subsystem

    Science.gov (United States)

    Kostin, V. N.; Minakova, T. E.

    2017-10-01

    The paper presents instantaneous selective short-circuit protection for the cabling of the underground part of a coal mine and central control algorithms as a Coal-Mine Power-Supply ACS Subsystem. In order to improve the reliability of electricity supply and reduce the mining equipment down-time, a dual channel relay protection and central control system is proposed as a subsystem of the coal-mine power-supply automated control system (PS ACS).

  13. Tono mine

    Energy Technology Data Exchange (ETDEWEB)

    Saito, Hiroshi; Yusa, Yasuhisa; Koide, Kaoru [Japan Nuclear Cycle Development Inst., Toki, Gifu (Japan). Tono Geoscience Center] (and others)

    1999-09-01

    This technical report provides a comprehensive presentation of the Geoscientific studies (GS)' performed since 1986, and a new work on the Earthquake frontier research for terrestrial subsurface (EFR)' plan performed since 1995 in and around the Tono mine in Gifu prefecture. Main objects of GS in Tono area to provide sufficient informations on deep underground geological environment for its performance assessment and to develop some methods on site characterization. At present, some major studies are under progress in such fields as hydrology, hydro-geochemistry, isotope chemistry of groundwater, nuclide retardation, mine-by experiments, and development on instruments. And, EFR is divided to three categories, two of which have been performed at Tono mine under their names of the 'Development of ACROSS (Accurately controlled routinely operated signal system) for detecting microscale crustal movements' and the 'Studies of precursory and co-seismic changes in rock stress, water level and groundwater chemistry'. Here were shown on geology and geoscientific studies on Tono mine and on earthquake frontier research for terrestrial subsurface. (G.K.)

  14. AUTOMATION OF CONVEYOR BELT TRANSPORT

    Directory of Open Access Journals (Sweden)

    Nenad Marinović

    1990-12-01

    Full Text Available Belt conveyor transport, although one of the most economical mining transport system, introduce many problems to mantain the continuity of the operation. Every stop causes economical loses. Optimal operation require correct tension of the belt, correct belt position and velocity and faultless rolls, which are together input conditions for automation. Detection and position selection of the faults are essential for safety to eliminate fire hazard and for efficient maintenance. Detection and location of idler roll faults are still open problem and up to now not solved successfully (the paper is published in Croatian.

  15. Data mining and education.

    Science.gov (United States)

    Koedinger, Kenneth R; D'Mello, Sidney; McLaughlin, Elizabeth A; Pardos, Zachary A; Rosé, Carolyn P

    2015-01-01

    An emerging field of educational data mining (EDM) is building on and contributing to a wide variety of disciplines through analysis of data coming from various educational technologies. EDM researchers are addressing questions of cognition, metacognition, motivation, affect, language, social discourse, etc. using data from intelligent tutoring systems, massive open online courses, educational games and simulations, and discussion forums. The data include detailed action and timing logs of student interactions in user interfaces such as graded responses to questions or essays, steps in rich problem solving environments, games or simulations, discussion forum posts, or chat dialogs. They might also include external sensors such as eye tracking, facial expression, body movement, etc. We review how EDM has addressed the research questions that surround the psychology of learning with an emphasis on assessment, transfer of learning and model discovery, the role of affect, motivation and metacognition on learning, and analysis of language data and collaborative learning. For example, we discuss (1) how different statistical assessment methods were used in a data mining competition to improve prediction of student responses to intelligent tutor tasks, (2) how better cognitive models can be discovered from data and used to improve instruction, (3) how data-driven models of student affect can be used to focus discussion in a dialog-based tutoring system, and (4) how machine learning techniques applied to discussion data can be used to produce automated agents that support student learning as they collaborate in a chat room or a discussion board. © 2015 John Wiley & Sons, Ltd.

  16. Data mining concepts and techniques

    CERN Document Server

    Han, Jiawei

    2005-01-01

    Our ability to generate and collect data has been increasing rapidly. Not only are all of our business, scientific, and government transactions now computerized, but the widespread use of digital cameras, publication tools, and bar codes also generate data. On the collection side, scanned text and image platforms, satellite remote sensing systems, and the World Wide Web have flooded us with a tremendous amount of data. This explosive growth has generated an even more urgent need for new techniques and automated tools that can help us transform this data into useful information and knowledge.Like the first edition, voted the most popular data mining book by KD Nuggets readers, this book explores concepts and techniques for the discovery of patterns hidden in large data sets, focusing on issues relating to their feasibility, usefulness, effectiveness, and scalability. However, since the publication of the first edition, great progress has been made in the development of new data mining methods, systems, and app...

  17. Data mining

    Energy Technology Data Exchange (ETDEWEB)

    Lee, K.; Kargupta, H.; Stafford, B.G.; Buescher, K.L.; Ravindran, B.

    1998-12-31

    This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The objective of this project was to develop and implement data mining technology suited to the analysis of large collections of unstructured data. This has taken the form of a software tool, PADMA (Parallel Data Mining Agents), which incorporates parallel data accessing, parallel scalable hierarchical clustering algorithms, and a web-based user interface for submitting Structured Query Language (SQL) queries and interactive data visualization. The authors have demonstrated the viability and scalability of PADMA by applying it to an unstructured text database of 25,000 documents running on an IBM SP2 at Argonne National Laboratory. The utility of PADMA for discovering patterns in data has also been demonstrated by applying it to laboratory test data for Hepatitis C patients and autopsy reports in collaboration with the University of New Mexico School of Medicine.

  18. Autonomous Systems: Habitat Automation

    Data.gov (United States)

    National Aeronautics and Space Administration — The Habitat Automation Project Element within the Autonomous Systems Project is developing software to automate the automation of habitats and other spacecraft. This...

  19. An Automation Planning Primer.

    Science.gov (United States)

    Paynter, Marion

    1988-01-01

    This brief planning guide for library automation incorporates needs assessment and evaluation of options to meet those needs. A bibliography of materials on automation planning and software reviews, library software directories, and library automation journals is included. (CLB)

  20. Genome cluster database. A sequence family analysis platform for Arabidopsis and rice.

    Science.gov (United States)

    Horan, Kevin; Lauricha, Josh; Bailey-Serres, Julia; Raikhel, Natasha; Girke, Thomas

    2005-05-01

    The genome-wide protein sequences from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) spp. japonica were clustered into families using sequence similarity and domain-based clustering. The two fundamentally different methods resulted in separate cluster sets with complementary properties to compensate the limitations for accurate family analysis. Functional names for the identified families were assigned with an efficient computational approach that uses the description of the most common molecular function gene ontology node within each cluster. Subsequently, multiple alignments and phylogenetic trees were calculated for the assembled families. All clustering results and their underlying sequences were organized in the Web-accessible Genome Cluster Database (http://bioinfo.ucr.edu/projects/GCD) with rich interactive and user-friendly sequence family mining tools to facilitate the analysis of any given family of interest for the plant science community. An automated clustering pipeline ensures current information for future updates in the annotations of the two genomes and clustering improvements. The analysis allowed the first systematic identification of family and singlet proteins present in both organisms as well as those restricted to one of them. In addition, the established Web resources for mining these data provide a road map for future studies of the composition and structure of protein families between the two species.

  1. Automated Budget System -

    Data.gov (United States)

    Department of Transportation — The Automated Budget System (ABS) automates management and planning of the Mike Monroney Aeronautical Center (MMAC) budget by providing enhanced capability to plan,...

  2. Text mining for the biocuration workflow.

    Science.gov (United States)

    Hirschman, Lynette; Burns, Gully A P C; Krallinger, Martin; Arighi, Cecilia; Cohen, K Bretonnel; Valencia, Alfonso; Wu, Cathy H; Chatr-Aryamontri, Andrew; Dowell, Karen G; Huala, Eva; Lourenço, Anália; Nash, Robert; Veuthey, Anne-Lise; Wiegers, Thomas; Winter, Andrew G

    2012-01-01

    Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on 'Text Mining for the BioCuration Workflow' at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community.

  3. Optimized mine ventilation on demand (OMVOD)

    International Nuclear Information System (INIS)

    Anderson, M.

    2009-01-01

    This paper provided an overview of the Optimized Mine Ventilation on Demand (OMVOD) system that is being installed at Xstrata Nickel Rim South Project and at Vale Inco's Totten Mine in Sudbury. The OMVOD system is designed to dynamically monitor and control air quality and quantity in real time and dilute and remove hazardous substances including diesel particulate matter (DPM), carbon monoxide (CO) and nitrous oxide (NO 2 ). It is also designed to control the thermal environment and provide ventilation for humans as well as mobile equipment engine combustion according to regulatory standards. The paper highlighted the OMVOD system optimization of energy, air quality measurement and control and production management of the mines through real time dynamic automation. Topics of discussion included real-time tracking and monitoring of diesel equipment; real-time tracking of underground miners; real-time evaluation of mine ventilation networks; and real-time control and optimization of ventilation equipment. ABB and Simsmart Technologies have joined forces to provide underground mining customers with a ventilation optimization solution. Simsmart's OMVOD provides proven real time/dynamic automation technology to significantly reduce energy costs, provide health and safety benefits as well as major capital cost savings while realizing an increase in production.

  4. Automated Event Service: Efficient and Flexible Searching for Earth Science Phenomena Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Develop an Automated Event Service system that: Methodically mines custom-defined events in the reanalysis data sets of global atmospheric models. Enables...

  5. Automation 2017

    CERN Document Server

    Zieliński, Cezary; Kaliczyńska, Małgorzata

    2017-01-01

    This book consists of papers presented at Automation 2017, an international conference held in Warsaw from March 15 to 17, 2017. It discusses research findings associated with the concepts behind INDUSTRY 4.0, with a focus on offering a better understanding of and promoting participation in the Fourth Industrial Revolution. Each chapter presents a detailed analysis of a specific technical problem, in most cases followed by a numerical analysis, simulation and description of the results of implementing the solution in a real-world context. The theoretical results, practical solutions and guidelines presented are valuable for both researchers working in the area of engineering sciences and practitioners looking for solutions to industrial problems. .

  6. Marketing automation

    Directory of Open Access Journals (Sweden)

    TODOR Raluca Dania

    2017-01-01

    Full Text Available The automation of the marketing process seems to be nowadays, the only solution to face the major changes brought by the fast evolution of technology and the continuous increase in supply and demand. In order to achieve the desired marketing results, businessis have to employ digital marketing and communication services. These services are efficient and measurable thanks to the marketing technology used to track, score and implement each campaign. Due to the technical progress, the marketing fragmentation, demand for customized products and services on one side and the need to achieve constructive dialogue with the customers, immediate and flexible response and the necessity to measure the investments and the results on the other side, the classical marketing approached had changed continue to improve substantially.

  7. Application of Modern Tools and Techniques for Mine Safety & Disaster Management

    Science.gov (United States)

    Kumar, Dheeraj

    2016-04-01

    The implementation of novel systems and adoption of improvised equipment in mines help mining companies in two important ways: enhanced mine productivity and improved worker safety. There is a substantial need for adoption of state-of-the-art automation technologies in the mines to ensure the safety and to protect health of mine workers. With the advent of new autonomous equipment used in the mine, the inefficiencies are reduced by limiting human inconsistencies and error. The desired increase in productivity at a mine can sometimes be achieved by changing only a few simple variables. Significant developments have been made in the areas of surface and underground communication, robotics, smart sensors, tracking systems, mine gas monitoring systems and ground movements etc. Advancement in information technology in the form of internet, GIS, remote sensing, satellite communication, etc. have proved to be important tools for hazard reduction and disaster management. This paper is mainly focused on issues pertaining to mine safety and disaster management and some of the recent innovations in the mine automations that could be deployed in mines for safe mining operations and for avoiding any unforeseen mine disaster.

  8. Siemens' innovative role in mining technology

    Energy Technology Data Exchange (ETDEWEB)

    1990-07-01

    The growth of the mining industry in South Africa has played a decisive role in the industrial development of the country. As mining activities expanded, the need for energy production increased and as of late mining is becoming more mechanised and the need for more energy as well as automation is growing. The origins of Siemens operations in South Africa date back to the humble beginnings of the mining era, when the company provided the first generator and floodlights to illuminate the famous 'Big Hole' of the diamond mine at Kimberley as well as hydro-electric plants in 1895 on the Crocodile River and Blyde River respectively to supply the newly established mines in the Lydenburg district with electric power. 7 figs.

  9. Coal Mine Permit Boundaries

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — ESRI ArcView shapefile depicting New Mexico coal mines permitted under the Surface Mining Control and Reclamation Act of 1977 (SMCRA), by either the NM Mining these...

  10. Ghana Mining Journal

    African Journals Online (AJOL)

    ... in the Ghana mining journal: Geology and Mineral Exploration, Mining, Quarrying, Geomechanics, Groundwater Studies, Hydrocarbon Development, Mineral Processing, Metallurgy, Material Science, Mineral Management Policies, Mineral Economics, Environmental Aspects, Computer Applications and Mining Education.

  11. Exploration and Mining Roadmap

    Energy Technology Data Exchange (ETDEWEB)

    none,

    2002-09-01

    This Exploration and Mining Technology Roadmap represents the third roadmap for the Mining Industry of the Future. It is based upon the results of the Exploration and Mining Roadmap Workshop held May 10 ñ 11, 2001.

  12. Uranium mining in Australia

    International Nuclear Information System (INIS)

    Anon.

    1984-01-01

    The mining of uranium in Australia is criticised in relation to it's environmental impact, economics and effects on mine workers and Aborigines. A brief report is given on each of the operating and proposed uranium mines in Australia

  13. Papers of the CIM Toronto 2005 mining industry conference and exhibition : Mining rocks. Online ed.

    International Nuclear Information System (INIS)

    2005-01-01

    This conference highlighted technical innovations and best business practices within Canada's mining industry. It provided an opportunity for geologists, engineers and mine operators to exchange the latest information concerning innovations, challenges and discoveries in the mining industry in Canada and internationally. A session on mine management focused on underground mining operations, maintenance engineering, open-pit operations and geotechnical engineering. A session on current projects focused on the activities involved with developing properties from the exploration phase through to production. Mine economics, geology, mine design and management practices were highlighted along with technology and advanced systems, underground technologies, open-pit technologies, metallurgy, and developments in mineral processing. The presentations also addressed the issue of how to ensure the development of mineral resources so they continue to be integrally important to Canada's economic prosperity. Some of the challenges facing the industry include environmental, community, human resource and automation issues. The trade show allowed leading equipment and service providers to exhibit the latest tools and equipment driving mine production. The exhibition included technology that has contributed to environmental, geotechnical, production, maintenance and processing performance and safety. More than 43 technical papers were presented at the conference, of which 5 have been indexed separately for inclusion in this database. refs., tabs., figs

  14. MouseMine: a new data warehouse for MGI.

    Science.gov (United States)

    Motenko, H; Neuhauser, S B; O'Keefe, M; Richardson, J E

    2015-08-01

    MouseMine (www.mousemine.org) is a new data warehouse for accessing mouse data from Mouse Genome Informatics (MGI). Based on the InterMine software framework, MouseMine supports powerful query, reporting, and analysis capabilities, the ability to save and combine results from different queries, easy integration into larger workflows, and a comprehensive Web Services layer. Through MouseMine, users can access a significant portion of MGI data in new and useful ways. Importantly, MouseMine is also a member of a growing community of online data resources based on InterMine, including those established by other model organism databases. Adopting common interfaces and collaborating on data representation standards are critical to fostering cross-species data analysis. This paper presents a general introduction to MouseMine, presents examples of its use, and discusses the potential for further integration into the MGI interface.

  15. Sentinel Mining

    DEFF Research Database (Denmark)

    Middelfart, Morten

    for example notify users that revenue might drop within two months if an increase in customer problems combined with a decrease in website traffic is observed, whereas a multidimensional sentinel could warn users that revenue might drop within two months if an increase in customer complaints in USA (drilldown...... into geography dimension) combined with a decrease in the money invested in customer support for laptop computers (drilldown into product dimension) is observed. The work leading to this thesis progressed from algorithms for regular sentinel mining with only one source and one target measure, into algorithms...

  16. Mining royalties

    Directory of Open Access Journals (Sweden)

    Jelenković Rade J.

    2014-01-01

    Full Text Available Mineral resources are finite and nonrenewable in the sense that their extraction permanently depletes a country's resource inventory. The role of governments should be to manage the exploitation of these resources to maximize the economic benefits to their community, consistent with the need to attract and retain the exploration and development capital necessary to continue to realize these benefits for as long as possible. In designing mineral sector taxation systems, policy makers must carefully seek to balance tax types, rates, and incentives that satisfy the needs of both the nation and the mining investor.

  17. Wikipedia Mining

    Science.gov (United States)

    Nakayama, Kotaro; Ito, Masahiro; Erdmann, Maike; Shirakawa, Masumi; Michishita, Tomoyuki; Hara, Takahiro; Nishio, Shojiro

    Wikipedia, a collaborative Wiki-based encyclopedia, has become a huge phenomenon among Internet users. It covers a huge number of concepts of various fields such as arts, geography, history, science, sports and games. As a corpus for knowledge extraction, Wikipedia's impressive characteristics are not limited to the scale, but also include the dense link structure, URL based word sense disambiguation, and brief anchor texts. Because of these characteristics, Wikipedia has become a promising corpus and a new frontier for research. In the past few years, a considerable number of researches have been conducted in various areas such as semantic relatedness measurement, bilingual dictionary construction, and ontology construction. Extracting machine understandable knowledge from Wikipedia to enhance the intelligence on computational systems is the main goal of "Wikipedia Mining," a project on CREP (Challenge for Realizing Early Profits) in JSAI. In this paper, we take a comprehensive, panoramic view of Wikipedia Mining research and the current status of our challenge. After that, we will discuss about the future vision of this challenge.

  18. Both Automation and Paper.

    Science.gov (United States)

    Purcell, Royal

    1988-01-01

    Discusses the concept of a paperless society and the current situation in library automation. Various applications of automation and telecommunications are addressed, and future library automation is considered. Automation at the Monroe County Public Library in Bloomington, Indiana, is described as an example. (MES)

  19. Data processing in management of Dolni Rozinka uranium mines

    International Nuclear Information System (INIS)

    Benes, B.

    1987-01-01

    In 1985, a qualitative inovation was introduced of data processing by the commissioning of the EC 1026 computer with a terminal network and a remote data communication system. The design jobs which are being gradually implemented are mainly oriented to the creating of an automated information system for operative control of mining production, data preparation in mining plants, and to the personnel, wages, material consumptions, etc. areas. (J.B.)

  20. Soft measures and incremental gains in mines; Mesures douces et gains incrementaux : mines

    Energy Technology Data Exchange (ETDEWEB)

    Laliberte, P. [Natural Resources Canada, Ottawa, ON (Canada). CANMET Mining and Mineral Sciences Laboratories

    2008-07-01

    This paper presented a variety of measures that mine operators can adopt to save energy. Researchers at the CANMET Mining and Mineral Sciences Laboratories of Natural Resources Canada have conducted a joint study with Hydro-Quebec to investigate the impact of alternate energy technologies and control systems on energy savings. The impacts of a range of technologies were evaluated and rates of energy efficiency were compared. Technologies included hybrid vehicles; fuel cell-powered vehicles; automated ventilation control systems; heat recovery; compressed air; and electrical mining equipment. Energy profiles for various industrial applications were included. This paper also provided details of computerized simulations currently being conducted to estimate the potential incremental gains associated with the use of technology innovations in mining applications. 9 tabs., 3 figs.

  1. Frontiers of biomedical text mining: current progress

    Science.gov (United States)

    Zweigenbaum, Pierre; Demner-Fushman, Dina; Yu, Hong; Cohen, Kevin B.

    2008-01-01

    It is now almost 15 years since the publication of the first paper on text mining in the genomics domain, and decades since the first paper on text mining in the medical domain. Enormous progress has been made in the areas of information retrieval, evaluation methodologies and resource construction. Some problems, such as abbreviation-handling, can essentially be considered solved problems, and others, such as identification of gene mentions in text, seem likely to be solved soon. However, a number of problems at the frontiers of biomedical text mining continue to present interesting challenges and opportunities for great improvements and interesting research. In this article we review the current state of the art in biomedical text mining or ‘BioNLP’ in general, focusing primarily on papers published within the past year. PMID:17977867

  2. Genomic Testing

    Science.gov (United States)

    ... Events and Multimedia Implementation Genetics 101 Family Health History Genomics and Diseases Genetic Counseling Genomic Testing Epidemiology Pathogen Genomics Resources Genomic Testing Recommend on Facebook Tweet Share Compartir Fact Sheet: Identifying Opportunities to ...

  3. Comparative genomics using data mining tools

    Indian Academy of Sciences (India)

    ... multivariate data on the proteins of each organism in an effort to classify the proteins into clusters. Interestingly, we found that most of the proteins in each organism cluster closely together, but there are a few 'outliers'. We focus on the outliers for the functional investigations, which may aid in revealing any unique features ...

  4. Technology visions for mining at Syncrude

    Energy Technology Data Exchange (ETDEWEB)

    Fair, A.; Oxenford, J.; Coward, J.; Lipsett, M. [Syncrude Canada Ltd., Ft. McMurray, AB (Canada)

    1999-01-01

    Technological developments that will affect operations at Syncrude Canada`s oil sands mining operations in Alberta during the next decade or two are discussed. Three types of changes are anticipated: (1) improvements to current mining technology, (2) new technologies that will radically alter the way in which mining is conducted, and (3) platform changes that represent significant advances between these two extremes. New technologies in the first category include the move to larger and more efficient mobile equipment such as shovels and trucks, improved wear materials to extend component life and reduce maintenance costs, improved contracting strategies, organizational structures, and mine planning and reporting systems. In the breakthrough category (category 2), development of such technologies as shallow in-situ mining, improved use of automation, and the development of modular and relocatable oil sand mining and bitumen extraction facilities are the most likely. Changes expected in the platform technologies (category 3) include improved equipment condition monitoring and diagnostic systems and the associated sensors and embedded analysis systems, and a greatly expanded communications infrastructure for voice, data and video to allow company-wide real time access to the information generated by these systems. 9 refs., 2 tabs., 8 figs.

