Sample records for accurate finished sequence

  1. Approaches for in silico finishing of microbial genome sequences

    PubMed Central

    Kremer, Frederico Schmitt; McBride, Alan John Alexander; Pinto, Luciano da Silva

    2017-01-01

    Abstract The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as “drafts”, incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases) tools that are available to facilitate genome finishing. PMID:28898352

  2. Approaches for in silico finishing of microbial genome sequences.

    PubMed

    Kremer, Frederico Schmitt; McBride, Alan John Alexander; Pinto, Luciano da Silva

    The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as "drafts", incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases) tools that are available to facilitate genome finishing.

  3. A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Jr., Richard A.

    This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted.more » PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Furthermore, our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.« less

  4. A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

    DOE PAGES

    Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Jr., Richard A.; ...

    2017-07-18

    This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted.more » PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Furthermore, our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.« less

  5. A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies.

    PubMed

    Utturkar, Sagar M; Klingeman, Dawn M; Hurt, Richard A; Brown, Steven D

    2017-01-01

    This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.

  6. A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

    PubMed Central

    Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Richard A.; Brown, Steven D.

    2017-01-01

    This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences. PMID:28769883

  7. Nearly Finished Genomes Produced Using Gel Microdroplet Culturing (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fitzsimmons, Michael

    2012-06-01

    Michael Fitzsimmons from Los Alamos National Laboratory gives a talk titled "Nearly Finished Genomes Produced Using Gel Microdroplet Culturing" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  8. Nearly Finished Genomes Produced Using Gel Microdroplet Culturing (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Fitzsimmons, Michael

    2018-01-22

    Michael Fitzsimmons from Los Alamos National Laboratory gives a talk titled "Nearly Finished Genomes Produced Using Gel Microdroplet Culturing" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  9. Automated Finishing with Autofinish

    PubMed Central

    Gordon, David; Desmarais, Cindy; Green, Phil

    2001-01-01

    Currently, the genome sequencing community is producing shotgun sequence data at a very high rate, but finishing (collecting additional directed sequence data to close gaps and improve the quality of the data) is not matching that rate. One reason for the difference is that shotgun sequencing is highly automated but finishing is not: Most finishing decisions, such as which directed reads to obtain and which specialized sequencing techniques to use, are made by people. If finishing rates are to increase to match shotgun sequencing rates, most finishing decisions also must be automated. The Autofinish computer program (which is part of the Consed computer software package) does this by automatically choosing finishing reads. Autofinish is able to suggest most finishing reads required for completion of each sequencing project, greatly reducing the amount of human attention needed. Autofinish sometimes completely finishes the project, with no human decisions required. It cannot solve the most complex problems, so we recommend that Autofinish be allowed to suggest reads for the first three rounds of finishing, and if the project still is not finished completely, a human finisher complete the work. We compared this Autofinish-Hybrid method of finishing against a human finisher in five different projects with a variety of shotgun depths by finishing each project twice—once with each method. This comparison shows that the Autofinish-Hybrid method saves many hours over a human finisher alone, while using roughly the same number and type of reads and closing gaps at roughly the same rate. Autofinish currently is in production use at several large sequencing centers. It is designed to be adaptable to the finishing strategy of the lab—it can finish using some or all of the following: resequencing reads, reverses, custom primer walks on either subclone templates or whole clone templates, PCR, or minilibraries. Autofinish has been used for finishing cDNA, genomic clones, and

  10. Finished Prokaryotic Genome Assemblies from a Low-cost Combination of Short and Long Reads (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yin, Shuangye

    2012-06-01

    Shuangye Yin on "Finished prokaryotic genome assemblies from a low-cost combination of short and long reads"; at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  11. High Throughput Plasmid Sequencing with Illumina and CLC Bio (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Athavale, Ajay

    2018-01-04

    Ajay Athavale (Monsanto) presents "High Throughput Plasmid Sequencing with Illumina and CLC Bio" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  12. Finishing and Special Motifs: Lessons Learned from CRISPR Analysis Using Next-Generation Draft Sequences (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Campbell, Catherine

    2018-01-22

    Catherine Campbell on "Finishing and Special Motifs: Lessons learned from CRISPR analysis using next-generation draft sequences" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  13. Finishing and Special Motifs: Lessons Learned from CRISPR Analysis Using Next-Generation Draft Sequences (7th Annual SFAF Meeting, 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Campbell, Catherine

    Catherine Campbell on "Finishing and Special Motifs: Lessons learned from CRISPR analysis using next-generation draft sequences" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  14. Fast, accurate and easy-to-pipeline methods for amplicon sequence processing

    NASA Astrophysics Data System (ADS)

    Antonielli, Livio; Sessitsch, Angela

    2016-04-01

    Next generation sequencing (NGS) technologies established since years as an essential resource in microbiology. While on the one hand metagenomic studies can benefit from the continuously increasing throughput of the Illumina (Solexa) technology, on the other hand the spreading of third generation sequencing technologies (PacBio, Oxford Nanopore) are getting whole genome sequencing beyond the assembly of fragmented draft genomes, making it now possible to finish bacterial genomes even without short read correction. Besides (meta)genomic analysis next-gen amplicon sequencing is still fundamental for microbial studies. Amplicon sequencing of the 16S rRNA gene and ITS (Internal Transcribed Spacer) remains a well-established widespread method for a multitude of different purposes concerning the identification and comparison of archaeal/bacterial (16S rRNA gene) and fungal (ITS) communities occurring in diverse environments. Numerous different pipelines have been developed in order to process NGS-derived amplicon sequences, among which Mothur, QIIME and USEARCH are the most well-known and cited ones. The entire process from initial raw sequence data through read error correction, paired-end read assembly, primer stripping, quality filtering, clustering, OTU taxonomic classification and BIOM table rarefaction as well as alternative "normalization" methods will be addressed. An effective and accurate strategy will be presented using the state-of-the-art bioinformatic tools and the example of a straightforward one-script pipeline for 16S rRNA gene or ITS MiSeq amplicon sequencing will be provided. Finally, instructions on how to automatically retrieve nucleotide sequences from NCBI and therefore apply the pipeline to targets other than 16S rRNA gene (Greengenes, SILVA) and ITS (UNITE) will be discussed.

  15. Signature Peptide-Enabled Metagenomics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    McMahon, Ben

    2018-01-11

    Ben McMahon of Los Alamos National Laboratory (LANL) presents "Signature Peptide-Enabled Metagenomics" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  16. Signature Peptide-Enabled Metagenomics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    McMahon, Ben

    2012-06-01

    Ben McMahon of Los Alamos National Laboratory (LANL) presents "Signature Peptide-Enabled Metagenomics" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  17. Draft versus finished sequence data for DNA and protein diagnostic signature development

    PubMed Central

    Gardner, Shea N.; Lam, Marisa W.; Smith, Jason R.; Torres, Clinton L.; Slezak, Tom R.

    2005-01-01

    Sequencing pathogen genomes is costly, demanding careful allocation of limited sequencing resources. We built a computational Sequencing Analysis Pipeline (SAP) to guide decisions regarding the amount of genomic sequencing necessary to develop high-quality diagnostic DNA and protein signatures. SAP uses simulations to estimate the number of target genomes and close phylogenetic relatives (near neighbors or NNs) to sequence. We use SAP to assess whether draft data are sufficient or finished sequencing is required using Marburg and variola virus sequences. Simulations indicate that intermediate to high-quality draft with error rates of 10−3–10−5 (∼8× coverage) of target organisms is suitable for DNA signature prediction. Low-quality draft with error rates of ∼1% (3× to 6× coverage) of target isolates is inadequate for DNA signature prediction, although low-quality draft of NNs is sufficient, as long as the target genomes are of high quality. For protein signature prediction, sequencing errors in target genomes substantially reduce the detection of amino acid sequence conservation, even if the draft is of high quality. In summary, high-quality draft of target and low-quality draft of NNs appears to be a cost-effective investment for DNA signature prediction, but may lead to underestimation of predicted protein signatures. PMID:16243783

  18. The PerkinElmer Omics Laboratory (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Smith, Todd

    2017-12-22

    Todd Smith of the PerkinElmer Omics Laboratory gives a talk about his lab and its work at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  19. The PerkinElmer Omics Laboratory (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Smith, Todd

    2012-06-01

    Todd Smith of the PerkinElmer Omics Laboratory gives a talk about his lab and its work at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  20. Finishing Using Next Generation Technologies

    ScienceCinema

    Van Tonder, Andries

    2018-01-16

    Andries van Tonder of Wellcome Trust Sanger Institute discusses a pipeline for finishing genomes to the gold standard on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  1. Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Patel, Kamlesh D.

    2018-01-22

    Kamlesh (Ken) Patel from Sandia National Laboratories (Livermore, California) presents "Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology " at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  2. Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Patel, Kamlesh D.

    2012-06-01

    Kamlesh (Ken) Patel from Sandia National Laboratories (Livermore, California) presents "Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology " at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  3. Sequencing intractable DNA to close microbial genomes.

    PubMed

    Hurt, Richard A; Brown, Steven D; Podar, Mircea; Palumbo, Anthony V; Elias, Dwayne A

    2012-01-01

    Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  4. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.

    PubMed

    Chin, Chen-Shan; Alexander, David H; Marks, Patrick; Klammer, Aaron A; Drake, James; Heiner, Cheryl; Clum, Alicia; Copeland, Alex; Huddleston, John; Eichler, Evan E; Turner, Stephen W; Korlach, Jonas

    2013-06-01

    We present a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing. Our method uses the longest reads as seeds to recruit all other reads for construction of highly accurate preassembled reads through a directed acyclic graph-based consensus procedure, which we follow with assembly using off-the-shelf long-read assemblers. In contrast to hybrid approaches, HGAP does not require highly accurate raw reads for error correction. We demonstrate efficient genome assembly for several microorganisms using as few as three SMRT Cell zero-mode waveguide arrays of sequencing and for BACs using just one SMRT Cell. Long repeat regions can be successfully resolved with this workflow. We also describe a consensus algorithm that incorporates SMRT sequencing primary quality values to produce de novo genome sequence exceeding 99.999% accuracy.

  5. Arbitrarily accurate twin composite π -pulse sequences

    NASA Astrophysics Data System (ADS)

    Torosov, Boyan T.; Vitanov, Nikolay V.

    2018-04-01

    We present three classes of symmetric broadband composite pulse sequences. The composite phases are given by analytic formulas (rational fractions of π ) valid for any number of constituent pulses. The transition probability is expressed by simple analytic formulas and the order of pulse area error compensation grows linearly with the number of pulses. Therefore, any desired compensation order can be produced by an appropriate composite sequence; in this sense, they are arbitrarily accurate. These composite pulses perform equally well as or better than previously published ones. Moreover, the current sequences are more flexible as they allow total pulse areas of arbitrary integer multiples of π .

  6. Introducing National Center for Genome Resources (NCGR) Informatics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Crow, John

    2018-01-22

    John Crow from the National Center for Genome Resources discusses his organization's informatics at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  7. Introducing National Center for Genome Resources (NCGR) Informatics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Crow, John

    2012-06-01

    John Crow from the National Center for Genome Resources discusses his organization's informatics at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  8. Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Sexton, David

    2018-01-22

    David Sexton (Baylor) gives a talk titled "Mercury: Next-gen Data Analysis and Annotation Pipeline" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  9. Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sexton, David

    2012-06-01

    David Sexton (Baylor) gives a talk titled "Mercury: Next-gen Data Analysis and Annotation Pipeline" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  10. A Hybrid Approach for the Automated Finishing of Bacterial Genomes

    PubMed Central

    Robins, William P.; Chin, Chen-Shan; Webster, Dale; Paxinos, Ellen; Hsu, David; Ashby, Meredith; Wang, Susana; Peluso, Paul; Sebra, Robert; Sorenson, Jon; Bullard, James; Yen, Jackie; Valdovino, Marie; Mollova, Emilia; Luong, Khai; Lin, Steven; LaMay, Brianna; Joshi, Amruta; Rowe, Lori; Frace, Michael; Tarr, Cheryl L.; Turnsek, Maryann; Davis, Brigid M; Kasarskis, Andrew; Mekalanos, John J.; Waldor, Matthew K.; Schadt, Eric E.

    2013-01-01

    Dramatic improvements in DNA sequencing technology have revolutionized our ability to characterize most genomic diversity. However, accurate resolution of large structural events has remained challenging due to the comparatively shorter read lengths of second-generation technologies. Emerging third-generation sequencing technologies, which yield markedly increased read length on rapid time scales and for low cost, have the potential to address assembly limitations. Here we combine sequencing data from second- and third-generation DNA sequencing technologies to assemble the two-chromosome genome of a recent Haitian cholera outbreak strain into two nearly finished contigs at > 99.9% accuracy. Complex regions with clinically significant structure were completely resolved. In separate control assemblies on experimental and simulated data for the canonical N16961 reference we obtain 14 and 8 scaffolds greater than 1kb, respectively, correcting several errors in the underlying source data. This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly. PMID:22750883

  11. Finished Genome Sequence of Bacillus cereus Strain 03BB87, a Clinical Isolate with B. anthracis Virulence Genes

    DOE PAGES

    Johnson, Shannon L.; Minogue, Timothy D.; Teshima, Hazuki; ...

    2015-01-15

    Bacillus cereus strain 03BB87, a blood culture isolate, originated in a 56-year-old male muller operator with a fatal case of pneumonia in 2003. Here we present the finished genome sequence of that pathogen, including a 5.46-Mb chromosome and two plasmids (209 and 52 Kb, respectively).

  12. Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the “Finished” C. elegans Genome

    PubMed Central

    Li, Runsheng; Hsieh, Chia-Ling; Young, Amanda; Zhang, Zhihong; Ren, Xiaoliang; Zhao, Zhongying

    2015-01-01

    Most next-generation sequencing platforms permit acquisition of high-throughput DNA sequences, but the relatively short read length limits their use in genome assembly or finishing. Illumina has recently released a technology called Synthetic Long-Read Sequencing that can produce reads of unusual length, i.e., predominately around 10 Kb. However, a systematic assessment of their use in genome finishing and assembly is still lacking. We evaluate the promise and deficiency of the long reads in these aspects using isogenic C. elegans genome with no gap. First, the reads are highly accurate and capable of recovering most types of repetitive sequences. However, the presence of tandem repetitive sequences prevents pre-assembly of long reads in the relevant genomic region. Second, the reads are able to reliably detect missing but not extra sequences in the C. elegans genome. Third, the reads of smaller size are more capable of recovering repetitive sequences than those of bigger size. Fourth, at least 40 Kbp missing genomic sequences are recovered in the C. elegans genome using the long reads. Finally, an N50 contig size of at least 86 Kbp can be achieved with 24×reads but with substantial mis-assembly errors, highlighting a need for novel assembly algorithm for the long reads. PMID:26039588

  13. Rapid Identification of Sequences for Orphan Enzymes to Power Accurate Protein Annotation

    PubMed Central

    Ojha, Sunil; Watson, Douglas S.; Bomar, Martha G.; Galande, Amit K.; Shearer, Alexander G.

    2013-01-01

    The power of genome sequencing depends on the ability to understand what those genes and their proteins products actually do. The automated methods used to assign functions to putative proteins in newly sequenced organisms are limited by the size of our library of proteins with both known function and sequence. Unfortunately this library grows slowly, lagging well behind the rapid increase in novel protein sequences produced by modern genome sequencing methods. One potential source for rapidly expanding this functional library is the “back catalog” of enzymology – “orphan enzymes,” those enzymes that have been characterized and yet lack any associated sequence. There are hundreds of orphan enzymes in the Enzyme Commission (EC) database alone. In this study, we demonstrate how this orphan enzyme “back catalog” is a fertile source for rapidly advancing the state of protein annotation. Starting from three orphan enzyme samples, we applied mass-spectrometry based analysis and computational methods (including sequence similarity networks, sequence and structural alignments, and operon context analysis) to rapidly identify the specific sequence for each orphan while avoiding the most time- and labor-intensive aspects of typical sequence identifications. We then used these three new sequences to more accurately predict the catalytic function of 385 previously uncharacterized or misannotated proteins. We expect that this kind of rapid sequence identification could be efficiently applied on a larger scale to make enzymology’s “back catalog” another powerful tool to drive accurate genome annotation. PMID:24386392

  14. Rapid identification of sequences for orphan enzymes to power accurate protein annotation.

    PubMed

    Ramkissoon, Kevin R; Miller, Jennifer K; Ojha, Sunil; Watson, Douglas S; Bomar, Martha G; Galande, Amit K; Shearer, Alexander G

    2013-01-01

    The power of genome sequencing depends on the ability to understand what those genes and their proteins products actually do. The automated methods used to assign functions to putative proteins in newly sequenced organisms are limited by the size of our library of proteins with both known function and sequence. Unfortunately this library grows slowly, lagging well behind the rapid increase in novel protein sequences produced by modern genome sequencing methods. One potential source for rapidly expanding this functional library is the "back catalog" of enzymology--"orphan enzymes," those enzymes that have been characterized and yet lack any associated sequence. There are hundreds of orphan enzymes in the Enzyme Commission (EC) database alone. In this study, we demonstrate how this orphan enzyme "back catalog" is a fertile source for rapidly advancing the state of protein annotation. Starting from three orphan enzyme samples, we applied mass-spectrometry based analysis and computational methods (including sequence similarity networks, sequence and structural alignments, and operon context analysis) to rapidly identify the specific sequence for each orphan while avoiding the most time- and labor-intensive aspects of typical sequence identifications. We then used these three new sequences to more accurately predict the catalytic function of 385 previously uncharacterized or misannotated proteins. We expect that this kind of rapid sequence identification could be efficiently applied on a larger scale to make enzymology's "back catalog" another powerful tool to drive accurate genome annotation.

  15. PanFunPro: Bacterial Pan-Genome Analysis Based on the Functional Profiles (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lukjancenko, Oksana

    2012-06-01

    Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  16. PanFunPro: Bacterial Pan-Genome Analysis Based on the Functional Profiles (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Lukjancenko, Oksana

    2018-01-10

    Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  17. SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences.

    PubMed

    Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

    2008-05-01

    Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of the features, which are

  18. SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences

    PubMed Central

    Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

    2008-01-01

    Background Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. Results SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. Conclusion The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of

  19. Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing

    PubMed Central

    Eastman, Alexander W.; Yuan, Ze-Chun

    2015-01-01

    Advances in sequencing technology have drastically increased the depth and feasibility of bacterial genome sequencing. However, little information is available that details the specific techniques and procedures employed during genome sequencing despite the large numbers of published genomes. Shotgun approaches employed by second-generation sequencing platforms has necessitated the development of robust bioinformatics tools for in silico assembly, and complete assembly is limited by the presence of repetitive DNA sequences and multi-copy operons. Typically, re-sequencing with multiple platforms and laborious, targeted Sanger sequencing are employed to finish a draft bacterial genome. Here we describe a novel strategy based on the identification and targeted sequencing of repetitive rDNA operons to expedite bacterial genome assembly and finishing. Our strategy was validated by finishing the genome of Paenibacillus polymyxa strain CR1, a bacterium with potential in sustainable agriculture and bio-based processes. An analysis of the 38 contigs contained in the P. polymyxa strain CR1 draft genome revealed 12 repetitive rDNA operons with varied intragenic and flanking regions of variable length, unanimously located at contig boundaries and within contig gaps. These highly similar but not identical rDNA operons were experimentally verified and sequenced simultaneously with multiple, specially designed primer sets. This approach also identified and corrected significant sequence rearrangement generated during the initial in silico assembly of sequencing reads. Our approach reduces the required effort associated with blind primer walking for contig assembly, increasing both the speed and feasibility of genome finishing. Our study further reinforces the notion that repetitive DNA elements are major limiting factors for genome finishing. Moreover, we provided a step-by-step workflow for genome finishing, which may guide future bacterial genome finishing projects. PMID

  20. Accurate RNA consensus sequencing for high-fidelity detection of transcriptional mutagenesis-induced epimutations.

    PubMed

    Reid-Bayliss, Kate S; Loeb, Lawrence A

    2017-08-29

    Transcriptional mutagenesis (TM) due to misincorporation during RNA transcription can result in mutant RNAs, or epimutations, that generate proteins with altered properties. TM has long been hypothesized to play a role in aging, cancer, and viral and bacterial evolution. However, inadequate methodologies have limited progress in elucidating a causal association. We present a high-throughput, highly accurate RNA sequencing method to measure epimutations with single-molecule sensitivity. Accurate RNA consensus sequencing (ARC-seq) uniquely combines RNA barcoding and generation of multiple cDNA copies per RNA molecule to eliminate errors introduced during cDNA synthesis, PCR, and sequencing. The stringency of ARC-seq can be scaled to accommodate the quality of input RNAs. We apply ARC-seq to directly assess transcriptome-wide epimutations resulting from RNA polymerase mutants and oxidative stress.

  1. Sequencing the Unrearranged Human Immunoglobin

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Warren, Rene

    2010-06-03

    Rene Warren from Canada's Michael Smith Genome Sciences Centre discusses sequencing and finishing the IgH heavy chain locus on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  2. Reducing assembly complexity of microbial genomes with single-molecule sequencing.

    PubMed

    Koren, Sergey; Harhay, Gregory P; Smith, Timothy P L; Bono, James L; Harhay, Dayna M; Mcvey, Scott D; Radune, Diana; Bergman, Nicholas H; Phillippy, Adam M

    2013-01-01

    The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads. Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.

  3. [Complete genome sequencing and sequence analysis of BCG Tice].

    PubMed

    Wang, Zhiming; Pan, Yuanlong; Wu, Jun; Zhu, Baoli

    2012-10-04

    The objective of this study is to obtain the complete genome sequence of Bacillus Calmette-Guerin Tice (BCG Tice), in order to provide more information about the molecular biology of BCG Tice and design more reasonable vaccines to prevent tuberculosis. We assembled the data from high-throughput sequencing with SOAPdenovo software, with many contigs and scaffolds obtained. There are many sequence gaps and physical gaps remained as a result of regional low coverage and low quality. We designed primers at the end of contigs and performed PCR amplification in order to link these contigs and scaffolds. With various enzymes to perform PCR amplification, adjustment of PCR reaction conditions, and combined with clone construction to sequence, all the gaps were finished. We obtained the complete genome sequence of BCG Tice and submitted it to GenBank of National Center for Biotechnology Information (NCBI). The genome of BCG Tice is 4334064 base pairs in length, with GC content 65.65%. The problems and strategies during the finishing step of BCG Tice sequencing are illuminated here, with the hope of affording some experience to those who are involved in the finishing step of genome sequencing. The microarray data were verified by our results.

  4. Use of Optical Mapping in Bacterial Genome Finishing

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kumar, Dibyendu

    2010-06-03

    Dibyendu Kumar from the University of Florida discusses whole-genome optical mapping to help validate bacterial genome assemblies on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  5. Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

    PubMed Central

    Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Cornelissen, Marion; Kellam, Paul; Reiss, Peter

    2018-01-01

    Abstract Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user’s choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver’s constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also

  6. Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.

    PubMed

    Wymant, Chris; Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ong, Swee Hoe; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Berkhout, Ben; Cornelissen, Marion; Kellam, Paul; Reiss, Peter; Fraser, Christophe

    2018-01-01

    Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver's constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied

  7. Calibration and prediction of removal function in magnetorheological finishing.

    PubMed

    Dai, Yifan; Song, Ci; Peng, Xiaoqiang; Shi, Feng

    2010-01-20

    A calibrated and predictive model of the removal function has been established based on the analysis of a magnetorheological finishing (MRF) process. By introducing an efficiency coefficient of the removal function, the model can be used to calibrate the removal function in a MRF figuring process and to accurately predict the removal function of a workpiece to be polished whose material is different from the spot part. Its correctness and feasibility have been validated by simulations. Furthermore, applying this model to the MRF figuring experiments, the efficiency coefficient of the removal function can be identified accurately to make the MRF figuring process deterministic and controllable. Therefore, all the results indicate that the calibrated and predictive model of the removal function can improve the finishing determinacy and increase the model applicability in a MRF process.

  8. Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platform (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Tremblay, Julien

    2018-01-22

    Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  9. Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platform (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tremblay, Julien

    2012-06-01

    Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  10. SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

    PubMed

    Liu, Kevin; Warnow, Tandy J; Holder, Mark T; Nelesen, Serita M; Yu, Jiaye; Stamatakis, Alexandros P; Linder, C Randal

    2012-01-01

    Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of

  11. Superficial roughness on composite surface, composite-enamel and composite-dentin junctions after different finishing and polishing procedures. Part II: roughness with diamond finishing and differences between enamel composite vs body composite.

    PubMed

    Ferraris, Federico; Conti, Alessandro

    2014-01-01

    The following study asks three principle questions relative to composite finishing and composite polishing: 1) Will the superficial roughness of different restoration surfaces have different values, utilizing the same polishing system (multistep), after finishing with the tungsten carbide or diamond bur? 2) Under the same conditions of finishing and polishing sequences, will the composite surfaces (C), the composite-enamel (CE) and composite-dentin (CD) interfaces show different roughness values? 3) Will the surface roughness of composites of different translucency in the various phases of finishing and polishing, and on different interfaces, have different results? The null hypothesis is represented by the fact that there are no significant differences on roughness of composite restorations when polishing, after finishing with tungsten carbide or diamond burs. Furthermore, the null hypothesis is that there are no significant differences on roughness between polishing on composite surface, composite-enamel and composite-dentin interfaces, and finally there are no differences on roughness after finishing and polishing of two composite with different translucency. For the study, 56 class V cavities were prepared on extracted teeth. Restorations were done in nanofilled composite Filtek XTE (3M Espe) in a standard fashion, and then finished and polished. The 28 buccal cavities were restored on the surface with composite enamel and the 28 palatals with composite body. Finishing was done with fine toothing burs in tungsten carbide (16 blades) or fine grit diamond burs (46 μm), and made by the same manufacturer (Komet). The second phase of finishing was done with burs (with the same form as already mentioned) ultrafine toothing tungsten carbide (30 blades) or with extra and ultrafine grit diamond (25 and 8 μm). The polishing phase for both of the earlier sequences was done with the application of three rubber tips with decreasing abrasiveness and an application with a

  12. The Finish Line.

    ERIC Educational Resources Information Center

    Cohen, Andrew

    1998-01-01

    Details what is expected in a good floor finish for athletic facilities, and explores the different categories of finishes and their content within the context of environmental regulation and manufacturing standards. Also discusses urethane finishings, the debate over using waterbased finishes, and the influence of regulatory control that may…

  13. Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS.

    PubMed

    Warris, Sven; Yalcin, Feyruz; Jackson, Katherine J L; Nap, Jan Peter

    2015-01-01

    To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis. With the Parallel SW Alignment Software (PaSWAS) it is possible (a) to have easy access to the computational power of NVIDIA-based general purpose graphics processing units (GPGPUs) to perform high-speed sequence alignments, and (b) retrieve relevant information such as score, number of gaps and mismatches. The software reports multiple hits per alignment. The added value of the new SW implementation is demonstrated with two test cases: (1) tag recovery in next generation sequence data and (2) isotype assignment within an immunoglobulin 454 sequence data set. Both cases show the usability and versatility of the new parallel Smith-Waterman implementation.

  14. A Novel Method for Accurate Operon Predictions in All SequencedProkaryotes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Price, Morgan N.; Huang, Katherine H.; Alm, Eric J.

    2004-12-01

    We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83% accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized transcripts. In Halobacterium NRC-1 and in Helicobacterpylori, our method correctly infers that genes in operons are separated by shorter distances than they are in E.coli, andmore » its predictions using distance alone are more accurate than distance-only predictions trained on a database of E.coli transcripts. We use microarray data from sixphylogenetically diverse prokaryotes to show that combining intergenic distance with comparative genomic measures further improves accuracy and that our method is broadly effective. Finally, we survey operon structure across 124 genomes, and find several surprises: H.pylori has many operons, contrary to previous reports; Bacillus anthracis has an unusual number of pseudogenes within conserved operons; and Synechocystis PCC6803 has many operons even though it has unusually wide spacings between conserved adjacent genes.« less

  15. MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

    PubMed

    Lee, Wan-Ping; Stromberg, Michael P; Ward, Alistair; Stewart, Chip; Garrison, Erik P; Marth, Gabor T

    2014-01-01

    MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me).

  16. MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

    PubMed Central

    Lee, Wan-Ping; Stromberg, Michael P.; Ward, Alistair; Stewart, Chip; Garrison, Erik P.; Marth, Gabor T.

    2014-01-01

    MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me). PMID:24599324

  17. Abrasive wear of resin composites as related to finishing and polishing procedures.

    PubMed

    Turssi, Cecilia P; Ferracane, Jack L; Serra, Mônica C

    2005-07-01

    Finishing and polishing procedures may cause topographical changes and introduce subsurface microcracks in dental composite restoratives. Since both of these effects may contribute toward the kinetics of wear, the purpose of this study was to assess and correlate the wear and surface roughness of minifilled and nanofilled composites finished and polished by different methods. Specimens (n=10) made of a minifilled and a nanofilled composite were finished and polished with one of the four sequences: (1) tungsten carbide burs plus Al(2)O(3)-impregnated brush (CbBr) or (2) tungsten carbide burs plus diamond-impregnated cup (CbCp), (3) diamond burs plus brush (DmBr) or (4) diamond burs plus cup (DmCp). As a control, abrasive papers were used. After surface roughness had been quantified, three-body abrasion was simulated using the OHSU wear machine. The wear facets were then scanned to measure wear depth and post-testing roughness. All sets of data were subjected to ANOVA and Tukey's tests (alpha=0.05). Pearson's correlation test was applied to check for the existence of a relationship between pre-testing roughness and wear. Significantly smoother surfaces were attained with the sequences CbBr and CbCp, whereas DmCp yielded the roughest surface. Regardless of the finishing/polishing technique, the nanofilled composite exhibited the lowest pre-testing roughness and wear. There was no correlation between the surface roughness achieved after finishing/polishing procedures and wear (p=0.3899). Nano-sized materials may have improved abrasive wear resistance over minifilled composites. The absence of correlation between wear and surface roughness produced by different finishing/polishing methods suggests that the latter negligibly influences material loss due to three-body abrasion.

  18. Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

    PubMed Central

    Hillier, LaDeana W.; Zody, Michael C.; Goldstein, Steve; She, Xinwe; Bult, Carol J.; Agarwala, Richa; Cherry, Joshua L.; DiCuccio, Michael; Hlavina, Wratko; Kapustin, Yuri; Meric, Peter; Maglott, Donna; Birtle, Zoë; Marques, Ana C.; Graves, Tina; Zhou, Shiguo; Teague, Brian; Potamousis, Konstantinos; Churas, Christopher; Place, Michael; Herschleb, Jill; Runnheim, Ron; Forrest, Daniel; Amos-Landgraf, James; Schwartz, David C.; Cheng, Ze; Lindblad-Toh, Kerstin; Eichler, Evan E.; Ponting, Chris P.

    2009-01-01

    The mouse (Mus musculus) is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer gaps and over 139 Mb more of novel sequence, compared with the earlier MGSCv3 draft genome assembly. In a comprehensive analysis of this revised genome sequence, we are now able to define 20,210 protein-coding genes, over a thousand more than predicted in the human genome (19,042 genes). In addition, we identified 439 long, non–protein-coding RNAs with evidence for transcribed orthologs in human. We analyzed the complex and repetitive landscape of 267 Mb of sequence that was missing or misassembled in the previously published assembly, and we provide insights into the reasons for its resistance to sequencing and assembly by whole-genome shotgun approaches. Duplicated regions within newly assembled sequence tend to be of more recent ancestry than duplicates in the published draft, correcting our initial understanding of recent evolution on the mouse lineage. These duplicates appear to be largely composed of sequence regions containing transposable elements and duplicated protein-coding genes; of these, some may be fixed in the mouse population, but at least 40% of segmentally duplicated sequences are copy number variable even among laboratory mouse strains. Mouse lineage-specific regions contain 3,767 genes drawn mainly from rapidly-changing gene families associated with reproductive functions. The finished mouse genome assembly, therefore, greatly improves our understanding of rodent-specific biology and allows the delineation of ancestral biological functions that are shared with human from derived functions that are not. PMID:19468303

  19. Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

    PubMed Central

    Burger, Lukas; van Nimwegen, Erik

    2008-01-01

    Accurate and large-scale prediction of protein–protein interactions directly from amino-acid sequences is one of the great challenges in computational biology. Here we present a new Bayesian network method that predicts interaction partners using only multiple alignments of amino-acid sequences of interacting protein domains, without tunable parameters, and without the need for any training examples. We first apply the method to bacterial two-component systems and comprehensively reconstruct two-component signaling networks across all sequenced bacteria. Comparisons of our predictions with known interactions show that our method infers interaction partners genome-wide with high accuracy. To demonstrate the general applicability of our method we show that it also accurately predicts interaction partners in a recent dataset of polyketide synthases. Analysis of the predicted genome-wide two-component signaling networks shows that cognates (interacting kinase/regulator pairs, which lie adjacent on the genome) and orphans (which lie isolated) form two relatively independent components of the signaling network in each genome. In addition, while most genes are predicted to have only a small number of interaction partners, we find that 10% of orphans form a separate class of ‘hub' nodes that distribute and integrate signals to and from up to tens of different interaction partners. PMID:18277381

  20. Apical extrusion of debris during the preparation of oval root canals: a comparative study between a full-sequence SAF system and a rotary file system supplemented by XP-endo finisher file.

    PubMed

    Kfir, Anda; Moza-Levi, Rotem; Herteanu, Moran; Weissman, Amir; Wigler, Ronald

    2018-03-01

    The purpose of this study was to assess the amount of apically extruded debris during the preparation of oval canals with either a rotary file system supplemented by the XP-endo Finisher file or a full-sequence self-adjusting file (SAF) system. Sixty mandibular incisors were randomly assigned to two groups: group A: stage 1-glide path preparation with Pre-SAF instruments. Stage 2-cleaning and shaping with SAF. Group B: stage 1-glide path preparation with ProGlider file. Stage 2-cleaning and shaping with ProTaper Next system. Stage 3-Final cleaning with XP-endo Finisher file. The debris extruded during each of the stages was collected, and the debris weights were compared between the groups and between the stages within the groups using t tests with a significance level set at P < 0.05. The complete procedure for group B resulted in significantly more extruded debris compared to group A. There was no significant difference between the stages in group A, while there was a significant difference between stage 2 and stages 1 and 3 in group B, but no significant difference between stages 1 and 3. Both instrumentation protocols resulted in extruded debris. Rotary file followed by XP-endo Finisher file extruded significantly more debris than a full-sequence SAF system. Each stage, in either procedure, had its own contribution to the extrusion of debris. Final preparation with XP-endo Finisher file contributes to the total amount of extruded debris, but the clinical relevance of the relative difference in the amount of apically extruded debris remains unclear.

  1. Accurate Sample Assignment in a Multiplexed, Ultrasensitive, High-Throughput Sequencing Assay for Minimal Residual Disease.

    PubMed

    Bartram, Jack; Mountjoy, Edward; Brooks, Tony; Hancock, Jeremy; Williamson, Helen; Wright, Gary; Moppett, John; Goulden, Nick; Hubank, Mike

    2016-07-01

    High-throughput sequencing (HTS) (next-generation sequencing) of the rearranged Ig and T-cell receptor genes promises to be less expensive and more sensitive than current methods of monitoring minimal residual disease (MRD) in patients with acute lymphoblastic leukemia. However, the adoption of new approaches by clinical laboratories requires careful evaluation of all potential sources of error and the development of strategies to ensure the highest accuracy. Timely and efficient clinical use of HTS platforms will depend on combining multiple samples (multiplexing) in each sequencing run. Here we examine the Ig heavy-chain gene HTS on the Illumina MiSeq platform for MRD. We identify errors associated with multiplexing that could potentially impact the accuracy of MRD analysis. We optimize a strategy that combines high-purity, sequence-optimized oligonucleotides, dual indexing, and an error-aware demultiplexing approach to minimize errors and maximize sensitivity. We present a probability-based, demultiplexing pipeline Error-Aware Demultiplexer that is suitable for all MiSeq strategies and accurately assigns samples to the correct identifier without excessive loss of data. Finally, using controls quantified by digital PCR, we show that HTS-MRD can accurately detect as few as 1 in 10(6) copies of specific leukemic MRD. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

  2. Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Peng, Ze

    2012-06-01

    Ze Peng from DOE JGI presents "Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  3. Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Peng, Ze

    2018-01-24

    Ze Peng from DOE JGI presents "Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  4. Comparative genomic analysis of single-molecule sequencing and hybrid approaches for finishing the Clostridium autoethanogenum JA1-1 strain DSM 10061 genome

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Brown, Steven D; Nagaraju, Shilpa; Utturkar, Sagar M

    Background Clostridium autoethanogenum strain JA1-1 (DSM 10061) is an acetogen capable of fermenting CO, CO2 and H2 (e.g. from syngas or waste gases) into biofuel ethanol and commodity chemicals such as 2,3-butanediol. A draft genome sequence consisting of 100 contigs has been published. Results A closed, high-quality genome sequence for C. autoethanogenum DSM10061 was generated using only the latest single-molecule DNA sequencing technology and without the need for manual finishing. It is assigned to the most complex genome classification based upon genome features such as repeats, prophage, nine copies of the rRNA gene operons. It has a low G +more » C content of 31.1%. Illumina, 454, Illumina/454 hybrid assemblies were generated and then compared to the draft and PacBio assemblies using summary statistics, CGAL, QUAST and REAPR bioinformatics tools and comparative genomic approaches. Assemblies based upon shorter read DNA technologies were confounded by the large number repeats and their size, which in the case of the rRNA gene operons were ~5 kb. CRISPR (Clustered Regularly Interspaced Short Paloindromic Repeats) systems among biotechnologically relevant Clostridia were classified and related to plasmid content and prophages. Potential associations between plasmid content and CRISPR systems may have implications for historical industrial scale Acetone-Butanol-Ethanol (ABE) fermentation failures and future large scale bacterial fermentations. While C. autoethanogenum contains an active CRISPR system, no such system is present in the closely related Clostridium ljungdahlii DSM 13528. A common prophage inserted into the Arg-tRNA shared between the strains suggests a common ancestor. However, C. ljungdahlii contains several additional putative prophages and it has more than double the amount of prophage DNA compared to C. autoethanogenum. Other differences include important metabolic genes for central metabolism (as an additional hydrogenase and the absence of a

  5. Ion Torren Semiconductor Sequencing Allows Rapid, Low Cost Sequencing of the Human Exome (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Jenkins, David

    2018-01-10

    David Jenkins on "Ion Torrent semiconductor sequencing allows rapid, low-cost sequencing of the human exome" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  6. Ion Torren Semiconductor Sequencing Allows Rapid, Low Cost Sequencing of the Human Exome (7th Annual SFAF Meeting, 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jenkins, David

    David Jenkins on "Ion Torrent semiconductor sequencing allows rapid, low-cost sequencing of the human exome" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  7. An atomic-scale and high efficiency finishing method of zirconia ceramics by using magnetorheological finishing

    NASA Astrophysics Data System (ADS)

    Luo, Hu; Guo, Meijian; Yin, Shaohui; Chen, Fengjun; Huang, Shuai; Lu, Ange; Guo, Yuanfan

    2018-06-01

    Zirconia ceramics is a valuable crucial material for fabricating functional components applied in aerospace, biology, precision machinery, military industry and other fields. However, the properties of its high brittleness and high hardness could seriously reduce its finishing efficiency and surface quality by conventional processing technology. In this work, we present a high efficiency and high-quality finishing process by using magnetorheological finishing (MRF), which employs the permanent magnetic yoke with straight air gap as excitation unit. The sub-nanoscale surface roughness and damage free surface can be obtained after magnetorheological finishing. The XRD results and SEM morphologies confirmed that the mechanical shear removal with ductile modes are the dominant material removal mechanism for the magnetorheological finishing of zirconia ceramic. With the developed experimental apparatus, the effects of workpiece speed, trough speed and work gap on material removal rate and surface roughness were systematically investigated. Zirconia ceramics finished to ultra-smooth surface with surface roughness less than Ra 1 nm was repeatedly achieved during the parametric experiments. Additionally, the highest material removal rate exceeded 1 mg/min when using diamond as an abrasive particle. Magnetorheological finishing promises to be an adaptable and efficient method for zirconia ceramics finishing.

  8. Ultra-smooth finishing of aspheric surfaces using CAST technology

    NASA Astrophysics Data System (ADS)

    Kong, John; Young, Kevin

    2014-06-01

    Growing applications for astronomical ground-based adaptive systems and air-born telescope systems demand complex optical surface designs combined with ultra-smooth finishing. The use of more sophisticated and accurate optics, especially aspheric ones, allows for shorter optical trains with smaller sizes and a reduced number of components. This in turn reduces fabrication and alignment time and costs. These aspheric components include the following: steep surfaces with large aspheric departures; more complex surface feature designs like stand-alone off-axis-parabola (OAP) and free form optics that combine surface complexity with a requirement for ultra-high smoothness, as well as special optic materials such as lightweight silicon carbide (SiC) for air-born systems. Various fabrication technologies for finishing ultra-smooth aspheric surfaces are progressing to meet these growing and demanding challenges, especially Magnetorheological Finishing (MRF) and ion-milling. These methods have demonstrated some good success as well as a certain level of limitations. Amongst them, computer-controlled asphere surface-finishing technology (CAST), developed by Precision Asphere Inc. (PAI), plays an important role in a cost effective manufacturing environment and has successfully delivered numerous products for the applications mentioned above. One of the most recent successes is the Gemini Planet Imager (GPI), the world's most powerful planet-hunting instrument, with critical aspheric components (seven OAPs and free form optics) made using CAST technology. GPI showed off its first images in a press release on January 7, 2014 . This paper reviews features of today's technologies in handling the ultra-smooth aspheric optics, especially the capabilities of CAST on these challenging products. As examples, three groups of aspheres deployed in astronomical optics systems, both polished and finished using CAST, will be discussed in detail.

  9. Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.

    PubMed

    Bauer, Markus; Klau, Gunnar W; Reinert, Knut

    2007-07-27

    The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA alignment algorithms have to take structural information into account. We present a graph-based representation for sequence-structure alignments, which we model as an integer linear program (ILP). We sketch how we compute an optimal or near-optimal solution to the ILP using methods from combinatorial optimization, and present results on a recently published benchmark set for RNA alignments. The implementation of our algorithm yields better alignments in terms of two published scores than the other programs that we tested: This is especially the case with an increasing number of input sequences. Our program LARA is freely available for academic purposes from http://www.planet-lisa.net.

  10. Use of Whole-Genus Genome Sequence Data To Develop a Multilocus Sequence Typing Tool That Accurately Identifies Yersinia Isolates to the Species and Subspecies Levels

    PubMed Central

    Hall, Miquette; Chattaway, Marie A.; Reuter, Sandra; Savin, Cyril; Strauch, Eckhard; Carniel, Elisabeth; Connor, Thomas; Van Damme, Inge; Rajakaruna, Lakshani; Rajendram, Dunstan; Jenkins, Claire; Thomson, Nicholas R.

    2014-01-01

    The genus Yersinia is a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species. Recently, the phylogenetic and population structure of the entire genus was elucidated through the genome sequence data of 241 strains encompassing every known species in the genus. Here we report the mining of this enormous data set to create a multilocus sequence typing-based scheme that can identify Yersinia strains to the species level to a level of resolution equal to that for whole-genome sequencing. Our assay is designed to be able to accurately subtype the important human-pathogenic species Yersinia enterocolitica to whole-genome resolution levels. We also report the validation of the scheme on 386 strains from reference laboratory collections across Europe. We propose that the scheme is an important molecular typing system to allow accurate and reproducible identification of Yersinia isolates to the species level, a process often inconsistent in nonspecialist laboratories. Additionally, our assay is the most phylogenetically informative typing scheme available for Y. enterocolitica. PMID:25339391

  11. Is multiple-sequence alignment required for accurate inference of phylogeny?

    PubMed

    Höhl, Michael; Ragan, Mark A

    2007-04-01

    the correct phylogeny as accurately as does an approach based on maximum-likelihood distance estimates of multiply aligned sequences.

  12. Carcass quality and meat tenderness of Hawaii pasture-finished cattle and Hawaii-originated, mainland feedlot-finished cattle.

    PubMed

    Kim, Yong Soo; Fukumoto, Glen Kazumi; Kim, Sunae

    2012-10-01

    The objective of this study was to compare the carcass quality and meat tenderness of Hawaii cattle finished on subtropical pasture with those of mainland US feedlot-finished cattle that were shipped from Hawaii after weaning. Rib-eye steak samples were collected from 30 feedlot-finished cattle harvested at a slaughter house in Washington State, USA and from 13 subtropical pasture-finished cattle harvested at a local slaughter house in Hawaii, then shipped to meat science laboratory at the University of Hawaii, Manoa. Samples were aged for 2 weeks at 4°C and frozen for later proximate analysis and meat tenderness measurement. Feedlot-finished cattle had significantly heavier carcass weight (353 vs 290 kg) and thicker backfat (13.5 vs 6.6 mm), but no significant difference was observed in rib-eye area between the two groups. Marbling score (Small) and United States Department of Agriculture quality grade (Choice) of the pasture-finished beef were not significantly (P < 0.05) different from those of feedlot-finished beef. The shear force value of pasture-finished beef (5.18 kg) was not statistically different (P < 0.05) from that of feedlot-finished beef (4.40 kg). In conclusion, results of this study suggest that Hawaii cattle finished on subtropical pasture produced as tender beef as mainland feedlot-finished cattle with less intramuscular fat.

  13. Case Report: Application of whole exome sequencing for accurate diagnosis of rare syndromes of mineralocorticoid excess

    PubMed Central

    Narayanan, Ranjit; Karuthedath Vellarikkal, Shamsudheen; Jayarajan, Rijith; Verma, Ankit; Dixit, Vishal; Scaria, Vinod; Sivasubbu, Sridhar

    2017-01-01

    Syndromes of mineralocorticoid excess (SME) are closely related clinical manifestations occurring within a specific set of diseases. Overlapping clinical manifestations of such syndromes often create a dilemma in accurate diagnosis, which is crucial for disease surveillance and management especially in rare genetic disorders. Here we demonstrate the use of whole exome sequencing (WES) for accurate diagnosis of rare SME and report that p.R337C variation in the HSD11B2 gene causes progressive apparent mineralocorticoid excess (AME) syndrome in a South Indian family of Mappila origin. PMID:29067160

  14. Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia

    PubMed Central

    2014-01-01

    Background Clostridium autoethanogenum strain JA1-1 (DSM 10061) is an acetogen capable of fermenting CO, CO2 and H2 (e.g. from syngas or waste gases) into biofuel ethanol and commodity chemicals such as 2,3-butanediol. A draft genome sequence consisting of 100 contigs has been published. Results A closed, high-quality genome sequence for C. autoethanogenum DSM10061 was generated using only the latest single-molecule DNA sequencing technology and without the need for manual finishing. It is assigned to the most complex genome classification based upon genome features such as repeats, prophage, nine copies of the rRNA gene operons. It has a low G + C content of 31.1%. Illumina, 454, Illumina/454 hybrid assemblies were generated and then compared to the draft and PacBio assemblies using summary statistics, CGAL, QUAST and REAPR bioinformatics tools and comparative genomic approaches. Assemblies based upon shorter read DNA technologies were confounded by the large number repeats and their size, which in the case of the rRNA gene operons were ~5 kb. CRISPR (Clustered Regularly Interspaced Short Paloindromic Repeats) systems among biotechnologically relevant Clostridia were classified and related to plasmid content and prophages. Potential associations between plasmid content and CRISPR systems may have implications for historical industrial scale Acetone-Butanol-Ethanol (ABE) fermentation failures and future large scale bacterial fermentations. While C. autoethanogenum contains an active CRISPR system, no such system is present in the closely related Clostridium ljungdahlii DSM 13528. A common prophage inserted into the Arg-tRNA shared between the strains suggests a common ancestor. However, C. ljungdahlii contains several additional putative prophages and it has more than double the amount of prophage DNA compared to C. autoethanogenum. Other differences include important metabolic genes for central metabolism (as an additional hydrogenase and the absence of a

  15. Sequencing Technologies Panel at SFAF

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Turner, Steve; Fiske, Haley; Knight, Jim

    2010-06-02

    From left to right: Steve Turner of Pacific Biosciences, Haley Fiske of Illumina, Jim Knight of Roche, Michael Rhodes of Life Technologies and Peter Vander Horn of Life Technologies' Single Molecule Sequencing group discuss new sequencing technologies and applications on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  16. Finished genome assembly of warm spring isolate Francisella novicida DPG 3A-IS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Johnson, Shannon L.; Minogue, Timothy D.; Daligault, Hajnalka E.

    2015-09-17

    We sequenced the complete genome of Francisella novicida DPG 3A-IS to closed and finished status. This is a warm spring isolate recovered from Hobo Warm Spring (Utah, USA). The last assembly is available in NCBI under accession number CP012037.

  17. The identification of complete domains within protein sequences using accurate E-values for semi-global alignment

    PubMed Central

    Kann, Maricel G.; Sheetlin, Sergey L.; Park, Yonil; Bryant, Stephen H.; Spouge, John L.

    2007-01-01

    The sequencing of complete genomes has created a pressing need for automated annotation of gene function. Because domains are the basic units of protein function and evolution, a gene can be annotated from a domain database by aligning domains to the corresponding protein sequence. Ideally, complete domains are aligned to protein subsequences, in a ‘semi-global alignment’. Local alignment, which aligns pieces of domains to subsequences, is common in high-throughput annotation applications, however. It is a mature technique, with the heuristics and accurate E-values required for screening large databases and evaluating the screening results. Hidden Markov models (HMMs) provide an alternative theoretical framework for semi-global alignment, but their use is limited because they lack heuristic acceleration and accurate E-values. Our new tool, GLOBAL, overcomes some limitations of previous semi-global HMMs: it has accurate E-values and the possibility of the heuristic acceleration required for high-throughput applications. Moreover, according to a standard of truth based on protein structure, two semi-global HMM alignment tools (GLOBAL and HMMer) had comparable performance in identifying complete domains, but distinctly outperformed two tools based on local alignment. When searching for complete protein domains, therefore, GLOBAL avoids disadvantages commonly associated with HMMs, yet maintains their superior retrieval performance. PMID:17596268

  18. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.

    PubMed

    Fungtammasan, Arkarachai; Ananda, Guruprasad; Hile, Suzanne E; Su, Marcia Shu-Wei; Sun, Chen; Harris, Robert; Medvedev, Paul; Eckert, Kristin; Makova, Kateryna D

    2015-05-01

    Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution. © 2015 Fungtammasan et al.; Published by Cold Spring Harbor Laboratory Press.

  19. Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer.

    PubMed

    Wang, Ji; Ke, Yue Hua; Zhang, Yong; Huang, Ke Qiang; Wang, Lei; Shen, Xin Xin; Dong, Xiao Ping; Xu, Wen Bo; Ma, Xue Jun

    2017-10-01

    Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Within the first minute (min) of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min (on average), 99% identity was achieved for 10 CA16 strains in a single run. MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use. Copyright © 2017 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  20. Finishing of wood

    Treesearch

    R. Sam Williams

    1999-01-01

    The primary function of any wood finish (paint, varnish, and stain, for example) is to protect the wood surface, help maintain a certain appearance, and provide a cleanable surface. Although wood can be used both outdoors and indoors without finishing, unfinished wood surfaces exposed to the weather change color, are roughened by photodegradation and surface checking,...

  1. Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing.

    PubMed

    Liu, Chang; Xiao, Fangzhou; Hoisington-Lopez, Jessica; Lang, Kathrin; Quenzel, Philipp; Duffy, Brian; Mitra, Robi David

    2018-04-03

    Oxford Nanopore Technologies' MinION has expanded the current DNA sequencing toolkit by delivering long read lengths and extreme portability. The MinION has the potential to enable expedited point-of-care human leukocyte antigen (HLA) typing, an assay routinely used to assess the immunologic compatibility between organ donors and recipients, but the platform's high error rate makes it challenging to type alleles with accuracy. We developed and validated accurate typing of HLA by Oxford nanopore (Athlon), a bioinformatic pipeline that i) maps nanopore reads to a database of known HLA alleles, ii) identifies candidate alleles with the highest read coverage at different resolution levels that are represented as branching nodes and leaves of a tree structure, iii) generates consensus sequences by remapping the reads to the candidate alleles, and iv) calls the final diploid genotype by blasting consensus sequences against the reference database. Using two independent data sets generated on the R9.4 flow cell chemistry, Athlon achieved a 100% accuracy in class I HLA typing at the two-field resolution. Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  2. Accurate estimation of object location in an image sequence using helicopter flight data

    NASA Technical Reports Server (NTRS)

    Tang, Yuan-Liang; Kasturi, Rangachar

    1994-01-01

    In autonomous navigation, it is essential to obtain a three-dimensional (3D) description of the static environment in which the vehicle is traveling. For a rotorcraft conducting low-latitude flight, this description is particularly useful for obstacle detection and avoidance. In this paper, we address the problem of 3D position estimation for static objects from a monocular sequence of images captured from a low-latitude flying helicopter. Since the environment is static, it is well known that the optical flow in the image will produce a radiating pattern from the focus of expansion. We propose a motion analysis system which utilizes the epipolar constraint to accurately estimate 3D positions of scene objects in a real world image sequence taken from a low-altitude flying helicopter. Results show that this approach gives good estimates of object positions near the rotorcraft's intended flight-path.

  3. Finishing Techniques for Silicon Nitride Bearings

    DTIC Science & Technology

    1976-03-01

    finishing procedures. Rolling contact fatigue lives of silicon nitride with selected smoother finishes tested at 800 ksi Hertz stress were an order...grinding. Rolling contact fatigue lives of silicon nitride with selected smoother finishes tested at 800 ksi Hertz stress were an order of magnitude...lives of silicon nitride with selected smoother finishes tested at 800 ksi Hertz stress were an order of magnitude longer than those

  4. Distribution of Salmonella serovars in breeding, nursery, and grow-to-finish pigs, and risk factors for shedding in ten farrow-to-finish swine farms in Alberta and Saskatchewan.

    PubMed

    Wilkins, Wendy; Rajić, Andrijana; Waldner, Cheryl; McFall, Margaret; Chow, Eva; Muckle, Anne; Rosengren, Leigh

    2010-04-01

    The study objectives were to investigate Salmonella prevalence, serovar distribution, and risk factors for shedding in 10 purposively selected farrow-to-finish farms in Saskatchewan and Alberta. Pooled fecal samples from the breeding and grow-finish phases and individual fecal samples from breeding, nursery, and grow-finish pigs were cultured for Salmonella; serotyping of isolates was performed. Pig and pen characteristics were recorded for each pig and pen sampled.Overall, 407/1143 (36%) of samples were Salmonella positive; within-farm prevalence ranged from 1% to 79%. Sows, nursery, and grow-finish pigs accounted for 43%, 29%, and 28% of positive samples, respectively. More Salmonella were detected in pooled pen than individual pig samples (P < 0.001). Among 418 Salmonella isolates, there were 19 distinct serovars; the most common were S. Derby (28.5%), S. Typhimurium, var. Copenhagen (19.1%), S. Putten (11.8%), S. Infantis (6.8%), and S. Mbandaka (6.1%). Sows were more likely to shed Salmonella than nursery or grow-finisher (OR 2.9, P < 0.001) pigs. Pelleted feed (OR 8.2, P < 0.001) and nose-to-nose pig contact through pens (OR 2.2, P = 0.005) were associated with increased Salmonella prevalence. Significant differences in serovar distribution were detected among production phases. The use of pooled pen samples is recommended as a more efficient means for accurate evaluation of Salmonella status in different phases of pig production. The breeding herd might be an important source of Salmonella persistence within farrow-to-finish farms and should be targeted in control efforts. The latter might also apply to the use of pelleted feed, which remains the most consistently reported significant risk factor for Salmonella shedding in pigs.

  5. Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation.

    PubMed

    Ralph, Duncan K; Matsen, Frederick A

    2016-01-01

    VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D, or J genes, or from an N-addition (a.k.a. non-templated insertion). Previous work has used simple parametric distributions to model transitions from state to state in a hidden Markov model (HMM) of VDJ recombination, and assumed that mutations occur via the same process across sites. However, codon frame and other effects have been observed to violate these parametric assumptions for such coding sequences, suggesting that a non-parametric approach to modeling the recombination process could be useful. In our paper, we find that indeed large modern data sets suggest a model using parameter-rich per-allele categorical distributions for HMM transition probabilities and per-allele-per-position mutation probabilities, and that using such a model for inference leads to significantly improved results. We present an accurate and efficient BCR sequence annotation software package using a novel HMM "factorization" strategy. This package, called partis (https://github.com/psathyrella/partis/), is built on a new general-purpose HMM compiler that can perform efficient inference given a simple text description of an HMM.

  6. NexGen Production – Sequencing and Analysis

    ScienceCinema

    Muzny, Donna

    2018-01-16

    Donna Muzny of the Baylor College of Medicine Human Genome Sequencing Center discusses next generation sequencing platforms and evaluating pipeline performance on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  7. Sequencing Complex Genomic Regions

    ScienceCinema

    Eichler, Evan

    2018-02-12

    Evan Eichler, Howard Hughes Medical Investigator at the University of Washington, gives the May 28, 2009 keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM. Part 1 of 2

  8. 27 CFR 25.231 - Finished beer.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Finished beer. 25.231... OF THE TREASURY LIQUORS BEER Beer Purchased From Another Brewer § 25.231 Finished beer. (a) A brewer may obtain beer in barrels and kegs, finished and ready for sale from another brewer. The purchasing...

  9. 27 CFR 25.231 - Finished beer.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false Finished beer. 25.231... OF THE TREASURY ALCOHOL BEER Beer Purchased From Another Brewer § 25.231 Finished beer. (a) A brewer may obtain beer in barrels and kegs, finished and ready for sale from another brewer. The purchasing...

  10. 27 CFR 25.231 - Finished beer.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Finished beer. 25.231... OF THE TREASURY LIQUORS BEER Beer Purchased From Another Brewer § 25.231 Finished beer. (a) A brewer may obtain beer in barrels and kegs, finished and ready for sale from another brewer. The purchasing...

  11. 27 CFR 25.231 - Finished beer.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2013-04-01 2013-04-01 false Finished beer. 25.231... OF THE TREASURY ALCOHOL BEER Beer Purchased From Another Brewer § 25.231 Finished beer. (a) A brewer may obtain beer in barrels and kegs, finished and ready for sale from another brewer. The purchasing...

  12. 27 CFR 25.231 - Finished beer.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Finished beer. 25.231... OF THE TREASURY LIQUORS BEER Beer Purchased From Another Brewer § 25.231 Finished beer. (a) A brewer may obtain beer in barrels and kegs, finished and ready for sale from another brewer. The purchasing...

  13. JSC Metal Finishing Waste Minimization Methods

    NASA Technical Reports Server (NTRS)

    Sullivan, Erica

    2003-01-01

    THe paper discusses the following: Johnson Space Center (JSC) has achieved VPP Star status and is ISO 9001 compliant. The Structural Engineering Division in the Engineering Directorate is responsible for operating the metal finishing facility at JSC. The Engineering Directorate is responsible for $71.4 million of space flight hardware design, fabrication and testing. The JSC Metal Finishing Facility processes flight hardware to support the programs in particular schedule and mission critical flight hardware. The JSC Metal Finishing Facility is operated by Rothe Joint Venture. The Facility provides following processes: anodizing, alodining, passivation, and pickling. JSC Metal Finishing Facility completely rebuilt in 1998. Total cost of $366,000. All new tanks, electrical, plumbing, and ventilation installed. Designed to meet modern safety, environmental, and quality requirements. Designed to minimize contamination and provide the highest quality finishes.

  14. Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.

    PubMed

    Neuwald, Andrew F

    2009-08-01

    The patterns of sequence similarity and divergence present within functionally diverse, evolutionarily related proteins contain implicit information about corresponding biochemical similarities and differences. A first step toward accessing such information is to statistically analyze these patterns, which, in turn, requires that one first identify and accurately align a very large set of protein sequences. Ideally, the set should include many distantly related, functionally divergent subgroups. Because it is extremely difficult, if not impossible for fully automated methods to align such sequences correctly, researchers often resort to manual curation based on detailed structural and biochemical information. However, multiply-aligning vast numbers of sequences in this way is clearly impractical. This problem is addressed using Multiply-Aligned Profiles for Global Alignment of Protein Sequences (MAPGAPS). The MAPGAPS program uses a set of multiply-aligned profiles both as a query to detect and classify related sequences and as a template to multiply-align the sequences. It relies on Karlin-Altschul statistics for sensitivity and on PSI-BLAST (and other) heuristics for speed. Using as input a carefully curated multiple-profile alignment for P-loop GTPases, MAPGAPS correctly aligned weakly conserved sequence motifs within 33 distantly related GTPases of known structure. By comparison, the sequence- and structurally based alignment methods hmmalign and PROMALS3D misaligned at least 11 and 23 of these regions, respectively. When applied to a dataset of 65 million protein sequences, MAPGAPS identified, classified and aligned (with comparable accuracy) nearly half a million putative P-loop GTPase sequences. A C++ implementation of MAPGAPS is available at http://mapgaps.igs.umaryland.edu. Supplementary data are available at Bioinformatics online.

  15. 9 CFR 381.309 - Finished product inspection.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Finished product inspection. (a) Finished product inspections must be handled according to: (1) A HACCP.... (b)-(c) [Reserved] (d) Procedures for finished product inspections where the HACCP plan for thermally...

  16. Sequencing, Assembly and Analysis of Human Microbial Communities

    ScienceCinema

    Petrosino, Joe

    2018-02-02

    Joe Petrosino of Baylor College of Medicine discusses using next generation sequencing technologies to study human microbial communities associated with health and disease on June 4, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  17. POLLUTION PREVENTION IN THE METAL FINISHING INDUSTRY

    EPA Science Inventory

    A broad overview of the metal finishing processes in pollution prevention. The volume of hazardous/toxic waste streams produced from metal finishing operations is significant. It is common for product surfaces to undergo more than 10 finishing steps. The elimination of any of ...

  18. Fundamental Bounds for Sequence Reconstruction from Nanopore Sequencers.

    PubMed

    Magner, Abram; Duda, Jarosław; Szpankowski, Wojciech; Grama, Ananth

    2016-06-01

    Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic analysis of the impact of insertion-deletion (indel) errors in nanopore sequencers. In particular, we consider the following problems: (i) for given indel error characteristics and rate, what is the probability of accurate reconstruction as a function of sequence length; (ii) using replicated extrusion (the process of passing a DNA strand through the nanopore), what is the number of replicas needed to accurately reconstruct the true sequence with high probability? Our results provide a number of important insights: (i) the probability of accurate reconstruction of a sequence from a single sample in the presence of indel errors tends quickly (i.e., exponentially) to zero as the length of the sequence increases; and (ii) replicated extrusion is an effective technique for accurate reconstruction. We show that for typical distributions of indel errors, the required number of replicas is a slow function (polylogarithmic) of sequence length - implying that through replicated extrusion, we can sequence large reads using nanopore sequencers. Moreover, we show that in certain cases, the required number of replicas can be related to information-theoretic parameters of the indel error distributions.

  19. 25 CFR 301.8 - Finish.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 2 2010-04-01 2010-04-01 false Finish. 301.8 Section 301.8 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER AND TURQUOISE PRODUCTS; STANDARDS § 301.8 Finish. All silver is to be hand polished. ...

  20. 27 CFR 19.601 - Finished products records.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... Finished products records. (a) Bottling and packaging. A proprietor must maintain daily transaction records and a daily summary record of the kind and quantity of finished products bottled or packaged within... daily records of the disposition of finished products from the processing account at the distilled...

  1. Finishing bacterial genome assemblies with Mix.

    PubMed

    Soueidan, Hayssam; Maurier, Florence; Groppi, Alexis; Sirand-Pugnet, Pascal; Tardy, Florence; Citti, Christine; Dupuy, Virginie; Nikolski, Macha

    2013-01-01

    Among challenges that hamper reaping the benefits of genome assembly are both unfinished assemblies and the ensuing experimental costs. First, numerous software solutions for genome de novo assembly are available, each having its advantages and drawbacks, without clear guidelines as to how to choose among them. Second, these solutions produce draft assemblies that often require a resource intensive finishing phase. In this paper we address these two aspects by developing Mix , a tool that mixes two or more draft assemblies, without relying on a reference genome and having the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a set of paths in the extension graph that maximizes the cumulative contig length. We evaluate the performance of Mix on bacterial NGS data from the GAGE-B study and apply it to newly sequenced Mycoplasma genomes. Resulting final assemblies demonstrate a significant improvement in the overall assembly quality. In particular, Mix is consistent by providing better overall quality results even when the choice is guided solely by standard assembly statistics, as is the case for de novo projects. Mix is implemented in Python and is available at https://github.com/cbib/MIX, novel data for our Mycoplasma study is available at http://services.cbib.u-bordeaux2.fr/mix/.

  2. Accurate estimation of short read mapping quality for next-generation genome sequencing

    PubMed Central

    Ruffalo, Matthew; Koyutürk, Mehmet; Ray, Soumya; LaFramboise, Thomas

    2012-01-01

    Motivation: Several software tools specialize in the alignment of short next-generation sequencing reads to a reference sequence. Some of these tools report a mapping quality score for each alignment—in principle, this quality score tells researchers the likelihood that the alignment is correct. However, the reported mapping quality often correlates weakly with actual accuracy and the qualities of many mappings are underestimated, encouraging the researchers to discard correct mappings. Further, these low-quality mappings tend to correlate with variations in the genome (both single nucleotide and structural), and such mappings are important in accurately identifying genomic variants. Approach: We develop a machine learning tool, LoQuM (LOgistic regression tool for calibrating the Quality of short read mappings, to assign reliable mapping quality scores to mappings of Illumina reads returned by any alignment tool. LoQuM uses statistics on the read (base quality scores reported by the sequencer) and the alignment (number of matches, mismatches and deletions, mapping quality score returned by the alignment tool, if available, and number of mappings) as features for classification and uses simulated reads to learn a logistic regression model that relates these features to actual mapping quality. Results: We test the predictions of LoQuM on an independent dataset generated by the ART short read simulation software and observe that LoQuM can ‘resurrect’ many mappings that are assigned zero quality scores by the alignment tools and are therefore likely to be discarded by researchers. We also observe that the recalibration of mapping quality scores greatly enhances the precision of called single nucleotide polymorphisms. Availability: LoQuM is available as open source at http://compbio.case.edu/loqum/. Contact: matthew.ruffalo@case.edu. PMID:22962451

  3. Forest Products Laboratory natural finish

    Treesearch

    J. M. Black; D. F. Laughnan; E. A. Mraz

    1979-01-01

    A simple and durable exterior natural finish developed at the Forest Products Laboratory is described. The finish is classified as a semi-transparent oil-base penetrating stain that effectively retains much of the natural grain and texture of wood when exposed to the weather. The directions for preparation are included as are the recommendations for application to both...