  5. Mining ergonomics

    Energy Technology Data Exchange (ETDEWEB)

    McPhee, B.

    2007-02-15

    Changes in work practices and a drive for greater productivity have introduced a range of emerging issues in ergonomics in mining. Some of the practices appear to be at odds with the need to improve general occupational health and safety. Longer shift lengths and fatigue, mental overload and underload, intermittent heavy physical work, reduced task variation, sedentary work in fixed postures and whole-body vibration all have risks for health and safety. The increasing age of some of the workforce is of concern. There appears to be a need to recognise these as potential causes of health problems. The article gives a review of these problems are reports on research findings. 36 refs., 3 figs.

  6. Data mining.

    Science.gov (United States)

    Cupples, L Adrienne; Bailey, Julia; Cartier, Kevin C; Falk, Catherine T; Liu, Kuang-Yu; Ye, Yuanqing; Yu, Robert; Zhang, Heping; Zhao, Hongyu

    2005-01-01

    Group 14 used data-mining strategies to evaluate a number of issues, including appropriate diagnosis, haplotype estimation, genetic linkage and association studies, and type I error. Methods ranged from exploratory analyses, to machine learning strategies (neural networks, supervised learning, and tree-based methods), to false discovery rate control of type I errors. The general motivations were to find the "story" in the data and to summarize information from a multitude of measures. Several methods illustrated strategies for better trait definition, using summarization of related traits. In the few studies that sought to identify genes for alcoholism, there was little agreement among the different strategies, likely reflecting the complexities of the disease. Nevertheless, Group 14 found that these methods offered strategies to gain a better understanding of the complex pathways by which disease develops.

  7. Uranium mining

    International Nuclear Information System (INIS)

    Cheeseman, E.W.

    1980-01-01

    The international uranium market appears to be currently over-supplied with a resultant softening in prices. Buyers on the international market are unhappy about some of the restrictions placed on sales by the government, and Canadian sales may suffer as a result. About 64 percent of Canada's shipments come from five operating Ontario mines, with the balance from Saskatchewan. Several other properties will be producing within the next few years. In spite of the adverse effects of the Three Mile Island incident and the default by the T.V.A. of their contract, some 3 600 tonnes of new uranium sales were completed during the year. The price for uranium had stabilized at US $42 - $44 by mid 1979, but by early 1980 had softened somewhat. The year 1979 saw the completion of major environmental hearings in Ontario and Newfoundland and the start of the B.C. inquiry. Two more hearings are scheduled for Saskatchewan in 1980. The Elliot Lake uranium mining expansion hearings are reviewed, as are other recent hearings. In the production of uranium for nuclear fuel cycle, environmental matters are of major concern to the industry, the public and to governments. Research is being conducted to determine the most effective method for removing radium from tailings area effluents. Very stringent criteria are being drawn up by the regulatory agencies that must be met by the industry in order to obtain an operating licence from the AECB. These criteria cover seepages from the tailings basin and through the tailings retention dam, seismic stability, and both short and long term management of the tailings waste management area. (auth)

  8. MetReS, an Efficient Database for Genomic Applications.

    Science.gov (United States)

    Vilaplana, Jordi; Alves, Rui; Solsona, Francesc; Mateo, Jordi; Teixidó, Ivan; Pifarré, Marc

    2018-02-01

    MetReS (Metabolic Reconstruction Server) is a genomic database that is shared between two software applications that address important biological problems. Biblio-MetReS is a data-mining tool that enables the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the processes of interest and their function. The main goal of this work was to identify the areas where the performance of the MetReS database performance could be improved and to test whether this improvement would scale to larger datasets and more complex types of analysis. The study was started with a relational database, MySQL, which is the current database server used by the applications. We also tested the performance of an alternative data-handling framework, Apache Hadoop. Hadoop is currently used for large-scale data processing. We found that this data handling framework is likely to greatly improve the efficiency of the MetReS applications as the dataset and the processing needs increase by several orders of magnitude, as expected to happen in the near future.

  9. Uses of antimicrobial genes from microbial genome

    Science.gov (United States)

    Sorek, Rotem; Rubin, Edward M.

    2013-08-20

    We describe a method for mining microbial genomes to discover antimicrobial genes and proteins having broad spectrum of activity. Also described are antimicrobial genes and their expression products from various microbial genomes that were found using this method. The products of such genes can be used as antimicrobial agents or as tools for molecular biology.

  10. Application for trackless mining technique in Benxi uranium mine

    International Nuclear Information System (INIS)

    Chen Bingguo

    1998-01-01

    The author narrates the circumstances achieving constructional target in Benxi Uranium Mine under relying on advance of science and technology and adopting small trackless mining equipment, presents the application of trackless mining equipment at mining small mine and complex mineral deposit and discusses the unique superiority of trackless mining technique in development work, mining preparation work and backstoping

  11. South African mining experience

    Energy Technology Data Exchange (ETDEWEB)

    Buck, J.D. (British Coal Corporation (UK). North Selby Mine)

    1992-09-01

    The article details the author's visit to South Africa on the 1990 Institution of Mining Electrical and Mining Mechanical Engineers Travelling Scholarship. The author undertook to visit to six coal mines (including two opencast mines and one rail loading terminal), four local engineering manufacturers, three power stations, three gold mines, two diamond mines (both in Botswana), a steel and vanadium works, the 1990 Mining Electra exhibition and the head offices of the Anglo American Corporation of South Africa. 4 figs., 2 tabs.

  12. Review of the application of ergonomics design of trackless mining equipment (TME) - lessons and challenges

    CSIR Research Space (South Africa)

    James, JP

    2007-06-01

    Full Text Available Despite increasing levels of trackless mining automation in South African mines, there is a distinct lack of design focus specific to the human operator tasked with driving machines for prolonged periods of the working shift. In many instances...

  13. The application of data mining to flow cytometry.

    Science.gov (United States)

    Nguyen, Andy N D

    2002-05-01

    Data mining is the process of automating information discovery to detect useful patterns, correlations, and trends. Existing data must be fitted into a representative model from which useful information can be derived through a variety of algorithms. The routine generation of vast amounts of data make flow cytometry a logical target for the application of data mining. This informative unit discusses the steps of the data-mining process using the immunophenotyping of hematologic neoplasms to demonstrate the application. The author describes several types of algorithms and provides a useful resource list of commercially available tools.

  14. Genome bioinformatics of tomato and potato

    NARCIS (Netherlands)

    Datema, E.

    2011-01-01

    In the past two decades genome sequencing has developed from a laborious and costly technology employed by large international consortia to a widely used, automated and affordable tool used worldwide by many individual research groups. Genome sequences of many food animals and crop plants have been

  15. Genome bioinformatics of tomato and potato

    NARCIS (Netherlands)

    Datema, E.

    2011-01-01

    In the past two decades genome sequencing has developed from a laborious and costly technology employed by large international consortia to a widely used, automated and affordable tool used worldwide by many individual research groups. Genome sequences of many food animals and crop plants have

  16. Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes

    Science.gov (United States)

    The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of high-quality gene structure annotations challenging. In response, we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here, we report the use of MAKER-...

  17. Data mining for ontology development.

    Energy Technology Data Exchange (ETDEWEB)

    Davidson, George S.; Strasburg, Jana (Pacific Northwest National Laboratory, Richland, WA); Stampf, David (Brookhaven National Laboratory, Upton, NY); Neymotin,Lev (Brookhaven National Laboratory, Upton, NY); Czajkowski, Carl (Brookhaven National Laboratory, Upton, NY); Shine, Eugene (Savannah River National Laboratory, Aiken, SC); Bollinger, James (Savannah River National Laboratory, Aiken, SC); Ghosh, Vinita (Brookhaven National Laboratory, Upton, NY); Sorokine, Alexandre (Oak Ridge National Laboratory, Oak Ridge, TN); Ferrell, Regina (Oak Ridge National Laboratory, Oak Ridge, TN); Ward, Richard (Oak Ridge National Laboratory, Oak Ridge, TN); Schoenwald, David Alan

    2010-06-01

    A multi-laboratory ontology construction effort during the summer and fall of 2009 prototyped an ontology for counterfeit semiconductor manufacturing. This effort included an ontology development team and an ontology validation methods team. Here the third team of the Ontology Project, the Data Analysis (DA) team reports on their approaches, the tools they used, and results for mining literature for terminology pertinent to counterfeit semiconductor manufacturing. A discussion of the value of ontology-based analysis is presented, with insights drawn from other ontology-based methods regularly used in the analysis of genomic experiments. Finally, suggestions for future work are offered.

  18. The application and implementation of optimized mine ventilation on demand (OMVOD) at the Xstrata Nickel Rim South Mine, Sudbury, Ontario

    International Nuclear Information System (INIS)

    Bartsch, E.; Laine, M.; Andersen, M.

    2010-01-01

    An Optimized Mine Ventilation on Demand (OMVOD) system has been installed at the Xstrata Nickel Rim South Mine in Sudbury. Developed by Simsmart Technologies, the OMVOD system monitors and controls air quality and quantity through real time dynamic automation. A ventilation on demand (VOD) system was needed to remove diesel particulate matter (DPM), carbon monoxide (CO) and nitrogen dioxide (NO 2 ). This paper described the real-time tracking and monitoring of the OMVOD system and optimization of ventilation equipment. Simsmart's OMVOD system was shown to reduce energy costs while improve air quality in the underground mine. 7 refs., 3 tabs., 8 figs.

  19. Autonomy and Automation

    Science.gov (United States)

    Shively, Jay

    2017-01-01

    A significant level of debate and confusion has surrounded the meaning of the terms autonomy and automation. Automation is a multi-dimensional concept, and we propose that Remotely Piloted Aircraft Systems (RPAS) automation should be described with reference to the specific system and task that has been automated, the context in which the automation functions, and other relevant dimensions. In this paper, we present definitions of automation, pilot in the loop, pilot on the loop and pilot out of the loop. We further propose that in future, the International Civil Aviation Organization (ICAO) RPAS Panel avoids the use of the terms autonomy and autonomous when referring to automated systems on board RPA. Work Group 7 proposes to develop, in consultation with other workgroups, a taxonomy of Levels of Automation for RPAS.

  20. An automated swimming respirometer

    DEFF Research Database (Denmark)

    STEFFENSEN, JF; JOHANSEN, K; BUSHNELL, PG

    1984-01-01

    An automated respirometer is described that can be used for computerized respirometry of trout and sharks.......An automated respirometer is described that can be used for computerized respirometry of trout and sharks....

  1. Configuration Management Automation (CMA) -

    Data.gov (United States)

    Department of Transportation — Configuration Management Automation (CMA) will provide an automated, integrated enterprise solution to support CM of FAA NAS and Non-NAS assets and investments. CMA...

  2. Mining with communities

    International Nuclear Information System (INIS)

    Veiga, Marcello M.; Scoble, Malcolm; McAllister, Mary Louise

    2001-01-01

    To be considered as sustainable, a mining community needs to adhere to the principles of ecological sustainability, economic vitality and social equity. These principles apply over a long time span, covering both the life of the mine and post-mining closure. The legacy left by a mine to the community after its closure is emerging as a significant aspect of its planning. Progress towards sustainability is made when value is added to a community with respect to these principles by the mining operation during its life cycle. This article presents a series of cases to demonstrate the diverse potential challenges to achieving a sustainable mining community. These case studies of both new and old mining communities are drawn mainly from Canada and from locations abroad where Canadian companies are now building mines. The article concludes by considering various approaches that can foster sustainable mining communities and the role of community consultation and capacity building. (author)

  3. Mission-Critical Mobile Broadband Communications in Open Pit Mines

    DEFF Research Database (Denmark)

    Uzeda Garcia, Luis Guilherme; Portela Lopes de Almeida, Erika; Barbosa, Viviane S. B.

    2016-01-01

    The need for continuous safety improvements and increased operational efficiency is driving the mining industry through a transition towards automated operations. From a communications perspective, this transition introduces a new set of high-bandwidth business- and mission-critical applications...

  4. A Simulator to Enhance Teaching and Learning of Mining Methods ...

    African Journals Online (AJOL)

    Audio visual education that incorporates devices and materials which involve sight, sound, or both has become a sine qua non in recent times in the teaching and learning process. An automated physical model of mining methods aided with video instructions was designed and constructed by harnessing locally available ...

  5. De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies.

    Science.gov (United States)

    Karamitros, Timokratis; Harrison, Ian; Piorkowska, Renata; Katzourakis, Aris; Magiorkinis, Gkikas; Mbisa, Jean Lutamyo

    2016-01-01

    Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging. To improve the assembly of HHV-1 genomes we have employed a hybrid genome assembly protocol using data from two sequencing technologies: the short-read Roche 454 and the long-read Oxford Nanopore MinION sequencers. We sequenced 18 HHV-1 cell culture-isolated clinical specimens collected from immunocompromised patients undergoing antiviral therapy. The susceptibility of the samples to several antivirals was determined by plaque reduction assay. Hybrid genome assembly resulted in a decrease in the number of contigs in 6 out of 7 samples and an increase in N(G)50 and N(G)75 of all 7 samples sequenced by both technologies. The approach also enhanced the detection of non-canonical contigs including a rearrangement between the unique (UL) and repeat (T/IRL) sequence regions of one sample that was not detectable by assembly of 454 reads alone. We detected several known and novel resistance-associated mutations in UL23 and UL30 genes. Genome-wide genetic variability ranged from genomes will be useful in determining genetic determinants of drug resistance, virulence, pathogenesis and viral evolution. The numerous, complex repeat regions of the HHV-1 genome currently remain a barrier towards this goal.

  6. Automation in College Libraries.

    Science.gov (United States)

    Werking, Richard Hume

    1991-01-01

    Reports the results of a survey of the "Bowdoin List" group of liberal arts colleges. The survey obtained information about (1) automation modules in place and when they had been installed; (2) financing of automation and its impacts on the library budgets; and (3) library director's views on library automation and the nature of the…

  7. ENCODE whole-genome data in the UCSC Genome Browser

    Science.gov (United States)

    Rosenbloom, Kate R.; Dreszer, Timothy R.; Pheasant, Michael; Barber, Galt P.; Meyer, Laurence R.; Pohl, Andy; Raney, Brian J.; Wang, Ting; Hinrichs, Angie S.; Zweig, Ann S.; Fujita, Pauline A.; Learned, Katrina; Rhead, Brooke; Smith, Kayla E.; Kuhn, Robert M.; Karolchik, Donna; Haussler, David; Kent, W. James

    2010-01-01

    The Encyclopedia of DNA Elements (ENCODE) project is an international consortium of investigators funded to analyze the human genome with the goal of producing a comprehensive catalog of functional elements. The ENCODE Data Coordination Center at The University of California, Santa Cruz (UCSC) is the primary repository for experimental results generated by ENCODE investigators. These results are captured in the UCSC Genome Bioinformatics database and download server for visualization and data mining via the UCSC Genome Browser and companion tools (Rhead et al. The UCSC Genome Browser Database: update 2010, in this issue). The ENCODE web portal at UCSC (http://encodeproject.org or http://genome.ucsc.edu/ENCODE) provides information about the ENCODE data and convenient links for access. PMID:19920125

  8. Locating previously unknown patterns in data-mining results: a dual data- and knowledge-mining method

    Directory of Open Access Journals (Sweden)

    Knaus William A

    2006-03-01

    Full Text Available Abstract Background Data mining can be utilized to automate analysis of substantial amounts of data produced in many organizations. However, data mining produces large numbers of rules and patterns, many of which are not useful. Existing methods for pruning uninteresting patterns have only begun to automate the knowledge acquisition step (which is required for subjective measures of interestingness, hence leaving a serious bottleneck. In this paper we propose a method for automatically acquiring knowledge to shorten the pattern list by locating the novel and interesting ones. Methods The dual-mining method is based on automatically comparing the strength of patterns mined from a database with the strength of equivalent patterns mined from a relevant knowledgebase. When these two estimates of pattern strength do not match, a high "surprise score" is assigned to the pattern, identifying the pattern as potentially interesting. The surprise score captures the degree of novelty or interestingness of the mined pattern. In addition, we show how to compute p values for each surprise score, thus filtering out noise and attaching statistical significance. Results We have implemented the dual-mining method using scripts written in Perl and R. We applied the method to a large patient database and a biomedical literature citation knowledgebase. The system estimated association scores for 50,000 patterns, composed of disease entities and lab results, by querying the database and the knowledgebase. It then computed the surprise scores by comparing the pairs of association scores. Finally, the system estimated statistical significance of the scores. Conclusion The dual-mining method eliminates more than 90% of patterns with strong associations, thus identifying them as uninteresting. We found that the pruning of patterns using the surprise score matched the biomedical evidence in the 100 cases that were examined by hand. The method automates the acquisition of

  9. Technological advances in telecommunications for mines

    Energy Technology Data Exchange (ETDEWEB)

    Waye, P.M.Y.; Yewen, R. [Mine Radio Systemic Inc., Stouffville, ON (Canada)

    2002-01-01

    As mines utilize more automation in mining operations to improve efficiency and safety, a corresponding increasing demand is placed on the transport of information. Some of the recent technological advances in underground telecommunications are described for various data, voice and video applications. In particular, two new innovative underground communication systems are described, one with highspeed data at 30 Mbps and the other for mine-wide evacuation and safety applications. The high-speed data system incorporates state-of-the-art data networking technologies and the existing leaky-cable, narrow-band radio channels. The new system provides over the same basic infrastructure - the highspeed data network at 30 Mbps TCP/IP Ethernet with 100 Base-T interconnection, plus 32 narrow-band radio channels. The second system is a system for mine-wide evacuation with 'through-the-earth' communication infrastructure. Emergency situations can be communicated to and from all the miners within seconds through a central control location. The technology involved does not require leaky cable or any other similar transmission media installation. Many applications are possible, including warning miners of emergency situations, mine rescue operation to communicate with trapped miners, and regular reporting from miners working alone.

  10. Contract Mining versus Owner Mining – The Way Forward | Suglo ...

    African Journals Online (AJOL)

    Ghana Mining Journal ... By contracting out one or more of their mining operations, the mining companies can concentrate on their core businesses. This paper reviews ... The general trends in the mining industry show that contract mining will be the way forward for most mines under various circumstances in the future.

  11. Optimization of mining design of Hongwei uranium mine

    International Nuclear Information System (INIS)

    Wu Sanmao; Yuan Baixiang

    2012-01-01

    Combined with the mining conditions of Hongwei uranium mine, optimization schemes for hoisting cage, mine drainge,ore transport, mine wastewater treatment, power-supply system,etc are put forward in the mining design of the mine. Optimized effects are analyzed from the aspects of technique, economy, and energy saving and reducing emissions. (authors)

  12. Automated Single Cell Data Decontamination Pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Tennessen, Kristin [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Pati, Amrita [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.

    2014-03-21

    Recent technological advancements in single-cell genomics have encouraged the classification and functional assessment of microorganisms from a wide span of the biospheres phylogeny.1,2 Environmental processes of interest to the DOE, such as bioremediation and carbon cycling, can be elucidated through the genomic lens of these unculturable microbes. However, contamination can occur at various stages of the single-cell sequencing process. Contaminated data can lead to wasted time and effort on meaningless analyses, inaccurate or erroneous conclusions, and pollution of public databases. A fully automated decontamination tool is necessary to prevent these instances and increase the throughput of the single-cell sequencing process

  13. Automation in Clinical Microbiology

    Science.gov (United States)

    Ledeboer, Nathan A.

    2013-01-01

    Historically, the trend toward automation in clinical pathology laboratories has largely bypassed the clinical microbiology laboratory. In this article, we review the historical impediments to automation in the microbiology laboratory and offer insight into the reasons why we believe that we are on the cusp of a dramatic change that will sweep a wave of automation into clinical microbiology laboratories. We review the currently available specimen-processing instruments as well as the total laboratory automation solutions. Lastly, we outline the types of studies that will need to be performed to fully assess the benefits of automation in microbiology laboratories. PMID:23515547

  14. Automation of industrial bioprocesses.

    Science.gov (United States)

    Beyeler, W; DaPra, E; Schneider, K

    2000-01-01

    The dramatic development of new electronic devices within the last 25 years has had a substantial influence on the control and automation of industrial bioprocesses. Within this short period of time the method of controlling industrial bioprocesses has changed completely. In this paper, the authors will use a practical approach focusing on the industrial applications of automation systems. From the early attempts to use computers for the automation of biotechnological processes up to the modern process automation systems some milestones are highlighted. Special attention is given to the influence of Standards and Guidelines on the development of automation systems.

  15. Text mining for the biocuration workflow

    Science.gov (United States)

    Hirschman, Lynette; Burns, Gully A. P. C; Krallinger, Martin; Arighi, Cecilia; Cohen, K. Bretonnel; Valencia, Alfonso; Wu, Cathy H.; Chatr-Aryamontri, Andrew; Dowell, Karen G.; Huala, Eva; Lourenço, Anália; Nash, Robert; Veuthey, Anne-Lise; Wiegers, Thomas; Winter, Andrew G.

    2012-01-01

    Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on ‘Text Mining for the BioCuration Workflow’ at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community. PMID:22513129

  16. Mines and Mineral Resources

    Data.gov (United States)

    Department of Homeland Security — Mines in the United States According to the Homeland Security Infrastructure Program Tiger Team Report Table E-2.V.1 Sub-Layer Geographic Names, a mine is defined as...

  17. Uranium mining in Australia

    International Nuclear Information System (INIS)

    Anon.

    1980-01-01

    Known uranium deposits and the companies involved in uranium mining and exploration in Australia are listed. The status of the development of the deposits is outlined and reasons for delays to mining are given

  18. Mining Ostrava '93

    International Nuclear Information System (INIS)

    1993-04-01

    Part I of the Proceedings contains 55 contributions, out of which 2 deal with environmental impacts of undermining during coal mining, and of shocks and vibrations during underground coal mining. (Z.S.)