  4. Kinetic model for the formation of acrylamide during the finish-frying of commercial french fries.

    PubMed

    Parker, Jane K; Balagiannis, Dimitrios P; Higley, Jeremy; Smith, Gordon; Wedzicha, Bronislaw L; Mottram, Donald S

    2012-09-12

    Acrylamide is formed from reducing sugars and asparagine during the preparation of French fries. The commercial preparation of French fries is a multistage process involving the preparation of frozen, par-fried potato strips for distribution to catering outlets, where they are finish-fried. The initial blanching, treatment in glucose solution, and par-frying steps are crucial because they determine the levels of precursors present at the beginning of the finish-frying process. To minimize the quantities of acrylamide in cooked fries, it is important to understand the impact of each stage on the formation of acrylamide. Acrylamide, amino acids, sugars, moisture, fat, and color were monitored at time intervals during the frying of potato strips that had been dipped in various concentrations of glucose and fructose during a typical pretreatment. A mathematical model based on the fundamental chemical reaction pathways of the finish-frying was developed, incorporating moisture and temperature gradients in the fries. This showed the contribution of both glucose and fructose to the generation of acrylamide and accurately predicted the acrylamide content of the final fries.

  5. Finishing Well

    NASA Astrophysics Data System (ADS)

    Riendeau, Diane

    2011-05-01

    As we finish this publishing cycle, I'd like to thank all the readers who sent in video clips. If you have a YouTube clip that you use in class, please send the link and a brief description to driendeau@dist113.org.

  6. Best of both worlds : clear exterior finishes : in search of finishes that protect wood without hiding its natural beauty

    Treesearch

    Tom Daniels; Marc Hirsch; Ken McClelland; Alan Ross; Sam Williams

    2000-01-01

    In recent years, a number of clear wood finishes have been developed that protect wood while accentuating its natural beauty. The focus of this publication is on those finishes having little visible pigment. In some cases, the pigments are included but are finely ground to create a coating that is transparent to visible light. Most natural clear wood finishes are...

  7. Surface finish measurement studies

    NASA Technical Reports Server (NTRS)

    Teague, E. C.

    1983-01-01

    The performance of stylus instruments for measuring the topography of National Transonic Facility (NTF) model surfaces both for monitoring during fabrication and as an absolute measurement of topography was evaluated. It was found that the shop-grade instruments can damage the surface of models and that their use for monitoring fabrication procedures can lead to surface finishes that are substantially out of range in critical areas of the leading edges. The development of a prototype light-scattering instrument which would allow for rapid assessment of the surface finish of a model is also discussed.

  8. Non-invasive prenatal diagnosis of achondroplasia and thanatophoric dysplasia: next-generation sequencing allows for a safer, more accurate, and comprehensive approach

    PubMed Central

    Chitty, Lyn S; Mason, Sarah; Barrett, Angela N; McKay, Fiona; Lench, Nicholas; Daley, Rebecca; Jenkins, Lucy A

    2015-01-01

    Abstract Objective Accurate prenatal diagnosis of genetic conditions can be challenging and usually requires invasive testing. Here, we demonstrate the potential of next-generation sequencing (NGS) for the analysis of cell-free DNA in maternal blood to transform prenatal diagnosis of monogenic disorders. Methods Analysis of cell-free DNA using a PCR and restriction enzyme digest (PCR–RED) was compared with a novel NGS assay in pregnancies at risk of achondroplasia and thanatophoric dysplasia. Results PCR–RED was performed in 72 cases and was correct in 88.6%, inconclusive in 7% with one false negative. NGS was performed in 47 cases and was accurate in 96.2% with no inconclusives. Both approaches were used in 27 cases, with NGS giving the correct result in the two cases inconclusive with PCR–RED. Conclusion NGS provides an accurate, flexible approach to non-invasive prenatal diagnosis of de novo and paternally inherited mutations. It is more sensitive than PCR–RED and is ideal when screening a gene with multiple potential pathogenic mutations. These findings highlight the value of NGS in the development of non-invasive prenatal diagnosis for other monogenic disorders. © 2015 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. What's already known about this topic? Non-invasive prenatal diagnosis (NIPD) using PCR-based methods has been reported for the detection or exclusion of individual paternally inherited or de novo alleles in maternal plasma. What does this study add? NIPD using next generation sequencing provides an accurate, more sensitive approach which can be used to detect multiple mutations in a single assay and so is ideal when screening a gene with multiple potential pathogenic mutations. Next generation sequencing thus provides a flexible approach to non-invasive prenatal diagnosis ideal for use in a busy service laboratory. PMID:25728633

  9. Accurate multiplex polony sequencing of an evolved bacterial genome.

    PubMed

    Shendure, Jay; Porreca, Gregory J; Reppas, Nikos B; Lin, Xiaoxia; McCutcheon, John P; Rosenbaum, Abraham M; Wang, Michael D; Zhang, Kun; Mitra, Robi D; Church, George M

    2005-09-09

    We describe a DNA sequencing technology in which a commonly available, inexpensive epifluorescence microscope is converted to rapid nonelectrophoretic DNA sequencing automation. We apply this technology to resequence an evolved strain of Escherichia coli at less than one error per million consensus bases. A cell-free, mate-paired library provided single DNA molecules that were amplified in parallel to 1-micrometer beads by emulsion polymerase chain reaction. Millions of beads were immobilized in a polyacrylamide gel and subjected to automated cycles of sequencing by ligation and four-color imaging. Cost per base was roughly one-ninth as much as that of conventional sequencing. Our protocols were implemented with off-the-shelf instrumentation and reagents.

  10. Deterministic magnetorheological finishing of optical aspheric mirrors

    NASA Astrophysics Data System (ADS)

    Song, Ci; Dai, Yifan; Peng, Xiaoqiang; Li, Shengyi; Shi, Feng

    2009-05-01

    A new method magnetorheological finishing (MRF) used for deterministical finishing of optical aspheric mirrors is applied to overcome some disadvantages including low finishing efficiency, long iterative time and unstable convergence in the process of conventional polishing. Based on the introduction of the basic principle of MRF, the key techniques to implement deterministical MRF are also discussed. To demonstrate it, a 200 mm diameter K9 class concave asphere with a vertex radius of 640mm was figured on MRF polish tool developed by ourselves. Through one process about two hours, the surface accuracy peak-to-valley (PV) is improved from initial 0.216λ to final 0.179λ and root-mean-square (RMS) is improved from 0.027λ to 0.017λ (λ = 0.6328um ). High-precision and high-efficiency convergence of optical aspheric surface error shows that MRF is an advanced optical manufacturing method that owns high convergence ratio of surface figure, high precision of optical surfacing, stabile and controllable finishing process. Therefore, utilizing MRF to finish optical aspheric mirrors determinately is credible and stabile; its advantages can be also used for finishing optical elements on varieties of types such as plane mirrors and spherical mirrors.

  11. Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21).

    PubMed

    Chang, Yun-Juan; Land, Miriam; Hauser, Loren; Chertkov, Olga; Del Rio, Tijana Glavina; Nolan, Matt; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Ovchinikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Mavromatis, Konstantinos; Liolios, Konstantinos; Brettin, Thomas; Fiebig, Anne; Rohde, Manfred; Abt, Birte; Göker, Markus; Detter, John C; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla

    2011-10-15

    Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum 'Chloroflexi'. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum 'Chloroflexi'. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the genetic redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  12. Sequencing Centers Panel at SFAF

    ScienceCinema

    Schilkey, Faye; Ali, Johar; Grafham, Darren; Muzny, Donna; Fulton, Bob; Fitzgerald, Mike; Hostetler, Jessica; Daum, Chris

    2018-02-13

    From left to right: Faye Schilkey of NCGR, Johar Ali of OICR, Darren Grafham of Wellcome Trust Sanger Institute, Donna Muzny of the Baylor College of Medicine, Bob Fulton of Washington University, Mike Fitzgerald of the Broad Institute, Jessica Hostetler of the J. Craig Venter Institute and Chris Daum of the DOE Joint Genome Institute discuss sequencing technologies, applications and pipelines on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  13. Sequencing Centers Panel at SFAF

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Schilkey, Faye; Ali, Johar; Grafham, Darren

    From left to right: Faye Schilkey of NCGR, Johar Ali of OICR, Darren Grafham of Wellcome Trust Sanger Institute, Donna Muzny of the Baylor College of Medicine, Bob Fulton of Washington University, Mike Fitzgerald of the Broad Institute, Jessica Hostetler of the J. Craig Venter Institute and Chris Daum of the DOE Joint Genome Institute discuss sequencing technologies, applications and pipelines on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  14. A highly sensitive and accurate gene expression analysis by sequencing ("bead-seq") for a single cell.

    PubMed

    Matsunaga, Hiroko; Goto, Mari; Arikawa, Koji; Shirai, Masataka; Tsunoda, Hiroyuki; Huang, Huan; Kambara, Hideki

    2015-02-15

    Analyses of gene expressions in single cells are important for understanding detailed biological phenomena. Here, a highly sensitive and accurate method by sequencing (called "bead-seq") to obtain a whole gene expression profile for a single cell is proposed. A key feature of the method is to use a complementary DNA (cDNA) library on magnetic beads, which enables adding washing steps to remove residual reagents in a sample preparation process. By adding the washing steps, the next steps can be carried out under the optimal conditions without losing cDNAs. Error sources were carefully evaluated to conclude that the first several steps were the key steps. It is demonstrated that bead-seq is superior to the conventional methods for single-cell gene expression analyses in terms of reproducibility, quantitative accuracy, and biases caused during sample preparation and sequencing processes. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Engineered Polymerases Enable Novel Sequencing Applications (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Appel, Maryke

    2018-01-15

    Maryke Appel on "Engineered polymerases provide improved NGS library amplification and enable novel sequencing applications" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  16. NMRDSP: an accurate prediction of protein shape strings from NMR chemical shifts and sequence data.

    PubMed

    Mao, Wusong; Cong, Peisheng; Wang, Zhiheng; Lu, Longjian; Zhu, Zhongliang; Li, Tonghua

    2013-01-01

    Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are exploited to predict protein structures in conjunction with computational approaches. Here we demonstrate a novel approach, NMRDSP, which can accurately predict the protein shape string based on nuclear magnetic resonance chemical shifts and structural profiles obtained from sequence data. The NMRDSP uses six chemical shifts (HA, H, N, CA, CB and C) and eight elements of structure profiles as features, a non-redundant set (1,003 entries) as the training set, and a conditional random field as a classification algorithm. For an independent testing set (203 entries), we achieved an accuracy of 75.8% for S8 (the eight states accuracy) and 87.8% for S3 (the three states accuracy). This is higher than only using chemical shifts or sequence data, and confirms that the chemical shift and the structure profile are significant features for shape string prediction and their combination prominently improves the accuracy of the predictor. We have constructed the NMRDSP web server and believe it could be employed to provide a solid platform to predict other protein structures and functions. The NMRDSP web server is freely available at http://cal.tongji.edu.cn/NMRDSP/index.jsp.

  17. COPS: A Sensitive and Accurate Tool for Detecting Somatic Copy Number Alterations Using Short-Read Sequence Data from Paired Samples

    PubMed Central

    Krishnan, Neeraja M.; Gaur, Prakhar; Chaudhary, Rakshit; Rao, Arjun A.; Panda, Binay

    2012-01-01

    Copy Number Alterations (CNAs) such as deletions and duplications; compose a larger percentage of genetic variations than single nucleotide polymorphisms or other structural variations in cancer genomes that undergo major chromosomal re-arrangements. It is, therefore, imperative to identify cancer-specific somatic copy number alterations (SCNAs), with respect to matched normal tissue, in order to understand their association with the disease. We have devised an accurate, sensitive, and easy-to-use tool, COPS, COpy number using Paired Samples, for detecting SCNAs. We rigorously tested the performance of COPS using short sequence simulated reads at various sizes and coverage of SCNAs, read depths, read lengths and also with real tumor:normal paired samples. We found COPS to perform better in comparison to other known SCNA detection tools for all evaluated parameters, namely, sensitivity (detection of true positives), specificity (detection of false positives) and size accuracy. COPS performed well for sequencing reads of all lengths when used with most upstream read alignment tools. Additionally, by incorporating a downstream boundary segmentation detection tool, the accuracy of SCNA boundaries was further improved. Here, we report an accurate, sensitive and easy to use tool in detecting cancer-specific SCNAs using short-read sequence data. In addition to cancer, COPS can be used for any disease as long as sequence reads from both disease and normal samples from the same individual are available. An added boundary segmentation detection module makes COPS detected SCNA boundaries more specific for the samples studied. COPS is available at ftp://115.119.160.213 with username “cops” and password “cops”. PMID:23110103

  18. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.

    PubMed

    Koren, Sergey; Phillippy, Adam M

    2015-02-01

    Like a jigsaw puzzle with large pieces, a genome sequenced with long reads is easier to assemble. However, recent sequencing technologies have favored lowering per-base cost at the expense of read length. This has dramatically reduced sequencing cost, but resulted in fragmented assemblies, which negatively affect downstream analyses and hinder the creation of finished (gapless, high-quality) genomes. In contrast, emerging long-read sequencing technologies can now produce reads tens of kilobases in length, enabling the automated finishing of microbial genomes for under $1000. This promises to improve the quality of reference databases and facilitate new studies of chromosomal structure and variation. We present an overview of these new technologies and the methods used to assemble long reads into complete genomes. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  19. Finishability of CCA pressure-treated wood

    Treesearch

    Alan Ross; Richard Carlson; William Feist; Steven Bussjaeger

    2000-01-01

    Thus, a need arose for the development of surface finishes for CCA-treated wood that could address the special requirements of this substrate and provide protection against the ravages of water, sunlight, mildew, and other aspects of weathering and wear. Initially, this need was not addressed, most wood preserving companies had little expertise in surface finishes and...

  20. CAPSULE REPORT - MANAGING CYANIDE IN METAL FINISHING

    EPA Science Inventory

    The purpose of this document is to provide guidance to surface finishing manufacturers, metal finishing decision maker and regulators on management practices and control technologies for managing cyanide in the workplace. This information can benefit key industry stakeholder gro...

  1. Analysis of Metagenomic Sequences: From Megabases to Terabases

    ScienceCinema

    Krypides, Nikos

    2018-05-04

    Nikos Krypides of the DOE Joint Genome Institute discusses metagenomics and the challenge of dealing with terabases of data on June 4, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  2. Seshat: A Web service for accurate annotation, validation, and analysis of TP53 variants generated by conventional and next-generation sequencing.

    PubMed

    Tikkanen, Tuomas; Leroy, Bernard; Fournier, Jean Louis; Risques, Rosa Ana; Malcikova, Jitka; Soussi, Thierry

    2018-07-01

    Accurate annotation of genomic variants in human diseases is essential to allow personalized medicine. Assessment of somatic and germline TP53 alterations has now reached the clinic and is required in several circumstances such as the identification of the most effective cancer therapy for patients with chronic lymphocytic leukemia (CLL). Here, we present Seshat, a Web service for annotating TP53 information derived from sequencing data. A flexible framework allows the use of standard file formats such as Mutation Annotation Format (MAF) or Variant Call Format (VCF), as well as common TXT files. Seshat performs accurate variant annotations using the Human Genome Variation Society (HGVS) nomenclature and the stable TP53 genomic reference provided by the Locus Reference Genomic (LRG). In addition, using the 2017 release of the UMD_TP53 database, Seshat provides multiple statistical information for each TP53 variant including database frequency, functional activity, or pathogenicity. The information is delivered in standardized output tables that minimize errors and facilitate comparison of mutational data across studies. Seshat is a beneficial tool to interpret the ever-growing TP53 sequencing data generated by multiple sequencing platforms and it is freely available via the TP53 Website, http://p53.fr or directly at http://vps338341.ovh.net/. © 2018 Wiley Periodicals, Inc.

  3. METAL FINISHING FACILITY POLLUTION PREVENTION TOOL (MFFPPT)

    EPA Science Inventory

    The Metal Finishing Facility Pollution Tool (MFFPPT) is being developed to allow the metal finishing industry an easy method to evaluate potential pollution prevention options. In order to reduce the quantity of pollutants generated by a process, the sources of pollutants within ...

  4. NCMS PWB Surface Finishes Team project summary

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kokas, J.; DeSantis, C.; Wenger, G.

    1996-04-01

    The NCMS PWB Surface Finishes Consortium is just about at the end of the five year program. Dozens of projects related to surface finishes and PWB solder-ability were performed by the team throughout the program, and many of them are listed in this paper. They are listed with a cross reference to where and when a technical paper was presented describing the results of the research. However, due to time and space constraints, this paper can summarize the details of only three of the major research projects accomplished by the team. The first project described is an ``Evaluation of PWBmore » Surface Finishes.`` It describes the solderability, reliability, and wire bondability of numerous surface finishes. The second project outlined is an ``Evaluation of PWB Solderability Test Methods.`` The third project outlined is the ``Development and Evaluation of Organic Solderability Preservatives.``« less

  5. Characterization of M40J Desized and Finished Fibers

    NASA Technical Reports Server (NTRS)

    Allred, Ronald E.; Gosau, Jan-M.; Shin, E. Eugene; McCorkle, Linda; O'Malley, Michelle; Sutter, James K.; Wheeler, Don

    1990-01-01

    A viewgraph presentation on desized and finished M40J carbon fibers shown. The topics include: 1) Program Goals and Prior Year Results Summary; 2) Continuous Desizing and Finishing System Development; 3) Characterizzation of Desized and Finished M40J Carbon Fibers and 4) Conclusions and Future Work.

  6. 27 CFR 19.601 - Finished products records.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2013-04-01 2013-04-01 false Finished products records..., DEPARTMENT OF THE TREASURY ALCOHOL DISTILLED SPIRITS PLANTS Records and Reports Processing Records § 19.601 Finished products records. (a) Bottling and packaging. A proprietor must maintain daily transaction records...

  7. 27 CFR 19.601 - Finished products records.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Finished products records..., DEPARTMENT OF THE TREASURY LIQUORS DISTILLED SPIRITS PLANTS Records and Reports Processing Records § 19.601 Finished products records. (a) Bottling and packaging. A proprietor must maintain daily transaction records...

  8. 27 CFR 19.601 - Finished products records.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false Finished products records..., DEPARTMENT OF THE TREASURY ALCOHOL DISTILLED SPIRITS PLANTS Records and Reports Processing Records § 19.601 Finished products records. (a) Bottling and packaging. A proprietor must maintain daily transaction records...

  9. [Experimental analysis of finishing lines in ceramometal restorations].

    PubMed

    Gascón, F; Gil, J A; Fons, A; Badal, R

    1990-11-01

    The preparation is the first step of any tooth reconstruction. The biological integration of the protesis is depending on the marginal adaptation (finish line of the preparation), occlusal adaptation (occlusal reduction), longevity of the restoration (retention and luting) and esthetics. The effect the two finish line of the preparation is studied using experimental design. In porcelain-fused-to-metal the finish line of the preparation in chanfer is superior at the beveled shoulder, because proportioning better marginal adaptation.

  10. DNA barcode data accurately assign higher spider taxa

    PubMed Central

    Coddington, Jonathan A.; Agnarsson, Ingi; Cheng, Ren-Chung; Čandek, Klemen; Driskell, Amy; Frick, Holger; Gregorič, Matjaž; Kostanjšek, Rok; Kropf, Christian; Kweskin, Matthew; Lokovšek, Tjaša; Pipan, Miha; Vidergar, Nina

    2016-01-01

    The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of

  11. Towards the Perfect Genome Sequence (Opening Keynote) (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Weinstock, George

    2018-04-30

    George Weinstock, associate director at the Genome Institute at Washington University, delivered the opening keynote "Towards the Perfect Genome Sequence" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  12. Towards the Perfect Genome Sequence (Opening Keynote) (7th Annual SFAF Meeting, 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Weinstock, George

    2012-06-01

    George Weinstock, associate director at the Genome Institute at Washington University, delivered the opening keynote "Towards the Perfect Genome Sequence" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  13. Solder flow over fine line PWB surface finishes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hosking, F.M.; Hernandez, C.L.

    1998-08-01

    The rapid advancement of interconnect technology has stimulated the development of alternative printed wiring board (PWB) surface finishes to enhance the solderability of standard copper and solder-coated surfaces. These new finishes are based on either metallic or organic chemistries. As part of an ongoing solderability study, Sandia National Laboratories has investigated the solder flow behavior of two azole-based organic solderability preservations, immersion Au, immersion Ag, electroless Pd, and electroless Pd/Ni on fine line copper features. The coated substrates were solder tested in the as-fabricated and environmentally-stressed conditions. Samples were processed through an inerted reflow machine. The azole-based coatings generally providedmore » the most effective protection after aging. Thin Pd over Cu yielded the best wetting results of the metallic coatings, with complete dissolution of the Pd overcoat and wetting of the underlying Cu by the flowing solder. Limited wetting was measured on the thicker Pd and Pd over Ni finishes, which were not completely dissolved by the molten solder. The immersion Au and Ag finishes yielded the lowest wetted lengths, respectively. These general differences in solderability were directly attributed to the type of surface finish which the solder came in contact with. The effects of circuit geometry, surface finish, stressing, and solder processing conditions are discussed.« less

  14. Accurate and exact CNV identification from targeted high-throughput sequence data.

    PubMed

    Nord, Alex S; Lee, Ming; King, Mary-Claire; Walsh, Tom

    2011-04-12

    Massively parallel sequencing of barcoded DNA samples significantly increases screening efficiency for clinically important genes. Short read aligners are well suited to single nucleotide and indel detection. However, methods for CNV detection from targeted enrichment are lacking. We present a method combining coverage with map information for the identification of deletions and duplications in targeted sequence data. Sequencing data is first scanned for gains and losses using a comparison of normalized coverage data between samples. CNV calls are confirmed by testing for a signature of sequences that span the CNV breakpoint. With our method, CNVs can be identified regardless of whether breakpoints are within regions targeted for sequencing. For CNVs where at least one breakpoint is within targeted sequence, exact CNV breakpoints can be identified. In a test data set of 96 subjects sequenced across ~1 Mb genomic sequence using multiplexing technology, our method detected mutations as small as 31 bp, predicted quantitative copy count, and had a low false-positive rate. Application of this method allows for identification of gains and losses in targeted sequence data, providing comprehensive mutation screening when combined with a short read aligner.

  15. Defining Genome Project Standards in a New Era of Sequencing

    ScienceCinema

    Chain, Patrick

    2018-01-16

    Patrick Chain of the DOE Joint Genome Institute gives a talk on behalf of the International Genome Sequencing Standards Consortium on the need for intermediate genome classifications between "draft" and "finished".

  16. Finishing procedures in orthodontic-surgical cases.

    PubMed

    Brunel, Jean-Michel

    2015-09-01

    To ensure optimal results, we must do our utmost to achieve targets based on order, symmetry and precision, our ultimate aim being to strive towards the desired harmony, planned contrast and exact proportions. Orthodontic-surgical treatments require specific finishing procedures, which most often call for multidisciplinary, or even transdisciplinary, collaboration. Finishing will involve the dental arches just as much as the orofacial environment. Above all, treatment of this kind demands a highly targeted approach in combination with well-defined and perfectly executed techniques. To finish a case satisfactorily, reasonable targets should be aimed for to ensure they are achieved. One must be ambitious and yet wise. A tight alliance of surgeon and orthodontist will nurture convincing and achievable projects and good, lifelong outcomes. Following the consolidation phase, roughly 4 to 6 weeks post-surgery, we can initiate the final orthodontic treatment, which, in effect, constitutes a mini-treatment in its own right. "Details make perfection, but perfection is not a detail" (Leonardo Da Vinci). "A lucid mind is the ante-chamber of intelligence" (Léo Ferré). In the order of life, every form of unity is always unique, and if each of us is unique, it is because everyone else is too. Ambition, wisdom, lucidity and efficiency will guarantee a successful result, the successful result. We must not be mere observers of our treatments, but the architect, project manager and site foreman at one and the same time. One could talk ad infinitum about finishing orthodontic-surgical cases because everything else leads up to the case-finishing and even the fullest description could never be exhaustive. Copyright © 2015 CEO. Published by Elsevier Masson SAS. All rights reserved.

  17. BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.

    PubMed

    Bartels, Daniela; Kespohl, Sebastian; Albaum, Stefan; Drüke, Tanja; Goesmann, Alexander; Herold, Julia; Kaiser, Olaf; Pühler, Alfred; Pfeiffer, Friedhelm; Raddatz, Günter; Stoye, Jens; Meyer, Folker; Schuster, Stephan C

    2005-04-01

    We provide the graphical tool BACCardI for the construction of virtual clone maps from standard assembler output files or BLAST based sequence comparisons. This new tool has been applied to numerous genome projects to solve various problems including (a) validation of whole genome shotgun assemblies, (b) support for contig ordering in the finishing phase of a genome project, and (c) intergenome comparison between related strains when only one of the strains has been sequenced and a large insert library is available for the other. The BACCardI software can seamlessly interact with various sequence assembly packages. Genomic assemblies generated from sequence information need to be validated by independent methods such as physical maps. The time-consuming task of building physical maps can be circumvented by virtual clone maps derived from read pair information of large insert libraries.

  18. 16 CFR 1508.7 - Construction and finishing.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... REGULATIONS REQUIREMENTS FOR FULL-SIZE BABY CRIBS § 1508.7 Construction and finishing. (a) All wood surfaces shall be smooth and free from splinters. (b) All wood parts shall be free from splits, cracks, or other... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Construction and finishing. 1508.7 Section...

  19. A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences.

    PubMed

    Alcantara, Luiz Carlos Junior; Cassol, Sharon; Libin, Pieter; Deforche, Koen; Pybus, Oliver G; Van Ranst, Marc; Galvão-Castro, Bernardo; Vandamme, Anne-Mieke; de Oliveira, Tulio

    2009-07-01

    Human immunodeficiency virus type-1 (HIV-1), hepatitis B and C and other rapidly evolving viruses are characterized by extremely high levels of genetic diversity. To facilitate diagnosis and the development of prevention and treatment strategies that efficiently target the diversity of these viruses, and other pathogens such as human T-lymphotropic virus type-1 (HTLV-1), human herpes virus type-8 (HHV8) and human papillomavirus (HPV), we developed a rapid high-throughput-genotyping system. The method involves the alignment of a query sequence with a carefully selected set of pre-defined reference strains, followed by phylogenetic analysis of multiple overlapping segments of the alignment using a sliding window. Each segment of the query sequence is assigned the genotype and sub-genotype of the reference strain with the highest bootstrap (>70%) and bootscanning (>90%) scores. Results from all windows are combined and displayed graphically using color-coded genotypes. The new Virus-Genotyping Tools provide accurate classification of recombinant and non-recombinant viruses and are currently being assessed for their diagnostic utility. They have incorporated into several HIV drug resistance algorithms including the Stanford (http://hivdb.stanford.edu) and two European databases (http://www.umcutrecht.nl/subsite/spread-programme/ and http://www.hivrdb.org.uk/) and have been successfully used to genotype a large number of sequences in these and other databases. The tools are a PHP/JAVA web application and are freely accessible on a number of servers including: http://bioafrica.mrc.ac.za/rega-genotype/html/, http://lasp.cpqgm.fiocruz.br/virus-genotype/html/, http://jose.med.kuleuven.be/genotypetool/html/.

  20. 16 CFR 1509.8 - Construction and finishing.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... REGULATIONS REQUIREMENTS FOR NON-FULL-SIZE BABY CRIBS § 1509.8 Construction and finishing. (a) All wood surfaces of non-full-size baby cribs shall be smooth and free from splinters. (b) All wood parts of non... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Construction and finishing. 1509.8 Section...

  1. Surface Finish after Laser Metal Deposition

    NASA Astrophysics Data System (ADS)

    Rombouts, M.; Maes, G.; Hendrix, W.; Delarbre, E.; Motmans, F.

    Laser metal deposition (LMD) is an additive manufacturing technology for the fabrication of metal parts through layerwise deposition and laser induced melting of metal powder. The poor surface finish presents a major limitation in LMD. This study focuses on the effects of surface inclination angle and strategies to improve the surface finish of LMD components. A substantial improvement in surface quality of both the side and top surfaces has been obtained by laser remelting after powder deposition.

  2. Ultra-low roughness magneto-rheological finishing for EUV mask substrates

    NASA Astrophysics Data System (ADS)

    Dumas, Paul; Jenkins, Richard; McFee, Chuck; Kadaksham, Arun J.; Balachandran, Dave K.; Teki, Ranganath

    2013-09-01

    EUV mask substrates, made of titania-doped fused silica, ideally require sub-Angstrom surface roughness, sub-30 nm flatness, and no bumps/pits larger than 1 nm in height/depth. To achieve the above specifications, substrates must undergo iterative global and local polishing processes. Magnetorheological finishing (MRF) is a local polishing technique which can accurately and deterministically correct substrate figure, but typically results in a higher surface roughness than the current requirements for EUV substrates. We describe a new super-fine MRF® polishing fluid whichis able to meet both flatness and roughness specifications for EUV mask blanks. This eases the burden on the subsequent global polishing process by decreasing the polishing time, and hence the defectivity and extent of figure distortion.

  3. EPA'S METAL FINISHING FACILITY POLLUTION PREVENTION TOOL - 2002

    EPA Science Inventory

    To help metal finishing facilities meet the goal of profitable pollution prevention, the USEPA is developing the Metal Finishing Facility Pollution Prevention Tool (MFFP2T), a computer program that estimates the rate of solid, liquid waste generation and air emissions. This progr...

  4. Role of alginate in antibacterial finishing of textiles.

    PubMed

    Li, Jiwei; He, Jinmei; Huang, Yudong

    2017-01-01

    Antibacterial finishing of textiles has been introduced as a necessary process for various purposes especially creating a fabric with antimicrobial activities. Currently, the textile industry continues to look for textiles antimicrobial finishing process based on sustainable biopolymers from the viewpoints of environmental friendliness, industrialization, and economic concerns. This paper reviews the role of alginate, a sustainable biopolymer, in the development of antimicrobial textiles, including both basic physicochemical properties of alginate such as preparation, chemical structure, molecular weight, solubility, viscosity, and sol-gel transformation property. Then different processing routes (e.g. nanocomposite coating, ionic cross-linking coating, and Layer-by-Layer coating) for the antibacterial finishing of textiles by using alginate are revised in some detail. The achievements in this area have increased our knowledge of alginate application in the field of textile industry and promoted the development of green textile finishing. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Hi-Plex for Simple, Accurate, and Cost-Effective Amplicon-based Targeted DNA Sequencing.

    PubMed

    Pope, Bernard J; Hammet, Fleur; Nguyen-Dumont, Tu; Park, Daniel J

    2018-01-01

    Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguyen-Dumont et al., Biotechniques 58:33-36, 2015). At its core is the principle of using gene-specific primers (GSPs) to "seed" (or target) the reaction and universal primers to "drive" the majority of the reaction. In this manner, effects on amplification efficiencies across the target amplicons can, to a large extent, be restricted to early seeding cycles. Product sizes are defined within a relatively narrow range to enable high-specificity size selection, replication uniformity across target sites (including in the context of fragmented input DNA such as that derived from fixed tumor specimens (Nguyen-Dumont et al., Biotechniques 55:69-74, 2013; Nguyen-Dumont et al., Anal Biochem 470:48-51, 2015), and application of high-specificity genetic variant calling algorithms (Pope et al., Source Code Biol Med 9:3, 2014; Park et al., BMC Bioinformatics 17:165, 2016). Hi-Plex offers a streamlined workflow that is suitable for testing large numbers of specimens without the need for automation.

  6. Drywall Finishing Manual.

    ERIC Educational Resources Information Center

    Lengert, Gerald

    This manual, a self-study guide for apprentices in the drywall finishing trade in British Columbia, attempts to establish standards for the trade. It tells how to produce a properly taped and filled drywall surface and describes what that surface should look like. The standards emphasize quality work that can be realistically achieved on the job.…

  7. 40 CFR 63.1347 - Standards for raw and finish mills.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 11 2010-07-01 2010-07-01 true Standards for raw and finish mills. 63... and Operating Limits § 63.1347 Standards for raw and finish mills. The owner or operator of each new or existing raw mill or finish mill at a facility which is a major source subject to the provisions...

  8. The Release 6 reference sequence of the Drosophila melanogaster genome

    DOE PAGES

    Hoskins, Roger A.; Carlson, Joseph W.; Wan, Kenneth H.; ...

    2015-01-14

    Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy andmore » middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.« less

  9. The Release 6 reference sequence of the Drosophila melanogaster genome

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hoskins, Roger A.; Carlson, Joseph W.; Wan, Kenneth H.

    Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy andmore » middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.« less

  10. Effect of Burnishing Parameters on Surface Finish

    NASA Astrophysics Data System (ADS)

    Shirsat, Uddhav; Ahuja, Basant; Dhuttargaon, Mukund

    2017-08-01

    Burnishing is cold working process in which hard balls are pressed against the surface, resulting in improved surface finish. The surface gets compressed and then plasticized. This is a highly finishing process which is becoming more popular. Surface quality of the product improves its aesthetic appearance. The product made up of aluminum material is subjected to burnishing process during which kerosene is used as a lubricant. In this study factors affecting burnishing process such as burnishing force, speed, feed, work piece diameter and ball diameter are considered as input parameters while surface finish is considered as an output parameter In this study, experiments are designed using 25 factorial design in order to analyze the relationship between input and output parameters. The ANOVA technique and F-test are used for further analysis.