  19. Mining in El Salvador

    DEFF Research Database (Denmark)

    Pacheco Cueva, Vladimir

    2014-01-01

    In this guest article, Vladimir Pacheco, a social scientist who has worked on mining and human rights shares his perspectives on a current campaign against mining in El Salvador – Central America’s smallest but most densely populated country.......In this guest article, Vladimir Pacheco, a social scientist who has worked on mining and human rights shares his perspectives on a current campaign against mining in El Salvador – Central America’s smallest but most densely populated country....

  20. MONITORING OF MINING

    Directory of Open Access Journals (Sweden)

    Berislav Šebečić

    1996-12-01

    Full Text Available The way mining was monitored in the past depended on knowledge, interest and the existing legal regulations. Documentary evidence about this work can be found in archives, libraries and museums. In particular, there is the rich archival material (papers and books concerning the work of the one-time Imperial and Royal Mining Captaincies in Zagreb, Zadar, Klagenfurt and Split, A minor part of the documentation has not yet been transferred to Croatia. From mining handbooks and books we can also find out about mining in Croatia. In the context of Austro-Hungary. For example, we can find out that the first governorships in Zagreb and Zadar headed the Ban, Count Jelacic and Baron Mamula were also the top mining authorities, though this, probably from political motives, was suppressed in the guides and inventories or the Mining Captaincies. At the end of the 1850s, Croatia produced 92-94% of sea salt, up to 8.5% of sulphur, 19.5% of asphalt and 100% of oil for the Austro-Hungarian empire. From data about mining in the Split Mining Captaincy, prepared for the Philadephia Exhibition, it can be seen that in the exploratory mining operations in which there were 33,372 independent mines declared in 1925 they were looking mainly for bauxite (60,0%, then dark coal (19,0%, asphalts (10.3% and lignites (62%. In 1931, within the area covered by the same captaincy, of 74 declared mines, only 9 were working. There were five coal mines, three bauxite mines and one for asphalt. I suggest that within state institution, the Mining Captaincy or Authority be renewed, or that a Mining and Geological Authority be set ap, which would lead to the more complete affirmation of Croatian mining (the paper is published in Croatian.

  1. Mine drainage treatment

    OpenAIRE

    Golomeova, Mirjana; Zendelska, Afrodita; Krstev, Boris; Golomeov, Blagoj; Krstev, Aleksandar

    2012-01-01

    Water flowing from underground and surface mines and contains high concentrations of dissolved metals is called mine drainage. Mine drainage can be categorized into several basic types by their alkalinity or acidity. Sulfide rich and carbonate poor materials are expected to produce acidic drainage, and alkaline rich materials, even with significant sulfide concentrations, often produce net alkaline water. Mine drainages are dangerous because pollutants may decompose in the environment. In...

  2. The mining methods at the Fraisse mine

    International Nuclear Information System (INIS)

    Heurley, P.; Vervialle, J.P.

    1985-01-01

    The Fraisse mine is one of the four underground mines of the La Crouzille mining divisions of Cogema. Faced with the necessity to mechanize its workings, this mine also had to satisfy a certain number of stringent demands. This has led to concept of four different mining methods for the four workings at present in active operation at this pit, which nevertheless preserve the basic ideas of the methods of top slicing under concrete slabs (TSS) or horizontal cut-and-fill stopes (CFS). An electric scooptram is utilized. With this type of vehicle the stringent demands for the introduction of means for fire fighting and prevention are reduced to a minimum. Finally, the dimensions of the vehicles and the operation of these methods result in a net-to-gross tonnages of close to 1, i.e. a maximum output, combined with a minimum of contamination [fr

  3. National Underground Mines Inventory

    Science.gov (United States)

    1983-10-01

    washing facilities near the mine entrance at ground level. Telephones and/or radio phones are generally placed throughout mines for communication...023 0206001 04 000 0206002 04 000 0206003 04 000 ARKANSAS LIMESTONE OPERATION 0300051 05 065 261360 GUION MINE AND MILL 0300313 05 065 254100 EL DORADO

  4. Data Mining for CRM

    Science.gov (United States)

    Thearling, Kurt

    Data Mining technology allows marketing organizations to better understand their customers and respond to their needs. This chapter describes how Data Mining can be combined with customer relationship management to help drive improved interactions with customers. An example showing how to use Data Mining to drive customer acquisition activities is presented.

  5. Mined-out land

    International Nuclear Information System (INIS)

    Reinsalu, Enno; Toomik, Arvi; Valgma, Ingo

    2002-01-01

    Estonian mineral resources are deposited in low depth and mining fields are large, therefore vast areas are affected by mining. There are at least 800 deposits with total area of 6,000 km 2 and about the same number of underground mines, surface mines, peat fields, quarries, and sand and gravel pits. The deposits cover more than 10% of Estonian mainland. The total area of operating mine claims exceeds 150 km 2 that makes 0.3 % of Estonian area. The book is written mainly for the people who are living or acting in the area influenced by mining. The observations and research could benefit those who are interested in geography and environment, who follow formation and look of mined-out landscapes. The book contains also warnings for careless people on and under the surface of the mined-out land. Part of the book contains results of the research made in 1968-1993 by the first two authors working at the Estonian branch of A.Skochinsky Institute of Mining. Since 1990, Arvi Toomik continued this study at the Northeastern section of the Institute of Ecology of Tallinn Pedagogical University. Enno Reinsalu studied aftereffects of mining at the Mining Department of Tallinn Technical University from 1998 to 2000. Geographical Information System for Mining was studied by Ingo Valgma within his doctoral dissertation, and this book is one of the applications of his study

  6. Mine waste management

    International Nuclear Information System (INIS)

    Hutchinson, I.P.G.; Ellison, R.D.

    1992-01-01

    This book reports on mine waste management. Topics covered include: Performance review of modern mine waste management units; Mine waste management requirements; Prediction of acid generation potential; Attenuation of chemical constituents; Climatic considerations; Liner system design; Closure requirements; Heap leaching; Ground water monitoring; and Economic impact evaluation

  7. Mining and the Environment

    International Development Research Centre (IDRC) Digital Library (Canada)

    These include technology-policy initiatives for education and innovation incentives for garimpo mining, as well as the adaptation of mining legislation to ...... in this area: it has had several significant international projects (participating in the development of mining projects in Venezuela, Argentina, Colombia, and Ecuador).

  8. Mountaintop mining consequences

    Science.gov (United States)

    M.A. Palmer; E.S. Bernhardt; W.H. Schlesinger; K.N. Eshleman; E. Foufoula-Georgiou; M.S. Hendryx; A.D. Lemly; G.E. Likens; O.L. Loucks; M.E. Power; P.S. White; P.R. Wilcock

    2010-01-01

    There has been a global, 30-year increase in surface mining (1), which is now the dominant driver of land-use change in the central Appalachian ecoregion of the United States (2). One major form of such mining, mountaintop mining with valley fills (MTM/VF) (3), is widespread throughout eastern Kentucky, West Virginia (WV), and southwestern Virginia. Upper elevation...

  9. Ghana Mining Journal: Contact

    African Journals Online (AJOL)

    Principal Contact. Professor Daniel Mireku-Gyimah Editor-in-Chief University of Mines & Technology Ghana Mining Journal University of Mines & Technology P. O. BOX 237 Tarkwa Ghana Phone: +233 362 20280/20324. Fax: +233 362 20306. Email: dm.gyimah@umat.edu.gh ...

  10. De Novo Assembly of Human Herpes Virus Type 1 (HHV-1 Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies.

    Directory of Open Access Journals (Sweden)

    Timokratis Karamitros

    Full Text Available Human herpesvirus type 1 (HHV-1 has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging. To improve the assembly of HHV-1 genomes we have employed a hybrid genome assembly protocol using data from two sequencing technologies: the short-read Roche 454 and the long-read Oxford Nanopore MinION sequencers. We sequenced 18 HHV-1 cell culture-isolated clinical specimens collected from immunocompromised patients undergoing antiviral therapy. The susceptibility of the samples to several antivirals was determined by plaque reduction assay. Hybrid genome assembly resulted in a decrease in the number of contigs in 6 out of 7 samples and an increase in N(G50 and N(G75 of all 7 samples sequenced by both technologies. The approach also enhanced the detection of non-canonical contigs including a rearrangement between the unique (UL and repeat (T/IRL sequence regions of one sample that was not detectable by assembly of 454 reads alone. We detected several known and novel resistance-associated mutations in UL23 and UL30 genes. Genome-wide genetic variability ranged from <1% to 53% of amino acids in each gene exhibiting at least one substitution within the pool of samples. The UL23 gene had one of the highest genetic variabilities at 35.2% in keeping with its role in development of drug resistance. The assembly of accurate, full-length HHV-1 genomes will be useful in determining genetic determinants of drug resistance, virulence, pathogenesis and viral evolution. The numerous, complex repeat regions of the HHV-1 genome currently remain a barrier towards this goal.

  11. A MINE alternative to D-optimal designs for the linear model.

    Directory of Open Access Journals (Sweden)

    Amanda M Bouffier

    Full Text Available Doing large-scale genomics experiments can be expensive, and so experimenters want to get the most information out of each experiment. To this end the Maximally Informative Next Experiment (MINE criterion for experimental design was developed. Here we explore this idea in a simplified context, the linear model. Four variations of the MINE method for the linear model were created: MINE-like, MINE, MINE with random orthonormal basis, and MINE with random rotation. Each method varies in how it maximizes the MINE criterion. Theorem 1 establishes sufficient conditions for the maximization of the MINE criterion under the linear model. Theorem 2 establishes when the MINE criterion is equivalent to the classic design criterion of D-optimality. By simulation under the linear model, we establish that the MINE with random orthonormal basis and MINE with random rotation are faster to discover the true linear relation with p regression coefficients and n observations when p>>n. We also establish in simulations with n<100, p=1000, σ=0.01 and 1000 replicates that these two variations of MINE also display a lower false positive rate than the MINE-like method and additionally, for a majority of the experiments, for the MINE method.

  12. Advances in Computer, Communication, Control and Automation

    CERN Document Server

    011 International Conference on Computer, Communication, Control and Automation

    2012-01-01

    The volume includes a set of selected papers extended and revised from the 2011 International Conference on Computer, Communication, Control and Automation (3CA 2011). 2011 International Conference on Computer, Communication, Control and Automation (3CA 2011) has been held in Zhuhai, China, November 19-20, 2011. This volume  topics covered include signal and Image processing, speech and audio Processing, video processing and analysis, artificial intelligence, computing and intelligent systems, machine learning, sensor and neural networks, knowledge discovery and data mining, fuzzy mathematics and Applications, knowledge-based systems, hybrid systems modeling and design, risk analysis and management, system modeling and simulation. We hope that researchers, graduate students and other interested readers benefit scientifically from the proceedings and also find it stimulating in the process.

  13. Mining planing introduction

    International Nuclear Information System (INIS)

    Toledo, R.D.

    1985-01-01

    Basic concepts concerning mining parameters, plan establishment and typical procedure methods applied throughout the physical execution of mining operations are here determined, analyzed and discussed. Technological and economic aspects of the exploration phase are presented as well as general mathematical and statistical methods for estimating, analyzing and representing mineral deposits which are virtually essential for good mining project execution. The characterization of important mineral substances and the basic parameters of mining works are emphasized in conjunction with long, medium and short term mining planning. Finally, geological modelling, ore reserves calculations and final economic evaluations are considered using a hypothetical example in order to consolidate the main elaborated ideas. (D.J.M.) [pt

  14. Recent advances in remote coal mining machine sensing, guidance, and teleoperation

    Energy Technology Data Exchange (ETDEWEB)

    Ralston, J.C.; Hainsworth, D.W.; Reid, D.C.; Anderson, D.L.; McPhee, R.J. [CSIRO Exploration & Minerals, Kenmore, Qld. (Australia)

    2001-10-01

    Some recent applications of sensing, guidance and telerobotic technology in the coal mining industry are presented. Of special interest is the development of semi or fully autonomous systems to provide remote guidance and communications for coal mining equipment. The use of radar and inertial based sensors are considered in an attempt to solve the horizontal and lateral guidance problems associated with mining equipment automation. Also described is a novel teleoperated robot vehicle with unique communications capabilities, called the Numbat, which is used in underground mine safety and reconnaissance missions.

  15. Data mining in radiology

    International Nuclear Information System (INIS)

    Kharat, Amit T; Singh, Amarjit; Kulkarni, Vilas M; Shah, Digish

    2014-01-01

    Data mining facilitates the study of radiology data in various dimensions. It converts large patient image and text datasets into useful information that helps in improving patient care and provides informative reports. Data mining technology analyzes data within the Radiology Information System and Hospital Information System using specialized software which assesses relationships and agreement in available information. By using similar data analysis tools, radiologists can make informed decisions and predict the future outcome of a particular imaging finding. Data, information and knowledge are the components of data mining. Classes, Clusters, Associations, Sequential patterns, Classification, Prediction and Decision tree are the various types of data mining. Data mining has the potential to make delivery of health care affordable and ensure that the best imaging practices are followed. It is a tool for academic research. Data mining is considered to be ethically neutral, however concerns regarding privacy and legality exists which need to be addressed to ensure success of data mining

  16. Radiation monitoring in mining

    International Nuclear Information System (INIS)

    Shalaev, I.L.; Komodov, A.A.; Lebedev, Yu.A.; Lutsenko, K.S.; Pavlov, I.V.; Pashchenko, L.P.; Ryabov, N.V.; Saltykov, L.D.; Shishkin, V.I.

    1980-01-01

    The tasks and organization of radiation monitoring under the conditions of the uranium mines are considered. Main radiation hazard in uranium mines represent contamination of mine atmosphere with short - living daughter products of radon decay (DRP), external γ-irradiation of personnel and concentrations of long-living α-emitters in mine atmosphere. The following interconnected tasks of radiation monitoring under the mine conditions are pointed out: environmental radiation monitoring at enterprises, personnel monitoring and counting estimation of environmental radiation at the enterprise and determination of necessary measures to decrease the personnel irradiation levels. Organization of monitoring of mine atmosphere contamination and individual DRP intake, monitoring of parameters affecting the environmental radiation monitoring of external γ-irradiation and contamination of mine atmosphere with long-living radioactive aerosols are considered in detail. The problem of radiation monitoring data registration and representation is studied [ru

  17. Automation systems for radioimmunoassay

    International Nuclear Information System (INIS)

    Yamasaki, Paul

    1974-01-01

    The application of automation systems for radioimmunoassay (RIA) was discussed. Automated systems could be useful in the second step, of the four basic processes in the course of RIA, i.e., preparation of sample for reaction. There were two types of instrumentation, a semi-automatic pipete, and a fully automated pipete station, both providing for fast and accurate dispensing of the reagent or for the diluting of sample with reagent. Illustrations of the instruments were shown. (Mukohata, S.)

  18. Automated stopcock actuator

    OpenAIRE

    Vandehey, N. T.; O\\'Neil, J. P.

    2015-01-01

    Introduction We have developed a low-cost stopcock valve actuator for radiochemistry automation built using a stepper motor and an Arduino, an open-source single-board microcontroller. The con-troller hardware can be programmed to run by serial communication or via two 5–24 V digital lines for simple integration into any automation control system. This valve actuator allows for automated use of a single, disposable stopcock, providing a number of advantages over stopcock manifold systems ...

  19. Automated Analysis of Accountability

    DEFF Research Database (Denmark)

    Bruni, Alessandro; Giustolisi, Rosario; Schürmann, Carsten

    2017-01-01

    that are amenable to automated verification. Our definitions are general enough to be applied to different classes of protocols and different automated security verification tools. Furthermore, we point out formally the relation between verifiability and accountability. We validate our definitions...... with the automatic verification of three protocols: a secure exam protocol, Google’s Certificate Transparency, and an improved version of Bingo Voting. We find through automated verification that all three protocols satisfy verifiability while only the first two protocols meet accountability....

  20. Application of text mining in the biomedical domain.

    Science.gov (United States)

    Fleuren, Wilco W M; Alkema, Wynand

    2015-03-01

    In recent years the amount of experimental data that is produced in biomedical research and the number of papers that are being published in this field have grown rapidly. In order to keep up to date with developments in their field of interest and to interpret the outcome of experiments in light of all available literature, researchers turn more and more to the use of automated literature mining. As a consequence, text mining tools have evolved considerably in number and quality and nowadays can be used to address a variety of research questions ranging from de novo drug target discovery to enhanced biological interpretation of the results from high throughput experiments. In this paper we introduce the most important techniques that are used for a text mining and give an overview of the text mining tools that are currently being used and the type of problems they are typically applied for. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Management Planning for Workplace Automation.

    Science.gov (United States)

    McDole, Thomas L.

    Several factors must be considered when implementing office automation. Included among these are whether or not to automate at all, the effects of automation on employees, requirements imposed by automation on the physical environment, effects of automation on the total organization, and effects on clientele. The reasons behind the success or…

  2. Laboratory Automation and Middleware.

    Science.gov (United States)

    Riben, Michael

    2015-06-01

    The practice of surgical pathology is under constant pressure to deliver the highest quality of service, reduce errors, increase throughput, and decrease turnaround time while at the same time dealing with an aging workforce, increasing financial constraints, and economic uncertainty. Although not able to implement total laboratory automation, great progress continues to be made in workstation automation in all areas of the pathology laboratory. This report highlights the benefits and challenges of pathology automation, reviews middleware and its use to facilitate automation, and reviews the progress so far in the anatomic pathology laboratory. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Automated cloning methods.; TOPICAL

    International Nuclear Information System (INIS)

    Collart, F.

    2001-01-01

    Argonne has developed a series of automated protocols to generate bacterial expression clones by using a robotic system designed to be used in procedures associated with molecular biology. The system provides plate storage, temperature control from 4 to 37 C at various locations, and Biomek and Multimek pipetting stations. The automated system consists of a robot that transports sources from the active station on the automation system. Protocols for the automated generation of bacterial expression clones can be grouped into three categories (Figure 1). Fragment generation protocols are initiated on day one of the expression cloning procedure and encompass those protocols involved in generating purified coding region (PCR)

  4. Economics of mine water treatment

    OpenAIRE

    Dvořáček, Jaroslav; Vidlář, Jiří; Štěrba, Jiří; Heviánková, Silvie; Vaněk, Michal; Barták, Pavel

    2012-01-01

    Mine water poses a significant problem in lignite coal mining. The drainage of mine water is the fundamental prerequisite of mining operations. Under the legislation of the Czech Republic, mine water that discharges into surface watercourse is subject to the permission of the state administration body in the water management sector. The permission also stipulates the limits for mine water pollution. Therefore, mine water has to be purified prior to discharge. Although all...

  5. Complacency and Automation Bias in the Use of Imperfect Automation.

    Science.gov (United States)

    Wickens, Christopher D; Clegg, Benjamin A; Vieane, Alex Z; Sebok, Angelia L

    2015-08-01

    We examine the effects of two different kinds of decision-aiding automation errors on human-automation interaction (HAI), occurring at the first failure following repeated exposure to correctly functioning automation. The two errors are incorrect advice, triggering the automation bias, and missing advice, reflecting complacency. Contrasts between analogous automation errors in alerting systems, rather than decision aiding, have revealed that alerting false alarms are more problematic to HAI than alerting misses are. Prior research in decision aiding, although contrasting the two aiding errors (incorrect vs. missing), has confounded error expectancy. Participants performed an environmental process control simulation with and without decision aiding. For those with the aid, automation dependence was created through several trials of perfect aiding performance, and an unexpected automation error was then imposed in which automation was either gone (one group) or wrong (a second group). A control group received no automation support. The correct aid supported faster and more accurate diagnosis and lower workload. The aid failure degraded all three variables, but "automation wrong" had a much greater effect on accuracy, reflecting the automation bias, than did "automation gone," reflecting the impact of complacency. Some complacency was manifested for automation gone, by a longer latency and more modest reduction in accuracy. Automation wrong, creating the automation bias, appears to be a more problematic form of automation error than automation gone, reflecting complacency. Decision-aiding automation should indicate its lower degree of confidence in uncertain environments to avoid the automation bias. © 2015, Human Factors and Ergonomics Society.

  6. Automated recognition of malignancy mentions in biomedical literature

    Directory of Open Access Journals (Sweden)

    Liberman Mark Y

    2006-11-01

    Full Text Available Abstract Background The rapid proliferation of biomedical text makes it increasingly difficult for researchers to identify, synthesize, and utilize developed knowledge in their fields of interest. Automated information extraction procedures can assist in the acquisition and management of this knowledge. Previous efforts in biomedical text mining have focused primarily upon named entity recognition of well-defined molecular objects such as genes, but less work has been performed to identify disease-related objects and concepts. Furthermore, promise has been tempered by an inability to efficiently scale approaches in ways that minimize manual efforts and still perform with high accuracy. Here, we have applied a machine-learning approach previously successful for identifying molecular entities to a disease concept to determine if the underlying probabilistic model effectively generalizes to unrelated concepts with minimal manual intervention for model retraining. Results We developed a named entity recognizer (MTag, an entity tagger for recognizing clinical descriptions of malignancy presented in text. The application uses the machine-learning technique Conditional Random Fields with additional domain-specific features. MTag was tested with 1,010 training and 432 evaluation documents pertaining to cancer genomics. Overall, our experiments resulted in 0.85 precision, 0.83 recall, and 0.84 F-measure on the evaluation set. Compared with a baseline system using string matching of text with a neoplasm term list, MTag performed with a much higher recall rate (92.1% vs. 42.1% recall and demonstrated the ability to learn new patterns. Application of MTag to all MEDLINE abstracts yielded the identification of 580,002 unique and 9,153,340 overall mentions of malignancy. Significantly, addition of an extensive lexicon of malignancy mentions as a feature set for extraction had minimal impact in performance. Conclusion Together, these results suggest that the

  7. Automated recognition of malignancy mentions in biomedical literature.

    Science.gov (United States)

    Jin, Yang; McDonald, Ryan T; Lerman, Kevin; Mandel, Mark A; Carroll, Steven; Liberman, Mark Y; Pereira, Fernando C; Winters, Raymond S; White, Peter S

    2006-11-07

    The rapid proliferation of biomedical text makes it increasingly difficult for researchers to identify, synthesize, and utilize developed knowledge in their fields of interest. Automated information extraction procedures can assist in the acquisition and management of this knowledge. Previous efforts in biomedical text mining have focused primarily upon named entity recognition of well-defined molecular objects such as genes, but less work has been performed to identify disease-related objects and concepts. Furthermore, promise has been tempered by an inability to efficiently scale approaches in ways that minimize manual efforts and still perform with high accuracy. Here, we have applied a machine-learning approach previously successful for identifying molecular entities to a disease concept to determine if the underlying probabilistic model effectively generalizes to unrelated concepts with minimal manual intervention for model retraining. We developed a named entity recognizer (MTag), an entity tagger for recognizing clinical descriptions of malignancy presented in text. The application uses the machine-learning technique Conditional Random Fields with additional domain-specific features. MTag was tested with 1,010 training and 432 evaluation documents pertaining to cancer genomics. Overall, our experiments resulted in 0.85 precision, 0.83 recall, and 0.84 F-measure on the evaluation set. Compared with a baseline system using string matching of text with a neoplasm term list, MTag performed with a much higher recall rate (92.1% vs. 42.1% recall) and demonstrated the ability to learn new patterns. Application of MTag to all MEDLINE abstracts yielded the identification of 580,002 unique and 9,153,340 overall mentions of malignancy. Significantly, addition of an extensive lexicon of malignancy mentions as a feature set for extraction had minimal impact in performance. Together, these results suggest that the identification of disparate biomedical entity classes in

  8. Genome Modeling System: A Knowledge Management Platform for Genomics.

    Directory of Open Access Journals (Sweden)

    Malachi Griffith

    2015-07-01

    Full Text Available In this work, we present the Genome Modeling System (GMS, an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395 and matched lymphoblastoid line (HCC1395BL. These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms.

  9. Pig genome sequence - analysis and publication strategy

    DEFF Research Database (Denmark)

    Archibald, Alan L.; Bolund, Lars; Churcher, Carol

    2010-01-01

    BACKGROUND: The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing. RESULTS: Assemblies...... of the BAC clone derived genome sequence have been annotated using the Pre-Ensembl and Ensembl automated pipelines and made accessible through the Pre-Ensembl/Ensembl browsers. The current annotated genome assembly (Sscrofa9) was released with Ensembl 56 in September 2009. A revised assembly (Sscrofa10......) is under construction and will incorporate whole genome shotgun sequence (WGS) data providing > 30x genome coverage. The WGS sequence, most of which comprise short Illumina/Solexa reads, were generated from DNA from the same single Duroc sow as the source of the BAC library from which clones were...

  10. Data mining, mining data : energy consumption modelling

    Energy Technology Data Exchange (ETDEWEB)

    Dessureault, S. [Arizona Univ., Tucson, AZ (United States)

    2007-09-15

    Most modern mining operations are accumulating large amounts of data on production and business processes. Data, however, provides value only if it can be translated into information that appropriate users can utilize. This paper emphasized that a new technological focus should emerge, notably how to concentrate data into information; analyze information sufficiently to become knowledge; and, act on that knowledge. Researchers at the Mining Information Systems and Operations Management (MISOM) laboratory at the University of Arizona have created a method to transform data into action. The data-to-action approach was exercised in the development of an energy consumption model (ECM), in partnership with a major US-based copper mining company, 2 software companies, and the MISOM laboratory. The approach begins by integrating several key data sources using data warehousing techniques, and increasing the existing level of integration and data cleaning. An online analytical processing (OLAP) cube was also created to investigate the data and identify a subset of several million records. Data mining algorithms were applied using the information that was isolated by the OLAP cube. The data mining results showed that traditional cost drivers of energy consumption are poor predictors. A comparison was made between traditional methods of predicting energy consumption and the prediction formed using data mining. Traditionally, in the mines for which data were available, monthly averages of tons and distance are used to predict diesel fuel consumption. However, this article showed that new information technology can be used to incorporate many more variables into the budgeting process, resulting in more accurate predictions. The ECM helped mine planners improve the prediction of energy use through more data integration, measure development, and workflow analysis. 5 refs., 11 figs.

  11. REPARATION : ribosome profiling assisted (re-)annotation of bacterial genomes

    OpenAIRE

    Ndah, Elvis; Jonckheere, Veronique; Giess, Adam; Valen, Eivind; Menschaert, Gerben; Van Damme, Petra

    2017-01-01

    Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated methods depend heavily on sequence composition and often underestimate the complexity of the proteome. We developed RibosomeE Profiling Assisted (re-)AnnotaTION (REPARATION), a de novo machine learning algorithm that takes advantage of experimental protein synthesis evidence from ribosome profiling (Ribo-seq) to delineate...

  12. REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes

    OpenAIRE

    Ndah, Elvis; Jonckheere, Veronique; Giess, Adam; Valen, Eivind; Menschaert, Gerben; Van Damme, Petra

    2017-01-01

    Abstract Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated methods depend heavily on sequence composition and often underestimate the complexity of the proteome. We developed RibosomeE Profiling Assisted (re-)AnnotaTION (REPARATION), a de novo machine learning algorithm that takes advantage of experimental protein synthesis evidence from ribosome profiling (Ribo-seq) to ...

  13. Automated System Marketplace 1994.

    Science.gov (United States)

    Griffiths, Jose-Marie; Kertis, Kimberly

    1994-01-01

    Reports results of the 1994 Automated System Marketplace survey based on responses from 60 vendors. Highlights include changes in the library automation marketplace; estimated library systems revenues; minicomputer and microcomputer-based systems; marketplace trends; global markets and mergers; research needs; new purchase processes; and profiles…

  14. Automation benefits BWR customers

    International Nuclear Information System (INIS)

    Anon.

    1982-01-01

    A description is given of the increasing use of automation at General Electric's Wilmington fuel fabrication plant. Computerised systems and automated equipment perform a large number of inspections, inventory and process operations, and new advanced systems are being continuously introduced to reduce operator errors and expand product reliability margins. (U.K.)

  15. Automate functional testing

    Directory of Open Access Journals (Sweden)

    Ramesh Kalindri

    2014-06-01

    Full Text Available Currently, software engineers are increasingly turning to the option of automating functional tests, but not always have successful in this endeavor. Reasons range from low planning until over cost in the process. Some principles that can guide teams in automating these tests are described in this article.

  16. Automation in Warehouse Development

    NARCIS (Netherlands)

    Hamberg, R.; Verriet, J.

    2012-01-01

    The warehouses of the future will come in a variety of forms, but with a few common ingredients. Firstly, human operational handling of items in warehouses is increasingly being replaced by automated item handling. Extended warehouse automation counteracts the scarcity of human operators and

  17. Identity Management Processes Automation

    Directory of Open Access Journals (Sweden)

    A. Y. Lavrukhin

    2010-03-01

    Full Text Available Implementation of identity management systems consists of two main parts, consulting and automation. The consulting part includes development of a role model and identity management processes description. The automation part is based on the results of consulting part. This article describes the most important aspects of IdM implementation.

  18. Work and Programmable Automation.

    Science.gov (United States)

    DeVore, Paul W.

    A new industrial era based on electronics and the microprocessor has arrived, an era that is being called intelligent automation. Intelligent automation, in the form of robots, replaces workers, and the new products, using microelectronic devices, require significantly less labor to produce than the goods they replace. The microprocessor thus…

  19. Library Automation in Pakistan.

    Science.gov (United States)

    Haider, Syed Jalaluddin

    1998-01-01

    Examines the state of library automation in Pakistan. Discusses early developments; financial support by the Netherlands Library Development Project (Pakistan); lack of automated systems in college/university and public libraries; usage by specialist libraries; efforts by private-sector libraries and the National Library in Pakistan; commonly used…

  20. Library Automation Style Guide.

    Science.gov (United States)

    Gaylord Bros., Liverpool, NY.

    This library automation style guide lists specific terms and names often used in the library automation industry. The terms and/or acronyms are listed alphabetically and each is followed by a brief definition. The guide refers to the "Chicago Manual of Style" for general rules, and a notes section is included for the convenience of individual…

  1. Planning for Office Automation.

    Science.gov (United States)

    Sherron, Gene T.

    1982-01-01

    The steps taken toward office automation by the University of Maryland are described. Office automation is defined and some types of word processing systems are described. Policies developed in the writing of a campus plan are listed, followed by a section on procedures adopted to implement the plan. (Author/MLW)

  2. The Automated Office.

    Science.gov (United States)

    Naclerio, Nick

    1979-01-01

    Clerical personnel may be able to climb career ladders as a result of office automation and expanded job opportunities in the word processing area. Suggests opportunities in an automated office system and lists books and periodicals on word processing for counselors and teachers. (MF)

  3. Automating the Small Library.

    Science.gov (United States)

    Skapura, Robert

    1987-01-01

    Discusses the use of microcomputers for automating school libraries, both for entire systems and for specific library tasks. Highlights include available library management software, newsletters that evaluate software, constructing an evaluation matrix, steps to consider in library automation, and a brief discussion of computerized card catalogs.…

  4. Coal mine site reclamation

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2013-02-15

    Coal mine sites can have significant effects on local environments. In addition to the physical disruption of land forms and ecosystems, mining can also leave behind a legacy of secondary detrimental effects due to leaching of acid and trace elements from discarded materials. This report looks at the remediation of both deep mine and opencast mine sites, covering reclamation methods, back-filling issues, drainage and restoration. Examples of national variations in the applicable legislation and in the definition of rehabilitation are compared. Ultimately, mine site rehabilitation should return sites to conditions where land forms, soils, hydrology, and flora and fauna are self-sustaining and compatible with surrounding land uses. Case studies are given to show what can be achieved and how some landscapes can actually be improved as a result of mining activity.

  5. Gold-Mining

    DEFF Research Database (Denmark)

    Raaballe, J.; Grundy, B.D.

    2002-01-01

    of operating gold mines. Asymmetric information on the reserves in the mine implies that, at a high enough price of gold, the manager of high type finds the extraction value of the company to be higher than the current market value of the non-operating gold mine. Due to this under valuation the maxim of market...... value maximization forces the manager of high type to extract the gold.The implications are three-fold. First, all managers (except the lowest type) extract the gold too soon compared to the first-best policy of leaving the gold in the mine forever. Second, a manager of high type extracts the gold......  Based on standard option pricing arguments and assumptions (including no convenience yield and sustainable property rights), we will not observe operating gold mines. We find that asymmetric information on the reserves in the gold mine is a necessary and sufficient condition for the existence...

  6. Advances in inspection automation

    Science.gov (United States)

    Weber, Walter H.; Mair, H. Douglas; Jansen, Dion; Lombardi, Luciano

    2013-01-01

    This new session at QNDE reflects the growing interest in inspection automation. Our paper describes a newly developed platform that makes the complex NDE automation possible without the need for software programmers. Inspection tasks that are tedious, error-prone or impossible for humans to perform can now be automated using a form of drag and drop visual scripting. Our work attempts to rectify the problem that NDE is not keeping pace with the rest of factory automation. Outside of NDE, robots routinely and autonomously machine parts, assemble components, weld structures and report progress to corporate databases. By contrast, components arriving in the NDT department typically require manual part handling, calibrations and analysis. The automation examples in this paper cover the development of robotic thickness gauging and the use of adaptive contour following on the NRU reactor inspection at Chalk River.

  7. Automated model building

    CERN Document Server

    Caferra, Ricardo; Peltier, Nicholas

    2004-01-01

    This is the first book on automated model building, a discipline of automated deduction that is of growing importance Although models and their construction are important per se, automated model building has appeared as a natural enrichment of automated deduction, especially in the attempt to capture the human way of reasoning The book provides an historical overview of the field of automated deduction, and presents the foundations of different existing approaches to model construction, in particular those developed by the authors Finite and infinite model building techniques are presented The main emphasis is on calculi-based methods, and relevant practical results are provided The book is of interest to researchers and graduate students in computer science, computational logic and artificial intelligence It can also be used as a textbook in advanced undergraduate courses

  8. Automation in Warehouse Development

    CERN Document Server

    Verriet, Jacques

    2012-01-01

    The warehouses of the future will come in a variety of forms, but with a few common ingredients. Firstly, human operational handling of items in warehouses is increasingly being replaced by automated item handling. Extended warehouse automation counteracts the scarcity of human operators and supports the quality of picking processes. Secondly, the development of models to simulate and analyse warehouse designs and their components facilitates the challenging task of developing warehouses that take into account each customer’s individual requirements and logistic processes. Automation in Warehouse Development addresses both types of automation from the innovative perspective of applied science. In particular, it describes the outcomes of the Falcon project, a joint endeavour by a consortium of industrial and academic partners. The results include a model-based approach to automate warehouse control design, analysis models for warehouse design, concepts for robotic item handling and computer vision, and auton...

  9. Automation in Immunohematology

    Directory of Open Access Journals (Sweden)

    Meenu Bajpai

    2012-01-01

    Full Text Available There have been rapid technological advances in blood banking in South Asian region over the past decade with an increasing emphasis on quality and safety of blood products. The conventional test tube technique has given way to newer techniques such as column agglutination technique, solid phase red cell adherence assay, and erythrocyte-magnetized technique. These new technologies are adaptable to automation and major manufacturers in this field have come up with semi and fully automated equipments for immunohematology tests in the blood bank. Automation improves the objectivity and reproducibility of tests. It reduces human errors in patient identification and transcription errors. Documentation and traceability of tests, reagents and processes and archiving of results is another major advantage of automation. Shifting from manual methods to automation is a major undertaking for any transfusion service to provide quality patient care with lesser turnaround time for their ever increasing workload. This article discusses the various issues involved in the process.

  10. Uranium mining in Saskatchewan

    International Nuclear Information System (INIS)

    Scales, M.

    2006-01-01

    The mines of northern Saskatchewan make Canada the worlds leading uranium producer in Canada supplied 29% of global demand, or 11.60 million tonnes of the metal in 2004. Here are two bright ideas - how to mine an orebody by neither pit nor underground method, and how to mine high-grade ore without miners - that Cogema and Cameco are pursuing in the Athabasca Basin

  11. A mine of energy

    International Nuclear Information System (INIS)

    Fallon, M.

    1982-01-01

    In July 1978 the then Union Corporation (which is a wholly-owned Subsidiary of the larger Gencor Group) announced its intention to develop Beisa mine in the Orange Free State. They started up a medium sized uranium mine with gold as a by-product. The main idea was for the processing of uranium. The planning of the uranium recovery plant, the actual mining, and the recovery and extraction of uranium are discussed

  12. Novel mining methods

    CSIR Research Space (South Africa)

    Monchusi, B

    2012-10-01

    Full Text Available Biennial Conference Presented by: Dr. Bessie Monchusi Date: 10 October 2012 Background ? CSIR 2012 Slide 2 Conglomerate - Carbon Leader Reef Au Contents ? Fundamental Earth Science Research ? Applied Collaborative Research ? CSIR 2012 Slide 3... Question? ? How do we change our mining processes to mine the 50cm reefs efficiently, economically and safely? ? CSIR 2012 Slide 4 ? CSIR 2012 Slide 5 Vision: Autonomous Mining Systems ? Rock breaking ? Rock removal ? Support ? Environmental...

  13. Implementation of paste backfill mining technology in Chinese coal mines.

    Science.gov (United States)

    Chang, Qingliang; Chen, Jianhang; Zhou, Huaqiang; Bai, Jianbiao

    2014-01-01

    Implementation of clean mining technology at coal mines is crucial to protect the environment and maintain balance among energy resources, consumption, and ecology. After reviewing present coal clean mining technology, we introduce the technology principles and technological process of paste backfill mining in coal mines and discuss the components and features of backfill materials, the constitution of the backfill system, and the backfill process. Specific implementation of this technology and its application are analyzed for paste backfill mining in Daizhuang Coal Mine; a practical implementation shows that paste backfill mining can improve the safety and excavation rate of coal mining, which can effectively resolve surface subsidence problems caused by underground mining activities, by utilizing solid waste such as coal gangues as a resource. Therefore, paste backfill mining is an effective clean coal mining technology, which has widespread application.

  14. Implementation of Paste Backfill Mining Technology in Chinese Coal Mines

    Directory of Open Access Journals (Sweden)

    Qingliang Chang

    2014-01-01

    Full Text Available Implementation of clean mining technology at coal mines is crucial to protect the environment and maintain balance among energy resources, consumption, and ecology. After reviewing present coal clean mining technology, we introduce the technology principles and technological process of paste backfill mining in coal mines and discuss the components and features of backfill materials, the constitution of the backfill system, and the backfill process. Specific implementation of this technology and its application are analyzed for paste backfill mining in Daizhuang Coal Mine; a practical implementation shows that paste backfill mining can improve the safety and excavation rate of coal mining, which can effectively resolve surface subsidence problems caused by underground mining activities, by utilizing solid waste such as coal gangues as a resource. Therefore, paste backfill mining is an effective clean coal mining technology, which has widespread application.

  15. Treatment of mine-water from decommissioning uranium mines

    International Nuclear Information System (INIS)

    Fan Quanhui

    2002-01-01

    Treatment methods for mine-water from decommissioning uranium mines are introduced and classified. The suggestions on optimal treatment methods are presented as a matter of experience with decommissioned Chenzhou Uranium Mine

  16. Implementation of Paste Backfill Mining Technology in Chinese Coal Mines

    Science.gov (United States)

    Chang, Qingliang; Zhou, Huaqiang; Bai, Jianbiao

    2014-01-01

    Implementation of clean mining technology at coal mines is crucial to protect the environment and maintain balance among energy resources, consumption, and ecology. After reviewing present coal clean mining technology, we introduce the technology principles and technological process of paste backfill mining in coal mines and discuss the components and features of backfill materials, the constitution of the backfill system, and the backfill process. Specific implementation of this technology and its application are analyzed for paste backfill mining in Daizhuang Coal Mine; a practical implementation shows that paste backfill mining can improve the safety and excavation rate of coal mining, which can effectively resolve surface subsidence problems caused by underground mining activities, by utilizing solid waste such as coal gangues as a resource. Therefore, paste backfill mining is an effective clean coal mining technology, which has widespread application. PMID:25258737

  17. Mine ventilation engineering

    Energy Technology Data Exchange (ETDEWEB)

    Hall, C.J.

    1981-01-01

    This book on mine ventilation covers psychometrics, airflow through roadways and ducts, natural ventilation, fans, instruments, ventilation surveys, auxiliary ventilation, air quality, and planning and economics.

  18. Uranium mining and milling

    International Nuclear Information System (INIS)

    Floeter, W.

    1976-01-01

    In this report uranium mining and milling are reviewed. The fuel cycle, different types of uranium geological deposits, blending of ores, open cast and underground mining, the mining cost and radiation protection in mines are treated in the first part of this report. In the second part, the milling of uranium ores is treated, including process technology, acid and alkaline leaching, process design for physical and chemical treatment of the ores, and the cost. Each chapter is clarified by added figures, diagrams, tables, and flowsheets. (HK) [de

  19. Mining and processing of uranium ores in the USSR

    International Nuclear Information System (INIS)

    Laskorin, B.N.; Mamilov, V.A.; Korejsho, Yu.A.

    1983-01-01

    Experience gained in uranium ore mining by modern methods in combination with underground and heap leaching is summarized. More intensive processing of low-grade ores has been achieved through the use of autoclave leaching, sorptive treatment of thick pulps, extractive separation of pure uranium compounds, automated continuous sorption devices of high efficiency for processing the underground- and heap-leaching liquors, natural and mine water, and recovery of molybdenum, vanadium, scandium, rare earths and phosphate fertilizers from low-grade ores. Production of ion-exchangers and extractants has been developed and processes for concomitant recovery of copper, gold, ionium, tungsten, caesium, zirconium, tantalum, nickel and cobalt have been designed. (author)

  20. Data mining approach to model the diagnostic service management.

    Science.gov (United States)

    Lee, Sun-Mi; Lee, Ae-Kyung; Park, Il-Su

    2006-01-01

    Korea has National Health Insurance Program operated by the government-owned National Health Insurance Corporation, and diagnostic services are provided every two year for the insured and their family members. Developing a customer relationship management (CRM) system using data mining technology would be useful to improve the performance of diagnostic service programs. Under these circumstances, this study developed a model for diagnostic service management taking into account the characteristics of subjects using a data mining approach. This study could be further used to develop an automated CRM system contributing to the increase in the rate of receiving diagnostic services.

  1. Assessment of reliability and efficiency of mining coal seams located above or below extracted coal seams with support coal pillars. [USSR

    Energy Technology Data Exchange (ETDEWEB)

    Batmanov, Yu.K.; Bakhtin, A.F.; Bulavka, E.I.

    1981-04-01

    Mining thin (under 1.1 m) coal seams located above or below extracted thicker coal seams in which coal support pillars were left is one of the ways of increasing coal output without major investment in Donbass coal mines. It is planned that by 1985 25 thin coal seams will be mined in the Donbass. Investigations show that mining thin coal seams with gradients up to 12 degrees by a system of raise faces without leaving coal pillars is economical using mining systems available at present. This mining scheme is economical also in the case of coal seams located in zones of geologic dislocations. Using integrated mining systems (coal cutter, powered supports and face conveyor) in this coal seams would reduce mining cost from 0.2 to 0.3 rubles/t. Using automated integrated mining systems is economical in working faces with coal output exceeding 900 t/d. (3 refs.) (In Russian)

  2. Mining machinery - bigger and better

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2009-07-15

    The article describes the latest mining equipment available to meet the global demand for coal from some major manufacture - Atlas Copco, Caterpillar Global Mining, Joy Mining Machinery, Liebherr Great Britain Ltd., Longwall Associates and Sandvik. 6 photos.