  11. Chemically Accelerated Vibratory Surface Finishing (CAVSF)

    DTIC Science & Technology

    2009-02-01

    media) • End-roughness and micro structure of different C- steels • Material removal and roughness changes versus the amount of treatment solution in...surface finishing (CAVSF) Visual appearance of strip steel test pieces during the CAVSF process. 0-120 minutes = acid treatment 120-135 minutes = water... steel during the super-finishing process 0 50 100 150 200 250 300 350 0 50 100 150 200 250 Time minutes R e m o v e d m a t e r i a l m i c r

  12. Toward Magnetorheological Finishing of Magnetic Materials

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Shafrir, S.N.; Lambropoulos, J.C.; Jacobs, S.D.

    2007-10-24

    Magnetorheological finishing (MRF) is a precision finishing process traditionally limited to processing only nonmagnetic materials, e.g., optical glasses, ceramics, polymers, and metals. Here we demonstrate that MRF can be used for material removal from magnetic material surfaces. Our approach is to place an MRF spot on machined surfaces of magnetic WC-Co materials. The resulting surface roughness is comparable to that produced on nonmagnetic materials. This spotting technique may be used to evaluate the depth of subsurface damage, or deformed layer, induced by earlier manufacturing steps, such as grinding and lapping.

  13. Legume finishing provides beef with positive human dietary fatty acid ratios and consumer preference comparable with grain-finished beef.

    PubMed

    Chail, A; Legako, J F; Pitcher, L R; Griggs, T C; Ward, R E; Martini, S; MacAdam, J W

    2016-05-01

    Consumer liking, proximate composition, pH, Warner-Bratzler shear force, fatty acid composition, and volatile compounds were determined from the LM (longissimus thoracis) of cattle ( = 6 per diet) finished on conventional feedlot (USUGrain), legume, and grass forage diets. Forage diets included a condensed tannin-containing perennial legume, birdsfoot trefoil (; USUBFT), and a grass, meadow brome ( Rehmann; USUGrass). Moreover, representative retail forage (USDA Certified Organic Grass-fed [OrgGrass]) and conventional beef (USDA Choice, Grain-fed; ChGrain) were investigated ( = 6 per retail type). The ChGrain had the greatest ( < 0.05) intramuscular fat (IMF) percentage followed by USUGrain, the IMF percentage of which was greater ( < 0.05) than that of USUGrass and OrgGrass. The IMF content of USUBFT was similar ( > 0.05) to that of both USUGrain and USUGrass. Both grain-finished beef treatments were rated greater ( < 0.05) for flavor, tenderness, fattiness, juiciness, and overall liking compared with USUGrass and OrgGrass. Consumer liking of USUBFT beef tenderness, fattiness, and overall liking were comparable ( > 0.05) with that of USUGrain and ChGrain. Flavor liking was rated greatest ( < 0.05) for USUGrain and ChGrain, and that of USUBFT was intermediate ( > 0.05) to those of ChGrain, USUGrass, and OrgGrass. Cumulative SFA and MUFA concentrations were greatest ( < 0.05) in ChGrain and USUGrain, whereas USUGrass and OrgGrass had lower ( < 0.05) concentrations. Concentrations of cumulative SFA and MUFA in USUBFT were intermediate and similar ( > 0.05) to those of USUGrain and USUGrass. Each forage-finished beef treatment, USUGrass, OrgGrass, and USUBFT, had lower ( < 0.001) ratios of -6:-3 fatty acids. Hexanal was the most numerically abundant volatile compound. The concentration of hexanal increased with increasing concentrations of total PUFA. Among all the lipid degradation products (aldehydes, alcohols, furans, carboxylic acids, and ketones) measured in this

  14. A Rapid Whole Genome Sequencing and Analysis System Supporting Genomic Epidemiology (7th Annual SFAF Meeting, 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    FitzGerald, Michael

    2012-06-01

    Michael FitzGerald on "A rapid whole genome sequencing and analysis system supporting genomic epidemiology" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  15. A Rapid Whole Genome Sequencing and Analysis System Supporting Genomic Epidemiology (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    FitzGerald, Michael

    2018-01-11

    Michael FitzGerald on "A rapid whole genome sequencing and analysis system supporting genomic epidemiology" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  16. Clear exterior finishes : finding the balance between aesthetics and durability

    Treesearch

    Tom Daniel; Marc S. Hirsch; Ken McClelland; Alan S. Ross; R. Sam Williams

    2004-01-01

    Consumers can easily be confused by the abundance of choices to make when selecting a clear wood finish. There are many types of clear finishes with different characteristics and product claims. This article is designed to help consumers sort out the different finishes and effectively choose which product would be best for their purpose. First, we cover the causes and...

  17. Evaluation of several finishes on severely weathered wood

    Treesearch

    R. Sam Williams; Peter Sotos; William Feist

    1999-01-01

    Alkyd-, oil-modified-latex-, and latex-based finishes were applied to severely weathered western redcedar and redwood boards that did not have any surface treatment to ameliorate the weathered surface prior to painting. Six finishes were evaluated annually for 11 years for cracking, flaking, erosion, mildew growth, discoloration, and general appearance. Low-solids-...

  18. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.

    PubMed

    Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver

    2012-07-15

    In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license.

  19. Sequence Data for Clostridium autoethanogenum using Three Generations of Sequencing Technologies

    DOE PAGES

    Utturkar, Sagar M.; Klingeman, Dawn Marie; Bruno-Barcena, José M.; ...

    2015-04-14

    During the past decade, DNA sequencing output has been mostly dominated by the second generation sequencing platforms which are characterized by low cost, high throughput and shorter read lengths for example, Illumina. The emergence and development of so called third generation sequencing platforms such as PacBio has permitted exceptionally long reads (over 20 kb) to be generated. Due to read length increases, algorithm improvements and hybrid assembly approaches, the concept of one chromosome, one contig and automated finishing of microbial genomes is now a realistic and achievable task for many microbial laboratories. In this paper, we describe high quality sequencemore » datasets which span three generations of sequencing technologies, containing six types of data from four NGS platforms and originating from a single microorganism, Clostridium autoethanogenum. The dataset reported here will be useful for the scientific community to evaluate upcoming NGS platforms, enabling comparison of existing and novel bioinformatics approaches and will encourage interest in the development of innovative experimental and computational methods for NGS data.« less

  20. Droplet Digital™ PCR Next-Generation Sequencing Library QC Assay.

    PubMed

    Heredia, Nicholas J

    2018-01-01

    Digital PCR is a valuable tool to quantify next-generation sequencing (NGS) libraries precisely and accurately. Accurately quantifying NGS libraries enable accurate loading of the libraries on to the sequencer and thus improve sequencing performance by reducing under and overloading error. Accurate quantification also benefits users by enabling uniform loading of indexed/barcoded libraries which in turn greatly improves sequencing uniformity of the indexed/barcoded samples. The advantages gained by employing the Droplet Digital PCR (ddPCR™) library QC assay includes the precise and accurate quantification in addition to size quality assessment, enabling users to QC their sequencing libraries with confidence.

  1. [The statistical analysis for the use of the 55,787 finished resin teeth].

    PubMed

    Wu, Shu-hong; Yu, Hai-yang; Wang, Lu; Xu, Ling; Xiao, Zhi-li

    2010-08-01

    To analyze the use situation of finished resin teeth for the different location, and to provide reference for manufacturers of finished resin teeth and all the buyers. To analyze the use situation of finished resin teeth in the Dental Laboratory of the Affiliated Hospital of Stomatology of Chongqing Medical University from January 2006 to December 2008 by using statistic methods. During the use of 55,787 finished resin teeth, the study found some rules. (1) The top use of finished resin teeth was D6 with the percentage of 5.31%, and the lowest use of finished resin teeth was D3 with the percentage of 1.94%. (2) Except the maxillary canines and the mandibular lateral incisors, there was no significant difference between the usage of other same name finished resin teeth (P > 0.05). (3) Among all finished resin teeth, the usage of section B exceeded section A, and the usage of maxillary finished resin teeth exceeded mandibular finished resin teeth (P < 0.05). (4) The use of the complete denture and single complete denture was about 1/3 of the total usage of finished resin teeth. (5) Except the use situation of complete denture and single complete denture, the frequency of simultaneously using mandibular left and right central incisors was the most with the percentage of 81.46%, for the frequency of simultaneously using maxillary left and right canines was 43.26% of the total, which was the lowest. There is significant difference in the use frequency of finished resin teeth for different location. For such reason, the manufacturers should produce finished resin teeth pro rata as well as the buyers for their purchase.

  2. Magnetorheological finishing: a perfect solution to nanofinishing requirements

    NASA Astrophysics Data System (ADS)

    Sidpara, Ajay

    2014-09-01

    Finishing of optics for different applications is the most important as well as difficult step to meet the specification of optics. Conventional grinding or other polishing processes are not able to reduce surface roughness beyond a certain limit due to high forces acting on the workpiece, embedded abrasive particles, limited control over process, etc. Magnetorheological finishing (MRF) process provides a new, efficient, and innovative way to finish optical materials as well many metals to their desired level of accuracy. This paper provides an overview of MRF process for different applications, important process parameters, requirement of magnetorheological fluid with respect to workpiece material, and some areas that need to be explored for extending the application of MRF process.

  3. 7 CFR 58.525 - Storage of finished product.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 3 2011-01-01 2011-01-01 false Storage of finished product. 58.525 Section 58.525... Procedures § 58.525 Storage of finished product. Cottage cheese after packaging shall be promptly stored at a... distribution and storage prior to sale the product should be maintained at a temperature of 45 °F. or lower...

  4. 7 CFR 58.525 - Storage of finished product.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 3 2013-01-01 2013-01-01 false Storage of finished product. 58.525 Section 58.525... Procedures § 58.525 Storage of finished product. Cottage cheese after packaging shall be promptly stored at a... distribution and storage prior to sale the product should be maintained at a temperature of 45 °F. or lower...

  5. 7 CFR 58.525 - Storage of finished product.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Storage of finished product. 58.525 Section 58.525... Procedures § 58.525 Storage of finished product. Cottage cheese after packaging shall be promptly stored at a... distribution and storage prior to sale the product should be maintained at a temperature of 45 °F. or lower...

  6. RapTOR: Automated Sequencing Library Preparation and Suppression for Rapid Pathogen Characterization (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Lane, Todd

    2018-05-18

    Todd Lane on "RapTOR: Automated sequencing library preparation and suppression for rapid pathogen characterization" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  7. RapTOR: Automated Sequencing Library Preparation and Suppression for Rapid Pathogen Characterization (7th Annual SFAF Meeting, 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lane, Todd

    2012-06-01

    Todd Lane on "RapTOR: Automated sequencing library preparation and suppression for rapid pathogen characterization" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  8. En Route to the Clinic: Diagnostic Sequencing Applications Using the Ion Torrent (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Muzny, Donna

    2018-01-15

    Donna Muzny on "En route to the clinic: Diagnostic sequencing applications using the Ion Torrent" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  9. Effect of bamboo vinegar powder as an antibiotic alternative on the digesta bacteria communities of finishing pigs.

    PubMed

    Qu, Huan; Huang, Yanjie; Shi, Yinghao; Liu, Ying; Wu, Shenglong; Bao, Wenbin

    2018-05-18

    This study investigated the use for bamboo vinegar powder as an antibiotic alternative in the diet of growing-finishing pigs by examining their digestive bacterial communities. Forty-five Duroc × Landrace × Yorkshire growing-finishing pigs were randomly allocated to five diet groups: 0%,0.5%, 1.0%, or 1.5% bamboo vinegar levels and antibiotics. After 37 days, the digesta in duodenum of four pigs from each treatment were analyzed for their bacterial community compositions using 16S rRNA gene sequencing. Addition of 1.5% bamboo vinegar powder had the most similar effect on the intestinal microflora to that of antibiotics, indicating its potential to promote the growth and development of finishing pigs. We also found the 1.5% bamboo vinegar powder group to have an increased abundance of Firmicute/Bacteroidetes compared with the other bamboo vinegar powder groups, which may enhance the ability of the host to absorb food energy and store more body fat. Additionally, the effects of bamboo vinegar powder on promoting the abundances of Lactobacillus and Thalassospira and on inhibiting Streptococcus and Prevotella growth revealed it may play an important role in animal production. Moreover, functional predictions of microbes via PICRUSt indicated that feed supplemented with 1.5% bamboo vinegar powder could promote many vital metabolic pathways.

  10. Wall Finishes; Carpentry: 901895.

    ERIC Educational Resources Information Center

    Dade County Public Schools, Miami, FL.

    The course outline is designed to provide instruction in selecting, preparing, and installing wall finishing materials. Prerequisites for the course include mastery of building construction plans, foundations and walls, and basic mathematics. Intended for use in grades 11 and 12, the course contains five blocks of study totaling 135 hours of…

  11. Construction of a Dip Tank for Finishing Wood Siding or Decking

    Treesearch

    Mark Knaebe

    2013-01-01

    Dipping new siding or decking pieces before installation is faster than finishing after installation, and it gets finish on the backside and ends of the pieces, thereby extending their service life. This method is appropriate for any penetrating finish, such as waterrepellent preservatives or semitransparent stains. It may also be used to pre-treat siding with water-...

  12. Sunrayce 97 Finish Sets Records

    Science.gov Websites

    in Indianapolis,, Sunrayce 97 roared to a record finish in Colorado Springs. Winning the event , followed closely by the University of Waterloo, and the University of Minnesota. The event started in

  13. CANVAS FINISH TO REMOVE FLOAT MARKS. View is to the ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    CANVAS FINISH TO REMOVE FLOAT MARKS. View is to the northwest of deck finishing operations - South Fork Trinity River Bridge, State Highway 299 spanning South Fork Trinity River, Salyer, Trinity County, CA

  14. Genome, Epigenome and RNA sequences of Monozygotic Twins Discordant for Multiple Sclerosis

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Miller, Neil

    2010-06-02

    Neil Miller, Deputy Director of Software Engineering at the National Center for Genome Resources, discusses a monozygotic twin study on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  15. Genome, Epigenome and RNA sequences of Monozygotic Twins Discordant for Multiple Sclerosis

    ScienceCinema

    Miller, Neil

    2018-01-22

    Neil Miller, Deputy Director of Software Engineering at the National Center for Genome Resources, discusses a monozygotic twin study on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  16. Provenance of the oil in par-fried French fries after finish frying.

    PubMed

    Al-Khusaibi, Mohammed; Gordon, Michael H; Lovegrove, Julie A; Niranjan, Keshavan

    2012-01-01

    Frozen par-fried French fries are finish-fried either by using the same type of oil used for par frying, or a different type. The nutritive quality of the final oil contained in the product depends on the relative amounts and the fatty acid (FA) composition of the oils used for par frying and finish frying. With the aim of understanding the provenance of the oil in the final product, par-fried French fries-either purchased ready or prepared in the laboratory-were finish fried in oils different from the ones used for par frying. The moisture content, oil content, and FA compositions of the par-fried and finish-fried products were experimentally determined, and the relative amounts of each of the oils present in the final product were calculated using the FAs as markers and undertaking a mass balance on each component FA. The results demonstrate that 89% to 93% of the total oil in the final product originates from the finish-frying step. The study also shows that a significant proportion of the oil absorbed during par frying is expelled from the product during finish frying. Further, the expulsion of par-frying oil was found to occur in the early stages of the finish-frying step. Experiments involving different combinations of par-frying and finish-frying oils showed that the relative proportions of the 2 oils did not depend on the individual fatty acid profiles. This study concludes that any positive health benefits of using an oil having a favorable FA profile for par frying, can potentially be lost, if the oil used for finish frying has a less favorable composition. This paper estimates the relative amounts of oil in French fries that have been fried in 2 stages-a par-frying step and a finish-frying step-which is commonly practiced in food service establishments as well as homes. The 2 key conclusions are: (1) nearly 90% of the oil content of the final product is the one used for finish frying; that is, a processor may use very good oil for par frying but if the

  17. School Building Finishing and Economy. The School Building Economy Series, No. 6.

    ERIC Educational Resources Information Center

    Connecticut State Dept. of Education, Hartford.

    Materials, elements, and methods of economical school construction are illustrated through explanatory outlines and accompany photographs and diagrams. Finishing elements covered include--(1) finished floorings, (2) ceilings and acoustical finishes, (3) carpentry and millwork, (4) chalkboards and tackboards, (5) toilet partitions, (6) finishing…

  18. FINISHED CASTINGS ARE ONLY GROUND BEFORE THEY ARE SHIPPED TO ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    FINISHED CASTINGS ARE ONLY GROUND BEFORE THEY ARE SHIPPED TO CUSTOMERS WHO COMPLETE THE FINISHING IN THEIR OWN MACHINE SHOPS. - Southern Ductile Casting Company, Grinding & Shipping, 2217 Carolina Avenue, Bessemer, Jefferson County, AL

  19. Orthodontic treatment outcomes obtained by application of a finishing protocol

    PubMed Central

    Carvajal-Flórez, Alvaro; Barbosa-Lis, Diana María; Zapata-Noreña, Oscar Arturo; Marín-Velásquez, Julissa Andrea; Afanador-Bayona, Sergio Andrés

    2016-01-01

    ABSTRACT Objective: To evaluate the results of a finishing protocol implemented in patients treated in the Orthodontics graduate program at Universidad de Antioquia. Evaluation was carried out by means of the criteria set by the Objective Grading System (OGS) of the American Board of Orthodontics (ABO). Methods: Cast models and panoramic radiographs of 34 patients were evaluated. The intervention group (IG) consisted of 17 patients (19.88 ± 4.4 years old) treated under a finishing protocol. This protocol included training in finishing, application of a finishing guide, brackets repositioning and patient's follow-up. Results of the IG were compared to a control group of 17 patients (21.88 ± 7.0 years old) selected by stratified randomization without finishing intervention (CG). Results: The scores for both CG and IG were 38.00 ± 9.0 and 31.41 ± 9.6 (p = 0.048), respectively. The score improved significantly in the IG group, mainly regarding marginal ridges (CG: 5.59 ± 2.2; IG: 3.65 ± 1.8) (p = 0.009) and root angulation (CG: 7.59 ± 2.8; IG: 4.88 ± 2.6) (p = 0.007). Criteria that did not improve, but had the highest scores were: alignment (CG: 6.35 ± 2.7; IG: 6.82 ± 2.8) (p = 0.62) and buccolingual inclination (CG: 3.6 ± 5.88; IG: 5.29 ± 3.9) (p = 0.65). Conclusions: Standardization and implementation of a finishing protocol contributed to improve clinical performance in the Orthodontics graduate program, as expressed by occlusal outcomes. Greater emphasis should be given on the finishing phase to achieve lower scores in the ABO grading system. PMID:27275620

  20. NATIONAL METAL FINISHING ENVIRONMENTAL R&D PLAN - AN UPDATE

    EPA Science Inventory

    This document is an update to the National Metal Finishing Environmental R&D Plan (EPA/600/R-97/095), dated September 1997. The 1997 Plan and Update are available on the National Metal Finishing Resource Center's web site, www.nmfrc.org. The primary purpose in preparing an up...

  1. Simulation of Magnetic Field Assisted Finishing (MFAF) Process Utilizing Smart MR Polishing Tool

    NASA Astrophysics Data System (ADS)

    Barman, Anwesa; Das, Manas

    2017-02-01

    Magnetic field assisted finishing process is an advanced finishing process. This process is capable of producing nanometer level surface finish. In this process magnetic field is applied to control the finishing forces using magnetorheological polishing medium. In the current study, permanent magnet is used to provide the required magnetic field in the finishing zone. The working gap between the workpiece and the magnet is filled with MR fluid which is used as the polishing brush to remove surface undulations from the top surface of the workpiece. In this paper, the distribution of magnetic flux density on the workpiece surface and behaviour of MR polishing medium during finishing are analyzed using commercial finite element packages (Ansys Maxwell® and Comsol®). The role of magnetic force in the indentation of abrasive particles on the workpiece surface is studied. A two-dimensional simulation study of the steady, laminar, and incompressible MR fluid flow behaviour during finishing process is carried out. The material removal and surface roughness modelling of the finishing process are also presented. The indentation force by a single active abrasive particle on the workpiece surface is modelled during simulation. The velocity profile of MR fluid with and without application of magnetic field is plotted. It shows non-Newtonian property without application of magnetic field. After that the total material displacement due to one abrasive particle is plotted. The simulated roughness profile is in a good agreement with the experimental results. The conducted study will help in understanding the fluid behavior and the mechanism of finishing during finishing process. Also, the modelling and simulation of the process will help in achieving better finishing performance.

  2. Feed-conversion ratio of finisher pigs in the USA.

    PubMed

    Losinger, W C

    1998-10-09

    Although the feed-conversion ratio is recognized as a prominent indicator of profitability for pork producers, only 212 (50.7%) of 418 producers who were asked the feed-conversion ratio for finisher pigs provided a response during the USA National Animal Health Monitoring System 1995 National Swine Study. Of these, 126 (59.4%) producers furnished a feed-conversion ratio which they characterized as having been calculated from records, while 86 (40.6%) gave a response that they characterized as estimated or guessed. Feed-conversion ratios ranged from 2.18 to 5.91 kg of feed fed for each kg of live-body weight gained during the grower/finisher phase, with a mean of 3.28 and a standard deviation of 0.52. Stepwise regression revealed the following management factors to be associated with improved feed-conversion ratios: > or = 3 different rations fed during the grower/finisher phase (P < 0.01); no rations mixed on the farm (P < 0.05); and not giving chlortetracycline in feed or water as a disease preventive or growth promotant (P < 0.01). In addition, operations where > or = 3000 pigs entered the grower/finisher-production phase during the six-month period prior to interview had a better mean feed-conversion ratio than operations where < 3000 pigs entered the grower/finisher phase (P < 0.01).

  3. Wall finish selection in hospital design: a survey of facility managers.

    PubMed

    Lavy, Sarel; Dixit, Manish K

    2012-01-01

    This paper seeks to analyze healthcare facility managers' perceptions regarding the materials used for interior wall finishes and the criteria used to select them. It also examines differences in wall finish materials and the selection process in three major hospital spaces: emergency, surgery, and in-patient units. These findings are compared with healthcare designers' perceptions on similar issues, as currently documented in the literature. Hospital design and the materials used for hospital construction have a considerable effect on the environment and health of patients. A 2002 survey revealed which characteristics healthcare facility designers consider when selecting materials for healthcare facilities; however, no similar study has examined the views of facility managers on building finish selection. A 22-question survey questionnaire was distributed to 210 facility managers of metropolitan, for-profit hospitals in Texas; IRB approval was obtained. Respondents were asked to rank 10 interior wall finish materials and 11 selection criteria for wall finishes. Data from 48 complete questionnaires were analyzed using descriptive statistics and nonparametric statistical analysis methods. The study found no statistically significant differences in terms of wall finish materials or the characteristics for material selection in the three major spaces studied. It identified facility managers' four most-preferred wall finish materials and the five-most preferred characteristics, with a statistical confidence level of greater than 95%. The paper underscores the importance of incorporating all perspectives: facility designers and facility managers should work together toward achieving common organizational goals.

  4. A survey of telerobotic surface finishing

    NASA Astrophysics Data System (ADS)

    Höglund, Thomas; Alander, Jarmo; Mantere, Timo

    2018-05-01

    This is a survey of research published on the subjects of telerobotics, haptic feedback, and mixed reality applied to surface finishing. The survey especially focuses on how visuo-haptic feedback can be used to improve a grinding process using a remote manipulator or robot. The benefits of teleoperation and reasons for using haptic feedback are presented. The use of genetic algorithms for optimizing haptic sensing is briefly discussed. Ways of augmenting the operator's vision are described. Visual feedback can be used to find defects and analyze the quality of the surface resulting from the surface finishing process. Visual cues can also be used to aid a human operator in manipulating a robot precisely and avoiding collisions.

  5. Surface texture of resin-modified glass ionomer cements: effects of finishing/polishing time.

    PubMed

    Yap, A U J; Ong, S B; Yap, W Y; Tan, W S; Yeo, J C

    2002-01-01

    This study compared the surface texture of resin-modified glass ionomer cements after immediate and delayed finishing with different finishing/polishing systems. Class V preparations were made on the buccal and lingual/palatal surfaces of 64 freshly extracted teeth. The cavities on each tooth were restored with Fuji II LC (GC) and Photac-Fil Quick (3M-ESPE) according to manufacturers' instructions. Immediately after light-polymerization, gross finishing was done with 8-fluted tungsten carbide burs. The teeth were then randomly divided into four groups of 16 teeth. Half of the teeth in each group were finished immediately, while the remaining half were finished after one-week storage in distilled water at 37 degrees C. The following finishing/polishing systems were employed: (a) Robot Carbides; (b) Super-Snap system; (c) OneGloss and (d) CompoSite Polishers. The mean surface roughness (microm; n=8) in vertical (RaV) and horizontal (RaH) axis was measured using a profilometer. Data was subjected to ANOVA/Scheffe's tests and Independent Samples t-test at significance level 0.05. Ra values were generally lower in both vertical and horizontal axis with delayed finishing/polishing. Although significant differences in RaV and RaH values were observed among several systems with immediate finishing/polishing, only one (Fuji II LC: RaH - Super-Snap < Robot Carbides) was observed with delayed finishing.

  6. New Generation Sequencing Technology Panel at SFAF-Part II

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fiske, Haley; Turner, Steve; Rhodes, Michael

    2009-05-27

    From left to right: Haley Fiske of Illumina Inc., Steve Turner of Pacific Biosciences, Michael Rhodes of Applied Biosystems, Patrice Milos of Helicos Biosciences and Tim Harkins of Roche Diagnostics answer questions in a forum moderated by Bob Fulton at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  7. New Generation Sequencing Technology Panel at SFAF-Part I

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fiske, Haley; Turner, Steve; Rhodes, Michael

    2009-05-27

    From left to right: Haley Fiske of Illumina Inc., Steve Turner of Pacific Biosciences, Michael Rhodes of Applied Biosystems, Patrice Milos of Helicos Biosciences and Tim Harkins of Roche Diagnostics answer questions in a forum moderated by Bob Fulton at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  8. Electro-rheological finishing for optical surfaces

    NASA Astrophysics Data System (ADS)

    Cheng, Haobo; Wang, Peng

    2009-05-01

    Many polishing techniques such as fixed-abrasive polishing, abrasive-free polishing and magnetorheological finishing etc., have been developed. Meanwhile, a new technique is proposed using the mixture of the electro-rheological (Er) fluid with abrasives as polishing slurry, which is a special process does not require pad. Electrorheological fluid is a special suspension liquid, whose viscosity has an approximate proportional relation with the electric strength applied. When the field strength reaches a certain limit, the phase transition occurs and the liquid acquires a solid like character, and while the electric field is removed, the fluid regains its original viscosity during the order of milliseconds. In this research work, we employed the characteristics of viscosity change of Er fluid to hold the polishing particles for micromachining. A point-contact electro-rheological finishing (Erf) tool was designed with a tip diameter 0.5~1mm. Both the anode and the cathode of the electric field were combined in the tool. The electric field could be controllable. When the tool moves across the profile of the work piece, by controlling the electric field strength as well as the other manufacturing parameters we can assure the deterministic material removal. Furthermore, the electro-rheological finishing process has been planned in detailed.

  9. An Integrated Tool to Study MHC Region: Accurate SNV Detection and HLA Genes Typing in Human MHC Region Using Targeted High-Throughput Sequencing

    PubMed Central

    Liu, Xiao; Xu, Yinyin; Liang, Dequan; Gao, Peng; Sun, Yepeng; Gifford, Benjamin; D’Ascenzo, Mark; Liu, Xiaomin; Tellier, Laurent C. A. M.; Yang, Fang; Tong, Xin; Chen, Dan; Zheng, Jing; Li, Weiyang; Richmond, Todd; Xu, Xun; Wang, Jun; Li, Yingrui

    2013-01-01

    The major histocompatibility complex (MHC) is one of the most variable and gene-dense regions of the human genome. Most studies of the MHC, and associated regions, focus on minor variants and HLA typing, many of which have been demonstrated to be associated with human disease susceptibility and metabolic pathways. However, the detection of variants in the MHC region, and diagnostic HLA typing, still lacks a coherent, standardized, cost effective and high coverage protocol of clinical quality and reliability. In this paper, we presented such a method for the accurate detection of minor variants and HLA types in the human MHC region, using high-throughput, high-coverage sequencing of target regions. A probe set was designed to template upon the 8 annotated human MHC haplotypes, and to encompass the 5 megabases (Mb) of the extended MHC region. We deployed our probes upon three, genetically diverse human samples for probe set evaluation, and sequencing data show that ∼97% of the MHC region, and over 99% of the genes in MHC region, are covered with sufficient depth and good evenness. 98% of genotypes called by this capture sequencing prove consistent with established HapMap genotypes. We have concurrently developed a one-step pipeline for calling any HLA type referenced in the IMGT/HLA database from this target capture sequencing data, which shows over 96% typing accuracy when deployed at 4 digital resolution. This cost-effective and highly accurate approach for variant detection and HLA typing in the MHC region may lend further insight into immune-mediated diseases studies, and may find clinical utility in transplantation medicine research. This one-step pipeline is released for general evaluation and use by the scientific community. PMID:23894464

  10. Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens.

    PubMed

    Reynolds, Sheila M; Bilmes, Jeff A; Noble, William Stafford

    2010-07-08

    DNA in eukaryotes is packaged into a chromatin complex, the most basic element of which is the nucleosome. The precise positioning of the nucleosome cores allows for selective access to the DNA, and the mechanisms that control this positioning are important pieces of the gene expression puzzle. We describe a large-scale nucleosome pattern that jointly characterizes the nucleosome core and the adjacent linkers and is predominantly characterized by long-range oscillations in the mono, di- and tri-nucleotide content of the DNA sequence, and we show that this pattern can be used to predict nucleosome positions in both Homo sapiens and Saccharomyces cerevisiae more accurately than previously published methods. Surprisingly, in both H. sapiens and S. cerevisiae, the most informative individual features are the mono-nucleotide patterns, although the inclusion of di- and tri-nucleotide features results in improved performance. Our approach combines a much longer pattern than has been previously used to predict nucleosome positioning from sequence-301 base pairs, centered at the position to be scored-with a novel discriminative classification approach that selectively weights the contributions from each of the input features. The resulting scores are relatively insensitive to local AT-content and can be used to accurately discriminate putative dyad positions from adjacent linker regions without requiring an additional dynamic programming step and without the attendant edge effects and assumptions about linker length modeling and overall nucleosome density. Our approach produces the best dyad-linker classification results published to date in H. sapiens, and outperforms two recently published models on a large set of S. cerevisiae nucleosome positions. Our results suggest that in both genomes, a comparable and relatively small fraction of nucleosomes are well-positioned and that these positions are predictable based on sequence alone. We believe that the bulk of the

  11. 40 CFR 463.30 - Applicability; description of the finishing water subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS PLASTICS MOLDING AND FORMING POINT SOURCE CATEGORY Finishing... the finishing water subcategory are processes where water comes in contact with the plastic product...

  12. 40 CFR 463.30 - Applicability; description of the finishing water subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS PLASTICS MOLDING AND FORMING POINT SOURCE CATEGORY Finishing... the finishing water subcategory are processes where water comes in contact with the plastic product...

  13. Protecting wood decks from biodegradation and weathering : evaluation of deck finish systems

    Treesearch

    J. J. Morrell; P. F. Schneider; R. Sam Williams

    2001-01-01

    Mildew resistance, water repellency, and overall finish appearance were evaluated for 32 deck finishes on western redcedar (Thuja plicata D. Donn.) and Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) after 12, 21, and 39 months of outdoor exposure in western Oregon. The finishes were either solvent-borne or waterborne; were ei- ther clear, tinted, or lightly...

  14. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

    PubMed

    Mirarab, Siavash; Nguyen, Nam; Guo, Sheng; Wang, Li-San; Kim, Junhyong; Warnow, Tandy

    2015-05-01

    We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate--slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory.

  15. Accurate and High-Coverage Immune Repertoire Sequencing Reveals Characteristics of Antibody Repertoire Diversification in Young Children with Malaria

    NASA Astrophysics Data System (ADS)

    Jiang, Ning

    Accurately measuring the immune repertoire sequence composition, diversity, and abundance is important in studying repertoire response in infections, vaccinations, and cancer immunology. Using molecular identifiers (MIDs) to tag mRNA molecules is an effective method in improving the accuracy of immune repertoire sequencing (IR-seq). However, it is still difficult to use IR-seq on small amount of clinical samples to achieve a high coverage of the repertoire diversities. This is especially challenging in studying infections and vaccinations where B cell subpopulations with fewer cells, such as memory B cells or plasmablasts, are often of great interest to study somatic mutation patterns and diversity changes. Here, we describe an approach of IR-seq based on the use of MIDs in combination with a clustering method that can reveal more than 80% of the antibody diversity in a sample and can be applied to as few as 1,000 B cells. We applied this to study the antibody repertoires of young children before and during an acute malaria infection. We discovered unexpectedly high levels of somatic hypermutation (SHM) in infants and revealed characteristics of antibody repertoire development in young children that would have a profound impact on immunization in children.

  16. Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

    PubMed

    Kisand, Veljo; Lettieri, Teresa

    2013-04-01

    De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (<450 bps), which are presumed to aid in the analysis of uncharacterized genomes. The array of tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes

  17. Concrete Finisher Program. Apprenticeship Training.

    ERIC Educational Resources Information Center

    Alberta Learning, Edmonton. Apprenticeship and Industry Training.

    This document presents information about the apprenticeship training program of Alberta, Canada, in general and the concrete finishing program in particular. The first part of the document discusses the following items: Alberta's apprenticeship and industry training system; the apprenticeship and industry training committee structure; local…

  18. Non-invasive prenatal diagnosis of achondroplasia and thanatophoric dysplasia: next-generation sequencing allows for a safer, more accurate, and comprehensive approach.