  3. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines when...

  4. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  5. Systematic review automation technologies

    Science.gov (United States)

    2014-01-01

    Systematic reviews, a cornerstone of evidence-based medicine, are not produced quickly enough to support clinical practice. The cost of production, availability of the requisite expertise and timeliness are often quoted as major contributors for the delay. This detailed survey of the state of the art of information systems designed to support or automate individual tasks in the systematic review, and in particular systematic reviews of randomized controlled clinical trials, reveals trends that see the convergence of several parallel research projects. We surveyed literature describing informatics systems that support or automate the processes of systematic review or each of the tasks of the systematic review. Several projects focus on automating, simplifying and/or streamlining specific tasks of the systematic review. Some tasks are already fully automated while others are still largely manual. In this review, we describe each task and the effect that its automation would have on the entire systematic review process, summarize the existing information system support for each task, and highlight where further research is needed for realizing automation for the task. Integration of the systems that automate systematic review tasks may lead to a revised systematic review workflow. We envisage the optimized workflow will lead to system in which each systematic review is described as a computer program that automatically retrieves relevant trials, appraises them, extracts and synthesizes data, evaluates the risk of bias, performs meta-analysis calculations, and produces a report in real time. PMID:25005128

  6. On-Site School Library Automation: Automation Anywhere with Laptops.

    Science.gov (United States)

    Gunn, Holly; Oxner, June

    2000-01-01

    Four years after the Halifax Regional School Board was formed through amalgamation, over 75% of its school libraries were automated. On-site automation with laptops was a quicker, more efficient way of automating than sending a shelf list to the Technical Services Department. The Eastern Shore School Library Automation Project was a successful…

  7. Developing image processing meta-algorithms with data mining of multiple metrics.

    Science.gov (United States)

    Leung, Kelvin; Cunha, Alexandre; Toga, A W; Parker, D Stott

    2014-01-01

    People often use multiple metrics in image processing, but here we take a novel approach of mining the values of batteries of metrics on image processing results. We present a case for extending image processing methods to incorporate automated mining of multiple image metric values. Here by a metric we mean any image similarity or distance measure, and in this paper we consider intensity-based and statistical image measures and focus on registration as an image processing problem. We show how it is possible to develop meta-algorithms that evaluate different image processing results with a number of different metrics and mine the results in an automated fashion so as to select the best results. We show that the mining of multiple metrics offers a variety of potential benefits for many image processing problems, including improved robustness and validation.

  8. Perspectives on genome mapping and marker-assisted breeding of ...

    African Journals Online (AJOL)

    The second one would be to have access to a whole genome sequence so that candidate genes in a fine mapping interval delimited by flanking markers could be mined, reannotated and then analysed in association mapping. A fully public draft of the E. grandis genome will be sequenced by the US Department of Energy ...

  9. Physics Mining of Multi-Source Data Sets

    Science.gov (United States)

    Helly, John; Karimabadi, Homa; Sipes, Tamara

    2012-01-01

    Powerful new parallel data mining algorithms can produce diagnostic and prognostic numerical models and analyses from observational data. These techniques yield higher-resolution measures than ever before of environmental parameters by fusing synoptic imagery and time-series measurements. These techniques are general and relevant to observational data, including raster, vector, and scalar, and can be applied in all Earth- and environmental science domains. Because they can be highly automated and are parallel, they scale to large spatial domains and are well suited to change and gap detection. This makes it possible to analyze spatial and temporal gaps in information, and facilitates within-mission replanning to optimize the allocation of observational resources. The basis of the innovation is the extension of a recently developed set of algorithms packaged into MineTool to multi-variate time-series data. MineTool is unique in that it automates the various steps of the data mining process, thus making it amenable to autonomous analysis of large data sets. Unlike techniques such as Artificial Neural Nets, which yield a blackbox solution, MineTool's outcome is always an analytical model in parametric form that expresses the output in terms of the input variables. This has the advantage that the derived equation can then be used to gain insight into the physical relevance and relative importance of the parameters and coefficients in the model. This is referred to as physics-mining of data. The capabilities of MineTool are extended to include both supervised and unsupervised algorithms, handle multi-type data sets, and parallelize it.

  10. Automated electron microprobe

    International Nuclear Information System (INIS)

    Thompson, K.A.; Walker, L.R.

    1986-01-01

    The Plant Laboratory at the Oak Ridge Y-12 Plant has recently obtained a Cameca MBX electron microprobe with a Tracor Northern TN5500 automation system. This allows full stage and spectrometer automation and digital beam control. The capabilities of the system include qualitative and quantitative elemental microanalysis for all elements above and including boron in atomic number, high- and low-magnification imaging and processing, elemental mapping and enhancement, and particle size, shape, and composition analyses. Very low magnification, quantitative elemental mapping using stage control (which is of particular interest) has been accomplished along with automated size, shape, and composition analysis over a large relative area

  11. Operational proof of automation

    International Nuclear Information System (INIS)

    Jaerschky, R.; Reifenhaeuser, R.; Schlicht, K.

    1976-01-01

    Automation of the power plant process may imply quite a number of problems. The automation of dynamic operations requires complicated programmes often interfering in several branched areas. This reduces clarity for the operating and maintenance staff, whilst increasing the possibilities of errors. The synthesis and the organization of standardized equipment have proved very successful. The possibilities offered by this kind of automation for improving the operation of power plants will only sufficiently and correctly be turned to profit, however, if the application of these technics of equipment is further improved and if its volume is tallied with a definite etc. (orig.) [de

  12. Chef infrastructure automation cookbook

    CERN Document Server

    Marschall, Matthias

    2013-01-01

    Chef Infrastructure Automation Cookbook contains practical recipes on everything you will need to automate your infrastructure using Chef. The book is packed with illustrated code examples to automate your server and cloud infrastructure.The book first shows you the simplest way to achieve a certain task. Then it explains every step in detail, so that you can build your knowledge about how things work. Eventually, the book shows you additional things to consider for each approach. That way, you can learn step-by-step and build profound knowledge on how to go about your configuration management

  13. A Recommendation Algorithm for Automating Corollary Order Generation

    Science.gov (United States)

    Klann, Jeffrey; Schadow, Gunther; McCoy, JM

    2009-01-01

    Manual development and maintenance of decision support content is time-consuming and expensive. We explore recommendation algorithms, e-commerce data-mining tools that use collective order history to suggest purchases, to assist with this. In particular, previous work shows corollary order suggestions are amenable to automated data-mining techniques. Here, an item-based collaborative filtering algorithm augmented with association rule interestingness measures mined suggestions from 866,445 orders made in an inpatient hospital in 2007, generating 584 potential corollary orders. Our expert physician panel evaluated the top 92 and agreed 75.3% were clinically meaningful. Also, at least one felt 47.9% would be directly relevant in guideline development. This automated generation of a rough-cut of corollary orders confirms prior indications about automated tools in building decision support content. It is an important step toward computerized augmentation to decision support development, which could increase development efficiency and content quality while automatically capturing local standards. PMID:20351875

  14. Northeast Church Rock Mine

    Science.gov (United States)

    Northeast Church Rock Mine, a former uranium mine 17 miles northeast of Gallup, NM in the Pinedale Chapter of the Navajo Nation. EPA is working with NNEPA to oversee cleanup work by United Nuclear Corporation, a company owned by General Electric (GE).

  15. Underground Coal Mining

    Science.gov (United States)

    Hill, G. M.

    1980-01-01

    Computer program models coal-mining production, equipment failure and equipment repair. Underground mine is represented as collection of work stations requiring service by production and repair crews alternately. Model projects equipment availability and productivity, and indicates proper balance of labor and equipment. Program is in FORTRAN IV for batch execution; it has been implemented on UNIVAC 1108.

  16. Ghana - Mining and Development

    OpenAIRE

    P.C. Mohan

    2004-01-01

    The objectives of the project ($9.37 million, 1996-2001) were to (a) enhance the capacity of the mining sector institutions to carry out their functions of encouraging and regulating investments in the mining sector in an environmentally sound manner and (b) support the use of techniques and mechanisms that will improve productivity, financial viability and reduce the environmental impact of ...

  17. Minería de textos: la nueva generación de análisis de literatura científica en biología molecular y genómica Text-mining: the new generation of scientific literature analysis in molecular biology and genomics

    Directory of Open Access Journals (Sweden)

    Carmen Gálvez

    2008-01-01

    Full Text Available Una vez descifrado la secuencia del genoma humano, el paradigma de investigación ha cambiado dando paso a la descripción de las funciones de los genes y a futuros avances en la lucha contra enfermedades. Este nuevo contexto ha despertado el interés de la Bioinformática, que combina métodos de las Ciencias de la Vida con las Ciencias de la Información haciendo posible el acceso a la gran cantidad de información biológica almacenada en las bases de datos, y de la Genómica, dedicada al estudio de las interacciones de los genes y su influencia en el desarrollo de enfermedades. En este contexto, la minería de textos surge como un instrumento emergente para el análisis de la literatura científica. Una tarea habitual de la minería de textos en Biología Molecular y Genómica es el reconocimiento de entidades biológicas, tales como genes, proteínas y enfermedades. El paso siguiente en el proceso de minería lo constituye la dentificación entre entidades biológicas, tales como el tipo de interacción entre gen-gen, gen-enfermedad, gen-proteína, para interpretar funciones biológicas, o formular hipótesis de investigación. El objetivo de este trabajo es examinar el auge y las limitaciones la nueva generación de herramientas de análisis de la información en lenguaje natural, almacenada en bases de datos bibliográficas, como PubMed o MEDLINE.Since human genome sequences were first decoded, the paradigm of investigation has changed leading to the description of the functions of the genes and to future advances in the fight against diseases. This new context has awoke the interest of the Bioinformatics, that combines methods of the Life Science with the Information Sciences, making the access to the great quantity of biological information stored in the databases, and of the Genomics, dedicated to the study of the interactions of the genes and its influence in the development of diseases. In this context, the text mining arises like an

  18. A mine abutment

    Energy Technology Data Exchange (ETDEWEB)

    Ardashev, K.A.; Borisovets, V.A.; Kozel, A.M.

    1983-01-01

    The purpose of the invention is to increase the service life of the abutment between a mine shaft and near shaft drifts by eliminating the irregularity of the near shaft rock massif. The stated purpose is achieved by the fact that in the mine abutment, which includes a mine shaft and near shaft chambers, the mine shaft is made within the near shaft chambers with an expansion and is equipped with a cylindrical shell installed in its widened part with an inside cross section equal to the cross section of the shaft which with the shaft forms a cavity for positioning the near shaft chambers. Moreover, the mine shaft in the expansion zone may be made in the form of a cone in its upper part and in the form of a cylinder in its lower part.

  19. Text Mining for Protein Docking.

    Directory of Open Access Journals (Sweden)

    Varsha D Badal

    2015-12-01

    Full Text Available The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structures transformed structure prediction of proteins and protein complexes. Instead of exploring the enormous search space, predictive tools can simply proceed to the solution based on similarity to the existing, previously determined structures. A similar major paradigm shift is emerging due to the rapidly expanding amount of information, other than experimentally determined structures, which still can be used as constraints in biomolecular structure prediction. Automated text mining has been widely used in recreating protein interaction networks, as well as in detecting small ligand binding sites on protein structures. Combining and expanding these two well-developed areas of research, we applied the text mining to structural modeling of protein-protein complexes (protein docking. Protein docking can be significantly improved when constraints on the docking mode are available. We developed a procedure that retrieves published abstracts on a specific protein-protein interaction and extracts information relevant to docking. The procedure was assessed on protein complexes from Dockground (http://dockground.compbio.ku.edu. The results show that correct information on binding residues can be extracted for about half of the complexes. The amount of irrelevant information was reduced by conceptual analysis of a subset of the retrieved abstracts, based on the bag-of-words (features approach. Support Vector Machine models were trained and validated on the subset. The remaining abstracts were filtered by the best-performing models, which decreased the irrelevant information for ~ 25% complexes in the dataset. The extracted constraints were incorporated in the docking protocol and tested on the Dockground unbound

  20. Mobile robot competition. Underground mining: A challenging application in mobile robotics

    CSIR Research Space (South Africa)

    Green, J

    2011-09-01

    Full Text Available an expanding market. Keywords- mining robots; robot competition; academic competitions; ROBMECH 2011 I. INTRODUCTION Competitions form a valuable tool for academic institutions in directing their research and scholarly endeavours. They provide clear.... Technology forms a significant portion of this vision, and automation and remote control comprises one of three focus areas. The end goal is a mine where intelligent autonomous robots are standard and intelligent machines perform the activities...

  1. Statistical data analytics foundations for data mining, informatics, and knowledge discovery

    CERN Document Server

    Piegorsch, Walter W

    2015-01-01

      A comprehensive introduction to statistical methods for data mining and knowledge discovery.Applications of data mining and 'big data' increasingly take center stage in our modern, knowledge-driven society, supported by advances in computing power, automated data acquisition, social media development and interactive, linkable internet software.  This book presents a coherent, technical introduction to modern statistical learning and analytics, starting from the core foundations of statistics and probability. It includes an overview of probability and statistical distributions, basic

  2. Automation Interface Design Development

    Data.gov (United States)

    National Aeronautics and Space Administration — Our research makes its contributions at two levels. At one level, we addressed the problems of interaction between humans and computers/automation in a particular...

  3. Automated Vehicles Symposium 2014

    CERN Document Server

    Beiker, Sven; Road Vehicle Automation 2

    2015-01-01

    This paper collection is the second volume of the LNMOB series on Road Vehicle Automation. The book contains a comprehensive review of current technical, socio-economic, and legal perspectives written by experts coming from public authorities, companies and universities in the U.S., Europe and Japan. It originates from the Automated Vehicle Symposium 2014, which was jointly organized by the Association for Unmanned Vehicle Systems International (AUVSI) and the Transportation Research Board (TRB) in Burlingame, CA, in July 2014. The contributions discuss the challenges arising from the integration of highly automated and self-driving vehicles into the transportation system, with a focus on human factors and different deployment scenarios. This book is an indispensable source of information for academic researchers, industrial engineers, and policy makers interested in the topic of road vehicle automation.

  4. Fixed automated spray technology.

    Science.gov (United States)

    2011-04-19

    This research project evaluated the construction and performance of Boschungs Fixed Automated : Spray Technology (FAST) system. The FAST system automatically sprays de-icing material on : the bridge when icing conditions are about to occur. The FA...

  5. Automated Vehicles Symposium 2015

    CERN Document Server

    Beiker, Sven

    2016-01-01

    This edited book comprises papers about the impacts, benefits and challenges of connected and automated cars. It is the third volume of the LNMOB series dealing with Road Vehicle Automation. The book comprises contributions from researchers, industry practitioners and policy makers, covering perspectives from the U.S., Europe and Japan. It is based on the Automated Vehicles Symposium 2015 which was jointly organized by the Association of Unmanned Vehicle Systems International (AUVSI) and the Transportation Research Board (TRB) in Ann Arbor, Michigan, in July 2015. The topical spectrum includes, but is not limited to, public sector activities, human factors, ethical and business aspects, energy and technological perspectives, vehicle systems and transportation infrastructure. This book is an indispensable source of information for academic researchers, industrial engineers and policy makers interested in the topic of road vehicle automation.

  6. Automation synthesis modules review

    International Nuclear Information System (INIS)

    Boschi, S.; Lodi, F.; Malizia, C.; Cicoria, G.; Marengo, M.

    2013-01-01

    The introduction of 68 Ga labelled tracers has changed the diagnostic approach to neuroendocrine tumours and the availability of a reliable, long-lived 68 Ge/ 68 Ga generator has been at the bases of the development of 68 Ga radiopharmacy. The huge increase in clinical demand, the impact of regulatory issues and a careful radioprotection of the operators have boosted for extensive automation of the production process. The development of automated systems for 68 Ga radiochemistry, different engineering and software strategies and post-processing of the eluate were discussed along with impact of automation with regulations. - Highlights: ► Generators availability and robust chemistry boosted for the huge diffusion of 68Ga radiopharmaceuticals. ► Different technological approaches for 68Ga radiopharmaceuticals will be discussed. ► Generator eluate post processing and evolution to cassette based systems were the major issues in automation. ► Impact of regulations on the technological development will be also considered

  7. One-step sample preparation of positive blood cultures for the direct detection of methicillin-sensitive and -resistant Staphylococcus aureus and methicillin-resistant coagulase-negative staphylococci within one hour using the automated GenomEra CDX™ PCR system.

    Science.gov (United States)

    Hirvonen, J J; von Lode, P; Nevalainen, M; Rantakokko-Jalava, K; Kaukoranta, S-S

    2012-10-01

    A method for the rapid detection of methicillin-sensitive and -resistant Staphylococcus aureus (MSSA and MRSA, respectively) and methicillin-resistant coagulase-negative staphylococci (MRCoNS) with a straightforward sample preparation protocol of blood cultures using an automated homogeneous polymerase chain reaction (PCR) assay, the GenomEra™ MRSA/SA (Abacus Diagnostica Oy, Turku, Finland), is presented. In total, 316 BacT/Alert (bioMérieux, Marcy l'Etoile, France) and 433 BACTEC (Becton Dickinson, Sparks, MD, USA) blood culture bottles were analyzed, including 725 positive cultures containing Gram-positive cocci in clusters (n = 419) and other Gram stain forms (n = 361), as well as 24 signal- and growth-negative bottles. Detection sensitivities for MSSA, MRSA, and MRCoNS were 99.4 % (158/159), 100.0 % (9/9), and 99.3 % (132/133), respectively. One false-positive MRSA result was detected from a non-staphylococci-containing bottle, yielding a specificity of 99.8 %. The lowest detectable amount of viable cells in the blood culture sample was 4 × 10(4) CFU/mL. The results were available within one hour after microbial growth detection and the two-step, time-resolved fluorometric (TRF) measurement mode employed by the GenomEra CDX™ instrument showed no interference from blood, charcoal, or culture media. The method described lacks all sample purification steps and allows reliable and simplified pathogen detection also in clinical microbiology laboratory settings without specialized molecular microbiology competence.

  8. Disassembly automation automated systems with cognitive abilities

    CERN Document Server

    Vongbunyong, Supachai

    2015-01-01

    This book presents a number of aspects to be considered in the development of disassembly automation, including the mechanical system, vision system and intelligent planner. The implementation of cognitive robotics increases the flexibility and degree of autonomy of the disassembly system. Disassembly, as a step in the treatment of end-of-life products, can allow the recovery of embodied value left within disposed products, as well as the appropriate separation of potentially-hazardous components. In the end-of-life treatment industry, disassembly has largely been limited to manual labor, which is expensive in developed countries. Automation is one possible solution for economic feasibility. The target audience primarily comprises researchers and experts in the field, but the book may also be beneficial for graduate students.

  9. Automated Lattice Perturbation Theory

    Energy Technology Data Exchange (ETDEWEB)

    Monahan, Christopher

    2014-11-01

    I review recent developments in automated lattice perturbation theory. Starting with an overview of lattice perturbation theory, I focus on the three automation packages currently "on the market": HiPPy/HPsrc, Pastor and PhySyCAl. I highlight some recent applications of these methods, particularly in B physics. In the final section I briefly discuss the related, but distinct, approach of numerical stochastic perturbation theory.

  10. Automated ISMS control auditability

    OpenAIRE

    Suomu, Mikko

    2015-01-01

    This thesis focuses on researching a possible reference model for automated ISMS’s (Information Security Management System) technical control auditability. The main objective was to develop a generic framework for automated compliance status monitoring of the ISO27001:2013 standard which could be re‐used in any ISMS system. The framework was tested with Proof of Concept (PoC) empirical research in a test infrastructure which simulates the framework target deployment environment. To fulfi...

  11. Marketing automation supporting sales

    OpenAIRE

    Sandell, Niko

    2016-01-01

    The past couple of decades has been a time of major changes in marketing. Digitalization has become a permanent part of marketing and at the same time enabled efficient collection of data. Personalization and customization of content are playing a crucial role in marketing when new customers are acquired. This has also created a need for automation to facilitate the distribution of targeted content. As a result of successful marketing automation more information of the customers is gathered ...

  12. Automated security management

    CERN Document Server

    Al-Shaer, Ehab; Xie, Geoffrey

    2013-01-01

    In this contributed volume, leading international researchers explore configuration modeling and checking, vulnerability and risk assessment, configuration analysis, and diagnostics and discovery. The authors equip readers to understand automated security management systems and techniques that increase overall network assurability and usability. These constantly changing networks defend against cyber attacks by integrating hundreds of security devices such as firewalls, IPSec gateways, IDS/IPS, authentication servers, authorization/RBAC servers, and crypto systems. Automated Security Managemen

  13. Automated lattice data generation

    Directory of Open Access Journals (Sweden)

    Ayyar Venkitesh

    2018-01-01

    Full Text Available The process of generating ensembles of gauge configurations (and measuring various observables over them can be tedious and error-prone when done “by hand”. In practice, most of this procedure can be automated with the use of a workflow manager. We discuss how this automation can be accomplished using Taxi, a minimal Python-based workflow manager built for generating lattice data. We present a case study demonstrating this technology.

  14. Mining Balanced Sequential Patterns in RTS Games 1

    OpenAIRE

    Bosc, Guillaume; Kaytoue, Mehdi; Raïssi, Chedy; Boulicaut, Jean-François; Tan, Philip

    2014-01-01

    International audience; The video game industry has grown enormously over the last twenty years, bringing new challenges to the artificial intelli-gence and data analysis communities. We tackle here the problem of automatic discovery of strategies in real-time strategy games through pattern mining. Such patterns are the basic units for many tasks such as automated agent design, but also to build tools for the profession-ally played video games in the electronic sports scene. Our formal-izatio...

  15. Boosting association rule mining in large datasets via Gibbs sampling

    Science.gov (United States)

    Qian, Guoqi; Rao, Calyampudi Radhakrishna; Sun, Xiaoying; Wu, Yuehua

    2016-01-01

    Current algorithms for association rule mining from transaction data are mostly deterministic and enumerative. They can be computationally intractable even for mining a dataset containing just a few hundred transaction items, if no action is taken to constrain the search space. In this paper, we develop a Gibbs-sampling–induced stochastic search procedure to randomly sample association rules from the itemset space, and perform rule mining from the reduced transaction dataset generated by the sample. Also a general rule importance measure is proposed to direct the stochastic search so that, as a result of the randomly generated association rules constituting an ergodic Markov chain, the overall most important rules in the itemset space can be uncovered from the reduced dataset with probability 1 in the limit. In the simulation study and a real genomic data example, we show how to boost association rule mining by an integrated use of the stochastic search and the Apriori algorithm. PMID:27091963

  16. Ideate about building green mine of uranium mining and metallurgy

    International Nuclear Information System (INIS)

    Shi Zuyuan

    2012-01-01

    Analysing the current situation of uranium mining and metallurgy; Setting up goals for green uranium mining and metallurgy, its fundamental conditions, Contents and measures. Putting forward an idea to combine green uranium mining and metallurgy with the state target for green mining, and keeping its own characteristics. (author)

  17. Tellurium Mobility Through Mine Environments

    Science.gov (United States)

    Dorsk, M.

    2015-12-01

    Tellurium is a rare metalloid that has received minimal research regarding environmental mobility. Observations of Tellurium mobility are mainly based on observations of related metalloids such as selenium and beryllium; yet little research has been done on specific Tellurium behavior. This laboratory work established the environmental controls that influence Tellurium mobility and chemical speciation in aqueous driven systems. Theoretical simulations show possible mobility of Te as Te(OH)3[+] at highly oxidizing and acidic conditions. Movement as TeO3[2-] under more basic conditions may also be possible in elevated Eh conditions. Mobility in reducing environments is theoretically not as likely. For a practical approach to investigate mobility conditions for Te, a site with known Tellurium content was chosen in Colorado. Composite samples were selected from the top, center and bottom of a tailings pile for elution experiments. These samples were disintegrated using a rock crusher and pulverized with an automated mortar and pestle. The material was then classified to 70 microns. A 10g sample split was digested in concentrated HNO3 and HF and analyzed by Atomic Absorption Spectroscopy to determine initial Te concentrations. Additional 10g splits from each location were subjected to elution in 100 mL of each of the following solutions; nitric acid to a pH of 1.0, sulfuric acid to a pH of 2.0, sodium hydroxide to a pH of 12, ammonium hydroxide to a pH of 10, a pine needle/soil tea from material within the vicinity of the collection site to a pH of 3.5 and lastly distilled water to serve as control with a pH of 7. Sulfuric acid was purposefully chosen to simulate acid mine drainage from the decomposition of pyrite within the mine tailings. Sample sub sets were also inundated with 10mL of a 3% hydrogen peroxide solution to induce oxidizing conditions. All collected eluates were then analyzed by atomic absorption spectroscopy (AAS) to measure Tellurium concentrations in

  18. Fuel cell mining vehicles: design, performance and advantages

    International Nuclear Information System (INIS)

    Betournay, M.C.; Miller, A.R.; Barnes, D.L.

    2003-01-01

    The potential for using fuel cell technology in underground mining equipment was discussed with reference to the risks associated with the operation of hydrogen vehicles, hydrogen production and hydrogen delivery systems. This paper presented some of the initiatives for mine locomotives and fuel cell stacks for underground environments. In particular, it presents the test results of the first applied industrial fuel cell vehicle in the world, a mining and tunneling locomotive. This study was part of an international initiative managed by the Fuel Cell Propulsion Institute which consists of several mining companies, mining equipment manufacturers, and fuel cell technology developers. Some of the obvious benefits of fuel cells for underground mining operations include no exhaust gases, lower electrical costs, significantly reduced maintenance, and lower ventilation costs. Another advantage is that the technology can be readily automated and computer-based for tele-remote operations. This study also quantified the cost and operational benefits associated with fuel cell vehicles compared to diesel vehicles. It is expected that higher vehicle productivity could render fuel cell underground vehicles cost-competitive. 6 refs., 1 tab

  19. Spatiotemporal Data Mining: A Computational Perspective

    Directory of Open Access Journals (Sweden)

    Shashi Shekhar

    2015-10-01

    Full Text Available Explosive growth in geospatial and temporal data as well as the emergence of new technologies emphasize the need for automated discovery of spatiotemporal knowledge. Spatiotemporal data mining studies the process of discovering interesting and previously unknown, but potentially useful patterns from large spatiotemporal databases. It has broad application domains including ecology and environmental management, public safety, transportation, earth science, epidemiology, and climatology. The complexity of spatiotemporal data and intrinsic relationships limits the usefulness of conventional data science techniques for extracting spatiotemporal patterns. In this survey, we review recent computational techniques and tools in spatiotemporal data mining, focusing on several major pattern families: spatiotemporal outlier, spatiotemporal coupling and tele-coupling, spatiotemporal prediction, spatiotemporal partitioning and summarization, spatiotemporal hotspots, and change detection. Compared with other surveys in the literature, this paper emphasizes the statistical foundations of spatiotemporal data mining and provides comprehensive coverage of computational approaches for various pattern families. ISPRS Int. J. Geo-Inf. 2015, 4 2307 We also list popular software tools for spatiotemporal data analysis. The survey concludes with a look at future research needs.

  20. An ISU study of asteroid mining

    Science.gov (United States)

    Burke, J. D.

    During the 1990 summer session of the International Space University, 59 graduate students from 16 countries carried out a design project on using the resources of near-earth asteroids. The results of the project, whose full report is now available from ISU, are summarized. The student team included people in these fields: architecture, business and management, engineering, life sciences, physical sciences, policy and law, resources and manufacturing, and satellite applications. They designed a project for transporting equipment and personnel to a near-earth asteroid, setting up a mining base there, and hauling products back for use in cislunar space. In addition, they outlined the needed precursor steps, beginning with expansion of present ground-based programs for finding and characterizing near-earth asteroids and continuing with automated flight missions to candidate bodies. (To limit the summer project's scope the actual design of these flight-mission precursors was excluded.) The main conclusions were that asteroid mining may provide an important complement to the future use of lunar resources, with the potential to provide large amounts of water and carbonaceous materials for use off earth. However, the recovery of such materials from presently known asteroids did not show an economic gain under the study assumptions; therefore, asteroid mining cannot yet be considered a prospective business.

  1. Advanced Data Mining of Leukemia Cells Micro-Arrays

    Directory of Open Access Journals (Sweden)

    Ryan M. Pierce

    2009-12-01

    Full Text Available This paper provides continuation and extensions of previous research by Segall and Pierce (2009a that discussed data mining for micro-array databases of Leukemia cells for primarily self-organized maps (SOM. As Segall and Pierce (2009a and Segall and Pierce (2009b the results of applying data mining are shown and discussed for the data categories of microarray databases of HL60, Jurkat, NB4 and U937 Leukemia cells that are also described in this article. First, a background section is provided on the work of others pertaining to the applications of data mining to micro-array databases of Leukemia cells and micro-array databases in general. As noted in predecessor article by Segall and Pierce (2009a, micro-array databases are one of the most popular functional genomics tools in use today. This research in this paper is intended to use advanced data mining technologies for better interpretations and knowledge discovery as generated by the patterns of gene expressions of HL60, Jurkat, NB4 and U937 Leukemia cells. The advanced data mining performed entailed using other data mining tools such as cubic clustering criterion, variable importance rankings, decision trees, and more detailed examinations of data mining statistics and study of other self-organized maps (SOM clustering regions of workspace as generated by SAS Enterprise Miner version 4. Conclusions and future directions of the research are also presented.

  2. Implementation of Paste Backfill Mining Technology in Chinese Coal Mines

    OpenAIRE

    Chang, Qingliang; Chen, Jianhang; Zhou, Huaqiang; Bai, Jianbiao

    2014-01-01

    Implementation of clean mining technology at coal mines is crucial to protect the environment and maintain balance among energy resources, consumption, and ecology. After reviewing present coal clean mining technology, we introduce the technology principles and technological process of paste backfill mining in coal mines and discuss the components and features of backfill materials, the constitution of the backfill system, and the backfill process. Specific implementation of this technology a...

  3. Australian uranium mining policy

    International Nuclear Information System (INIS)

    Fisk, B.

    1985-01-01

    Australian government policy is explained in terms of adherence to the Non-Proliferation Treaty. Two alleged uncertainties are discussed: the future of Australian mining industry as a whole -on which it is said that Australian uranium mines will continue to be developed; and detailed commercial policy of the Australian government - on which it is suggested that the three-mines policy of limited expansion of the industry would continue. Various aspects of policy, applying the principles of the NPT, are listed. (U.K.)

  4. Millstone: software for multiplex microbial genome analysis and engineering.

    Science.gov (United States)

    Goodman, Daniel B; Kuznetsov, Gleb; Lajoie, Marc J; Ahern, Brian W; Napolitano, Michael G; Chen, Kevin Y; Chen, Changping; Church, George M

    2017-05-25

    Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

  5. Rescue complex for coal mines

    Science.gov (United States)

    Yungmeyster, D. A.; Urazbakhtin, R. Yu

    2017-10-01

    The mining industry was potentially dangerous at all times, even with the use of modern equipment in mines, accidents continue to occur, including catastrophic ones. Accidents in mines are due to the presence of specific features in the conduct of mining operations. These include the inconsistency of mining and geological conditions, the contamination of the mine atmosphere due to the release of gases from minerals, the presence of self-igniting coal strata, which creates the danger of underground fires, gas explosions. The main cause of accidents is the irresponsibility of both the manager and the personnel who violate the safety rules during mining operations.

  6. Closedure - Mine Closure Technologies Resource

    Science.gov (United States)

    Kauppila, Päivi; Kauppila, Tommi; Pasanen, Antti; Backnäs, Soile; Liisa Räisänen, Marja; Turunen, Kaisa; Karlsson, Teemu; Solismaa, Lauri; Hentinen, Kimmo

    2015-04-01

    Closure of mining operations is an essential part of the development of eco-efficient mining and the Green Mining concept in Finland to reduce the environmental footprint of mining. Closedure is a 2-year joint research project between Geological Survey of Finland and Technical Research Centre of Finland that aims at developing accessible tools and resources for planning, executing and monitoring mine closure. The main outcome of the Closedure project is an updatable wiki technology-based internet platform (http://mineclosure.gtk.fi) in which comprehensive guidance on the mine closure is provided and main methods and technologies related to mine closure are evaluated. Closedure also provides new data on the key issues of mine closure, such as performance of passive water treatment in Finland, applicability of test methods for evaluating cover structures for mining wastes, prediction of water effluents from mine wastes, and isotopic and geophysical methods to recognize contaminant transport paths in crystalline bedrock.

  7. GWA study data mining and independent replication identify cardiomyopathy-associated 5 (CMYA5) as a risk gene for schizophrenia

    NARCIS (Netherlands)

    Chen, X.; Lee, G.; Maher, B. S.; Fanous, A. H.; Chen, J.; Zhao, Z.; Guo, A.; van den Oord, E.; Sullivan, P. F.; Shi, J.; Levinson, D. F.; Gejman, P. V.; Sanders, A.; Duan, J.; Owen, M. J.; Craddock, N. J.; O'Donovan, M. C.; Blackman, J.; Lewis, D.; Kirov, G. K.; Qin, W.; Schwab, S.; Wildenauer, D.; Chowdari, K.; Nimgaonkar, V.; Straub, R. E.; Weinberger, D. R.; O'Neill, F. A.; Walsh, D.; Bronstein, M.; Darvasi, A.; Lencz, T.; Malhotra, A. K.; Rujescu, D.; Giegling, I.; Werge, T.; Hansen, T.; Ingason, A.; Nöethen, M. M.; Rietschel, M.; Cichon, S.; Djurovic, S.; Andreassen, O. A.; Cantor, R. M.; Ophoff, R.; Corvin, A.; Morris, D. W.; Gill, M.; Pato, C. N.; Pato, M. T.; Macedo, A.; Gurling, H. M. D.; McQuillin, A.; Pimm, J.; Hultman, C.; Lichtenstein, P.; Sklar, P.; Purcell, S. M.; Scolnick, E.; St Clair, D.; Blackwood, D. H. R.; Kendler, K. S.; Kahn, René S.; Linszen, Don H.; van Os, Jim; Wiersma, Durk; Bruggeman, Richard; Cahn, Wiepke; de Haan, Lieuwe; Krabbendam, Lydia; Myin-Germeys, Inez; O'Donovan, Michael C.; Kirov, George K.; Craddock, Nick J.; Holmans, Peter A.; Williams, Nigel M.; Georgieva, Lyudmila; Nikolov, Ivan; Norton, N.; Williams, H.; Toncheva, Draga; Milanova, Vihra; Owen, Michael J.; Hultman, Christina M.; Lichtenstein, Paul; Thelander, Emma F.; Sullivan, Patrick; Morris, Derek W.; O'Dushlaine, Colm T.; Kenny, Elaine; Quinn, Emma M.; Gill, Michael; Corvin, Aiden; McQuillin, Andrew; Choudhury, Khalid; Datta, Susmita; Pimm, Jonathan; Thirumalai, Srinivasa; Puri, Vinay; Krasucki, Robert; Lawrence, Jacob; Quested, Digby; Bass, Nicholas; Gurling, Hugh; Crombie, Caroline; Fraser, Gillian; Kuan, Soh Leh; Walker, Nicholas; St Clair, David; Blackwood, Douglas H. R.; Muir, Walter J.; McGhee, Kevin A.; Pickard, Ben; Malloy, Pat; Maclean, Alan W.; van Beck, Margaret; Wray, Naomi R.; Macgregor, Stuart; Visscher, Peter M.; Pato, Michele T.; Medeiros, Helena; Middleton, Frank; Carvalho, Celia; Morley, Christopher; Fanous, Ayman; Conti, David; Knowles, James A.; Ferreira, Carlos Paz; Macedo, Antonio; Azevedo, M. Helena; Pato, Carlos N.; Stone, Jennifer L.; Ruderfer, Douglas M.; Kirby, Andrew N.; Ferreira, Manuel A. R.; Daly, Mark J.; Purcell, Shaun M.; Sklar, Pamela; Chambert, Kimberly; Kuruvilla, Finny; Gabriel, Stacey B.; Ardlie, Kristin; Moran, Jennifer L.; Scolnick, Edward M.

    2011-01-01

    We conducted data-mining analyses using the Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE) and molecular genetics of schizophrenia genome-wide association study supported by the genetic association information network (MGS-GAIN) schizophrenia data sets and performed

  8. Ensemble Data Mining Methods

    Data.gov (United States)

    National Aeronautics and Space Administration — Ensemble Data Mining Methods, also known as Committee Methods or Model Combiners, are machine learning methods that leverage the power of multiple models to achieve...

  9. Acid mine drainage

    Science.gov (United States)

    Bigham, Jerry M.; Cravotta, Charles A.

    2016-01-01

    Acid mine drainage (AMD) consists of metal-laden solutions produced by the oxidative dissolution of iron sulfide minerals exposed to air, moisture, and acidophilic microbes during the mining of coal and metal deposits. The pH of AMD is usually in the range of 2–6, but mine-impacted waters at circumneutral pH (5–8) are also common. Mine drainage usually contains elevated concentrations of sulfate, iron, aluminum, and other potentially toxic metals leached from rock that hydrolyze and coprecipitate to form rust-colored encrustations or sediments. When AMD is discharged into surface waters or groundwaters, degradation of water quality, injury to aquatic life, and corrosion or encrustation of engineered structures can occur for substantial distances. Prevention and remediation strategies should consider the biogeochemical complexity of the system, the longevity of AMD pollution, the predictive power of geochemical modeling, and the full range of available field technologies for problem mitigation.

  10. Mining activities at Neyveli

    International Nuclear Information System (INIS)

    Boopathy, P.V.; Rathinavel, R.

    1993-01-01

    Mining activities at lignite areas around Neyveli are described. Measures taken to safeguard the environment from despoliation of land, air pollution, noise pollution and effluents are described. (M.G.B.)

  11. Data mining in agriculture

    CERN Document Server

    Mucherino, Antonio; Pardalos, Panos M

    2009-01-01

    Data Mining in Agriculture represents a comprehensive effort to provide graduate students and researchers with an analytical text on data mining techniques applied to agriculture and environmental related fields. This book presents both theoretical and practical insights with a focus on presenting the context of each data mining technique rather intuitively with ample concrete examples represented graphically and with algorithms written in MATLAB®. Examples and exercises with solutions are provided at the end of each chapter to facilitate the comprehension of the material. For each data mining technique described in the book variants and improvements of the basic algorithm are also given. Also by P.J. Papajorgji and P.M. Pardalos: Advances in Modeling Agricultural Systems, 'Springer Optimization and its Applications' vol. 25, ©2009.

  12. Coal mine subsidence

    International Nuclear Information System (INIS)

    Rahall, N.J.

    1991-05-01

    This paper examines the efficacy of the Department of the Interior's Office of Surface Mining Reclamation and Enforcement's (OSMRE) efforts to implement the federally assisted coal mine subsidence insurance program. Coal mine subsidence, a gradual settling of the earth's surface above an underground mine, can damage nearby land and property. To help protect property owners from subsidence-related damage, the Congress passed legislation in 1984 authorizing OSMRE to make grants of up to $3 million to each state to help the states establish self-sustaining, state-administered insurance programs. Of the 21 eligible states, six Colorado, Indiana, Kentucky, Ohio, West Virginia, and Wyoming applied for grants. This paper reviews the efforts of these six states to develop self-sustaining insurance programs and assessed OSMRE's oversight of those efforts

  13. Acid Mine Drainage Treatment

    National Research Council Canada - National Science Library

    Fripp, Jon

    2000-01-01

    .... Acid mine drainage (AMD) can have severe impacts to aquatic resources, can stunt terrestrial plant growth and harm wetlands, contaminate groundwater, raise water treatment costs, and damage concrete and metal structures...

  14. Ventilation of uranium mines

    International Nuclear Information System (INIS)

    Francois, Y.; Pradel, J.; Zettwoog, P.; Dumas, M.

    1975-01-01

    In the first part of the paper the authors describe the ventilation of French mines in terms of the primary ventilation system, which brings the outside air close to the working places using the overall structure of the mine to form the airways, and the secondary ventilation system, which is for the distribution of the primary air or for the ventilation of the development drifts and blind tunnels. Brief mention is made of the French regulations on the ventilation of mines in general and uranium mines in particular. The authors describe the equipment used and discuss the installed capacities and air flow per man and per working place. The difficulties encountered in properly ventilating various types of working places are mentioned, such as sublevel development drifts, reinforced stopes, and storage chambers with an artificial crown. The second part of the paper is devoted to computer calculations of the primary ventilation system. It is explained why the Commissariat a l'energie atomique has found it necessary to make these calculations. Without restating the mathematical theories underlying the methods employed, the authors demonstrate how simple measuring instruments and a small-size computer can be used to solve the ventilation problems arising in French mines. Emphasis is given to the layout of the ventilation system and to air flow and negative pressure measurements at the base of the mine. The authors show how calculations can be applied to new heading operations, a change in resistance, the replacement or addition of a ventilator, and a new air inlet or outlet. The authors come to the conclusion that since ventilation is at present the most reliable way of avoiding the pollution of mines, a thorough knowledge of the capabilities in this respect can often help improve working conditions. Despite the progress made, however, constant surveillance of the ventilation systems in uranium mines by a separate team with no responsibility for production problems is

  15. Mining through controversies

    OpenAIRE

    Lyytimäki, Jari; Peltonen, Lasse

    2016-01-01

    The economic, social and ecological implications of the extraction of mineral resources have been increasingly discussed under the heading of the social licence to operate. In Finland, critical public framings characterized by impressions of failed economic promises, unreliable technology and environmental hazards have dominated the recent mining debate. Operators probing for opportunities to establish new mines have faced critical public reactions. Changes to legislation, natural resource ma...

  16. Bauxite Mining Sustainably

    Science.gov (United States)

    Atkins, Patrick R.; Bayliss, Chris; Ward, Sam

    In 1990, the International Aluminum Institute began a program to report on the bauxite mining and rehabilitation activities of the worldwide industry. A survey process was initiated and reports were published in 1992, 2000 and 2004. The most recent report includes extensive data on mines representing over 70% of the world's output of bauxite and includes a more detailed focus on the social and economic as well as the environmental performance of the industry.

  17. Applied data mining

    CERN Document Server

    Xu, Guandong

    2013-01-01

    Data mining has witnessed substantial advances in recent decades. New research questions and practical challenges have arisen from emerging areas and applications within the various fields closely related to human daily life, e.g. social media and social networking. This book aims to bridge the gap between traditional data mining and the latest advances in newly emerging information services. It explores the extension of well-studied algorithms and approaches into these new research arenas.

  18. Changing the Tooth-to-Tail Ratio Using Robotics and Automation to Beat Sequestration

    Science.gov (United States)

    2015-10-01

    tracking inventory , notifying its human handler of a hazardous condition, complying with a schedule, and preparing a load-out of tools and parts. The...Taking Over Pilbara Mining Operations in Shift to Automation,” ABC News, 25 April 2014, http://www.abc.net.au/news/2014-04-25/computer-controlled

  19. Sustainable mining management

    International Nuclear Information System (INIS)

    Tejera Oliver, J. L.