    PubMed

    Chitty, Lyn S; Mason, Sarah; Barrett, Angela N; McKay, Fiona; Lench, Nicholas; Daley, Rebecca; Jenkins, Lucy A

    2015-07-01

    Accurate prenatal diagnosis of genetic conditions can be challenging and usually requires invasive testing. Here, we demonstrate the potential of next-generation sequencing (NGS) for the analysis of cell-free DNA in maternal blood to transform prenatal diagnosis of monogenic disorders. Analysis of cell-free DNA using a PCR and restriction enzyme digest (PCR-RED) was compared with a novel NGS assay in pregnancies at risk of achondroplasia and thanatophoric dysplasia. PCR-RED was performed in 72 cases and was correct in 88.6%, inconclusive in 7% with one false negative. NGS was performed in 47 cases and was accurate in 96.2% with no inconclusives. Both approaches were used in 27 cases, with NGS giving the correct result in the two cases inconclusive with PCR-RED. NGS provides an accurate, flexible approach to non-invasive prenatal diagnosis of de novo and paternally inherited mutations. It is more sensitive than PCR-RED and is ideal when screening a gene with multiple potential pathogenic mutations. These findings highlight the value of NGS in the development of non-invasive prenatal diagnosis for other monogenic disorders. © 2015 John Wiley & Sons, Ltd.

  19. Enhancing Surface Finish of Additively Manufactured Titanium and Cobalt Chrome Elements Using Laser Based Finishing

    NASA Astrophysics Data System (ADS)

    Gora, Wojciech S.; Tian, Yingtao; Cabo, Aldara Pan; Ardron, Marcus; Maier, Robert R. J.; Prangnell, Philip; Weston, Nicholas J.; Hand, Duncan P.

    Additive manufacturing (AM) offers the possibility of creating a complex free form object as a single element, which is not possible using traditional mechanical machining. Unfortunately the typically rough surface finish of additively manufactured parts is unsuitable for many applications. As a result AM parts must be post-processed; typically mechanically machined and/or and polished using either chemical or mechanical techniques (both of which have their limitations). Laser based polishing is based on remelting of a very thin surface layer and it offers potential as a highly repeatable, higher speed process capable of selective area polishing, and without any waste problems (no abrasives or liquids). In this paper an in-depth investigation of CW laser polishing of titanium and cobalt chrome AM elements is presented. The impact of different scanning strategies, laser parameters and initial surface condition on the achieved surface finish is evaluated.

  20. Potential of Silanes for Chromate Replacement in Metal Finishing Industries

    DTIC Science & Technology

    2002-09-16

    POTENTIAL OF SILANES FOR CHROMATE REPLACEMENT IN METAL FINISHING INDUSTRIES Wim J. van Ooij*, Danqing Zhu, Vignesh Palanivel, J. Anna Lamar...18 2 POTENTIAL OF SILANES FOR CHROMATE REPLACEMENT IN METAL FINISHING INDUSTRIES Wim J. van Ooij, Danqing Zhu, Vignesh Palanivel, J. Anna Lamar

  1. Fulfilling the Promise of a Sequenced Human Genome – Part II

    ScienceCinema

    Green, Eric

    2018-02-02

    Eric Green, scientific director of the National Human Genome Research Institute (NHGRI), gives the opening keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM on May 27, 2009. Part 2 of 2

  2. Fulfilling the Promise of a Sequenced Human Genome – Part I

    ScienceCinema

    Green, Eric

    2018-02-02

    Eric Green, scientific director of the National Human Genome Research Institute (NHGRI), gives the opening keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM on May 27, 2009. Part 1 of 2

  3. 40 CFR 425.40 - Applicability; description of the retan-wet finish-sides subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... retan-wet finish-sides subcategory. 425.40 Section 425.40 Protection of Environment ENVIRONMENTAL... CATEGORY Retan-Wet Finish-Sides Subcategory § 425.40 Applicability; description of the retan-wet finish-sides subcategory. The provisions of this subpart are applicable to process wastewater discharges...

  4. 40 CFR 425.40 - Applicability; description of the retan-wet finish-sides subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... retan-wet finish-sides subcategory. 425.40 Section 425.40 Protection of Environment ENVIRONMENTAL... POINT SOURCE CATEGORY Retan-Wet Finish-Sides Subcategory § 425.40 Applicability; description of the retan-wet finish-sides subcategory. The provisions of this subpart are applicable to process wastewater...

  5. 40 CFR 425.40 - Applicability; description of the retan-wet finish-sides subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... retan-wet finish-sides subcategory. 425.40 Section 425.40 Protection of Environment ENVIRONMENTAL... POINT SOURCE CATEGORY Retan-Wet Finish-Sides Subcategory § 425.40 Applicability; description of the retan-wet finish-sides subcategory. The provisions of this subpart are applicable to process wastewater...

  6. 40 CFR 425.40 - Applicability; description of the retan-wet finish-sides subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... retan-wet finish-sides subcategory. 425.40 Section 425.40 Protection of Environment ENVIRONMENTAL... POINT SOURCE CATEGORY Retan-Wet Finish-Sides Subcategory § 425.40 Applicability; description of the retan-wet finish-sides subcategory. The provisions of this subpart are applicable to process wastewater...

  7. Nitenpyram degradation in finished drinking water.

    PubMed

    Noestheden, Matthew; Roberts, Simon; Hao, Chunyan

    2016-07-15

    Neonicotinoid pesticides and their metabolites have been indicated as contributing factors in the decline of honey bee colonies. A thorough understanding of neonicotinoid toxicity requires knowledge of their metabolites and environmental breakdown products. This work investigated the rapid degradation of the neonicotinoid nitenpyram in finished drinking water. Nitenpyram reaction products were characterized using liquid chromatography/quadrupole time-of-flight mass spectrometry (LC/QTOFMS). A software algorithm that compared degraded and control samples was utilized to facilitate efficient data reduction. Fragmentation pathways for six reaction products and nitenpyram were proposed using predictive software and manual product ion analysis. This study showed that nitenpyram degradation in unpreserved finished drinking water was likely the result of oxidation, hydrolysis and reaction with Cl2 . Structures for six nitenpyram reaction products were proposed that suggest the C9/C11 olefin as the key reactive site. Similarities between the identified nitenpyram reaction products and imidacloprid metabolites highlight the importance of this study, as the toxicity of neonicotinoids to pollinators has been linked to their metabolites. Based on the proposed reaction mechanisms, the identified nitenpyram reaction products in finished drinking water could also be present in the environment and water treatment facilities. As such, identifying these degradation products will aid in evaluating the environmental impact of neonicotinoid pesticides. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  8. Surface finishing. [for aircraft wings

    NASA Technical Reports Server (NTRS)

    Kinzler, J. A.; Heffernan, J. T.; Fehrenkamp, L. G.; Lee, W. S. (Inventor)

    1977-01-01

    A surface of an article adapted for relative motion with a fluid environment is finished by coating the surface with a fluid adhesive. The adhesive is covered with a sheet of flexible film material under tension, and the adhesive is set while maintaining tension on the film material.

  9. Acidic magnetorheological finishing of infrared polycrystalline materials.

    PubMed

    Salzman, S; Romanofsky, H J; West, G; Marshall, K L; Jacobs, S D; Lambropoulos, J C

    2016-10-20

    Chemical-vapor-deposited (CVD) ZnS is an example of a polycrystalline material that is difficult to polish smoothly via the magnetorheological finishing (MRF) technique. When MRF-polished, the internal infrastructure of the material tends to manifest on the surface as millimeter-sized "pebbles," and the surface roughness observed is considerably high. The fluid's parameters important to developing a magnetorheological (MR) fluid that is capable of polishing CVD ZnS smoothly were previously discussed and presented. These parameters were acidic pH (∼4.5) and low viscosity (∼47  cP). MRF with such a unique MR fluid was shown to reduce surface artifacts in the form of pebbles; however, surface microroughness was still relatively high because of the absence of a polishing abrasive in the formulation. In this study, we examine the effect of two polishing abrasives-alumina and nanodiamond-on the surface finish of several CVD ZnS substrates, and on other important IR polycrystalline materials that were finished with acidic MR fluids containing these two polishing abrasives. Surface microroughness results obtained were as low as ∼28  nm peak-to-valley and ∼6-nm root mean square.

  10. Acidic magnetorheological finishing of infrared polycrystalline materials

    DOE PAGES

    Salzman, S.; Romanofsky, H. J.; West, G.; ...

    2016-10-12

    Here, chemical-vapor–deposited (CVD) ZnS is an example of a polycrystalline material that is difficult to polish smoothly via the magnetorheological–finishing (MRF) technique. When MRF-polished, the internal infrastructure of the material tends to manifest on the surface as millimeter-sized “pebbles,” and the surface roughness observed is considerably high. The fluid’s parameters important to developing a magnetorheological (MR) fluid that is capable of polishing CVD ZnS smoothly were previously discussed and presented. These parameters were acidic pH (~4.5) and low viscosity (~47 cP). MRF with such a unique MR fluid was shown to reduce surface artifacts in the form of pebbles; however,more » surface microroughness was still relatively high because of the absence of a polishing abrasive in the formulation. In this study, we examine the effect of two polishing abrasives—alumina and nanodiamond—on the surface finish of several CVD ZnS substrates, and on other important IR polycrystalline materials that were finished with acidic MR fluids containing these two polishing abrasives. Surface microroughness results obtained were as low as ~28 nm peak-to-valley and ~6-nm root mean square.« less

  11. ABACAS: algorithm-based automatic contiguation of assembled sequences

    PubMed Central

    Assefa, Samuel; Keane, Thomas M.; Otto, Thomas D.; Newbold, Chris; Berriman, Matthew

    2009-01-01

    Summary: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated. Availability and Implementation: ABACAS is implemented in Perl and is freely available for download from http://abacas.sourceforge.net Contact: sa4@sanger.ac.uk PMID:19497936

  12. Accurate phylogenetic classification of DNA fragments based onsequence composition

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    McHardy, Alice C.; Garcia Martin, Hector; Tsirigos, Aristotelis

    2006-05-01

    Metagenome studies have retrieved vast amounts of sequenceout of a variety of environments, leading to novel discoveries and greatinsights into the uncultured microbial world. Except for very simplecommunities, diversity makes sequence assembly and analysis a verychallenging problem. To understand the structure a 5 nd function ofmicrobial communities, a taxonomic characterization of the obtainedsequence fragments is highly desirable, yet currently limited mostly tothose sequences that contain phylogenetic marker genes. We show that forclades at the rank of domain down to genus, sequence composition allowsthe very accurate phylogenetic 10 characterization of genomic sequence.We developed a composition-based classifier, PhyloPythia, for de novophylogenetic sequencemore » characterization and have trained it on adata setof 340 genomes. By extensive evaluation experiments we show that themethodis accurate across all taxonomic ranks considered, even forsequences that originate fromnovel organisms and are as short as 1kb.Application to two metagenome datasets 15 obtained from samples ofphosphorus-removing sludge showed that the method allows the accurateclassification at genus level of most sequence fragments from thedominant populations, while at the same time correctly characterizingeven larger parts of the samples at higher taxonomic levels.« less

  13. Chronicle of 65 years of wood finishing research at the Forest Products Laboratory

    Treesearch

    Thomas M. Gorman; William C. Feist

    1989-01-01

    For 65 years, the Forest Products Laboratory (FPL) in Madison, Wisconsin, has had a continuous and extensive program of research on finishing wood for outdoor use. The research has stressed the fundamental aspects of wood weathering and the interactions of pretreatments and finishes on wood surfaces. This report outlines the history of the FPL wood finishing research...

  14. Durability of exterior natural wood finishes in the Pacific Northwest

    Treesearch

    William C. Feist; Edward A. Mraz

    1980-01-01

    There is a growing demand for natural exterior wood finishes that retain the original attractive appearance of wood with the least change in color and masking of grain. A number of experimental finishes are being evaluated for their performance in the cool, moist climate of Olympia, Wash. This study, started in 1966, has included observations on the weathering...

  15. Rapid and accurate pyrosequencing of angiosperm plastid genomes

    PubMed Central

    Moore, Michael J; Dhingra, Amit; Soltis, Pamela S; Shaw, Regina; Farmerie, William G; Folta, Kevin M; Soltis, Douglas E

    2006-01-01

    Background Plastid genome sequence information is vital to several disciplines in plant biology, including phylogenetics and molecular biology. The past five years have witnessed a dramatic increase in the number of completely sequenced plastid genomes, fuelled largely by advances in conventional Sanger sequencing technology. Here we report a further significant reduction in time and cost for plastid genome sequencing through the successful use of a newly available pyrosequencing platform, the Genome Sequencer 20 (GS 20) System (454 Life Sciences Corporation), to rapidly and accurately sequence the whole plastid genomes of the basal eudicot angiosperms Nandina domestica (Berberidaceae) and Platanus occidentalis (Platanaceae). Results More than 99.75% of each plastid genome was simultaneously obtained during two GS 20 sequence runs, to an average depth of coverage of 24.6× in Nandina and 17.3× in Platanus. The Nandina and Platanus plastid genomes shared essentially identical gene complements and possessed the typical angiosperm plastid structure and gene arrangement. To assess the accuracy of the GS 20 sequence, over 45 kilobases of sequence were generated for each genome using conventional sequencing. Overall error rates of 0.043% and 0.031% were observed in GS 20 sequence for Nandina and Platanus, respectively. More than 97% of all observed errors were associated with homopolymer runs, with ~60% of all errors associated with homopolymer runs of 5 or more nucleotides and ~50% of all errors associated with regions of extensive homopolymer runs. No substitution errors were present in either genome. Error rates were generally higher in the single-copy and noncoding regions of both plastid genomes relative to the inverted repeat and coding regions. Conclusion Highly accurate and essentially complete sequence information was obtained for the Nandina and Platanus plastid genomes using the GS 20 System. More importantly, the high accuracy observed in the GS 20 plastid

  16. Lung Sliding Identification Is Less Accurate in the Left Hemithorax.

    PubMed

    Piette, Eric; Daoust, Raoul; Lambert, Jean; Denault, André

    2017-02-01

    The aim of our study was to compare the accuracy of lung sliding identification for the left and right hemithoraxes, using prerecorded short US sequences, in a group of physicians with mixed clinical and US training. A total of 140 US sequences of a complete respiratory cycle were recorded in the operating room. Each sequence was divided in two, yielding 140 sequences of present lung sliding and 140 sequences of absent lung sliding. Of these 280 sequences, 40 were randomly repeated to assess intraobserver variability, for a total of 320 sequences. Descriptive data, the mean accuracy of each participant, as well as the rate of correct answers for each of the original 280 sequences were tabulated and compared for different subgroups of clinical and US training. A video with examples of present and absent lung sliding and a lung pulse was shown before testing. Two sessions were planned to facilitate the participation of 75 clinicians. In the first group, the rate of accurate lung sliding identification was lower in the left hemithorax than in the right (67.0% [interquartile range (IQR), 43.0-83.0] versus 80.0% [IQR, 57.0-95.0]; P < .001). In the second group, the rate of accurate lung sliding identification was also lower in the left hemithorax than in the right (76.3% [IQR, 42.9-90.9] versus 88.7% [IQR, 63.1-96.9]; P = .001). Mean accuracy rates were 67.5% (95% confidence interval, 65.7-69.4) in the first group and 73.1% (95% confidence interval, 70.7-75.5) in the second (P < .001). Lung sliding identification seems less accurate in the left hemithorax when using a short US examination. This study was done on recorded US sequences and should be repeated in a live clinical situation to confirm our results. © 2016 by the American Institute of Ultrasound in Medicine.

  17. THE USEPA'S METAL FINISHING FACILITY POLLUTION PREVENTION TOOL (MFFP2T)

    EPA Science Inventory

    The USEPA has developed a pre-release version of a process simulation tool, the Metal Finishing Facility Pollution Prevention Tool (MFFP2T), for the metal finishing industry. This presentation will provide a demonstration of the current version of this tool. The presentation will...

  18. THE USEPA'S METAL FINISHING FACILITY POLLUTION PREVENTION TOOL (MFFP2T)

    EPA Science Inventory

    The USEPA has developed a pre-release version of a process simulation tool, the Metal Finishing Facility Pollution Prevention Tool (MFFP2T), for the metal finishing industry. This presentation will provide a demonstration of the current version of this tool. The presentation wi...

  19. Evaluation of ENEPIG and Immersion Silver Surface Finishes Under Drop Loading

    NASA Astrophysics Data System (ADS)

    Pearl, Adam; Osterman, Michael; Pecht, Michael

    2016-01-01

    The effect of printed circuit board surface finish on the drop loading reliability of ball grid array (BGA) solder interconnects has been examined. The finishes examined include electroless nickel/electroless palladium/immersion gold (ENEPIG) and immersion silver (ImAg). For the ENEPIG finish, the effect of the Pd plating layer thickness was evaluated by testing two different thicknesses: 0.05 μm and 0.15 μm. BGA components were assembled onto the boards using either eutectic Sn-Pb or Sn-3.0Ag-0.5Cu (SAC305) solder. Prior to testing, the assembled boards were aged at 100°C for 24 h or 500 h. The boards were then subjected to multiple 1500-g drop tests. Failure analysis indicated the primary failure site for the BGAs to be the solder balls at the board-side solder interface. Cratering of the board laminate under the solder-attached pads was also observed. In all cases, isothermal aging reduced the number of drops to failure. The components soldered onto the boards with the 0.15- μm-Pd ENEPIG finish with the SAC305 solder had the highest characteristic life, at 234 drops to failure, compared with the other finish-solder combinations.

  20. APPROACHING ZERO DISCHARGE IN SURFACE FINISHING

    EPA Science Inventory

    This document provides guidance to surface finishing manufacturers on control technologies and process changes for approaching zero discharge (AZD). AZD is a key theme underlying the Strategic Goals Program (SGP). The SGP is a cooperative effort between the EPA nd the American El...

  1. Design and Feasibility Testing of the truth FinishIt Tobacco Countermarketing Brand Equity Scale.

    PubMed

    Evans, W Douglas; Rath, Jessica; Pitzer, Lindsay; Hair, Elizabeth C; Snider, Jeremy; Cantrell, Jennifer; Vallone, Donna

    2016-07-01

    The original truth campaign was a branded, national smoking prevention mass media effort focused on at-risk youth ages 12-17. Today the truth brand focuses on the goal of finishing tobacco (truth FinishIt). There have been significant changes in the tobacco control landscape, leading FinishIt to focus on 15- to 21-year-olds. The present article reports on formative research and media monitoring data collected to pilot test a new truth FinishIt brand equity scale. The goals of this study were to (a) content analyze truth FinishIt mass media ads, (b) assess truth's social media and followers' perceptions of truth's digital brand identity, and (c) develop and feasibility test a new version of the truth FinishIt brand equity scale using data from an existing Truth Initiative media monitoring study. Through factor analysis, we identified a brand equity scale, as in previous research, consisting of 4 main constructs: brand loyalty, leadership/satisfaction, personality, and awareness. Targeted truth attitudes and beliefs about social perceptions, acceptability, and industry-related beliefs were regressed on the higher order factor and each of the 4 individual brand equity factors. Ordinary least squares regression models generally showed associations in the expected directions (positive for anti-tobacco and negative for pro-tobacco) between targeted attitudes/beliefs and truth FinishIt brand equity. This study succeeded in developing and validating a new truth FinishIt brand equity scale. The scale may be a valuable metric for future campaign evaluation. Future studies should examine the effects of truth FinishIt brand equity on tobacco use behavioral outcomes over time.

  2. 46 CFR 116.422 - Ceilings, linings, trim, interior finish and decorations.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Ceilings, linings, trim, interior finish and decorations... PASSENGERS CONSTRUCTION AND ARRANGEMENT Fire Protection § 116.422 Ceilings, linings, trim, interior finish... accommodation spaces may have a combustible veneer trim and decorations that do not meet the requirements of...

  3. 46 CFR 116.422 - Ceilings, linings, trim, interior finish and decorations.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 4 2011-10-01 2011-10-01 false Ceilings, linings, trim, interior finish and decorations... PASSENGERS CONSTRUCTION AND ARRANGEMENT Fire Protection § 116.422 Ceilings, linings, trim, interior finish... accommodation spaces may have a combustible veneer trim and decorations that do not meet the requirements of...

  4. Comparison of calculated and experimentally determined SID of CP and AA in complex diets differing in AA contents for grower finisher pigs.

    PubMed

    Büsing, K; Berk, A; Müller, S; Kieckhäven, S; Krüger, K; Zeyner, A

    2017-10-01

    In practice, the content of standardized ileal digestible AA in complex feeds for pigs is calculated on the basis of tabulated values for individual feedstuffs. It comes into question, however, whether this truly reflects an accurate content based upon the estimate made for the individual feedstuffs. The objective of this study was to compare standardized ileal digestibility (SID) of crude protein (CP) and selected AA in complex feeds for grower and finisher pigs either calculated or experimentally determined. Six diets with increasing AA levels were prepared for grower (BW from 30 to 70 kg) and finisher (BW from 70 to 120 kg) feed. Crystalline L-lys, DL-met and L-thr were added to both diets, L-trp and L-val only to the grower feed. SID of both CP and AA was calculated from feed tables and experimentally determined in six adult minipigs (MINILEWE) with ileorectal anastomosis. With increasing AA levels, experimentally determined SID of supplemented AA increased (p < 0.05), but SID of CP (p ≥ 0.05) was not affected. In both grower and finisher feed, calculated and experimentally determined SID of CP, Met, Cys, Trp, Ile and Tyr differed by more than 2% units, but those of Lys and His only in the finisher feed. Yet this effect was not directly consistent. The margin of error following estimation of SID of AA via tabulated values for individual feedstuffs, however, seems to be acceptable for practical use. Journal of Animal Physiology and Animal Nutrition © 2017 Blackwell Verlag GmbH.

  5. 21 CFR 181.26 - Drying oils as components of finished resins.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... classified as drying oils, when migrating from food-packaging material (as components of finished resins... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Drying oils as components of finished resins. 181.26 Section 181.26 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN...

  6. 21 CFR 181.26 - Drying oils as components of finished resins.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... classified as drying oils, when migrating from food-packaging material (as components of finished resins... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Drying oils as components of finished resins. 181.26 Section 181.26 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN...

  7. 21 CFR 181.26 - Drying oils as components of finished resins.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... classified as drying oils, when migrating from food-packaging material (as components of finished resins... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Drying oils as components of finished resins. 181.26 Section 181.26 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN...

  8. 21 CFR 181.26 - Drying oils as components of finished resins.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... food-packaging material (as components of finished resins) shall include: Chinawood oil (tung oil... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Drying oils as components of finished resins. 181.26 Section 181.26 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN...

  9. 21 CFR 181.26 - Drying oils as components of finished resins.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... classified as drying oils, when migrating from food-packaging material (as components of finished resins... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Drying oils as components of finished resins. 181.26 Section 181.26 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN...

  10. Studies on Application of Aroma Finish on Silk Fabric

    NASA Astrophysics Data System (ADS)

    Hipparagi, Sanganna Aminappa; Srinivasa, Thirumalappa; Das, Brojeswari; Naik, Subhas Venkatappa; Purushotham, Serampur Parappa

    2016-10-01

    Aromatic treatments on textiles have gained importance in the recent years. In the present article work has been done on fragrance finish application on silk material. Silk is an expensive natural fibre used for apparel purpose and known for its feel and appeal. Incorporation of fragrance material in silk product, will add more value to it. Present work focuses to impart durable aroma finish for silk products to be home washed or subjected to dry cleaning. Microencapsulated aroma chemical has been used for the treatment. Impregnation method, Exhaust method, Dip-Pad-Dry method and Spray method have been used to see the influence of application method on the uptake and performance. Evaluation of the aroma treated material has been done through subjective evaluation as per Odor Intensity Reference Scaling (OIRS). Effect of the aroma finishing on the physical properties of the fabric has also been studied. No adverse effect has been observed on the stiffness of the fabric after the aroma treatment.

  11. Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification.

    PubMed

    Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

    2015-05-01

    Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. ivan.borozan@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  12. Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

    PubMed Central

    Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

    2015-01-01

    Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Results: Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. Availability and implementation: All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. Contact: ivan.borozan@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25573913

  13. Effects of delayed finishing/polishing on surface roughness, hardness and gloss of tooth-coloured restorative materials.

    PubMed

    Yazici, A Ruya; Tuncer, Duygu; Antonson, Sibel; Onen, Alev; Kilinc, Evren

    2010-01-01

    The aim of this study was to investigate the effect of delayed finishing/polishing on the surface roughness, hardness and gloss of tooth-coloured restorative materials. Four different tooth-coloured restoratives: a flowable resin composite- Tetric Flow, a hybrid resin composite- Venus, a nanohybrid resin composite- Grandio, and a polyacid modified resin composite- Dyract Extra were used. 30 specimens were made for each material and randomly assigned into three groups. The first group was finished/polished immediately and the second group was finished/polished after 24 hours. The remaining 10 specimens served as control. The surface roughness of each sample was recorded using a laser profilometer. Gloss measurements were performed using a small-area glossmeter. Vickers microhardness measurements were performed from three locations on each specimen surface under 100g load and 10s dwell time. Data for surface roughness and hardness were analyzed by Kruskal Wallis test and data for gloss were subjected to one-way ANOVA and Tukey test (P <.05). The smoothest surfaces were obtained under Mylar strip for all materials. While there were no significant differences in surface roughness of immediate and delayed finished/polished Dyract Extra samples, immediately finished/polished Venus and Grandio samples showed significantly higher roughness than the delayed polished samples (P <.05). In Tetric Flow samples, immediately finishing/polishing provided smoother surface than delayed finishing/polishing (P <.05). The highest gloss values were recorded under Mylar strip for all materials. While delayed finishing/polishing resulted in a significantly higher gloss compared to immediate finishing/polishing in Venus samples (P <.05), no differences were observed between delayed or immediate finishing/polishing for the other materials (P>.05). The lowest hardness values were found under Mylar strip. Delayed finishing/polishing significantly increased the hardness of all materials. The

  14. Authorization basis supporting documentation for plutonium finishing plant

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    King, J.P., Fluor Daniel Hanford

    1997-03-05

    The identification and definition of the authorization basis for the Plutonium Finishing Plant (PFP) facility and operations are essential for compliance to DOE Order 5480.21, Unreviewed Safety Questions. The authorization basis, as defined in the Order, consists of those aspects of the facility design basis, i.e., the structures, systems and components (SSCS) and the operational requirements that are considered to be important to the safety of operations and are relied upon by DOE to authorize operation of the facility. These facility design features and their function in various accident scenarios are described in WHC-SD-CP-SAR-021, Plutonium Finishing Plant Final Safety Analysismore » Report (FSAR), Chapter 9, `Accident Analysis.` Figure 1 depicts the relationship of the Authorization Basis to its components and other information contained in safety documentation supporting the Authorization Basis. The PFP SSCs that are important to safety, collectively referred to as the `Safety Envelope` are discussed in various chapters of the FSAR and in WHC-SD-CP-OSR-010, Plutonium Finishing Plant Operational Safety Requirements. Other documents such as Criticality Safety Evaluation Reports (CSERS) address and support some portions of the Authorization Basis and Safety Envelope.« less

  15. Concrete Finisher: Apprenticeship Course Outline. Apprenticeship and Industry Training. 4805.2

    ERIC Educational Resources Information Center

    Alberta Advanced Education, 2005

    2005-01-01

    The graduate of the Concrete Finisher apprenticeship program is a certified journeyperson who will be able to: (1) perform tests to confirm concrete quality; (2) interpret building codes, plans and specifications as they apply to the trade; (3) place and finish concrete in a professional manner; (4) cut, patch, maintain and repair concrete…

  16. 21 CFR 820.80 - Receiving, in-process, and finished device acceptance.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Receiving, in-process, and finished device acceptance. 820.80 Section 820.80 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... acceptance to ensure that each production run, lot, or batch of finished devices meets acceptance criteria...

  17. 21 CFR 820.80 - Receiving, in-process, and finished device acceptance.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Receiving, in-process, and finished device acceptance. 820.80 Section 820.80 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... acceptance to ensure that each production run, lot, or batch of finished devices meets acceptance criteria...

  18. DEVELOPING A CAPE-OPEN COMPLIANT METAL FINISHING FACILITY POLLUTION PREVENTION TOOL (CO-MFFP2T)

    EPA Science Inventory

    The USEPA is developing a Computer Aided Process Engineering (CAPE) software tool for the metal finishing industry that helps users design efficient metal finishing processes that are less polluting to the environment. Metal finishing process lines can be simulated and evaluated...

  19. 40 CFR 410.40 - Applicability; description of the woven fabric finishing subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 28 2010-07-01 2010-07-01 true Applicability; description of the woven fabric finishing subcategory. 410.40 Section 410.40 Protection of Environment ENVIRONMENTAL PROTECTION... proofing, soil repellency application and a special finish application. ...

  20. 8. Finish line, marked by white poles, as viewed from ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. Finish line, marked by white poles, as viewed from infield tote board. Shown are all the best locations for viewing the finish line, including the Clubhouse on the left and Original Grandstand on the right. For a similar view taken in 1939 by a photographer for the Seattle Post-Intelligencer newspaper, see photo WA-201-24. (August 1993) - Longacres, 1621 Southwest Sixteenth Street, Renton, King County, WA

  1. 40 CFR 425.90 - Applicability; description of the retan-wet finish-splits subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS LEATHER TANNING AND FINISHING POINT SOURCE... resulting from any tannery which processes previously unhaired and tanned splits into finished leather by...

  2. The limits of protein sequence comparison?

    PubMed Central

    Pearson, William R; Sierk, Michael L

    2010-01-01

    Modern sequence alignment algorithms are used routinely to identify homologous proteins, proteins that share a common ancestor. Homologous proteins always share similar structures and often have similar functions. Over the past 20 years, sequence comparison has become both more sensitive, largely because of profile-based methods, and more reliable, because of more accurate statistical estimates. As sequence and structure databases become larger, and comparison methods become more powerful, reliable statistical estimates will become even more important for distinguishing similarities that are due to homology from those that are due to analogy (convergence). The newest sequence alignment methods are more sensitive than older methods, but more accurate statistical estimates are needed for their full power to be realized. PMID:15919194

  3. 76 FR 79221 - Penske Logistics, LLC, Customer Service Department General Motors and Tier Finished Goods...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-21

    ..., Customer Service Department General Motors and Tier Finished Goods/Finished Goods Division; a Subsidiary of... Manpower El Paso, TX; Amended Certification Regarding Eligibility To Apply for Worker Adjustment Assistance... should read Penske Logistics, LLC, Customer Service Department, General Motors and Tier Finished Goods...

  4. 40 CFR 425.40 - Applicability; description of the retan-wet finish-sides subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS LEATHER TANNING AND FINISHING POINT SOURCE... resulting from any tannery which processes previously tanned hides and skins (grain side only) into finished...

  5. 40 CFR Figure 1 to Subpart Tttt of... - Example Logs for Recording Leather Finish Use and HAP Content

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Finishing Operations Part 63, Subpt. TTTT, Fig. 1 Figure 1 to Subpart TTTT of Part 63—Example Logs for Recording Leather Finish Use and HAP Content Month:______Year:______ Finish Inventory Log Finish type Finish usage(pounds) HAP Content(mass fraction) Date and time Operator's name Product process operation Monthly...

  6. The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

    PubMed

    Mavromatis, Konstantinos; Land, Miriam L; Brettin, Thomas S; Quest, Daniel J; Copeland, Alex; Clum, Alicia; Goodwin, Lynne; Woyke, Tanja; Lapidus, Alla; Klenk, Hans Peter; Cottingham, Robert W; Kyrpides, Nikos C

    2012-01-01

    The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis. These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio).

  7. Cross-Cultural Consumer Acceptability and Purchase Intent of Forage-Finished Rib-Eye Steaks.

    PubMed

    Torrico, Damir Dennis; Wardy, Wisdom; Pujols, Kairy Dharali; Carabante, Kennet Mariano; Jirangrat, Wannita; Scaglia, Guillermo; Janes, Marlene E; Prinyawiwatkul, Witoon

    2015-10-01

    Rib-eye steaks, from 3 forage-finished systems (S1, S2, and S3) and 1 commercial steak (C), either cooked by 1-sided-grilling or 2-sided-grilling, were evaluated for sensory acceptability [overall appearance (ORA) and overall appearance of fat (OAF) for raw steaks; overall appearance (OCA), overall beef aroma (OBA), overall beef flavor (OBF), juiciness, tenderness and overall liking (OL) for cooked steaks] and purchase intent by Hispanic, Asian and U.S. consumers. They also indicated preferred degree of doneness and cooking methods. Cross-cultural differences in preferences and consumer acceptability of rib-eye steaks were observed. Grilling was the most preferred cooking method. Hispanics and Asians preferred medium and/or medium well, while U.S. consumers preferred medium and/or medium rare. For cooked steaks, the population effect was significant for all sensory attributes; Asians generally scored lower than did Hispanics and U.S. consumers. C and S3 generally had higher scores for all sensory attributes across 3 populations. Purchase intent for all forage-finished steaks was higher for Hispanics and U.S. consumers compared to Asians (50.0% to 77.8% compared with 43.2% to 65.9%). Attributes influencing purchase intent of forage-finished steaks differed among populations: tenderness (odds ratio = 1.4) for Hispanics, OCA (odds ratio = 1.5) for Asians, and OBF (odds ratio = 1.3) for U.S. consumers. Overall, this study demonstrated that the type of forage-finished system and ethnic differences influenced sensory acceptability and purchase intent of forage-finished rib-eye steaks. Demand for forage-finished beef has increased worldwide due to its potential health benefits. Little is known regarding the cross-cultural effects on the consumer acceptance of forage-finished beef. We evaluated sensory acceptance and purchase intent of raw and cooked forage-finished rib-eye steaks using Hispanic, Asian, and U.S. (White and African American) populations. This study

  8. From the Lab Bench: The challenges of finishing cattle on pasture

    USDA-ARS?s Scientific Manuscript database

    A column was written to discuss the challenges in Kentucky to finish beef calves on pasture. It might seem feasible to finish a calf in 24 months. This can be accomplished if the average daily weight gain is 1.0 pound per day, but the calves will spend almost half of those 24 months on pasture with ...

  9. Effect of Plasma Surface Finish on Wettability and Mechanical Properties of SAC305 Solder Joints

    NASA Astrophysics Data System (ADS)

    Kim, Kyoung-Ho; Koike, Junichi; Yoon, Jeong-Won; Yoo, Sehoon

    2016-12-01

    The wetting behavior, interfacial reactions, and mechanical reliability of Sn-Ag-Cu solder on a plasma-coated printed circuit board (PCB) substrate were evaluated under multiple heat-treatments. Conventional organic solderability preservative (OSP) finished PCBs were used as a reference. The plasma process created a dense and highly cross-linked polymer coating on the Cu substrates. The plasma finished samples had higher wetting forces and shorter zero-cross times than those with OSP surface finish. The OSP sample was degraded after sequential multiple heat treatments and reflow processes, whereas the solderability of the plasma finished sample was retained after multiple heat treatments. After the soldering process, similar microstructures were observed at the interfaces of the two solder joints, where the development of intermetallic compounds was observed. From ball shear tests, it was found that the shear force for the plasma substrate was consistently higher than that for the OSP substrate. Deterioration of the OSP surface finish was observed after multiple heat treatments. Overall, the plasma surface finish was superior to the conventional OSP finish with respect to wettability and joint reliability, indicating that it is a suitable material for the fabrication of complex electronic devices.

  10. Survey of quantitative antimicrobial consumption in two different pig finishing systems.

    PubMed

    Moreno, M A

    2012-09-29

    The primary objectives of this study were to: (a) collect on-farm antimicrobial use (AMU) data in fattener pigs employing two questionnaire-based surveys; (b) assess different quantitative measures for quantifying AMU in fattener pigs; (c) compare AMU in fattener pigs between two different management systems producing finishers: farrow-to-finish (FtF) farms versus finisher farms. Two questionnaires were designed both containing five groups of questions focused on the responder, the farm and AMU (eg, in-feed, in-drinking water and parenteral); both surveys were carried out by means of personal face-to-face interviews. Both surveys started with a sample size of 108 potentially eligible farms per survey; nevertheless, finally 67 finisher farms and 49 FtF farms were recruited. Overall percentages of animals exposed to antimicrobials (AM) were high (90 per cent in finisher farms and 54 per cent FtF farms); colistin (61 per cent and 33 per cent) and doxycycline (62 per cent and 23 per cent) were the most common AMs, followed by amoxicillin (51 per cent and 19 per cent) and lincomycin (49 per cent), respectively. Questionnaire-based surveys using face-to-face interviews are useful for capturing information regarding AMU at the farm level. Farm-level data per administration route can be used for comparative AMU analysis between farms. Nevertheless, for the analysis of the putative relationships between AMU and AM resistance, measures based on exposed animals or exposure events are needed.

  11. 40 CFR 410.50 - Applicability; description of the knit fabric finishing subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 29 2011-07-01 2009-07-01 true Applicability; description of the knit... AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Knit Fabric Finishing Subcategory § 410.50 Applicability; description of the knit fabric finishing subcategory. The...

  12. DEVELOPMENT OF THE U.S. EPA'S METAL FINISHING FACILITY POLLUTION PREVENTION TOOL

    EPA Science Inventory

    Metal finishing processes are a type of chemical processes and can be modeled using Computer Aided Process Engineering (CAPE). Currently, the U.S. EPA is developing the Metal Finishing Facility Pollution Prevention Tool (MFFP2T), a pollution prevention software tool for the meta...

  13. Efficient and Accurate Algorithm for Cleaved Fragments Prediction (CFPA) in Protein Sequences Dataset Based on Consensus and Its Variants: A Novel Degradomics Prediction Application.

    PubMed

    El-Assaad, Atlal; Dawy, Zaher; Nemer, Georges; Hajj, Hazem; Kobeissy, Firas H

    2017-01-01

    Degradomics is a novel discipline that involves determination of the proteases/substrate fragmentation profile, called the substrate degradome, and has been recently applied in different disciplines. A major application of degradomics is its utility in the field of biomarkers where the breakdown products (BDPs) of different protease have been investigated. Among the major proteases assessed, calpain and caspase proteases have been associated with the execution phases of the pro-apoptotic and pro-necrotic cell death, generating caspase/calpain-specific cleaved fragments. The distinction between calpain and caspase protein fragments has been applied to distinguish injury mechanisms. Advanced proteomics technology has been used to identify these BDPs experimentally. However, it has been a challenge to identify these BDPs with high precision and efficiency, especially if we are targeting a number of proteins at one time. In this chapter, we present a novel bioinfromatic detection method that identifies BDPs accurately and efficiently with validation against experimental data. This method aims at predicting the consensus sequence occurrences and their variants in a large set of experimentally detected protein sequences based on state-of-the-art sequence matching and alignment algorithms. After detection, the method generates all the potential cleaved fragments by a specific protease. This space and time-efficient algorithm is flexible to handle the different orientations that the consensus sequence and the protein sequence can take before cleaving. It is O(mn) in space complexity and O(Nmn) in time complexity, with N number of protein sequences, m length of the consensus sequence, and n length of each protein sequence. Ultimately, this knowledge will subsequently feed into the development of a novel tool for researchers to detect diverse types of selected BDPs as putative disease markers, contributing to the diagnosis and treatment of related disorders.

  14. Microfabrication Method using a Combination of Local Ion Implantation and Magnetorheological Finishing

    NASA Astrophysics Data System (ADS)

    Han, Jin; Kim, Jong-Wook; Lee, Hiwon; Min, Byung-Kwon; Lee, Sang Jo

    2009-02-01

    A new microfabrication method that combines localized ion implantation and magnetorheological finishing is proposed. The proposed technique involves two steps. First, selected regions of a silicon wafer are irradiated with gallium ions by using a focused ion beam system. The mechanical properties of the irradiated regions are altered as a result of the ion implantation. Second, the wafer is processed by using a magnetorheological finishing method. During the finishing process, the regions not implanted with ion are preferentially removed. The material removal rate difference is utilized for microfabrication. The mechanisms of the proposed method are discussed, and applications are presented.

  15. Comparison of gene expression and fatty acid profiles in concentrate and forage finished beef.

    PubMed

    Buchanan, J W; Garmyn, A J; Hilton, G G; VanOverbeke, D L; Duan, Q; Beitz, D C; Mateescu, R G

    2013-01-01

    Fatty acid profiles and intramuscular expression of genes involved in fatty acid metabolism were characterized in concentrate- (CO) and forage- (FO) based finishing systems. Intramuscular samples from the adductor were taken at slaughter from 99 heifers finished on a CO diet and 58 heifers finished on a FO diet. Strip loins were obtained at fabrication to evaluate fatty acid profiles of LM muscle for all 157 heifers by using gas chromatography fatty acid methyl ester analysis. Composition was analyzed for differences by using the General Linear Model (GLM) procedure in SAS. Differences in fatty acid profile included a greater atherogenic index, greater percentage total MUFA, decreased omega-3 to omega-6 ratio, decreased percentage total PUFA, and decreased percentage omega-3 fatty acids in CO- compared with FO-finished heifers (P<0.05). Fatty acid profiles from intramuscular samples were ranked by the atherogenic index, and 20 heifers with either a high (HAI; n=10) or low (LAI; n=10) atherogenic index were selected for gene expression analysis using real-time PCR (RT-PCR). Gene expression data for the 20 individuals were analyzed as a 2 by 2 factorial arrangement of treatments using the GLM procedure in SAS. There was no significant diet × atherogenic index interaction identified for any gene (P>0.05). Upregulation was observed for PPARγ, fatty acid synthase (FASN), and fatty acid binding protein 4 (FABP4) in FO-finished compared with CO-finished heifers in both atherogenic index categories (P<0.05). Upregulation of diglyceride acyl transferase 2 (DGAT2) was observed in FO-finished heifers with a HAI (P<0.05). Expression of steroyl Co-A desaturase (SCD) was upregulated in CO-finished heifers with a LAI, and downregulated in FO-finished heifers with a HAI (P<0.05). Expression of adiponectin (ADIPOQ) was significantly downregulated in CO-finished heifers with a HAI compared with all other categories (P<0.05). The genes identified in this study which exhibit

  16. Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells.

    PubMed

    Beltman, Joost B; Urbanus, Jos; Velds, Arno; van Rooij, Nienke; Rohr, Jan C; Naik, Shalin H; Schumacher, Ton N

    2016-04-02

    Next generation sequencing (NGS) of amplified DNA is a powerful tool to describe genetic heterogeneity within cell populations that can both be used to investigate the clonal structure of cell populations and to perform genetic lineage tracing. For applications in which both abundant and rare sequences are biologically relevant, the relatively high error rate of NGS techniques complicates data analysis, as it is difficult to distinguish rare true sequences from spurious sequences that are generated by PCR or sequencing errors. This issue, for instance, applies to cellular barcoding strategies that aim to follow the amount and type of offspring of single cells, by supplying these with unique heritable DNA tags. Here, we use genetic barcoding data from the Illumina HiSeq platform to show that straightforward read threshold-based filtering of data is typically insufficient to filter out spurious barcodes. Importantly, we demonstrate that specific sequencing errors occur at an approximately constant rate across different samples that are sequenced in parallel. We exploit this observation by developing a novel approach to filter out spurious sequences. Application of our new method demonstrates its value in the identification of true sequences amongst spurious sequences in biological data sets.

  17. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

    PubMed Central

    Mirarab, Siavash; Nguyen, Nam; Guo, Sheng; Wang, Li-San; Kim, Junhyong

    2015-01-01

    Abstract We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate—slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory. PMID:25549288

  18. Complete Genome Sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700▿

    PubMed Central

    Di Bonaventura, Maria Pia; DeSalle, Rob; Pop, Mihai; Nagarajan, Niranjan; Figurski, David H.; Fine, Daniel H.; Kaplan, Jeffrey B.; Planet, Paul J.

    2009-01-01

    We report the finished and annotated genome sequence of Aggregatibacter aphrophilus strain NJ8700, a strain isolated from the oral flora of a healthy individual, and discuss characteristics that may affect its dual roles in human health and disease. This strain has a rough appearance, and its genome contains genes encoding a type VI secretion system and several factors that may participate in host colonization. PMID:19447908

  19. Effect of Blade-surface Finish on Performance of a Single-stage Axial-flow Compressor

    NASA Technical Reports Server (NTRS)

    Moses, Jason J; Serovy, George, K

    1951-01-01

    A set of modified NACA 5509-34 rotor and stator blades was investigated with rough-machine, hand-filed, and highly polished surface finishes over a range of weight flows at six equivalent tip speeds from 672 to 1092 feet per second to determine the effect of blade-surface finish on the performance of a single-stage axial-flow compressor. Surface-finish effects decreased with increasing compressor speed and with decreasing flow at a given speed. In general, finishing blade surfaces below the roughness that may be considered aerodynamically smooth on the basis of an admissible-roughness formula will have no effect on compressor performance.

  20. Complete Genome Sequence of NEB 5-alpha, a Derivative of Escherichia coli K-12 DH5α.

    PubMed

    Anton, Brian P; Raleigh, Elisabeth A

    2016-11-10

    Escherichia coli K-12 DH5α is one of the most popular and widely available laboratory strains, but, surprisingly, no complete genome sequence has been publicly available. Here, we report the complete, finished sequence of NEB 5-alpha (DH5α fhuA2). It should serve as a useful reference for researchers working with DH5α. Copyright © 2016 Anton and Raleigh.

  1. The Adolescent Who Does Not Finish Anything.

    ERIC Educational Resources Information Center

    Breiner, Sander J.

    1985-01-01

    Practical information for therapists who deal with adolescents who do not finish tasks is presented. The relationship of task incompletion to neurosis, psychosis, depression, homosexuality, and drug abuse is described, and techniques and guidelines for treatment are provided. (Author)

  2. 40 CFR 141.511 - What is required of new finished water reservoirs?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Finished Water Reservoirs § 141.511 What is required of... 40 Protection of Environment 22 2010-07-01 2010-07-01 false What is required of new finished water...

  3. 40 CFR 141.511 - What is required of new finished water reservoirs?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Finished Water Reservoirs § 141.511 What is required of... 40 Protection of Environment 24 2012-07-01 2012-07-01 false What is required of new finished water...

  4. 40 CFR 141.511 - What is required of new finished water reservoirs?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Finished Water Reservoirs § 141.511 What is required of... 40 Protection of Environment 23 2011-07-01 2011-07-01 false What is required of new finished water...

  5. 40 CFR 141.511 - What is required of new finished water reservoirs?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Finished Water Reservoirs § 141.511 What is required of... 40 Protection of Environment 24 2013-07-01 2013-07-01 false What is required of new finished water...

  6. The topographic development and areal parametric characterization of a stratified surface polished by mass finishing

    NASA Astrophysics Data System (ADS)

    Walton, Karl; Blunt, Liam; Fleming, Leigh

    2015-09-01

    Mass finishing is amongst the most widely used finishing processes in modern manufacturing, in applications from deburring to edge radiusing and polishing. Processing objectives are varied, ranging from the cosmetic to the functionally critical. One such critical application is the hydraulically smooth polishing of aero engine component gas-washed surfaces. In this, and many other applications the drive to improve process control and finish tolerance is ever present. Considering its widespread use mass finishing has seen limited research activity, particularly with respect to surface characterization. The objectives of the current paper are to; characterise the mass finished stratified surface and its development process using areal surface parameters, provide guidance on the optimal parameters and sampling method to characterise this surface type for a given application, and detail the spatial variation in surface topography due to coupon edge shadowing. Blasted and peened square plate coupons in titanium alloy are wet (vibro) mass finished iteratively with increasing duration. Measurement fields are precisely relocated between iterations by fixturing and an image superimposition alignment technique. Surface topography development is detailed with ‘log of process duration’ plots of the ‘areal parameters for scale-limited stratified functional surfaces’, (the Sk family). Characteristic features of the Smr2 plot are seen to map out the processing of peak, core and dale regions in turn. These surface process regions also become apparent in the ‘log of process duration’ plot for Sq, where lower core and dale regions are well modelled by logarithmic functions. Surface finish (Ra or Sa) with mass finishing duration is currently predicted with an exponential model. This model is shown to be limited for the current surface type at a critical range of surface finishes. Statistical analysis provides a group of areal parameters including; Vvc, Sq, and Sdq

  7. Ultraaccurate genome sequencing and haplotyping of single human cells.

    PubMed

    Chu, Wai Keung; Edge, Peter; Lee, Ho Suk; Bansal, Vikas; Bafna, Vineet; Huang, Xiaohua; Zhang, Kun

    2017-11-21

    Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensive in vitro amplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false-positive calls per genome. Second, relatively short sequence reads contain little to no haplotype information. Here we report a method, which is dubbed SISSOR (single-stranded sequencing using microfluidic reactors), for accurate single-cell genome sequencing and haplotyping. A microfluidic processor is used to separate the Watson and Crick strands of the double-stranded chromosomal DNA in a single cell and to randomly partition megabase-size DNA strands into multiple nanoliter compartments for amplification and construction of barcoded libraries for sequencing. The separation and partitioning of large single-stranded DNA fragments of the homologous chromosome pairs allows for the independent sequencing of each of the complementary and homologous strands. This enables the assembly of long haplotypes and reduction of sequence errors by using the redundant sequence information and haplotype-based error removal. We demonstrated the ability to sequence single-cell genomes with error rates as low as 10 -8 and average 500-kb-long DNA fragments that can be assembled into haplotype contigs with N50 greater than 7 Mb. The performance could be further improved with more uniform amplification and more accurate sequence alignment. The ability to obtain accurate genome sequences and haplotype information from single cells will enable applications of genome sequencing for diverse clinical needs. Copyright © 2017 the Author(s). Published by PNAS.

  8. Effects of finishing/polishing techniques on microleakage of resin-modified glass ilonomer cement restorations.

    PubMed

    Yap, Adrian U J; Yap, W Y; Yeo, Egwin J C; Tan, Jane W S; Ong, Debbie S B

    2003-01-01

    This study investigated the effect of finishing/polishing techniques on the microleakage of resin-modified glass ionomer restorations. Class V preparations were made on the buccal and lingual/palatal surfaces of freshly extracted teeth. The cavities on each tooth were restored with Fuji II LC (FT [GC]) and Photac-Fil Quick (PF [3M-ESPE]) according to manufacturers' instructions. Immediately after light-polymerization, gross finishing was done with eight-fluted tungsten carbide burs. The teeth were then randomly divided into four groups and finishing/polishing was done with one of the following systems: (a) Robot Carbides (RC); (b) Super-Snap system (SS); (c) OneGloss (OG) and (d) CompoSite Polishers (CS). The sample size for each material-finishing/polishing system combination was eight. After finishing/polishing, the teeth were stored in distilled water at 37 degrees C for one week. The root apices were then sealed with acrylic and two coats of varnish was applied 1 mm beyond the restoration margins. The teeth were subsequently subjected to dye penetration testing (0.5% basic fuchsin), sectioned and scored. Data was analyzed using Kruskal-Wallis and Mann-Whitney U tests at a significance level of 0.05. Results of statistical analysis were as follows: Enamel margins: PF-OGfinishing/polishing technique, leakage at dentin margins was significantly greater than at enamel margins for FT. For PF, no significant difference in leakage scores was observed between dentin and enamel with the exception of finishing/polishing with OG. FT restorations had significantly less enamel and dentin leakage than PF restorations when treated with OG. The effect of finishing/polishing techniques on microleakage was both tissue and material dependent.

  9. Effect of finishing/polishing techniques and time on surface roughness of esthetic restorative materials.

    PubMed

    Madhyastha, Prashanthi Sampath; Hegde, Shreya; Srikant, N; Kotian, Ravindra; Iyer, Srividhya Sriraman

    2017-01-01

    Surface roughness associated with improper finishing/polishing of restorations can result in plaque accumulation, gingival irritation, surface staining, and poor esthetic of restored teeth. The study aimed to evaluate the efficiency of various finishing and polishing systems and time using various procedures on surface roughness of some esthetic restorative materials. In this in vitro study, samples of two composite materials, compomer and glass ionomer cement (GIC) materials, were fabricated. Finishing and polishing were done immediately ( n = 40) and after 1 week ( n = 40) using four systems (diamond bur + soflex discs; diamond bur + Astropol polishing brush; tungsten carbide bur + soflex discs; tungsten carbide bur + Astropol polishing brush). Surface roughness was measured using surface profilometer. Data were statistically analyzed by t -test (for each material and time period) and one-way analysis of variance followed by Tukey's post hoc (for finishing and polishing systems) at a significant level of P < 0.05. Analysis of time period, irrespective of finishing and polishing system showed that Ra values were greater ( P < 0.05) in delayed polishing in GIC > Z100 > Filtek P90 > Dyract AP, suggesting immediate polishing is better. Among the materials, Filtek P90 had the least Ra values indicating the smoothest surface among all materials, followed by Z100, Dyract AP, and GIC. Comparison of polishing and finishing systems irrespective of materials showed that Ra values were lower ( P > 0.05) in diamond + Astropol combination whereas diamond + soflex had the greatest Ra values. It might be concluded that: (i) Filtek P90 showed least Ra values followed by < Z100 < Dyract < GIC; (ii) immediate (24 h) finishing/polishing of materials is better than delayed; and (iii) among all these polishing systems, diamond bur-Astropol and Astrobrush showed good surface finish.

  10. DNA sequence requirements for the accurate transcription of a protein-coding plastid gene in a plastid in vitro system from mustard (Sinapis alba L.)

    PubMed Central

    Link, Gerhard

    1984-01-01

    A nuclease-treated plastid extract from mustard (Sinapis alba L.) allows efficient transcription of cloned plastid DNA templates. In this in vitro system, the major runoff transcript of the truncated gene for the 32 000 mol. wt. photosystem II protein was accurately initiated from a site close to or identical with the in vivo start site. By using plasmids with deletions in the 5'-flanking region of this gene as templates, a DNA region required for efficient and selective initiation was detected ˜28-35 nucleotides upstream of the transcription start site. This region contains the sequence element TTGACA, which matches the consensus sequence for prokaryotic `−35' promoter elements. In the absence of this region, a region ˜13-27 nucleotides upstream of the start site still enables a basic level of specific transcription. This second region contains the sequence element TATATAA, which matches the consensus sequence for the `TATA' box of genes transcribed by RNA polymerase II (or B). The region between the `TATA'-like element and the transcription start site is not sufficient but may be required for specific transcription of the plastid gene. This latter region contains the sequence element TATACT, which resembles the prokaryotic `−10' (Pribnow) box. Based on the structural and transcriptional features of the 5' upstream region, a `promoter switch' mechanism is proposed, which may account for the developmentally regulated expression of this plastid gene. ImagesFig. 1.Fig. 2.Fig. 3.Fig. 4.Figure 5. PMID:16453540

  11. Human Genome Sequencing in Health and Disease

    PubMed Central

    Gonzaga-Jauregui, Claudia; Lupski, James R.; Gibbs, Richard A.

    2013-01-01

    Following the “finished,” euchromatic, haploid human reference genome sequence, the rapid development of novel, faster, and cheaper sequencing technologies is making possible the era of personalized human genomics. Personal diploid human genome sequences have been generated, and each has contributed to our better understanding of variation in the human genome. We have consequently begun to appreciate the vastness of individual genetic variation from single nucleotide to structural variants. Translation of genome-scale variation into medically useful information is, however, in its infancy. This review summarizes the initial steps undertaken in clinical implementation of personal genome information, and describes the application of whole-genome and exome sequencing to identify the cause of genetic diseases and to suggest adjuvant therapies. Better analysis tools and a deeper understanding of the biology of our genome are necessary in order to decipher, interpret, and optimize clinical utility of what the variation in the human genome can teach us. Personal genome sequencing may eventually become an instrument of common medical practice, providing information that assists in the formulation of a differential diagnosis. We outline herein some of the remaining challenges. PMID:22248320

  12. SEM Evaluation of Surrounding Enamel after Finishing of Composite Restorations- Preliminary Results

    NASA Astrophysics Data System (ADS)

    Iovan, G.; Stoleriu, S.; Solomon, S.; Ghiorghe, A.; Sandu, A. V.; Andrian, S.

    2017-06-01

    The purpose of this study was to analyze the surface characteristics of the enamel adjacent to composite resin after finishing the restoration with different diamond and tungsten carbide burs. The topography of enamel was observed by using a scanning electron microscope. Finishing with extra-/ultra-fine carbide burs, and extra-fine diamond burs resulted in smooth surfaces. In few areas some superficial scratches with no clinical relevance were observed. Deep grooves were observed on the surface of enamel when fine diamond burs were used. Finishing of composite restorations with coarse burs should be avoided when there is a high risk of touching and scratching adjacent enamel during the procedure.

  13. Learning a Weighted Sequence Model of the Nucleosome Core and Linker Yields More Accurate Predictions in Saccharomyces cerevisiae and Homo sapiens

    PubMed Central

    Reynolds, Sheila M.; Bilmes, Jeff A.; Noble, William Stafford

    2010-01-01

    DNA in eukaryotes is packaged into a chromatin complex, the most basic element of which is the nucleosome. The precise positioning of the nucleosome cores allows for selective access to the DNA, and the mechanisms that control this positioning are important pieces of the gene expression puzzle. We describe a large-scale nucleosome pattern that jointly characterizes the nucleosome core and the adjacent linkers and is predominantly characterized by long-range oscillations in the mono, di- and tri-nucleotide content of the DNA sequence, and we show that this pattern can be used to predict nucleosome positions in both Homo sapiens and Saccharomyces cerevisiae more accurately than previously published methods. Surprisingly, in both H. sapiens and S. cerevisiae, the most informative individual features are the mono-nucleotide patterns, although the inclusion of di- and tri-nucleotide features results in improved performance. Our approach combines a much longer pattern than has been previously used to predict nucleosome positioning from sequence—301 base pairs, centered at the position to be scored—with a novel discriminative classification approach that selectively weights the contributions from each of the input features. The resulting scores are relatively insensitive to local AT-content and can be used to accurately discriminate putative dyad positions from adjacent linker regions without requiring an additional dynamic programming step and without the attendant edge effects and assumptions about linker length modeling and overall nucleosome density. Our approach produces the best dyad-linker classification results published to date in H. sapiens, and outperforms two recently published models on a large set of S. cerevisiae nucleosome positions. Our results suggest that in both genomes, a comparable and relatively small fraction of nucleosomes are well-positioned and that these positions are predictable based on sequence alone. We believe that the bulk of the

  14. Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model

    PubMed Central

    DeLeon, Orlando; Hodis, Hagit; O’Malley, Yunxia; Johnson, Jacklyn; Salimi, Hamid; Zhai, Yinjie; Winter, Elizabeth; Remec, Claire; Eichelberger, Noah; Van Cleave, Brandon; Puliadi, Ramya; Harrington, Robert D.; Stapleton, Jack T.; Haim, Hillel

    2017-01-01

    The envelope glycoproteins (Envs) of HIV-1 continuously evolve in the host by random mutations and recombination events. The resulting diversity of Env variants circulating in the population and their continuing diversification process limit the efficacy of AIDS vaccines. We examined the historic changes in Env sequence and structural features (measured by integrity of epitopes on the Env trimer) in a geographically defined population in the United States. As expected, many Env features were relatively conserved during the 1980s. From this state, some features diversified whereas others remained conserved across the years. We sought to identify “clues” to predict the observed historic diversification patterns. Comparison of viruses that cocirculate in patients at any given time revealed that each feature of Env (sequence or structural) exists at a defined level of variance. The in-host variance of each feature is highly conserved among individuals but can vary between different HIV-1 clades. We designate this property “volatility” and apply it to model evolution of features as a linear diffusion process that progresses with increasing genetic distance. Volatilities of different features are highly correlated with their divergence in longitudinally monitored patients. Volatilities of features also correlate highly with their population-level diversification. Using volatility indices measured from a small number of patient samples, we accurately predict the population diversity that developed for each feature over the course of 30 years. Amino acid variants that evolved at key antigenic sites are also predicted well. Therefore, small “fluctuations” in feature values measured in isolated patient samples accurately describe their potential for population-level diversification. These tools will likely contribute to the design of population-targeted AIDS vaccines by effectively capturing the diversity of currently circulating strains and addressing properties

  15. MAFsnp: A Multi-Sample Accurate and Flexible SNP Caller Using Next-Generation Sequencing Data

    PubMed Central

    Hu, Jiyuan; Li, Tengfei; Xiu, Zidi; Zhang, Hong

    2015-01-01

    Most existing statistical methods developed for calling single nucleotide polymorphisms (SNPs) using next-generation sequencing (NGS) data are based on Bayesian frameworks, and there does not exist any SNP caller that produces p-values for calling SNPs in a frequentist framework. To fill in this gap, we develop a new method MAFsnp, a Multiple-sample based Accurate and Flexible algorithm for calling SNPs with NGS data. MAFsnp is based on an estimated likelihood ratio test (eLRT) statistic. In practical situation, the involved parameter is very close to the boundary of the parametric space, so the standard large sample property is not suitable to evaluate the finite-sample distribution of the eLRT statistic. Observing that the distribution of the test statistic is a mixture of zero and a continuous part, we propose to model the test statistic with a novel two-parameter mixture distribution. Once the parameters in the mixture distribution are estimated, p-values can be easily calculated for detecting SNPs, and the multiple-testing corrected p-values can be used to control false discovery rate (FDR) at any pre-specified level. With simulated data, MAFsnp is shown to have much better control of FDR than the existing SNP callers. Through the application to two real datasets, MAFsnp is also shown to outperform the existing SNP callers in terms of calling accuracy. An R package “MAFsnp” implementing the new SNP caller is freely available at http://homepage.fudan.edu.cn/zhangh/softwares/. PMID:26309201

  16. 77 FR 12227 - Long Term 2 Enhanced Surface Water Treatment Rule: Uncovered Finished Water Reservoirs; Public...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-29

    ... Water Treatment Rule: Uncovered Finished Water Reservoirs; Public Meeting AGENCY: Environmental... review of the uncovered finished water reservoir requirement in the Long Term 2 Enhanced Surface Water... uncovered finished water reservoir requirement and the agency's Six Year Review process. EPA also plans to...

  17. Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov.

    PubMed Central

    Lagier, Jean-Christophe; Armougom, Fabrice; Mishra, Ajay Kumar; Nguyen, Thi-Tien; Raoult, Didier; Fournier, Pierre-Edouard

    2012-01-01

    Alistipes timonensis strain JC136T sp. nov. is the type strain of A. timonensis sp. nov., a new species within the genus Alistipes. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. A. timonensis is an obligate anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,497,779 bp long genome (one chromosome but no plasmid) contains 2,742 protein-coding and 50 RNA genes, including three rRNA genes. PMID:23408657

  18. Non-contiguous finished genome sequence and description of Oceanobacillus massiliensis sp. nov.

    PubMed Central

    Roux, Véronique; Million, Matthieu; Robert, Catherine; Magne, Alix; Raoult, Didier

    2013-01-01

    Oceanobacillus massiliensis strain N’DiopT sp. nov. is the type strain of O. massiliensis sp. nov., a new species within the genus Oceanobacillus. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. O. massiliensis is an aerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,532,675 bp long genome contains 3,519 protein-coding genes and 72 RNA genes, including between 6 and 8 rRNA operons. PMID:24976893

  19. AMMONIA EMISSION FACTORS FROM SWINE FINISHING OPERATIONS

    EPA Science Inventory

    The paper presents results from two new studies at swine finishing facilities. (NOTE: Concentrated animal feeding operations (CAFOs) are being examined in several regions of the U,.S. as major sources of ammonia and particulate matter precursors. EPA's National Risk Management Re...

  20. AMMONIA EMISSION FACTORS FROM SWINE FINISHING OPERATIONS

    EPA Science Inventory

    The paper presents results from two new studies at swine finishing facilities. (NOTE: Concentrated anaimal feeding operations (CAFOs) are being examined in several regions of the U.S. as major sources of ammonia and particulate matter precursors. EPA's National Risk Management Re...

  1. Wood properties affecting finish service life

    Treesearch

    R. Sam Williams; Charles Jourdain; George I. Daisey; Robert W. Springate

    2000-01-01

    Wood is a biological material that has widely different properties depending on species, geographic area where the tree grew, the growth conditions, size of the tree at harvest, sawing, and other manufacturing processes. Some of the more important wood properties as they relate to wood finishing are discussed, e.g., growth rate, density, knots, extractives, juvenile...

  2. Draft Genome Sequence of Streptomyces clavuligerus NRRL 3585, a Producer of Diverse Secondary Metabolites▿

    PubMed Central

    Song, Ju Yeon; Jeong, Haeyoung; Yu, Dong Su; Fischbach, Michael A.; Park, Hong-Seog; Kim, Jae Jong; Seo, Jeong-Sun; Jensen, Susan E.; Oh, Tae Kwang; Lee, Kye Joon; Kim, Jihyun F.

    2010-01-01

    Streptomyces clavuligerus is an important industrial strain that produces a number of antibiotics, including clavulanic acid and cephamycin C. A high-quality draft genome sequence of the S. clavuligerus NRRL 3585 strain was produced by employing a hybrid approach that involved Sanger sequencing, Roche/454 pyrosequencing, optical mapping, and partial finishing. Its genome, comprising four linear replicons, one chromosome, and four plasmids, carries numerous sets of genes involved in the biosynthesis of secondary metabolites, including a variety of antibiotics. PMID:20889745

  3. Effects of Wet and Dry Finishing and Polishing on Surface Roughness and Microhardness of Composite Resins

    PubMed Central

    Nasoohi, Negin; Hoorizad, Maryam

    2017-01-01

    Objectives: This study aimed to assess the effect of wet and dry finishing and polishing on microhardness and roughness of microhybrid and nanohybrid composites. Materials and Methods: Thirty samples were fabricated of each of the Polofil Supra and Aelite Aesthetic All-Purpose Body microhybrid and Grandio and Aelite Aesthetic Enamel nanohybrid composite resins. Each group (n=30) was divided into three subgroups of D, W and C (n=10). Finishing and polishing were performed dry in group D and under water coolant in group W. Group C served as the control group and did not receive finishing and polishing. Surface roughness of samples was measured by a profilometer and their hardness was measured by a Vickers hardness tester. Data were analyzed using two-way ANOVA (P<0.05). Results: The smoothest surfaces with the lowest microhardness were obtained under Mylar strip without finishing/polishing for all composites (P<0.0001). The highest surface roughness was recorded for dry finishing/polishing for all composites (P<0.0001). Dry finishing/polishing increased the microhardness of all composites (P<0.0001). Conclusions: Dry finishing and polishing increases the microhardness and surface roughness of microhybrid and nanohybrid composite resins. PMID:29104597

  4. History of magnetorheological finishing

    NASA Astrophysics Data System (ADS)

    Harris, Daniel C.