    2009-01-01

    Mining activities are carried out by the older man and have provided resources, since ancient times, for their development and progress. With the discovery of fire will show the first metals that have marked the civilizations of copper, bronze and iron, and is the prehistory of the Stone Age tools that man has made from the exploitation of quarries first. The industrial revolution of the nineteenth century is linked to coal and steel, and could not conceiver of todays society without oil and gas, without silicon and coltan. But the mines are often aggressive and, despite their need and what they contribute to the development are answered by the societies where are made. during recent years there has been growing international efforts to try to make the minimum requirements of sustainable exploitation (European Directives, GMI, GRI, etc.) In AENOR, and within the Technical Committee of Standardization 22 Mining and Explosives, chaired by AITEMIN, was established the subcommittee 3, chaired by IGME, where, with the participation of all stake holders, have developed some standards on sustainable mining management sustainable mining that will be a tool available to mining companies to demonstrate their sustainable use to Society. (Author)

  20. Mine for sale

    International Nuclear Information System (INIS)

    Beer, G.

    2006-01-01

    The newest Slovak brown coal mine - Bana Zahorie is in crisis. Despite the fact that experts believe that along with Bana Novaky, it has the most potential. The owners have started its liquidation. One of the walls has collapsed and another part flooded. Nobody was hurt, but some equipment is still underground. The mine had already lost equipment in the past. During an accident in 2000, equipment worth several tens of millions was destroyed. 'After the accident, mining had to be stopped and from a technical point of view that was the end of the joint stock company, Bana Zahorie Cary. The company could not raise the funds necessary to recover from the accident,' stated the Director of the mine, Jan Palkovic. But he stressed that only the joint stock company is in liquidation, the mine is still being ventilated and the water is being pumped out. But the company management still does not want to specify who will become the new owner of the lignite deposits in Zahorie. The Director promised to publish more details within several weeks. All competencies and mining rights of the former Bana Zahorie are being transferred to a new company - joint stock company Bana Cary. (author)

  1. Mine Waste at The Kherzet Youcef Mine : Environmental Characterization

    Science.gov (United States)

    Issaad, Mouloud; Boutaleb, Abdelhak; Kolli, Omar

    2017-04-01

    Mining activity in Algeria has existed since antiquity. But it was very important since the 20th century. This activity has virtually ceased since the beginning of the 1990s, leaving many mine sites abandoned (so-called orphan mines). The abandonment of mining today poses many environmental problems (soil pollution, contamination of surface water, mining collapses...). The mining wastes often occupy large volumes that can be hazardous to the environment and human health, often neglected in the past: Faulting geotechnical implementation, acid mine drainage (AMD), alkalinity, presence of pollutants and toxic substances (heavy metals, cyanide...). The study started already six years ago and it covers all mines located in NE Algeria, almost are stopped for more than thirty years. So the most important is to have an overview of all the study area. After the inventory job of the abandoned mines, the rock drainage prediction will help us to classify sites according to their acid generating potential.

  2. Comparative Genomics

    Indian Academy of Sciences (India)

    An important hallmark of biological research is the aspect of 'comparisons'. As the complete genome sequences of numerous organisms have become available, the emphasis in biology has shifted to comparisons at the genome level. Indeed, the last few years have witnessed an exponential rise in the number of ...

  3. Comparative Genomics

    Indian Academy of Sciences (India)

    structions of the tree of life, drug discovery programs, func- tion predictions of hypothetical proteins and genes, regula- tory motifs and other non-coding DNA motifs, and genome ... expertise in assembling sequences. Beginning with the complete genome sequence of the bacterial pathogen Haemophilus influenzae that was ...

  4. Synthetic Genetic Arrays: Automation of Yeast Genetics.

    Science.gov (United States)

    Kuzmin, Elena; Costanzo, Michael; Andrews, Brenda; Boone, Charles

    2016-04-01

    Genome-sequencing efforts have led to great strides in the annotation of protein-coding genes and other genomic elements. The current challenge is to understand the functional role of each gene and how genes work together to modulate cellular processes. Genetic interactions define phenotypic relationships between genes and reveal the functional organization of a cell. Synthetic genetic array (SGA) methodology automates yeast genetics and enables large-scale and systematic mapping of genetic interaction networks in the budding yeast,Saccharomyces cerevisiae SGA facilitates construction of an output array of double mutants from an input array of single mutants through a series of replica pinning steps. Subsequent analysis of genetic interactions from SGA-derived mutants relies on accurate quantification of colony size, which serves as a proxy for fitness. Since its development, SGA has given rise to a variety of other experimental approaches for functional profiling of the yeast genome and has been applied in a multitude of other contexts, such as genome-wide screens for synthetic dosage lethality and integration with high-content screening for systematic assessment of morphology defects. SGA-like strategies can also be implemented similarly in a number of other cell types and organisms, includingSchizosaccharomyces pombe,Escherichia coli, Caenorhabditis elegans, and human cancer cell lines. The genetic networks emerging from these studies not only generate functional wiring diagrams but may also play a key role in our understanding of the complex relationship between genotype and phenotype. © 2016 Cold Spring Harbor Laboratory Press.

  5. Automating the CMS DAQ

    Energy Technology Data Exchange (ETDEWEB)

    Bauer, G.; et al.

    2014-01-01

    We present the automation mechanisms that have been added to the Data Acquisition and Run Control systems of the Compact Muon Solenoid (CMS) experiment during Run 1 of the LHC, ranging from the automation of routine tasks to automatic error recovery and context-sensitive guidance to the operator. These mechanisms helped CMS to maintain a data taking efficiency above 90% and to even improve it to 95% towards the end of Run 1, despite an increase in the occurrence of single-event upsets in sub-detector electronics at high LHC luminosity.

  6. Control and automation systems

    International Nuclear Information System (INIS)

    Schmidt, R.; Zillich, H.

    1986-01-01

    A survey is given of the development of control and automation systems for energy uses. General remarks about control and automation schemes are followed by a description of modern process control systems along with process control processes as such. After discussing the particular process control requirements of nuclear power plants the paper deals with the reliability and availability of process control systems and refers to computerized simulation processes. The subsequent paragraphs are dedicated to descriptions of the operating floor, ergonomic conditions, existing systems, flue gas desulfurization systems, the electromagnetic influences on digital circuits as well as of light wave uses. (HAG) [de

  7. Automated nuclear materials accounting

    International Nuclear Information System (INIS)

    Pacak, P.; Moravec, J.

    1982-01-01

    An automated state system of accounting for nuclear materials data was established in Czechoslovakia in 1979. A file was compiled of 12 programs in the PL/1 language. The file is divided into four groups according to logical associations, namely programs for data input and checking, programs for handling the basic data file, programs for report outputs in the form of worksheets and magnetic tape records, and programs for book inventory listing, document inventory handling and materials balance listing. A similar automated system of nuclear fuel inventory for a light water reactor was introduced for internal purposes in the Institute of Nuclear Research (UJV). (H.S.)

  8. VRLane: a desktop virtual safety management program for underground coal mine

    Science.gov (United States)

    Li, Mei; Chen, Jingzhu; Xiong, Wei; Zhang, Pengpeng; Wu, Daozheng

    2008-10-01

    VR technologies, which generate immersive, interactive, and three-dimensional (3D) environments, are seldom applied to coal mine safety work management. In this paper, a new method that combined the VR technologies with underground mine safety management system was explored. A desktop virtual safety management program for underground coal mine, called VRLane, was developed. The paper mainly concerned about the current research advance in VR, system design, key techniques and system application. Two important techniques were introduced in the paper. Firstly, an algorithm was designed and implemented, with which the 3D laneway models and equipment models can be built on the basis of the latest mine 2D drawings automatically, whereas common VR programs established 3D environment by using 3DS Max or the other 3D modeling software packages with which laneway models were built manually and laboriously. Secondly, VRLane realized system integration with underground industrial automation. VRLane not only described a realistic 3D laneway environment, but also described the status of the coal mining, with functions of displaying the run states and related parameters of equipment, per-alarming the abnormal mining events, and animating mine cars, mine workers, or long-wall shearers. The system, with advantages of cheap, dynamic, easy to maintenance, provided a useful tool for safety production management in coal mine.

  9. Altering user' acceptance of automation through prior automation exposure.

    Science.gov (United States)

    Bekier, Marek; Molesworth, Brett R C

    2017-06-01

    Air navigation service providers worldwide see increased use of automation as one solution to overcome the capacity constraints imbedded in the present air traffic management (ATM) system. However, increased use of automation within any system is dependent on user acceptance. The present research sought to determine if the point at which an individual is no longer willing to accept or cooperate with automation can be manipulated. Forty participants underwent training on a computer-based air traffic control programme, followed by two ATM exercises (order counterbalanced), one with and one without the aid of automation. Results revealed after exposure to a task with automation assistance, user acceptance of high(er) levels of automation ('tipping point') decreased; suggesting it is indeed possible to alter automation acceptance. Practitioner Summary: This paper investigates whether the point at which a user of automation rejects automation (i.e. 'tipping point') is constant or can be manipulated. The results revealed after exposure to a task with automation assistance, user acceptance of high(er) levels of automation decreased; suggesting it is possible to alter automation acceptance.

  10. Sinbase: an integrated database to study genomics, genetics and comparative genomics in Sesamum indicum.

    Science.gov (United States)

    Wang, Linhai; Yu, Jingyin; Li, Donghua; Zhang, Xiurong

    2015-01-01

    Sesame (Sesamum indicum L.) is an ancient and important oilseed crop grown widely in tropical and subtropical areas. It belongs to the gigantic order Lamiales, which includes many well-known or economically important species, such as olive (Olea europaea), leonurus (Leonurus japonicus) and lavender (Lavandula spica), many of which have important pharmacological properties. Despite their importance, genetic and genomic analyses on these species have been insufficient due to a lack of reference genome information. The now available S. indicum genome will provide an unprecedented opportunity for studying both S. indicum genetic traits and comparative genomics. To deliver S. indicum genomic information to the worldwide research community, we designed Sinbase, a web-based database with comprehensive sesame genomic, genetic and comparative genomic information. Sinbase includes sequences of assembled sesame pseudomolecular chromosomes, protein-coding genes (27,148), transposable elements (372,167) and non-coding RNAs (1,748). In particular, Sinbase provides unique and valuable information on colinear regions with various plant genomes, including Arabidopsis thaliana, Glycine max, Vitis vinifera and Solanum lycopersicum. Sinbase also provides a useful search function and data mining tools, including a keyword search and local BLAST service. Sinbase will be updated regularly with new features, improvements to genome annotation and new genomic sequences, and is freely accessible at http://ocri-genomics.org/Sinbase/. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  11. Idaho: Library Automation and Connectivity.

    Science.gov (United States)

    Bolles, Charles

    1996-01-01

    Provides an overview of the development of cooperative library automation and connectivity in Idaho, including telecommunications capacity, library networks, the Internet, and the role of the state library. Information on six shared automation systems in Idaho is included. (LRW)

  12. Cardiovascular genomics.

    Science.gov (United States)

    Wung, Shu-Fen; Hickey, Kathleen T; Taylor, Jacquelyn Y; Gallek, Matthew J

    2013-03-01

    This article provides an update on cardiovascular genomics using three clinically relevant exemplars, including myocardial infarction (MI) and coronary artery disease (CAD), stroke, and sudden cardiac death (SCD). ORGANIZATIONAL CONSTRUCT: Recent advances in cardiovascular genomic research, testing, and clinical implications are presented. Genomic nurse experts reviewed and summarized recent salient literature to provide updates on three selected cardiovascular genomic conditions. Research is ongoing to discover comprehensive genetic markers contributing to many common forms of cardiovascular disease (CVD), including MI and stroke. However, genomic technologies are increasingly being used clinically, particularly in patients with long QT syndrome (LQTS) or hypertrophic cardiomyopathy (HCM) who are at risk for SCD. Currently, there are no clinically recommended genetic tests for many common forms of CVD even though direct-to-consumer genetic tests are being marketed to healthcare providers and the general public. On the other hand, genetic testing for patients with certain single gene conditions, including channelopathies (e.g., LQTS) and cardiomyopathies (e.g., HCM), is recommended clinically. Nurses play a pivotal role in cardiogenetics and are actively engaged in direct clinical care of patients and families with a wide variety of heritable conditions. It is important for nurses to understand current development of cardiovascular genomics and be prepared to translate the new genomic knowledge into practice. © 2013 Sigma Theta Tau International.

  13. Automating Shallow Seismic Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Steeples, Don W.

    2004-12-09

    This seven-year, shallow-seismic reflection research project had the aim of improving geophysical imaging of possible contaminant flow paths. Thousands of chemically contaminated sites exist in the United States, including at least 3,700 at Department of Energy (DOE) facilities. Imaging technologies such as shallow seismic reflection (SSR) and ground-penetrating radar (GPR) sometimes are capable of identifying geologic conditions that might indicate preferential contaminant-flow paths. Historically, SSR has been used very little at depths shallower than 30 m, and even more rarely at depths of 10 m or less. Conversely, GPR is rarely useful at depths greater than 10 m, especially in areas where clay or other electrically conductive materials are present near the surface. Efforts to image the cone of depression around a pumping well using seismic methods were only partially successful (for complete references of all research results, see the full Final Technical Report, DOE/ER/14826-F), but peripheral results included development of SSR methods for depths shallower than one meter, a depth range that had not been achieved before. Imaging at such shallow depths, however, requires geophone intervals of the order of 10 cm or less, which makes such surveys very expensive in terms of human time and effort. We also showed that SSR and GPR could be used in a complementary fashion to image the same volume of earth at very shallow depths. The primary research focus of the second three-year period of funding was to develop and demonstrate an automated method of conducting two-dimensional (2D) shallow-seismic surveys with the goal of saving time, effort, and money. Tests involving the second generation of the hydraulic geophone-planting device dubbed the ''Autojuggie'' showed that large numbers of geophones can be placed quickly and automatically and can acquire high-quality data, although not under rough topographic conditions. In some easy

  14. Methane emissions from coal mining

    International Nuclear Information System (INIS)

    Boyer, C.M.; Kelafant, J.R.; Kuuskraa, V.A.; Manger, K.C.; Kruger, D.

    1990-09-01

    The report estimates global methane emissions from coal mining on a country specific basis, evaluates the technologies available to degasify coal seams and assesses the economics of recovering methane liberated during mining. 33 to 64 million tonnes were liberated in 1987 from coal mining, 75 per cent of which came from China, the USSR, Poland and the USA. Methane emissions from coal mining are likely to increase. Emission levels vary between surface and underground mines. The methane currently removed from underground mines for safety reasons could be used in a number of ways, which may be economically attractive. 55 refs., 19 figs., 24 tabs

  15. Homology and phylogeny and their automated inference.

    Science.gov (United States)

    Fuellen, Georg

    2008-06-01

    The analysis of the ever-increasing amount of biological and biomedical data can be pushed forward by comparing the data within and among species. For example, an integrative analysis of data from the genome sequencing projects for various species traces the evolution of the genomes and identifies conserved and innovative parts. Here, I review the foundations and advantages of this "historical" approach and evaluate recent attempts at automating such analyses. Biological data is comparable if a common origin exists (homology), as is the case for members of a gene family originating via duplication of an ancestral gene. If the family has relatives in other species, we can assume that the ancestral gene was present in the ancestral species from which all the other species evolved. In particular, describing the relationships among the duplicated biological sequences found in the various species is often possible by a phylogeny, which is more informative than homology statements. Detecting and elaborating on common origins may answer how certain biological sequences developed, and predict what sequences are in a particular species and what their function is. Such knowledge transfer from sequences in one species to the homologous sequences of the other is based on the principle of 'my closest relative looks and behaves like I do', often referred to as 'guilt by association'. To enable knowledge transfer on a large scale, several automated 'phylogenomics pipelines' have been developed in recent years, and seven of these will be described and compared. Overall, the examples in this review demonstrate that homology and phylogeny analyses, done on a large (and automated) scale, can give insights into function in biology and biomedicine.

  16. The UCSC Genome Browser database: 2015 update

    Science.gov (United States)

    Rosenbloom, Kate R.; Armstrong, Joel; Barber, Galt P.; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Dreszer, Timothy R.; Fujita, Pauline A.; Guruvadoo, Luvina; Haeussler, Maximilian; Harte, Rachel A.; Heitner, Steve; Hickey, Glenn; Hinrichs, Angie S.; Hubley, Robert; Karolchik, Donna; Learned, Katrina; Lee, Brian T.; Li, Chin H.; Miga, Karen H.; Nguyen, Ngan; Paten, Benedict; Raney, Brian J.; Smit, Arian F. A.; Speir, Matthew L.; Zweig, Ann S.; Haussler, David; Kuhn, Robert M.; Kent, W. James

    2015-01-01

    Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), ‘mined the web’ for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled. PMID:25428374

  17. Automated HAZOP revisited

    DEFF Research Database (Denmark)

    Taylor, J. R.

    2017-01-01

    Hazard and operability analysis (HAZOP) has developed from a tentative approach to hazard identification for process plants in the early 1970s to an almost universally accepted approach today, and a central technique of safety engineering. Techniques for automated HAZOP analysis were developed...

  18. Automated data model evaluation

    International Nuclear Information System (INIS)

    Kazi, Zoltan; Kazi, Ljubica; Radulovic, Biljana

    2012-01-01

    Modeling process is essential phase within information systems development and implementation. This paper presents methods and techniques for analysis and evaluation of data model correctness. Recent methodologies and development results regarding automation of the process of model correctness analysis and relations with ontology tools has been presented. Key words: Database modeling, Data model correctness, Evaluation

  19. Automated Vehicle Monitoring System

    OpenAIRE

    Wibowo, Agustinus Deddy Arief; Heriansyah, Rudi

    2014-01-01

    An automated vehicle monitoring system is proposed in this paper. The surveillance system is based on image processing techniques such as background subtraction, colour balancing, chain code based shape detection, and blob. The proposed system will detect any human's head as appeared at the side mirrors. The detected head will be tracked and recorded for further action.

  20. Automated Accounting. Instructor Guide.

    Science.gov (United States)

    Moses, Duane R.

    This curriculum guide was developed to assist business instructors using Dac Easy Accounting College Edition Version 2.0 software in their accounting programs. The module consists of four units containing assignment sheets and job sheets designed to enable students to master competencies identified in the area of automated accounting. The first…

  1. Mechatronic Design Automation

    DEFF Research Database (Denmark)

    Fan, Zhun

    successfully design analogue filters, vibration absorbers, micro-electro-mechanical systems, and vehicle suspension systems, all in an automatic or semi-automatic way. It also investigates the very important issue of co-designing plant-structures and dynamic controllers in automated design of Mechatronic...

  2. Protokoller til Home Automation

    DEFF Research Database (Denmark)

    Kjær, Kristian Ellebæk

    2008-01-01

    computer, der kan skifte mellem foruddefinerede indstillinger. Nogle gange kan computeren fjernstyres over internettet, så man kan se hjemmets status fra en computer eller måske endda fra en mobiltelefon. Mens nævnte anvendelser er klassiske indenfor home automation, er yderligere funktionalitet dukket op...

  3. Automated Water Extraction Index

    DEFF Research Database (Denmark)

    Feyisa, Gudina Legese; Meilby, Henrik; Fensholt, Rasmus

    2014-01-01

    of various sorts of environmental noise and at the same time offers a stable threshold value. Thus we introduced a new Automated Water Extraction Index (AWEI) improving classification accuracy in areas that include shadow and dark surfaces that other classification methods often fail to classify correctly...

  4. Myths in test automation

    Directory of Open Access Journals (Sweden)

    Jazmine Francis

    2015-01-01

    Full Text Available Myths in automation of software testing is an issue of discussion that echoes about the areas of service in validation of software industry. Probably, the first though that appears in knowledgeable reader would be Why this old topic again? What's New to discuss the matter? But, for the first time everyone agrees that undoubtedly automation testing today is not today what it used to be ten or fifteen years ago, because it has evolved in scope and magnitude. What began as a simple linear scripts for web applications today has a complex architecture and a hybrid framework to facilitate the implementation of testing applications developed with various platforms and technologies. Undoubtedly automation has advanced, but so did the myths associated with it. The change in perspective and knowledge of people on automation has altered the terrain. This article reflects the points of views and experience of the author in what has to do with the transformation of the original myths in new versions, and how they are derived; also provides his thoughts on the new generation of myths.

  5. GWATCH: a web platform for automated gene association discovery analysis

    Science.gov (United States)

    2014-01-01

    Background As genome-wide sequence analyses for complex human disease determinants are expanding, it is increasingly necessary to develop strategies to promote discovery and validation of potential disease-gene associations. Findings Here we present a dynamic web-based platform – GWATCH – that automates and facilitates four steps in genetic epidemiological discovery: 1) Rapid gene association search and discovery analysis of large genome-wide datasets; 2) Expanded visual display of gene associations for genome-wide variants (SNPs, indels, CNVs), including Manhattan plots, 2D and 3D snapshots of any gene region, and a dynamic genome browser illustrating gene association chromosomal regions; 3) Real-time validation/replication of candidate or putative genes suggested from other sources, limiting Bonferroni genome-wide association study (GWAS) penalties; 4) Open data release and sharing by eliminating privacy constraints (The National Human Genome Research Institute (NHGRI) Institutional Review Board (IRB), informed consent, The Health Insurance Portability and Accountability Act (HIPAA) of 1996 etc.) on unabridged results, which allows for open access comparative and meta-analysis. Conclusions GWATCH is suitable for both GWAS and whole genome sequence association datasets. We illustrate the utility of GWATCH with three large genome-wide association studies for HIV-AIDS resistance genes screened in large multicenter cohorts; however, association datasets from any study can be uploaded and analyzed by GWATCH. PMID:25374661

  6. Driver Psychology during Automated Platooning

    NARCIS (Netherlands)

    Heikoop, D.D.