    2011-06-01

    Magnetorheological finishing (MRF) is a deterministic method for producing complex optics with figure accuracy <50 nm and surface roughness <1 nm. MRF was invented at the Luikov Institute of Heat and Mass Transfer in Minsk, Belarus in the late 1980s by a team led by William Kordonski. When the Soviet Union opened up, New York businessman Lowell Mintz was invited to Minsk in 1990 to explore possibilities for technology transfer. Mintz was told of the potential for MRF, but did not understand whether it had value. Mintz was referred to Harvey Pollicove at the Center for Optics Manufacturing of the University of Rochester. As a result of their conversation, they sent Prof. Steve Jacobs to visit Minsk and evaluate MRF. From Jacobs' positive findings, and with support from Lowell Mintz, Kordonski and his colleagues were invited in 1993 to work at the Center for Optics Manufacturing with Jacobs and Don Golini to refine MRF technology. A "preprototype" finishing machine was operating by 1994. Prof. Greg Forbes and doctoral student Paul Dumas developed algorithms for deterministic control of MRF. In 1996, Golini recognized the commercial potential of MRF, secured investment capital from Lowell Mintz, and founded QED Technologies. The first commercial MRF machine was unveiled in 1998. It was followed by more advanced models and by groundbreaking subaperture stitching interferometers for metrology. In 2006, QED was acquired by and became a division of Cabot Microelectronics. This paper recounts the history of the development of MRF and the founding of QED Technologies.

  5. 24 CFR 200.946 - Building product standards and certification program for exterior finish and insulation systems...

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... Glass Fiber Reinforcing Mesh for Use in Exterior Insulation and Finish Systems (EIFS), Class PB. (xv... certification program for exterior finish and insulation systems, use of Materials Bulletin UM 101. 200.946... product standards and certification program for exterior finish and insulation systems, use of Materials...

  6. 24 CFR 200.946 - Building product standards and certification program for exterior finish and insulation systems...

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... Glass Fiber Reinforcing Mesh for Use in Exterior Insulation and Finish Systems (EIFS), Class PB. (xv... certification program for exterior finish and insulation systems, use of Materials Bulletin UM 101. 200.946... product standards and certification program for exterior finish and insulation systems, use of Materials...

  7. Indexed variation graphs for efficient and accurate resistome profiling.

    PubMed

    Rowe, Will P M; Winn, Martyn D

    2018-05-14

    Antimicrobial resistance remains a major threat to global health. Profiling the collective antimicrobial resistance genes within a metagenome (the "resistome") facilitates greater understanding of antimicrobial resistance gene diversity and dynamics. In turn, this can allow for gene surveillance, individualised treatment of bacterial infections and more sustainable use of antimicrobials. However, resistome profiling can be complicated by high similarity between reference genes, as well as the sheer volume of sequencing data and the complexity of analysis workflows. We have developed an efficient and accurate method for resistome profiling that addresses these complications and improves upon currently available tools. Our method combines a variation graph representation of gene sets with an LSH Forest indexing scheme to allow for fast classification of metagenomic sequence reads using similarity-search queries. Subsequent hierarchical local alignment of classified reads against graph traversals enables accurate reconstruction of full-length gene sequences using a scoring scheme. We provide our implementation, GROOT, and show it to be both faster and more accurate than a current reference-dependent tool for resistome profiling. GROOT runs on a laptop and can process a typical 2 gigabyte metagenome in 2 minutes using a single CPU. Our method is not restricted to resistome profiling and has the potential to improve current metagenomic workflows. GROOT is written in Go and is available at https://github.com/will-rowe/groot (MIT license). will.rowe@stfc.ac.uk. Supplementary data are available at Bioinformatics online.

  8. Implementing Cleaner Printed Wiring Board Technologies: Surface Finishes

    EPA Pesticide Factsheets

    This document describes the problems, solutions, and time and effort involved in implementing alternative surface finish technologies, and this guide is produced as part of the DfE Printed Wiring Board Project

  9. IMPLEMENTATION OF USEPA'S METAL FINISHING FACILITY POLLUTION PREVENTION TOOL (MFFP2T) - 2003

    EPA Science Inventory

    To help metal finishing facilities meet the goal of profitable pollution prevention, the USEPA is developing the Metal Finishing Facility Pollution Prevention Tool (MFFP2T), a computer program that estimates the rate of solid, liquid waste generation and air emissions. This progr...

  10. Surface Finish Effects Using Coating Method on 3D Printing (FDM) Parts

    NASA Astrophysics Data System (ADS)

    Haidiezul, AHM; Aiman, AF; Bakar, B.

    2018-03-01

    One of three-dimensional (3-D) printing economical processes is by using Fused Deposition Modelling (FDM). The 3-D printed object was built using layer-by-layer approach which caused “stair stepping” effects. This situation leads to uneven surface finish which mostly affect the objects appearance for product designers in presenting their models or prototypes. The objective of this paper is to examine the surface finish effects from the application of XTC-3D coating developed by Smooth-On, USA on the 3D printed parts. From the experimental works, this study shows the application of XTC-3D coating to the 3-D printed parts has improve the surface finish by reducing the gap between the layer

  11. Performance, profitability and greenhouse gas emissions of alternative finishing strategies for Holstein-Friesian bulls and steers.

    PubMed

    Murphy, B; Crosson, P; Kelly, A K; Prendiville, R

    2018-02-06

    Modifying finishing strategies within established production systems has the potential to increase beef output and farm profit while reducing greenhouse gas (GHG) emissions. Thus, the objectives of this study were to investigate the effects of finishing duration on animal performance of Holstein-Friesian (HF) bulls and steers and evaluate the profitability and GHG emissions of these finishing strategies. A total of 90 HF calves were assigned to a complete randomised block design; three bull and three steer finishing strategies. Calves were rotationally grazed in a paddock system for the first season at pasture, housed and offered grass silage ad libitum plus 1.5 kg DM of concentrate per head daily for the first winter and returned to pasture for a second season. Bulls were slaughtered at 19 months of age and either finished indoors on concentrates ad libitum for 100 days (19AL), finished at pasture supplemented with 5 kg DM of concentrate per head daily for 100 (19SP) or 150 days (19LP). Steers were slaughtered at 21 months of age and finished at pasture, supplemented with 5 kg DM of concentrate per head daily for 60 (21SP) and 110 days (21LP) or slaughtered at 24 months of age and finished indoors over the second winter on grass silage ad libitum plus 5 kg DM of concentrate per head daily (24MO). The Grange Dairy Beef Systems Model and the Beef Systems Greenhouse Gas Emissions Model were used to evaluate profitability and GHG emissions, respectively. Average daily gain during the finishing period (P<0.001), live weight at slaughter (P<0.01), carcass weight (P<0.05) and fat score (P<0.001) were greater for 19AL than 19SP and 19LP, respectively. Similarly, concentrate dry matter intake was greater for 19AL than 19SP; 19LP was intermediate (P<0.001). Live weight at slaughter (P<0.001), carcass weight (P<0.001), conformation score (P<0.05) and fat score (P<0.001) were greater for 24MO than 21SP and 21LP, respectively. During the finishing period concentrate dry matter

  12. Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

    PubMed

    Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan; Brent, Michael R

    2009-07-01

    The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics. We present Pairagon, a pair hidden Markov model based cDNA-to-genome alignment program, as the most accurate aligner for sequences with high- and low-identity levels. We conducted a series of experiments testing alignment accuracy with varying sequence identity. We first created 'perfect' simulated cDNA sequences by splicing the sequences of exons in the reference genome sequences of fly and human. The complete reference genome sequences were then mutated to various degrees using a realistic mutation simulator and the perfect cDNAs were aligned to them using Pairagon and 12 other aligners. To validate these results with natural sequences, we performed cross-species alignment using orthologous transcripts from human, mouse and rat. We found that aligner accuracy is heavily dependent on sequence identity. For sequences with 100% identity, Pairagon achieved accuracy levels of >99.6%, with one quarter of the errors of any other aligner. Furthermore, for human/mouse alignments, which are only 85% identical, Pairagon achieved 87% accuracy, higher than any other aligner. Pairagon source and executables are freely available at http://mblab.wustl.edu/software/pairagon/

  13. Finished Genome Sequence of Escherichia coli K-12 Strain HMS174 (ATCC 47011).

    PubMed

    Mairhofer, Juergen; Krempl, Peter M; Thallinger, Gerhard G; Striedner, Gerald

    2014-11-20

    Escherichia coli strain K-12 substrain HMS174 is an engineered descendant of the E. coli K-12 wild-type strain. Like its ancestor, it is an important organism in biotechnological research and is used in fermentation processes for heterologous protein production. Here, we report the complete genome sequence of E. coli HMS174 (ATCC 47011). Copyright © 2014 Mairhofer et al.

  14. 40 CFR 425.10 - Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 31 2012-07-01 2012-07-01 false Applicability; description of the hair... FINISHING POINT SOURCE CATEGORY Hair Pulp, Chrome Tan, Retan-Wet Finish Subcategory § 425.10 Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory. The provisions of this subpart are...

  15. 40 CFR 425.10 - Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 31 2013-07-01 2013-07-01 false Applicability; description of the hair... FINISHING POINT SOURCE CATEGORY Hair Pulp, Chrome Tan, Retan-Wet Finish Subcategory § 425.10 Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory. The provisions of this subpart are...

  16. 40 CFR 425.20 - Applicability; description of the hair save, chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 31 2012-07-01 2012-07-01 false Applicability; description of the hair... FINISHING POINT SOURCE CATEGORY Hair Save, Chrome Tan, Retan-Wet Finish Subcategory § 425.20 Applicability; description of the hair save, chrome tan, retan-wet finish subcategory. The provisions of this subpart are...

  17. 40 CFR 425.10 - Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 30 2014-07-01 2014-07-01 false Applicability; description of the hair... FINISHING POINT SOURCE CATEGORY Hair Pulp, Chrome Tan, Retan-Wet Finish Subcategory § 425.10 Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory. The provisions of this subpart are...

  18. 40 CFR 425.20 - Applicability; description of the hair save, chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 30 2014-07-01 2014-07-01 false Applicability; description of the hair... FINISHING POINT SOURCE CATEGORY Hair Save, Chrome Tan, Retan-Wet Finish Subcategory § 425.20 Applicability; description of the hair save, chrome tan, retan-wet finish subcategory. The provisions of this subpart are...

  19. 40 CFR 425.20 - Applicability; description of the hair save, chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 31 2013-07-01 2013-07-01 false Applicability; description of the hair... FINISHING POINT SOURCE CATEGORY Hair Save, Chrome Tan, Retan-Wet Finish Subcategory § 425.20 Applicability; description of the hair save, chrome tan, retan-wet finish subcategory. The provisions of this subpart are...

  20. Predicting DNA hybridization kinetics from sequence

    NASA Astrophysics Data System (ADS)

    Zhang, Jinny X.; Fang, John Z.; Duan, Wei; Wu, Lucia R.; Zhang, Angela W.; Dalchau, Neil; Yordanov, Boyan; Petersen, Rasmus; Phillips, Andrew; Zhang, David Yu

    2018-01-01

    Hybridization is a key molecular process in biology and biotechnology, but so far there is no predictive model for accurately determining hybridization rate constants based on sequence information. Here, we report a weighted neighbour voting (WNV) prediction algorithm, in which the hybridization rate constant of an unknown sequence is predicted based on similarity reactions with known rate constants. To construct this algorithm we first performed 210 fluorescence kinetics experiments to observe the hybridization kinetics of 100 different DNA target and probe pairs (36 nt sub-sequences of the CYCS and VEGF genes) at temperatures ranging from 28 to 55 °C. Automated feature selection and weighting optimization resulted in a final six-feature WNV model, which can predict hybridization rate constants of new sequences to within a factor of 3 with ∼91% accuracy, based on leave-one-out cross-validation. Accurate prediction of hybridization kinetics allows the design of efficient probe sequences for genomics research.

  1. Using structure to explore the sequence alignment space of remote homologs.

    PubMed

    Kuziemko, Andrew; Honig, Barry; Petrey, Donald

    2011-10-01

    Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

  2. Comparative evaluation of different thermally modified wood samples finishing with UV-curable and waterborne coatings

    NASA Astrophysics Data System (ADS)

    Herrera, René; Muszyńska, Monika; Krystofiak, Tomasz; Labidi, Jalel

    2015-12-01

    Thermally modified wood has been developed as an industrial method to improve durability and dimensional stability of wood and thus extends the range of uses and service life of wood-based products. Despite the improvements gained by treatment, surface finishing using coatings prevents esthetical changes such as color degradation or occasional growth of mold adding protection in outdoor use and extending the service life of products. The wood finishing process was carried out with commercially available waterborne and UV-curable coatings on industrially modified at 192, 200, 212 °C and unmodified European ash (Fraxinus excelsior L.) wood, using an industrial rollers system and a laboratory brushing system. Changes caused by thermal treatment which could affect the surface finish were measured and compared with control samples, such as water uptake, wettability and acidity. Following the wood finishing, surface properties and esthetic changes were evaluated; as well as the coatings performance. Thermally modified wood presented improved adherence compared with unmodified wood with a significant improvement in samples modified at 212 °C, which also present the highest hardness when UV-cured. Finishes with UV-curing maintain the hydrophobic effect of thermally modified wood, whereas waterborne finishes increase the surface wettability. Thermal modification did not negatively influence on the elastic properties of the coated substrate and thus allows this material to be finished with different coating systems in the same conditions as unmodified wood.

  3. The Effectiveness of Finishing School Programmes from the Perspectives of Graduates and Employers

    ERIC Educational Resources Information Center

    Ali, Jamal; Eam, Lim Hock; Ismail, Russayani; Rahim, Fauziah Abdul; Isa, Filzah Md; Ismail, Ismi Arif

    2014-01-01

    Purpose: This study examined the effectiveness of Finishing School programmes in enhancing the employability of graduates from institutions of higher learning. The perceptions of the graduates and employers towards the effectiveness of the programmes were analyzed. The effectiveness of Finishing School programmes evaluated through a graduate…

  4. Influence of finishing systems on hydrophilic and lipophilic oxygen radical absorbance capacity (ORAC) in beef.

    PubMed

    Wu, C; Duckett, S K; Neel, J P S; Fontenot, J P; Clapham, W M

    2008-11-01

    The aim of this research was to: (1) develop a reliable extraction procedure and assay to determine antioxidant activity in meat products, and (2) assess the effect of beef finishing system (forage-finished: alfalfa, pearl millet or mixed pastures vs. concentrate-finished) on longissimus muscle antioxidant activity. The effect of extraction method (ethanol concentration and extraction time), protein removal, and sample preparation method (pulverization or freeze drying) were first evaluated to develop an antioxidant assay for meat products. Beef extracts prepared with low ethanol concentrations (20%) demonstrated higher hydrophilic ORAC. Protein removal prior to extraction reduced hydrophilic ORAC values. Sample preparation method influenced both hydrophilic and lipophilic ORAC, with pulverized samples containing higher hydrophilic and lipophilic ORAC values. Beef cattle finishing system (Forage: alfalfa, pearl millet, or natural pasture vs. concentrates) had little impact on muscle hydrophilic ORAC, but muscle from forage finished beef contained greater lipophilic ORAC. In addition, broiling of steaks reduced hydrophilic ORAC.

  5. An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments.

    PubMed

    Bansal, Vikas

    2018-01-01

    The short read lengths of current high-throughput sequencing technologies limit the ability to recover long-range haplotype information. Dilution pool methods for preparing DNA sequencing libraries from high molecular weight DNA fragments enable the recovery of long DNA fragments from short sequence reads. These approaches require computational methods for identifying the DNA fragments using aligned sequence reads and assembling the fragments into long haplotypes. Although a number of computational methods have been developed for haplotype assembly, the problem of identifying DNA fragments from dilution pool sequence data has not received much attention. We formulate the problem of detecting DNA fragments from dilution pool sequencing experiments as a genome segmentation problem and develop an algorithm that uses dynamic programming to optimize a likelihood function derived from a generative model for the sequence reads. This algorithm uses an iterative approach to automatically infer the mean background read depth and the number of fragments in each pool. Using simulated data, we demonstrate that our method, FragmentCut, has 25-30% greater sensitivity compared with an HMM based method for fragment detection and can also detect overlapping fragments. On a whole-genome human fosmid pool dataset, the haplotypes assembled using the fragments identified by FragmentCut had greater N50 length, 16.2% lower switch error rate and 35.8% lower mismatch error rate compared with two existing methods. We further demonstrate the greater accuracy of our method using two additional dilution pool datasets. FragmentCut is available from https://bansal-lab.github.io/software/FragmentCut. vibansal@ucsd.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  6. Characterisation of the joining zone of serially arranged hybrid semi-finished components

    NASA Astrophysics Data System (ADS)

    Behrens, B.-A.; Chugreev, A.; Matthias, T.

    2018-05-01

    Forming of already joined semi-finished products is an innovative approach to manufacture components which are well-adapted to external loads. This approach results in an economically and ecologically improved production by the targeted use of high-quality materials in component areas, which undergo high stresses. One possible production method for hybrid semi-finished products is friction welding. This welding method allows for the production of hybrid semi-finished products made of aluminium and steel as well as steel and steel. In this paper, the thermomechanical tensile and shear stresses causing a failure of the joined zone are experimentally determined through tension tests. These tests are performed with specimens whose joint zones are aligned with different angles to the load direction.

  7. Non contiguous-finished genome sequence and description of Enorma timonensis sp. nov.

    PubMed Central

    Ramasamy, Dhamodaran; Dubourg, Gregory; Robert, Catherine; Caputo, Aurelia; Papazian, Laurent; Raoult, Didier; Fournier, Pierre-Edouard

    2014-01-01

    Enorma timonensis strain GD5T sp. nov., is the type strain of E. timonensis sp. nov., a new member of the genus Enorma within the family Coriobacteriaceae. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old woman hospitalized for 3 months in an intensive care unit. E. timonensis is an obligate anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,365,123 bp long genome (1 chromosome but no plasmid) contains 2,060 protein-coding and 52 RNA genes, including 4 rRNA genes. PMID:25197477

  8. Non contiguous-finished genome sequence and description of Peptoniphilus obesi sp. nov.

    PubMed Central

    Mishra, Ajay Kumar; Hugon, Perrine; Lagier, Jean-Christophe; Nguyen, Thi-Thien; Robert, Catherine; Couderc, Carine; Raoult, Didier

    2013-01-01

    Peptoniphilus obesi strain ph1T sp. nov., is the type strain of P. obesi sp. nov., a new species within the genus Peptoniphilus. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. P. obesi strain ph1T is a Gram-positive, obligate anaerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,774,150 bp long genome (1 chromosome but no plasmid) contains 1,689 protein-coding and 29 RNA genes, including 5 rRNA genes. PMID:24019985

  9. Evidence for spontaneous retrieval of suspended but not finished prospective memories.

    PubMed

    Scullin, Michael K; Einstein, Gilles O; McDaniel, Mark A

    2009-06-01

    McDaniel and Einstein (2007) argued that prospective memories can be retrieved through spontaneous retrieval processes stimulated by the presence of a target cue. To test this claim, we investigated whether presenting a prospective memory cue during a task that did not require an intention to be performed spontaneously triggered remembering of that intention. In two experiments, participants performed an image-rating task in which a prospective memory task (to press the "Q" key when a target word appeared) was embedded. Then, participants were told that their intention was finished or suspended. Finally, participants performed a lexical decision task in which each target (and a matched control) word appeared. RTs were slower to target words than to control words when the intention was suspended but not when it was finished. These results suggest that target cues associated with suspended intentions can spontaneously trigger remembering but that finished intentions are quickly deactivated.

  10. Finishing of additively manufactured titanium alloy by shape adaptive grinding (SAG)

    NASA Astrophysics Data System (ADS)

    Beaucamp, Anthony T.; Namba, Yoshiharu; Charlton, Phillip; Jain, Samyak; Graziano, Arthur A.

    2015-06-01

    In recent years, rapid prototyping of titanium alloy components for medical and aeronautics application has become viable thanks to advances in technologies such as electron beam melting (EBM) and selective laser sintering (SLS). However, for many applications the high surface roughness generated by additive manufacturing techniques demands a post-finishing operation to improve the surface quality prior to usage. In this paper, the novel shape adaptive grinding process has been applied to finishing titanium alloy (Ti6Al4V) additively manufactured by EBM and SLS. It is shown that the micro-structured surface layer resulting from the melting process can be removed, and the surface can then be smoothed down to less than 10 nm Ra (starting from 4-5 μm Ra) using only three different diamond grit sizes. This paper also demonstrates application of the technology to freeform shapes, and documents the dimensional accuracy of finished artifacts.

  11. Effects of forage species or concentrate finishing on animal performance, carcass and meat quality.

    PubMed

    Duckett, S K; Neel, J P S; Lewis, R M; Fontenot, J P; Clapham, W M

    2013-03-01

    Angus-cross steers (n = 128; initial BW = 270 ± 3.8 kg) were used in a 3-yr study to assess effects of forage species grazed before slaughter versus concentrate finishing on carcass and meat quality. At the completion of the stockering phase, steers were randomly allotted to mixed pasture (MP; n = 36/yr) or corn-silage concentrate (CON; n = 12/yr) finishing treatments. At 40 d before harvest, MP steers were randomly divided into 3 forage species treatments: alfalfa (AL), pearl millet (PM), or mixed pasture (MP). Average daily BW gain was greater (P = 0.001) for CON than for forage-finished (FOR) steers during the early and overall finishing phase. During the late finishing phase when FOR steers were grazing difference forage species, ADG was greater (P = 0.03) for PM than MP or AL. Harvest weight and HCW were greater (P < 0.001) for CON than FOR due to the differences in animal performance. Total fat percentage of the 9th to 11th rib section was 46% less(P = 0.028) for FOR than CON due to reductions (P < 0.001) in the percentage of subcutaneous fat. Warner-Bratzler shear force (WBS) values at 14 d and 28 d of aging did not differ (P > 0.78) between CON and FOR and were not altered (P > 0.40) by forage species. Trained sensory panel juiciness, initial tenderness, and overall tenderness scores did not differ (P > 0.17) by finishing treatment or forage species. Beef flavor intensity was greater (P < 0.001) for CON than FOR. Beef flavor intensity was greater (P < 0.02) for AL and PM than MP. Off-flavor intensity was greater (P < 0.001) for all forage-fed steaks, regardless of forage species, than CON. Finishing on forages reduced (P = 0.003) total lipid content by 61% for the LM compared with CON finished cattle. Forage species grazed before harvest did not alter (P > 0.05) total lipid content of the LM. Oleic acid concentration and total MUFA of the LM were 21% and 22% less (P = 0.001) for FOR than CON. Concentrations of all individual [linolenic acid

  12. Deep Sequencing to Identify the Causes of Viral Encephalitis

    PubMed Central

    Chan, Benjamin K.; Wilson, Theodore; Fischer, Kael F.; Kriesel, John D.

    2014-01-01

    Deep sequencing allows for a rapid, accurate characterization of microbial DNA and RNA sequences in many types of samples. Deep sequencing (also called next generation sequencing or NGS) is being developed to assist with the diagnosis of a wide variety of infectious diseases. In this study, seven frozen brain samples from deceased subjects with recent encephalitis were investigated. RNA from each sample was extracted, randomly reverse transcribed and sequenced. The sequence analysis was performed in a blinded fashion and confirmed with pathogen-specific PCR. This analysis successfully identified measles virus sequences in two brain samples and herpes simplex virus type-1 sequences in three brain samples. No pathogen was identified in the other two brain specimens. These results were concordant with pathogen-specific PCR and partially concordant with prior neuropathological examinations, demonstrating that deep sequencing can accurately identify viral infections in frozen brain tissue. PMID:24699691

  13. Flame retardant finishing of cotton fabric based on synergistic compounds containing boron and nitrogen.

    PubMed

    Xie, Kongliang; Gao, Aiqin; Zhang, Yongsheng

    2013-10-15

    Boric acid and compound containing nitrogen, 2,4,6-tri[(2-hydroxy-3-trimethyl-ammonium)propyl]-1,3,5-triazine chloride (Tri-HTAC) were used to finish cotton fabric. The flame retardant properties of the finished cotton fabrics and the synergetic effects of boron and nitrogen elements were investigated and evaluated by limited oxygen index (LOI) method. The mechanism of cross-linking reaction among cotton fiber, Tri-HTAC, and boric acid was discussed by FTIR and element analysis. The thermal stability and surface morphology of the finished cotton fabrics were investigated by thermogravimetric analysis (TGA) and scanning electron microscope (SEM), respectively. The finishing system of the mixture containing boron and nitrogen showed excellent synergistic flame retardancy for cotton fabric. The cotton fabric finished with mixture system had excellent flame retardancy. The LOI value of the treated cotton fabric increased over 27.5. Tri-HTAC could form covalent bonds with cellulose fiber and boric acid. The flame retardant cotton fabric showed a slight decrease in tensile strength and whiteness. The surface morphology of flame retardant cotton fiber was smooth. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Drywall Finishing Apprenticeship. Course Outline (C-6).

    ERIC Educational Resources Information Center

    Lengert, Gerald

    This course outline was prepard to help apprentice drywall installers and teachers of drywall finishing courses to learn or teach the skills necessary for the apprenticeship course in British Columbia. The course outline consists of 11 tracks (units) that cover the following topics: estimating, job inspection, safety, applying bead, filling…

  15. Portable flooring protects finished surfaces, is easily moved

    NASA Technical Reports Server (NTRS)

    Carmody, R. J.

    1964-01-01

    To protect curved, finished surface and provide support for workmen, portable flooring has been made from rigid plastic foam blocks, faced with aluminum strips. Held together by nylon webbing, the flooring can be rolled up for easy carrying.

  16. Surface Finish and Residual Stresses Induced by Orthogonal Dry Machining of AA7075-T651

    PubMed Central

    Jomaa, Walid; Songmene, Victor; Bocher, Philippe

    2014-01-01

    The surface finish was extensively studied in usual machining processes (turning, milling, and drilling). For these processes, the surface finish is strongly influenced by the cutting feed and the tool nose radius. However, a basic understanding of tool/surface finish interaction and residual stress generation has been lacking. This paper aims to investigate the surface finish and residual stresses under the orthogonal cutting since it can provide this information by avoiding the effect of the tool nose radius. The orthogonal machining of AA7075-T651 alloy through a series of cutting experiments was performed under dry conditions. Surface finish was studied using height and amplitude distribution roughness parameters. SEM and EDS were used to analyze surface damage and built-up edge (BUE) formation. An analysis of the surface topography showed that the surface roughness was sensitive to changes in cutting parameters. It was found that the formation of BUE and the interaction between the tool edge and the iron-rich intermetallic particles play a determinant role in controlling the surface finish during dry orthogonal machining of the AA7075-T651 alloy. Hoop stress was predominantly compressive on the surface and tended to be tensile with increased cutting speed. The reverse occurred for the surface axial stress. The smaller the cutting feed, the greater is the effect of cutting speed on both axial and hoop stresses. By controlling the cutting speed and feed, it is possible to generate a benchmark residual stress state and good surface finish using dry machining. PMID:28788534

  17. A novel approach of magnetorheological abrasive fluid finishing with swirling-assisted inlet flow

    NASA Astrophysics Data System (ADS)

    Kheradmand, Saeid; Esmailian, Mojtaba; Fatahy, A.

    Abrasive flow machining has been the pioneer of new finishing processes. Rotating workpiece and imposing a magnetic field using magnetorheological working medium are some assisting manipulations to improve surface finishing, because they can increase the forces on the workpiece surface. Similarly, swirling the inlet flow using stationary swirler vanes, as a novel idea, may also increase forces on the surface, and then raise the material removal, with a lower expense and energy consumption compared with the case of workpiece rotation. Thus, in this paper, surface roughness improvement is studied in a pipe with rotating inlet flow of a magnetorheological finishing medium under imposing a magnetic field. The results are compared with the case of rotating workpiece, using 3D numerical simulation. The governing hydrodynamic parameters are investigated in both cases to monitor the flow variations. It is shown that surface roughness is improved by rotating inlet flow. However, it is found that finishing in the entrance length of swirling-assisted inlet flow can be so economical for short length workpieces, compared with the case of rotating workpiece, with very near Ra values. By comparison of the numerical results and published experimental data, current study also shows the ability of the numerical simulation, as an inexpensive and efficient tool, to predict the surface roughness changes in finishing processes.

  18. Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T.

    PubMed

    Elkins, James G; Hamilton-Brehm, Scott D; Lucas, Susan; Han, James; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne A; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Davenport, Karen W; Detter, John C; Han, Cliff S; Tapia, Roxanne; Land, Miriam L; Hauser, Loren; Kyrpides, Nikos C; Ivanova, Natalia N; Pagani, Ioanna; Bruce, David; Woyke, Tanja; Cottingham, Robert W

    2013-04-11

    Thermodesulfobacterium geofontis OPF15(T) (ATCC BAA-2454, JCM 18567) was isolated from Obsidian Pool, Yellowstone National Park, and grows optimally at 83°C. The 1.6-Mb genome sequence was finished at the Joint Genome Institute and has been deposited for future genomic studies pertaining to microbial processes and nutrient cycles in high-temperature environments.

  19. Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T

    PubMed Central

    Hamilton-Brehm, Scott D.; Lucas, Susan; Han, James; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Davenport, Karen W.; Detter, John C.; Han, Cliff S.; Tapia, Roxanne; Land, Miriam L.; Hauser, Loren; Kyrpides, Nikos C.; Ivanova, Natalia N.; Pagani, Ioanna; Bruce, David; Woyke, Tanja; Cottingham, Robert W.

    2013-01-01

    Thermodesulfobacterium geofontis OPF15T (ATCC BAA-2454, JCM 18567) was isolated from Obsidian Pool, Yellowstone National Park, and grows optimally at 83°C. The 1.6-Mb genome sequence was finished at the Joint Genome Institute and has been deposited for future genomic studies pertaining to microbial processes and nutrient cycles in high-temperature environments. PMID:23580711

  20. An Analysis of Metal Finishing Technology and its Status in Industrial Teacher-Education.

    ERIC Educational Resources Information Center

    Singletary, Thomas Alexander

    The purposes of this study were to analyze and describe metal finishing processes and to ascertain the extent to which these processes are taught in industrial teacher education programs. Handbooks and industrial literature were reviewed, and a survey of 165 teacher education departments was made to collect the data. Finishing processes were…

  1. Index selection in terminal sires improves lamb performance at finishing.

    PubMed

    Márquez, G C; Haresign, W; Davies, M H; Roehe, R; Bünger, L; Simm, G; Lewis, R M

    2013-01-01

    Lamb meat is often perceived by consumers as fatty, and consumption has decreased in recent decades. A lean growth index was developed in the UK for terminal sire breeds to increase carcass lean content and constrain fat content at a constant age end point. The purposes of this study were 1) to evaluate the effects of index selection of terminal sires on their crossbred offspring at finishing and 2) to evaluate its effectiveness within terminal sire breeds. Approximately 70% of lambs marketed in the UK have been sired by rams of breeds typically thought of as specialized terminal sires. The most widely used are Charollais, Suffolk, and Texel. These breeds participated in sire referencing schemes from the early 1990s by sharing rams among flocks selected on the lean growth index. From 1999 to 2002 approximately 15 "high" and 15 "low" lean growth index score rams were selected from within their sire referencing schemes and mated to Welsh and Scottish Mule ewes. Their crossbred offspring were commercially reared on 3 farms in the UK. Lambs were finished to an estimated 11% subcutaneous fat by visual evaluation. At finishing, lambs were weighed, ultrasonically scanned, and assessed for condition score and conformation. Records were obtained for 6356 lambs on finishing BW (FWT), ultrasonic muscle depth (UMD), ultrasonic fat depth, overall condition score (OCS), and conformation of gigot, loin, and shoulder. Ultrasonic fat depth was log transformed (logUFD) to approach normality. High-index-sired lambs were heavier at finishing (1.2±0.2 kg) with thicker UMD (0.7±0.2 mm) and less logUFD (0.08±0.01 mm; P<0.05). There were no differences in OCS or conformation based on the sire index or breed (P>0.08). Suffolk-sired lambs were heavier than Charollais (1.0±0.3 kg), which were heavier than Texel (0.9±0.3 kg; P<0.001). Texel-sired lambs had thicker UMD than Charollais (0.7±0.2 mm; P<0.001) but were not different than Suffolk. Charollais-sired lambs had greater log

  2. Disassembly Properties of Cementitious Finish Joints Using an Induction Heating Method

    PubMed Central

    Ahn, Jaecheol; Noguchi, Takafumi; Kitagaki, Ryoma

    2015-01-01

    Efficient maintenance and upgrading of a building during its lifecycle are difficult because a cementitious finish uses materials and parts with low disassembly properties. Additionally, the reuse and recycling processes during building demolition also present numerous problems from the perspective of environmental technology. In this study, an induction heating (IH) method was used to disassemble cementitious finish joints, which are widely used to join building members and materials. The IH rapidly and selectively heated and weakened these joints. The temperature elevation characteristics of the cementitious joint materials were measured as a function of several resistor types, including wire meshes and punching metals, which are usually used for cementitious finishing. The disassembly properties were evaluated through various tests using conductive resistors in cementitious joints such as mortar. When steel fiber, punching metal, and wire mesh were used as conductive resistors, the cementitious modifiers could be weakened within 30 s. Cementitious joints with conductive resistors also showed complete disassembly with little residual bond strength.