    2017-01-01

    With the rapid increase in vehicle automation technology, the call for understanding how humans behave while driving in an automated vehicle becomes more urgent. Vehicles that have automated systems such as Lane Keeping Assist (LKA) or Adaptive Cruise Control (ACC) not only support drivers in their

  7. Digital family histories for data mining.

    Science.gov (United States)

    Hoyt, Robert; Linnville, Steven; Chung, Hui-Min; Hutfless, Brent; Rice, Courtney

    2013-01-01

    As we move closer to ubiquitous electronic health records (EHRs), genetic, familial, and clinical information will need to be incorporated into EHRs as structured data that can be used for data mining and clinical decision support. While the Human Genome Project has produced new and exciting genomic data, the cost to sequence the human personal genome is high, and significant controversies regarding how to interpret genomic data exist. Many experts feel that the family history is a surrogate marker for genetic information and should be part of any paper-based or electronic health record. A digital family history is now part of the Meaningful Use Stage 2 menu objectives for EHR reimbursement, projected for 2014. In this study, a secure online family history questionnaire was designed to collect data on a unique cohort of Vietnam-era repatriated male veterans and a comparison group in order to compare participant and family disease rates on common medical disorders with a genetic component. This article describes our approach to create the digital questionnaire and the results of analyzing family history data on 319 male participants.

  8. Data mining in healthcare: decision making and precision

    Directory of Open Access Journals (Sweden)

    Ionuţ ŢĂRANU

    2016-05-01

    Full Text Available The trend of application of data mining in healthcare today is increased because the health sector is rich with information and data mining has become a necessity. Healthcare organizations generate and collect large volumes of information to a daily basis. Use of information technology enables automation of data mining and knowledge that help bring some interesting patterns which means eliminating manual tasks and easy data extraction directly from electronic records, electronic transfer system that will secure medical records, save lives and reduce the cost of medical services as well as enabling early detection of infectious diseases on the basis of advanced data collection. Data mining can enable healthcare organizations to anticipate trends in the patient's medical condition and behaviour proved by analysis of prospects different and by making connections between seemingly unrelated information. The raw data from healthcare organizations are voluminous and heterogeneous. It needs to be collected and stored in organized form and their integration allows the formation unite medical information system. Data mining in health offers unlimited possibilities for analyzing different data models less visible or hidden to common analysis techniques. These patterns can be used by healthcare practitioners to make forecasts, put diagnoses, and set treatments for patients in healthcare organizations.

  9. GarlicESTdb: an online database and mining tool for garlic EST sequences

    Directory of Open Access Journals (Sweden)

    Choi Sang-Haeng

    2009-05-01

    Full Text Available Abstract Background Allium sativum., commonly known as garlic, is a species in the onion genus (Allium, which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression. Description GarlicESTdb is an integrated database and mining tool for large-scale garlic (Allium sativum EST sequencing. A total of 21,595 ESTs collected from an in-house cDNA library were used to construct the database. The analysis pipeline is an automated system written in JAVA and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, storage of the analyzed information into MySQL databases, and graphic display of all processed data. A web application was implemented with the latest J2EE (Java 2 Platform Enterprise Edition software technology (JSP/EJB/JavaServlet for browsing and querying the database, for creation of dynamic web pages on the client side, and for mapping annotated enzymes to KEGG pathways, the AJAX framework was also used partially. The online resources, such as putative annotation, single nucleotide polymorphisms (SNP and tandem repeat data sets, can be searched by text, explored on the website, searched using BLAST, and downloaded. To archive more significant BLAST results, a curation system was introduced with which biologists can easily edit best-hit annotation

  10. Safety Research and Experimental Coal Mines

    Data.gov (United States)

    Federal Laboratory Consortium — Safety Research and Experimental Coal MinesLocation: Pittsburgh SiteThe Safety Research Coal Mine and Experimental Mine complex is a multi-purpose underground mine...

  11. Colombia, mining country. Vision a year 2019

    International Nuclear Information System (INIS)

    2006-01-01

    Scope of the state action for the mining sector, the performance of the mining sector, regional perceptions of mining development, construction of a long-term vision for the mining sector, the action plan and goals follow-up

  12. Genomic Imprinting

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 9. Genomic Imprinting - Some Interesting Implications for the Evolution of Social Behaviour. Raghavendra Gadagkar. General Article Volume 5 Issue 9 September 2000 pp 58-68 ...

  13. Recent developments in coal mining technology and their impact on miners' health.

    Science.gov (United States)

    Taylor, L D; Thakur, P C

    1993-01-01

    Advances in technology have significantly reduced the long-term health risks associated with underground coal mining. While the potential risks include exposure to hazardous substances and noise, the reduction of respirable dust in the workplace has been emphasized here because of the greater probability of exposure and the well-documented consequences. Since enactment of the Mine Health and Safety Act of 1969, great strides have been made in reducing worker exposure to respirable dust. As production rates continue to increase, particularly in longwall sections, continued advances in dust control technology will be required. These advances will be needed to meet existing, and perhaps even more stringent future, exposure limits. Mechanization has resulted in a significant reduction in exposure to hazards while increasing productivity. Use of remotely controlled equipment is also increasing rapidly, and efforts are underway to develop completely automated mining systems. These automated systems may further reduce the risk of health impairment due to the underground working environment.

  14. The Mining Rescue Service

    Energy Technology Data Exchange (ETDEWEB)

    Karabelly, J.

    1989-01-01

    The Czechoslovak Mining Rescue Service has been in existence for very many years. Its legal status was derived from safety regulations. New laws that became effective in 1988 are the first to specify that organizations engaged in mining acitivities are obliged to provide these services. Excerpts of important paragraphs and a brief summary of these laws are given. They show that many details of the Service's operations, structure, reponsibilities, powers and personnel selection are determined by law. The Rescue Service is also active in accident prevention. An important control function in respect to the activities of the Service and resources to be allocated to it is given to the various levels of mining inspectorates.

  15. Auxiliary mine ventilation manual

    International Nuclear Information System (INIS)

    Workplace Safety North

    2010-01-01

    An adequate ventilation system is needed for air quality and handling in a mine and is comprised of many different pieces of equipment for removing contaminated air and supplying fresh air and thereby provide a satisfactory working environment. This manual highlights auxiliary ventilation systems made up of small fans, ducts, tubes, air movers, deflectors and additional air flow controls which distribute fresh air delivered by the primary system to all areas. A review of auxiliary ventilation is provided. Design, operation and management issues are discussed and guidelines are furnished. This manual is limited to underground hard rock operations and does not address directly other, specific auxiliary systems, either in underground coal mines or uranium mines.

  16. Data mining methods

    CERN Document Server

    Chattamvelli, Rajan

    2015-01-01

    DATA MINING METHODS, Second Edition discusses both theoretical foundation and practical applications of datamining in a web field including banking, e-commerce, medicine, engineering and management. This book starts byintroducing data and information, basic data type, data category and applications of data mining. The second chapterbriefly reviews data visualization technology and importance in data mining. Fundamentals of probability and statisticsare discussed in chapter 3, and novel algorithm for sample covariants are derived. The next two chapters give an indepthand useful discussion of data warehousing and OLAP. Decision trees are clearly explained and a new tabularmethod for decision tree building is discussed. The chapter on association rules discusses popular algorithms andcompares various algorithms in summary table form. An interesting application of genetic algorithm is introduced inthe next chapter. Foundations of neural networks are built from scratch and the back propagation algorithm is derived...

  17. Mining and the environment

    International Nuclear Information System (INIS)

    Janecka, V.; Nemec, V.; Bradka, S.; Placek, V.; Sulovsky, P.

    1992-01-01

    The proceedings contain 30 contributions, out of which 9 have been inputted in INIS. They are concerned with uranium mines and mills in the Czech Republic. The impacts of the mining activities and of the mill tailings on the environment and the population are assessed, and it is concluded that the radiation hazard does not exceed that from natural background. Considerable attention is paid to the monitoring of the surroundings of mines and mills and to landscaping activities. Proposed technologies for the purification of waste waters from the chemical leaching process are described. Ways to eliminate environmental damage from abandoned tailings settling ponds are suggested. (M.D.). 18 tabs., 21 figs., 43 refs

  18. Journey from Data Mining to Web Mining to Big Data

    OpenAIRE

    Gupta, Richa

    2014-01-01

    This paper describes the journey of big data starting from data mining to web mining to big data. It discusses each of this method in brief and also provides their applications. It states the importance of mining big data today using fast and novel approaches.

  19. Unsupervised Tensor Mining for Big Data Practitioners.

    Science.gov (United States)

    Papalexakis, Evangelos E; Faloutsos, Christos

    2016-09-01

    Multiaspect data are ubiquitous in modern Big Data applications. For instance, different aspects of a social network are the different types of communication between people, the time stamp of each interaction, and the location associated to each individual. How can we jointly model all those aspects and leverage the additional information that they introduce to our analysis? Tensors, which are multidimensional extensions of matrices, are a principled and mathematically sound way of modeling such multiaspect data. In this article, our goal is to popularize tensors and tensor decompositions to Big Data practitioners by demonstrating their effectiveness, outlining challenges that pertain to their application in Big Data scenarios, and presenting our recent work that tackles those challenges. We view this work as a step toward a fully automated, unsupervised tensor mining tool that can be easily and broadly adopted by practitioners in academia and industry.

  20. Worldwide ISL Uranium Mining Outlook

    International Nuclear Information System (INIS)

    Boytsov, A.; Stander, S.; Martynenko, V.

    2014-01-01

    Contents: • ISL uranium production historical review and current status; • ISL versus conventional mining; • Acid versus alkaline ISL; • ISL cost considerations; • Principal criteria and parameters for ISL mining; • ISL production forecast and resources availability

  1. Swedish mines. Underground exploitation methods

    International Nuclear Information System (INIS)

    Paucard, A.

    1960-01-01

    Between 1949 and 1957, 10 engineers of the Mining research and exploitation department of the CEA visited 17 Swedish mines during 5 field trips. This paper presents a compilation of the information gathered during these field trips concerning the different underground mining techniques used in Swedish iron mines: mining with backfilling (Central Sweden and Boliden mines); mining without backfilling (mines of the polar circle area). The following techniques are described successively: pillar drawing and backfilled slices (Ammeberg, Falun, Garpenberg, Boliden group), sub-level pillar drawing (Grangesberg, Bloettberget, Haeksberg), empty room and sub-level pillar drawing (Bodas, Haksberg, Stripa, Bastkarn), storage chamber pillar drawing (Bodas, Haeksberg, Bastkarn), and pillar drawing by block caving (ldkerberget). Reprint of a paper published in Revue de l'Industrie Minerale, vol. 41, no. 12, 1959 [fr

  2. Gravity in a Mine Shaft.

    Science.gov (United States)

    Hall, Peter M.; Hall, David J.

    1995-01-01

    Discusses the effects of gravity, local density compared to the density of the earth, the mine shaft, centrifugal force, and air buoyancy on the weight of an object at the top and at the bottom of a mine shaft. (JRH)

  3. Generate a bioactive natural product library by mining bacterial cytochrome P450 patterns.

    Science.gov (United States)

    Liu, Xiangyang

    2016-06-01

    The increased number of annotated bacterial genomes provides a vast resource for genome mining. Several bacterial natural products with epoxide groups have been identified as pre-mRNA spliceosome inhibitors and antitumor compounds through genome mining. These epoxide-containing natural products feature a common biosynthetic characteristic that cytochrome P450s (CYPs) and its patterns such as epoxidases are employed in the tailoring reactions. The tailoring enzyme patterns are essential to both biological activities and structural diversity of natural products, and can be used for enzyme pattern-based genome mining. Recent development of direct cloning, heterologous expression, manipulation of the biosynthetic pathways and the CRISPR-CAS9 system have provided molecular biology tools to turn on or pull out nascent biosynthetic gene clusters to generate a microbial natural product library. This review focuses on a library of epoxide-containing natural products and their associated CYPs, with the intention to provide strategies on diversifying the structures of CYP-catalyzed bioactive natural products. It is conceivable that a library of diversified bioactive natural products will be created by pattern-based genome mining, direct cloning and heterologous expression as well as the genomic manipulation.

  4. Data mining mobile devices

    CERN Document Server

    Mena, Jesus

    2013-01-01

    With today's consumers spending more time on their mobiles than on their PCs, new methods of empirical stochastic modeling have emerged that can provide marketers with detailed information about the products, content, and services their customers desire.Data Mining Mobile Devices defines the collection of machine-sensed environmental data pertaining to human social behavior. It explains how the integration of data mining and machine learning can enable the modeling of conversation context, proximity sensing, and geospatial location throughout large communities of mobile users

  5. Data mining for dummies

    CERN Document Server

    Brown, Meta S

    2014-01-01

    Delve into your data for the key to success Data mining is quickly becoming integral to creating value and business momentum. The ability to detect unseen patterns hidden in the numbers exhaustively generated by day-to-day operations allows savvy decision-makers to exploit every tool at their disposal in the pursuit of better business. By creating models and testing whether patterns hold up, it is possible to discover new intelligence that could change your business''s entire paradigm for a more successful outcome. Data Mining for Dummies shows you why it doesn''t take a data scientist to gain

  6. A STUDY OF TEXT MINING METHODS, APPLICATIONS,AND TECHNIQUES

    OpenAIRE

    R. Rajamani*1 & S. Saranya2

    2017-01-01

    Data mining is used to extract useful information from the large amount of data. It is used to implement and solve different types of research problems. The research related areas in data mining are text mining, web mining, image mining, sequential pattern mining, spatial mining, medical mining, multimedia mining, structure mining and graph mining. Text mining also referred to text of data mining, it is also called knowledge discovery in text (KDT) or knowledge of intelligent text analysis. T...

  7. WIRELESS MINE WIDE TELECOMMUNICATIONS TECHNOLOGY

    Energy Technology Data Exchange (ETDEWEB)

    Zvi H. Meiksin

    2002-04-01

    Two industrial prototype units for through-the-earth wireless communication were constructed and tested. Preparation for a temporary installation in NIOSH's Lake Lynn mine for the through-the-earth and the in-mine system were completed. Progress was made in the programming of the in-mine system to provide data communication. Work has begun to implement a wireless interface between equipment controllers and our in-mine system.

  8. Comparative Opinion Mining: A Review

    OpenAIRE

    Varathan, Kasturi Dewi; Giachanou, Anastasia; Crestani, Fabio

    2017-01-01

    Opinion mining refers to the use of natural language processing, text analysis and computational linguistics to identify and extract subjective information in textual material. Opinion mining, also known as sentiment analysis, has received a lot of attention in recent times, as it provides a number of tools to analyse the public opinion on a number of different topics. Comparative opinion mining is a subfield of opinion mining that deals with identifying and extracting information that is exp...

  9. WIRELESS MINE WIDE TELECOMMUNICATIONS TECHNOLOGY

    International Nuclear Information System (INIS)

    Zvi H. Meiksin

    2002-01-01

    Two industrial prototype units for through-the-earth wireless communication were constructed and tested. Preparation for a temporary installation in NIOSH's Lake Lynn mine for the through-the-earth and the in-mine system were completed. Progress was made in the programming of the in-mine system to provide data communication. Work has begun to implement a wireless interface between equipment controllers and our in-mine system

  10. 30 CFR 77.1200 - Mine map.

    Science.gov (United States)

    2010-07-01

    ... Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR COAL MINE SAFETY AND HEALTH MANDATORY SAFETY STANDARDS, SURFACE COAL MINES AND SURFACE WORK AREAS OF UNDERGROUND COAL MINES Maps § 77.1200 Mine... boundary lines of the active areas of the mine; (c) Contour lines passing through whole number elevations...

  11. 78 FR 39531 - Mine Rescue Teams

    Science.gov (United States)

    2013-07-01

    ... Requirements for Underground Coal Mine Operators and Mine Rescue Teams Type of mine rescue team Requirement Mine-site Composite Contract State-sponsored * * * * * * * Team must include at least two YES active employees from each covered large mine and at least one active employee from each covered small mine. Team...

  12. 30 CFR 75.1200 - Mine map.

    Science.gov (United States)

    2010-07-01

    ... Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR COAL MINE SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Maps § 75.1200 Mine map. The operator of a coal mine shall have... mine drawn on scale. Such map shall show: (a) The active workings; (b) All pillared, worked out, and...

  13. in remediating acid mine drainage

    African Journals Online (AJOL)

    The management and treatment of contaminated mine water is one of the most urgent problems facing the South African mining industry. The cost advantage of permeable reactive barriers (PRBs) has seen their increased application as means of passively treating mine drainage. A PRB is built by placing a reactive material ...

  14. Review of South American mines

    International Nuclear Information System (INIS)

    Anon.

    1984-01-01

    A general overview is presented of the mining activity and plans for South America. The countries which are presented are Columbia, Argentina, Brazil, Venezuela, Chile, Peru, and Bolivia. The products of the mines include coal, bauxite, gold, iron, uranium, copper and numerous other minor materials. A discussion of current production, support and processing facilities, and mining strategies is also given

  15. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    Energy Technology Data Exchange (ETDEWEB)

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R

    2007-12-10

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  16. Genome-wide scale-free network inference for Candida albicans

    Directory of Open Access Journals (Sweden)

    Robert eAltwasser

    2012-02-01

    Full Text Available Discovery of essential genes in pathogenic organisms is an important step in the development of new medication. Despite a growing number of genome data available, still little is known about C. albicans, the major fungal pathogen. Most of the human population carries C. albicans as commensal, but it can cause systemic infection that may lead to the death of the host if the immune system is deteriorated. In many organisms central nodes in the interaction network (hubs play a crucial role for information and energy transport. Indeed, knock-outs of such hubs often leads to lethal phenotypes making them interesting drug targets. To identify these central genes via topological analysis, we inferred gene regulatory networks that are of sparse and scale-free. We collected information from various sources of information as prior knowledge to complement the limited expression data available. We utilise a linear regression algorithm to infer genome-wide gene regulatory interaction networks. To evaluate the predictive power of our approach, we used an automated text-mining system that scanned full-text research papers for known interactions. With the help of the compendium of known interactions, we also optimise the influence of the prior knowledge we obtained and the sparseness of the model to achieve best results. We compare the results of our approach with those of other state-of-the-art network inference methods and show that we outperform these methods. Finally we identified a number of hubs in the genome of the fungus and investigate their biological relevance.

  17. Microarray data and gene expression statistics for Saccharomyces cerevisiae exposed to simulated asbestos mine drainage

    Directory of Open Access Journals (Sweden)

    Heather E. Driscoll

    2017-08-01

    Full Text Available Here we describe microarray expression data (raw and normalized, experimental metadata, and gene-level data with expression statistics from Saccharomyces cerevisiae exposed to simulated asbestos mine drainage from the Vermont Asbestos Group (VAG Mine on Belvidere Mountain in northern Vermont, USA. For nearly 100 years (between the late 1890s and 1993, chrysotile asbestos fibers were extracted from serpentinized ultramafic rock at the VAG Mine for use in construction and manufacturing industries. Studies have shown that water courses and streambeds nearby have become contaminated with asbestos mine tailings runoff, including elevated levels of magnesium, nickel, chromium, and arsenic, elevated pH, and chrysotile asbestos-laden mine tailings, due to leaching and gradual erosion of massive piles of mine waste covering approximately 9 km2. We exposed yeast to simulated VAG Mine tailings leachate to help gain insight on how eukaryotic cells exposed to VAG Mine drainage may respond in the mine environment. Affymetrix GeneChip® Yeast Genome 2.0 Arrays were utilized to assess gene expression after 24-h exposure to simulated VAG Mine tailings runoff. The chemistry of mine-tailings leachate, mine-tailings leachate plus yeast extract peptone dextrose media, and control yeast extract peptone dextrose media is also reported. To our knowledge this is the first dataset to assess global gene expression patterns in a eukaryotic model system simulating asbestos mine tailings runoff exposure. Raw and normalized gene expression data are accessible through the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO Database Series GSE89875 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE89875.

  18. Data mining-aided materials discovery and optimization

    Directory of Open Access Journals (Sweden)

    Wencong Lu

    2017-09-01

    Full Text Available Recent developments in data mining-aided materials discovery and optimization are reviewed in this paper, and an introduction to the materials data mining (MDM process is provided using case studies. Both qualitative and quantitative methods in machine learning can be adopted in the MDM process to accomplish different tasks in materials discovery, design, and optimization. State-of-the-art techniques in data mining-aided materials discovery and optimization are demonstrated by reviewing the controllable synthesis of dendritic Co3O4 superstructures, materials design of layered double hydroxide, battery materials discovery, and thermoelectric materials design. The results of the case studies indicate that MDM is a powerful approach for use in materials discovery and innovation, and will play an important role in the development of the Materials Genome Initiative and Materials Informatics.

  19. Automated campaign system

    Science.gov (United States)

    Vondran, Gary; Chao, Hui; Lin, Xiaofan; Beyer, Dirk; Joshi, Parag; Atkins, Brian; Obrador, Pere

    2006-02-01

    To run a targeted campaign involves coordination and management across numerous organizations and complex process flows. Everything from market analytics on customer databases, acquiring content and images, composing the materials, meeting the sponsoring enterprise brand standards, driving through production and fulfillment, and evaluating results; all processes are currently performed by experienced highly trained staff. Presented is a developed solution that not only brings together technologies that automate each process, but also automates the entire flow so that a novice user could easily run a successful campaign from their desktop. This paper presents the technologies, structure, and process flows used to bring this system together. Highlighted will be how the complexity of running a targeted campaign is hidden from the user through technologies, all while providing the benefits of a professionally managed campaign.

  20. Rapid automated nuclear chemistry

    International Nuclear Information System (INIS)

    Meyer, R.A.

    1979-01-01

    Rapid Automated Nuclear Chemistry (RANC) can be thought of as the Z-separation of Neutron-rich Isotopes by Automated Methods. The range of RANC studies of fission and its products is large. In a sense, the studies can be categorized into various energy ranges from the highest where the fission process and particle emission are considered, to low energies where nuclear dynamics are being explored. This paper presents a table which gives examples of current research using RANC on fission and fission products. The remainder of this text is divided into three parts. The first contains a discussion of the chemical methods available for the fission product elements, the second describes the major techniques, and in the last section, examples of recent results are discussed as illustrations of the use of RANC