  3. Surface texture of resin-modified glass ionomer cements: effects of finishing/polishing systems.

    PubMed

    Yap, Adrian U J; Tan, W S; Yeo, J C; Yap, W Y; Ong, S B

    2002-01-01

    This study investigated the surface texture of two resin-modified glass ionomer cements (RMGICs) in the vertical and horizontal axis after treatment with different finishing/polishing systems. Class V preparations were made on the buccal and lingual/palatal surfaces of freshly extracted teeth. The cavities on each tooth were restored with Fuji II LC (GC) and Photac-Fil Quick (ESPE) according to manufacturers' instructions. Immediately after light-polymerization, gross finishing was done with 8-flute tungsten carbide burs. The teeth were then randomly divided into four groups and finished/polished with (a) Robot Carbides (RC); (b) Super-Snap system (SS); (c) OneGloss (OG) and (d) CompoSite Points (CS). The sample size for each material-finishing/polishing system combination was eight. The mean surface roughness (microm) in vertical (RaV) and horizontal (RaH) axis was measured using a profilometer. Data was subjected to ANOVA/Scheffe's tests and Independent Samples t-test at significance level 0.05. Mean RaV ranged from 0.59-1.31 and 0.83-1.52, while mean RaH ranged from 0.80-1.43 and 0.85-1.58 for Fuji II LC and Photac-Fil, respectively. Results of statistical analysis were as follows: Fuji II LC: RaV-RC, SSfinished with RC. The use of carbides (RC) and one-step rubber abrasive system (OG) for finishing/polishing of RMGICs is not recommended. Graded abrasive disk (SS) or two-step rubber abrasive (CS) systems should be used instead.

  4. Evaluation of marginal fit of two all-ceramic copings with two finish lines

    PubMed Central

    Subasi, Gulce; Ozturk, Nilgun; Inan, Ozgur; Bozogullari, Nalan

    2012-01-01

    Objectives: This in-vitro study investigated the marginal fit of two all-ceramic copings with 2 finish line designs. Methods: Forty machined stainless steel molar die models with two different margin designs (chamfer and rounded shoulder) were prepared. A total of 40 standardized copings were fabricated and divided into 4 groups (n=10 for each finish line-coping material). Coping materials tested were IPS e.max Press and Zirkonzahn; luting agent was Variolink II. Marginal fit was evaluated after cementation with a stereomicroscope (Leica MZ16). Two-way analysis of variance and Tukey-HSD test were performed to assess the influence of each finish line design and ceramic type on the marginal fit of 2 all-ceramic copings (α =.05). Results: Two-way analysis of variance revealed no statistically significant differences for marginal fit relative to finish lines (P=.362) and ceramic types (P=.065). Conclusion: Within the limitations of this study, both types of all-ceramic copings demonstrated that the mean marginal fit was considered acceptable for clinical application (⩽120 μm). PMID:22509119

  5. 40 CFR 63.5395 - How do I measure the density of a finish?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 13 2013-07-01 2012-07-01 true How do I measure the density of a... and Initial Compliance Requirements § 63.5395 How do I measure the density of a finish? (a) To determine the density of a finish, the reference method is EPA Method 24 of appendix A of 40 CFR part 60...

  6. 40 CFR 63.5395 - How do I measure the density of a finish?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 13 2014-07-01 2014-07-01 false How do I measure the density of a... and Initial Compliance Requirements § 63.5395 How do I measure the density of a finish? (a) To determine the density of a finish, the reference method is EPA Method 24 of appendix A of 40 CFR part 60...

  7. 40 CFR 63.5395 - How do I measure the density of a finish?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 13 2012-07-01 2012-07-01 false How do I measure the density of a... and Initial Compliance Requirements § 63.5395 How do I measure the density of a finish? (a) To determine the density of a finish, the reference method is EPA Method 24 of appendix A of 40 CFR part 60...

  8. CoDE-seq, an augmented whole-exome sequencing, enables the accurate detection of CNVs and mutations in Mendelian obesity and intellectual disability.

    PubMed

    Montagne, Louise; Derhourhi, Mehdi; Piton, Amélie; Toussaint, Bénédicte; Durand, Emmanuelle; Vaillant, Emmanuel; Thuillier, Dorothée; Gaget, Stefan; De Graeve, Franck; Rabearivelo, Iandry; Lansiaux, Amélie; Lenne, Bruno; Sukno, Sylvie; Desailloud, Rachel; Cnop, Miriam; Nicolescu, Ramona; Cohen, Lior; Zagury, Jean-François; Amouyal, Mélanie; Weill, Jacques; Muller, Jean; Sand, Olivier; Delobel, Bruno; Froguel, Philippe; Bonnefond, Amélie

    2018-05-16

    The molecular diagnosis of extreme forms of obesity, in which accurate detection of both copy number variations (CNVs) and point mutations, is crucial for an optimal care of the patients and genetic counseling for their families. Whole-exome sequencing (WES) has benefited considerably this molecular diagnosis, but its poor ability to detect CNVs remains a major limitation. We aimed to develop a method (CoDE-seq) enabling the accurate detection of both CNVs and point mutations in one step. CoDE-seq is based on an augmented WES method, using probes distributed uniformly throughout the genome. CoDE-seq was validated in 40 patients for whom chromosomal DNA microarray was available. CNVs and mutations were assessed in 82 children/young adults with suspected Mendelian obesity and/or intellectual disability and in their parents when available (n total  = 145). CoDE-seq not only detected all of the 97 CNVs identified by chromosomal DNA microarrays but also found 84 additional CNVs, due to a better resolution. When compared to CoDE-seq and chromosomal DNA microarrays, WES failed to detect 37% and 14% of CNVs, respectively. In the 82 patients, a likely molecular diagnosis was achieved in >30% of the patients. Half of the genetic diagnoses were explained by CNVs while the other half by mutations. CoDE-seq has proven cost-efficient and highly effective as it avoids the sequential genetic screening approaches currently used in clinical practice for the accurate detection of CNVs and point mutations. Copyright © 2018 The Authors. Published by Elsevier GmbH.. All rights reserved.

  9. Historian: accurate reconstruction of ancestral sequences and evolutionary rates.

    PubMed

    Holmes, Ian H

    2017-04-15

    Reconstruction of ancestral sequence histories, and estimation of parameters like indel rates, are improved by using explicit evolutionary models and summing over uncertain alignments. The previous best tool for this purpose (according to simulation benchmarks) was ProtPal, but this tool was too slow for practical use. Historian combines an efficient reimplementation of the ProtPal algorithm with performance-improving heuristics from other alignment tools. Simulation results on fidelity of rate estimation via ancestral reconstruction, along with evaluations on the structurally informed alignment dataset BAliBase 3.0, recommend Historian over other alignment tools for evolutionary applications. Historian is available at https://github.com/evoldoers/historian under the Creative Commons Attribution 3.0 US license. ihholmes+historian@gmail.com. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  10. BASIC: A Simple and Accurate Modular DNA Assembly Method.

    PubMed

    Storch, Marko; Casini, Arturo; Mackrow, Ben; Ellis, Tom; Baldwin, Geoff S

    2017-01-01

    Biopart Assembly Standard for Idempotent Cloning (BASIC) is a simple, accurate, and robust DNA assembly method. The method is based on linker-mediated DNA assembly and provides highly accurate DNA assembly with 99 % correct assemblies for four parts and 90 % correct assemblies for seven parts [1]. The BASIC standard defines a single entry vector for all parts flanked by the same prefix and suffix sequences and its idempotent nature means that the assembled construct is returned in the same format. Once a part has been adapted into the BASIC format it can be placed at any position within a BASIC assembly without the need for reformatting. This allows laboratories to grow comprehensive and universal part libraries and to share them efficiently. The modularity within the BASIC framework is further extended by the possibility of encoding ribosomal binding sites (RBS) and peptide linker sequences directly on the linkers used for assembly. This makes BASIC a highly versatile library construction method for combinatorial part assembly including the construction of promoter, RBS, gene variant, and protein-tag libraries. In comparison with other DNA assembly standards and methods, BASIC offers a simple robust protocol; it relies on a single entry vector, provides for easy hierarchical assembly, and is highly accurate for up to seven parts per assembly round [2].

  11. Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov.

    PubMed Central

    Padmanabhan, Roshan; Dubourg, Gregory; Nguyen, Thi-Thien; Couderc, Carine; Rossi-Tamisier, Morgane; Caputo, Aurelia; Raoult, Didier; Fournier, Pierre-Edouard

    2014-01-01

    Collinsella massiliensis strain GD3T is the type strain of Collinsella massiliensis sp. nov., a new species within the genus Collinsella. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old French Caucasoid woman who had been admitted to intensive care unit for Guillain-Barré syndrome. Collinsella massiliensis is a Gram-positive, obligate anaerobic, non motile and non sporulating bacillus. Here, we describe the features of this organism, together with the complete genome sequence and annotation. The genome is 2,319,586 bp long (1 chromosome, no plasmid), exhibits a G+C content of 65.8% and contains 2,003 protein-coding and 54 RNA genes, including 1 rRNA operon. PMID:25197489

  12. Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov.

    PubMed

    Padmanabhan, Roshan; Dubourg, Gregory; Nguyen, Thi-Thien; Couderc, Carine; Rossi-Tamisier, Morgane; Caputo, Aurelia; Raoult, Didier; Fournier, Pierre-Edouard

    2014-06-15

    Collinsella massiliensis strain GD3(T) is the type strain of Collinsella massiliensis sp. nov., a new species within the genus Collinsella. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old French Caucasoid woman who had been admitted to intensive care unit for Guillain-Barré syndrome. Collinsella massiliensis is a Gram-positive, obligate anaerobic, non motile and non sporulating bacillus. Here, we describe the features of this organism, together with the complete genome sequence and annotation. The genome is 2,319,586 bp long (1 chromosome, no plasmid), exhibits a G+C content of 65.8% and contains 2,003 protein-coding and 54 RNA genes, including 1 rRNA operon.

  13. Evaluation of Some Finishing Properties of Oil Palm Particleboard for Furniture Application

    NASA Astrophysics Data System (ADS)

    Ratnasingam, J.; Nyugen, V.; Ioras, F.

    The finishing properties of particleboard made from the Empty-Fruit Bunch (EFB) of oil palm (Elaeis guineensis Jacq.) were evaluated for its suitability for furniture applications, using different coating and overlay materials. The results found that the thick plastic-formica overlay provided the best surface finish, in terms of surface smoothness, adhesion strength and impact resistance. Although the polyurethane lacquer provided an acceptable finish, its quality and performance is not comparable to that of the thick plastic overlay. Despite the fact that the use of such overlay material may render the material not aesthetically appealing and limit it to concealed applications or where the thick overlay material is tolerated, its cost competitiveness and environmental friendliness may be able to position the oil palm particleboard as a substitute for the conventional wood-based particleboard in the furniture manufacturing industry.

  14. Meat goat kids finished on alfalfa, red clover or orchardgrass pastures: carcass merit and meat quality.

    PubMed

    Turner, K E; Cassida, K A; Zerby, H N

    2014-12-01

    This experiment was conducted in 2005-2007 to evaluate carcass and chevon (goat meat) quality parameters when meat-goat kids (n=72) were finished on alfalfa (Medicago sativa L; ALF); red clover (Trifolium pratense L.; RCG); or orchardgrass (Dactylis glomerata L.; OGR) pastures. Carcass conformation score was greater (P=0.08) when meat-goat kids were finished on ALF compared to OGR with RCG intermediate. Chevon meat samples from goats finished on the three pasture treatments did not differ in ash, intramuscular fat, or crude protein content or in concentrations of omega6 and omega3 fatty acids, or the omega6 to omega3 ratio. Goats finished on OGR had higher (P<0.001) 18:1 trans-11 fatty acids (FA) compared to ALF or RCG. Overall, meat-goat kids finished on ALF, RCG, or ORG produced desirable carcass weights for most niche markets in the USA. Chevon is a low-fat meat option with high desirable fatty acids for human diets. Published by Elsevier Ltd.

  15. Optimal Magnetorheological Fluid for Finishing of Chemical-Vapor-Deposited Zinc Sulfide

    NASA Astrophysics Data System (ADS)

    Salzman, Sivan

    Magnetorheological finishing (MRF) of polycrystalline, chemical-vapor- deposited zinc sulfide (ZnS) optics leaves visible surface artifacts known as "pebbles". These artifacts are a direct result of the material's inner structure that consists of cone-like features that grow larger (up to a few millimeters in size) as deposition takes place, and manifest on the top deposited surface as "pebbles". Polishing the pebble features from a CVD ZnS substrate to a flat, smooth surface to below 10 nm root-mean-square is challenging, especially for a non-destructive polishing process such as MRF. This work explores ways to improve the surface finish of CVD ZnS processed with MRF through modification of the magnetorheological (MR) fluid's properties. A materials science approach is presented to define the anisotropy of CVD ZnS through a combination of chemical and mechanical experiments and theoretical predictions. Magnetorheological finishing experiments with single crystal samples of ZnS, whose cuts and orientations represent most of the facets known to occur in the polycrystalline CVD ZnS, were performed to explore the influence of material anisotropy on the material removal rate during MRF. By adjusting the fluid's viscosity, abrasive type concentration, and pH to find the chemo-mechanical conditions that equalize removal rates among all single crystal facets during MRF, we established an optimized, novel MR formulation to polish CVD ZnS without degrading the surface finish of the optic.

  16. Why Do Photo Finish Images Look Weird?

    ERIC Educational Resources Information Center

    Gregorcic, Bor; Planinsic, Gorazd

    2012-01-01

    This paper deals with effects that appear on photographs of rotating objects when taken by a photo finish camera, a rolling shutter camera or a computer scanner. These effects are very similar to Roget's palisade illusion. A simple quantitative analysis of the images is also provided. The effects are explored using a computer scanner in a way that…

  17. Effect of Binder and Mold parameters on Collapsibility and Surface Finish of Gray Cast Iron No-bake Sand Molds

    NASA Astrophysics Data System (ADS)

    Srinivasulu Reddy, K.; Venkata Reddy, Vajrala; Mandava, Ravi Kumar

    2017-08-01

    Chemically bonded no-bake molds and cores have good mechanical properties and produce dimensionally accurate castings compared to green sand molds. Poor collapsibility property of CO2 hardened sodium silicate bonded sand mold and phenolic urethane no-bake (PUN) binder system, made the reclamation of the sands more important. In the present work fine silica sand is mixed with phenolic urethane no-bake binder and the sand sets in a very short time within few minutes. In this paper it is focused on optimizing the process parameters of PUN binder based sand castings for better collapsibility and surface finish of gray cast iron using Taguchi design. The findings were successfully verified through experiments.

  18. Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology.

    PubMed

    Bakhtiarizadeh, Mohammad Reza; Moradi-Shahrbabak, Mohammad; Ebrahimi, Mansour; Ebrahimie, Esmaeil

    2014-09-07

    Due to the central roles of lipid binding proteins (LBPs) in many biological processes, sequence based identification of LBPs is of great interest. The major challenge is that LBPs are diverse in sequence, structure, and function which results in low accuracy of sequence homology based methods. Therefore, there is a need for developing alternative functional prediction methods irrespective of sequence similarity. To identify LBPs from non-LBPs, the performances of support vector machine (SVM) and neural network were compared in this study. Comprehensive protein features and various techniques were employed to create datasets. Five-fold cross-validation (CV) and independent evaluation (IE) tests were used to assess the validity of the two methods. The results indicated that SVM outperforms neural network. SVM achieved 89.28% (CV) and 89.55% (IE) overall accuracy in identification of LBPs from non-LBPs and 92.06% (CV) and 92.90% (IE) (in average) for classification of different LBPs classes. Increasing the number and the range of extracted protein features as well as optimization of the SVM parameters significantly increased the efficiency of LBPs class prediction in comparison to the only previous report in this field. Altogether, the results showed that the SVM algorithm can be run on broad, computationally calculated protein features and offers a promising tool in detection of LBPs classes. The proposed approach has the potential to integrate and improve the common sequence alignment based methods. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. 40 CFR 63.5395 - How do I measure the density of a finish?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 12 2010-07-01 2010-07-01 true How do I measure the density of a... Initial Compliance Requirements § 63.5395 How do I measure the density of a finish? (a) To determine the density of a finish, the reference method is EPA Method 24 of appendix A of 40 CFR part 60. You may use...

  20. 40 CFR 63.5395 - How do I measure the density of a finish?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 12 2011-07-01 2009-07-01 true How do I measure the density of a... Initial Compliance Requirements § 63.5395 How do I measure the density of a finish? (a) To determine the density of a finish, the reference method is EPA Method 24 of appendix A of 40 CFR part 60. You may use...

  1. Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20T)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pati, Amrita; Gronow, Sabine; Lu, Megan

    2011-01-01

    Prevotella multisaccharivorax Sakamoto et al. 2005 is a species of the large genus Prevotella, which belongs to the family Prevotellaceae. The species is of medical interest because its members are able to cause diseases in the human oral cavity such as periodontitis, root caries and others. Although 77 Prevotella genomes have already been sequenced or are targeted for sequencing, this is only the second completed genome sequence of a type strain of a species within the genus Prevotella to be published. The 3,388,644 bp long genome is assembled in three non-contiguous contigs, harbors 2,876 protein-coding and 75 RNA genes andmore » is a part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

  2. Genotype x environment interactions for fatty acid profiles in Bos indicus and Bos taurus finished on pasture or grain.

    PubMed

    Bressan, M C; Rossato, L V; Rodrigues, E C; Alves, S P; Bessa, R J B; Ramos, E M; Gama, L T

    2011-01-01

    A study was conducted to characterize lipid profiles in the M. longissimus thoracis of commercial Brazilian beef and to assess how those profiles are influenced by finishing system, genetic group, and their interaction. Intramuscular fat (IMF) and fatty acid (FA) profiles were determined in 160 bulls of the Bos taurus (n = 75) and Bos indicus (n = 85) genetic groups, finished on pasture (n = 46) or with grain supplementation (n = 114) and slaughtered in a commercial abattoir. Finishing system had a major impact on the deposition of IMF, as well as on the concentration of SFA, PUFA, and their ratio, but genetic groups showed important differences in the ability to convert SFA into cis-9 MUFA and to convert 16:0 into 18:0. When compared with pasture-finished animals, those finished with grain had greater content of IMF and SFA (P < 0.01), similar amounts of MUFA (P > 0.05), and about one-half the amount of PUFA (P < 0.01). Except for MUFA, differences in FA profiles among finishing systems were mostly mediated through their effect on IMF, even though the relationship of IMF with groups of FA differed among finishing systems. Under grain finishing, B. taurus had less SFA and greater MUFA than B. indicus (P < 0.01), but no differences were observed in PUFA (P > 0.05). With pasture-finishing, no differences were observed among the 2 genetic groups in SFA and MUFA (P > 0.05), but PUFA were decreased in B. taurus (P < 0.01). When genetic groups were compared in grain-finishing, B. taurus had a decreased ability for elongation and B. indicus had a decreased aptitude for desaturation of FA. On the other hand, with pasture-finishing a greater deposition of intermediate FA from ruminal biohydrogenation was observed in B. indicus than in B. taurus. Overall, FA profiles were affected more by finishing system in B. indicus than in B. taurus.

  3. Metagenome assembly through clustering of next-generation sequencing data using protein sequences.

    PubMed

    Sim, Mikang; Kim, Jaebum

    2015-02-01

    The study of environmental microbial communities, called metagenomics, has gained a lot of attention because of the recent advances in next-generation sequencing (NGS) technologies. Microbes play a critical role in changing their environments, and the mode of their effect can be solved by investigating metagenomes. However, the difficulty of metagenomes, such as the combination of multiple microbes and different species abundance, makes metagenome assembly tasks more challenging. In this paper, we developed a new metagenome assembly method by utilizing protein sequences, in addition to the NGS read sequences. Our method (i) builds read clusters by using mapping information against available protein sequences, and (ii) creates contig sequences by finding consensus sequences through probabilistic choices from the read clusters. By using simulated NGS read sequences from real microbial genome sequences, we evaluated our method in comparison with four existing assembly programs. We found that our method could generate relatively long and accurate metagenome assemblies, indicating that the idea of using protein sequences, as a guide for the assembly, is promising. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. 30 CFR 18.33 - Finish of surface joints.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Finish of surface joints. 18.33 Section 18.33 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND APPROVAL OF MINING PRODUCTS ELECTRIC MOTOR-DRIVEN MINE EQUIPMENT AND ACCESSORIES Construction and Design...

  5. Study on mycoflora of poultry feed ingredients and finished feed in Iran.

    PubMed

    Ghaemmaghami, Seyed Soheil; Modirsaneii, Mehrdad; Khosravi, Ali Reza; Razzaghi-Abyaneh, Mehdi

    2016-02-01

    Unhygienic poultry feedstuffs can lead to nutrient losses and detrimental effect on poultry production and public health. In the present study, mycobiota and colony-forming units per gram in ingredients and finish poultry feed was evaluated with special reference to potentially mycotoxigenic fungi. Eighty five samples of corn, soybean meal and poultry finished feed were collected from nine poultry feed factories located in three provinces i.e. Tehran, Alborz and Qom in Iran from October 2014 to January 2015. Samples were cultured on Sabouraud dextrose agar (SDA), Aspergillus flavus and parasiticus agar (AFPA) and dichloran rosebengal chloramphenicol agar (DRBC) and incubated at 28 °C for 7-10 days. Purified fungal colonies were identified by a combination of macro- and microscopic morphological criteria. For determining the rate of fungal contamination, samples were cultured on SDA and colony forming units (CFUs) were calculated. A total of 384 fungal isolates belonging to 7 genera of filamentous fungi and yeasts were obtained from corn (124 isolates), soybean meal (92 isolates), and feed before (72 isolates), and after pelleting (96 isolates). The most prominent fungal isolate in corn, soybean meal and feed before pelleting (feed as mash form) was Fusarium but in feed after pelleting was Aspergillus. Among 5 Aspergillus species isolated, potentially aflatoxigenic A. flavus isolates was predominant in corn (46.6%), soybean meal (72.7%) and poultry finished feed (75%). CFUs results indicated that 9/22 corn samples (40.9%), none of 22 soybean meal samples, 19/41 finished feed (46.3%) were contaminated higher than the standard limit. Our results indicated that corn, soybean meal and finished feed of poultry feed mill are contaminated with various fungal genera by different levels sometimes higher that the standard limits. Contamination with potentially mycotoxigenic fungi especially Aspergillus species may be considered as a human public health hazard.

  6. 40 CFR 429.130 - Applicability; description of the finishing subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ..., fabrication, and by-product utilization timber processing operations not otherwise covered by specific... (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TIMBER PRODUCTS PROCESSING POINT SOURCE CATEGORY Finishing...

  7. A new seamless, smooth, interior, absorptive finishing system

    NASA Astrophysics Data System (ADS)

    D'Antonio, Peter

    2003-10-01

    Government architecture typically employs classic forms of vaults, domes and other focusing or reflective shapes, usually created with hard materials like concrete and plaster. The use of conventional porous absorption is typically rejected as an acoustical surface material for aesthetic reasons. Hence, many of these new and existing facilities have compromised speech intelligibility and music quality. Acousticians have sought a field-applied, absorptive finishing system that resembles a smooth plaster or painted drywall surface, since the dawn of architectural acoustics. Some success has been achieved using sprayed cellulose or cementitious materials, but surface smoothness has been a challenge. A new approach utilizing a thin microporous layer of mineral particles applied over a mineral wool panel will be described. This material can be applied to almost any shape surface, internally pigmented to match almost any color and renovated. Because of these unique characteristics the new seamless, absorptive, finishing system is being specified for many new and renovated spaces. Application examples will be presented.

  8. 40 CFR 427.80 - Applicability; description of the coating or finishing of asbestos textiles subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... coating or finishing of asbestos textiles subcategory. 427.80 Section 427.80 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS (CONTINUED) ASBESTOS MANUFACTURING POINT SOURCE CATEGORY Coating or Finishing of Asbestos Textiles Subcategory § 427.80 Applicability...

  9. 40 CFR 427.80 - Applicability; description of the coating or finishing of asbestos textiles subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... coating or finishing of asbestos textiles subcategory. 427.80 Section 427.80 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS ASBESTOS MANUFACTURING POINT SOURCE CATEGORY Coating or Finishing of Asbestos Textiles Subcategory § 427.80 Applicability; description...

  10. 40 CFR 427.80 - Applicability; description of the coating or finishing of asbestos textiles subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... coating or finishing of asbestos textiles subcategory. 427.80 Section 427.80 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS (CONTINUED) ASBESTOS MANUFACTURING POINT SOURCE CATEGORY Coating or Finishing of Asbestos Textiles Subcategory § 427.80 Applicability...

  11. 40 CFR 427.80 - Applicability; description of the coating or finishing of asbestos textiles subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... coating or finishing of asbestos textiles subcategory. 427.80 Section 427.80 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS (CONTINUED) ASBESTOS MANUFACTURING POINT SOURCE CATEGORY Coating or Finishing of Asbestos Textiles Subcategory § 427.80 Applicability...

  12. 40 CFR 427.80 - Applicability; description of the coating or finishing of asbestos textiles subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... coating or finishing of asbestos textiles subcategory. 427.80 Section 427.80 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS ASBESTOS MANUFACTURING POINT SOURCE CATEGORY Coating or Finishing of Asbestos Textiles Subcategory § 427.80 Applicability; description...

  13. "Miss! I'm Done!" Finishing Craft Assignments as a Situated Activity System in Preschool

    ERIC Educational Resources Information Center

    Deunk, Marjolein; Berenst, Jan; de Glopper, Kees

    2010-01-01

    We describe the Situated Activity System of finishing craft assignments in preschool: the specific, routinized way that child and teacher jointly close the child's craft assignment, employing a specific discourse pattern. We analyzed the interactions of 14 Dutch children between 2.1 and 3.10 years old while they were finishing their craft…

  14. Development of USTES Aptitude Test Battery for Photograph Finisher (Any Industry) I 976.886.

    ERIC Educational Resources Information Center

    Wisconsin State Employment Service, Madison.

    To develop General Aptitude Test Battery (GATB) norms for the occupation of photograph finisher, 59 female workers employed as photograph finishers in Wisconsin were administered all 12 tests of the GATB and the Research Questionnaire-Background during July 1969. Supervisory ratings of job proficiency were made at approximately the same time as…

  15. Course in Carpentry: Interior Finish. Workbook and Tests.

    ERIC Educational Resources Information Center

    Strazicich, Mirko, Ed.

    Designed for use in carpentry apprenticeship classes, this workbook contains nine units on carpentry skills in the area of interior finish, lists of recommended and required instructional materials, and nine unit tests. Each instructional unit includes a listing of performance statements and text covering skills addressed in individual performance…

  16. Illinois Occupational Skill Standards: Finishing and Distribution Cluster.

    ERIC Educational Resources Information Center

    Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

    This document, which is intended as a guide for work force preparation program providers, details the Illinois occupational skill standards for programs preparing students for employment in occupations in the finishing and distribution cluster. The document begins with a brief overview of the Illinois perspective on occupational skill standards…

  17. 40 CFR 141.510 - Is my system subject to the new finished water reservoir requirements?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... finished water reservoir requirements? 141.510 Section 141.510 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Finished Water Reservoirs § 141.510 Is...

  18. 40 CFR 141.510 - Is my system subject to the new finished water reservoir requirements?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... finished water reservoir requirements? 141.510 Section 141.510 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Finished Water Reservoirs § 141.510 Is...

  19. 11. Exterior detail view of northeast corner, showing stucco finish ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    11. Exterior detail view of northeast corner, showing stucco finish and woodwork details - American Railway Express Company Freight Building, 1060 Northeast Division Street, Bend, Deschutes County, OR

  20. Dust control technology usage patterns in the drywall finishing industry.

    PubMed

    Young-Corbett, Deborah E; Nussbaum, Maury A

    2009-06-01

    A telephone survey was conducted to quantify drywall finishing industry usage rates of dust control technology, identify barriers to technology adoption, and explore firm owner perception of risk. Industry use of the following technologies was described: wet methods, respiratory protection, pole sanders, ventilated sanders, and low-dust joint compound. A survey instrument composed of both Likert-type scaled items and open-ended items was developed and administered by telephone to the census population of the owners of member firms of trade associations: Finishing Contractors Association and Association of the Wall and Ceiling Industries. Of 857 firms, 264 interviews were completed. Along with descriptive statistics, results were analyzed to examine effects of firm size and union affiliation on responses. Responses to open-ended items were analyzed using content analysis procedures. Firm owners rated the risk of dust to productivity and customer satisfaction as low-moderate. Half rated the dust as having some impact on worker health, with higher impacts indicated by owners of small firms. Among the available control technologies, respiratory protection was used most frequently. Several barriers to implementation of the more effective control technologies were identified. Barriers associated with technology usability, productivity, and cost, as well as misperceptions of risk, should be addressed to improve dust control in the drywall finishing industry.

  1. Effect of different surface finishing/polishing procedures on color stability of esthetic restorative materials: A spectrophotometric evaluation

    PubMed Central

    Beltrami, Riccardo; Ceci, Matteo; De Pani, Gabriele; Vialba, Lodovico; Federico, Ricaldone; Poggio, Claudio; Colombo, Marco

    2018-01-01

    Objective: To evaluate the color stability of different esthetic restorative materials after surface finishing/polishing with different procedures. Materials and Methods: All materials were polymerized into silicone rubber rings to obtain specimens identical in size. Samples were randomly assigned into four groups (10 specimens of each composite for each group), and they were finished with different procedures: Control group (Group 1), three or two polishers interspersed with diamond grit (Groups 3 and 2, respectively), and one tungsten carbide bur + one polisher interspersed with diamond grit (Group 4). After staining process in coffee, a colorimetric evaluation according to the CIE L*a*b* system was performed by a blind trained operator at 7, 14, 21, and 28 days. Shapiro–Wilk test and Kruskal–Wallis analysis of variance were applied to assess significant differences among restorative materials. Means of the different polishing/finishing groups were compared with Scheffe's multiple comparison test at the 0.05 level of significance. Results: In control group, significant lower discolorations were recorded for Essentia, Admira Fusion, and Estelite. After finishing, Filtek Supreme XTE and Ceram.X Universal showed a significantly lower degree of staining. The finishing technique used for Group 4 produced higher color changes. Conclusions: Tungsten carbide burs produced the higher color variations; after finishing, the nanofilled composites showed lower discoloration than nanohybrid ones, and the time of exposure to the staining agent and the polishing/finishing technique influenced the color change. PMID:29657525

  2. 77 FR 61025 - Certain Prepregs, Laminates, and Finished Circuit Boards: Notice of Institution of Formal...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-05

    ... INTERNATIONAL TRADE COMMISSION [Inv. No. 337-TA-659] Certain Prepregs, Laminates, and Finished..., and the sale within the United States after importation of certain prepregs, laminates, and finished... for sale, and selling for importation into the United States prepregs and laminates that are the...

  3. BAC sequencing using pooled methods.

    PubMed

    Saski, Christopher A; Feltus, F Alex; Parida, Laxmi; Haiminen, Niina

    2015-01-01

    Shotgun sequencing and assembly of a large, complex genome can be both expensive and challenging to accurately reconstruct the true genome sequence. Repetitive DNA arrays, paralogous sequences, polyploidy, and heterozygosity are main factors that plague de novo genome sequencing projects that typically result in highly fragmented assemblies and are difficult to extract biological meaning. Targeted, sub-genomic sequencing offers complexity reduction by removing distal segments of the genome and a systematic mechanism for exploring prioritized genomic content through BAC sequencing. If one isolates and sequences the genome fraction that encodes the relevant biological information, then it is possible to reduce overall sequencing costs and efforts that target a genomic segment. This chapter describes the sub-genome assembly protocol for an organism based upon a BAC tiling path derived from a genome-scale physical map or from fine mapping using BACs to target sub-genomic regions. Methods that are described include BAC isolation and mapping, DNA sequencing, and sequence assembly.

  4. The Effect of Various Finish Line Configurations on the Marginal Seal and Occlusal Discrepancy of Cast Full Crowns After Cementation - An In-vitro Study.

    PubMed

    Nemane, Vaishali; Akulwar, Ravikumar Suryakanth; Meshram, Suresh

    2015-08-01

    The marginal fit of crowns is of clinical importance. It is found that marginal and occlusal discrepancies are commonly increased following cementation. The resistance of cementing materials is a factor that prevents cast restorations from being correctly seated. Different finish lines behave differently in facilitating the escape of the cement. When the escape path of the cement decreases, the crown fails to seat further. This study was planned with an aim to evaluate the effect of various finish lines on the marginal seal and occlusal seat of full crown preparations. Six stainless steel metal dies were machined to simulate molar crown preparations. The diameter was 10 mm and height was 6mm. The occlusal surface was kept flat and a small circular dimple was machined for reorientation of the wax pattern and metal copings, margins of various designs were machined accurately. The margins prepared were Group A- 90(0)C shoulder, Group B- Rounded shoulder, Group C- 45 degree sloped shoulder, Group D- Chamfer, Group E- Long chamfer, Group F- Feather edge. Full cast metal crowns of base metal alloy were fabricated over the metal dies. Zinc phosphate luting cement was used for the cementation. After twenty four hours, the cemented crown and die assembly were embedded in clear acrylic resin so as to hold the assembly together while sectioning. Twenty four hours later, all the samples were sectioned sagitally. The sectioned halves were focused under a stereomicroscope and the cement spaces were measured to the nearest micron. The cement thickness was measured at two points on the occlusal surface and one at each margin. Significant differences were observed in the occlusal seat and marginal seal of all the finish line configurations. The rounded shoulder had the best occlusal seat, followed by 90(0)C shoulder. The occlusal seat and marginal seal afforded by the shoulder finish lines were similar whereas there was a vast difference in the seating and sealing of long chamfer

  5. Fluoroalkyl Siloxanes as Liquid-Repellent Fabric Finishes. Part 2. The Homopolymers and their Copolymers with Alkyl Silanes

    DTIC Science & Technology

    1979-06-01

    LUOROALKYL SILOXANES AS LIQUID-JEPELLENT FABiRIC FINISHES YARUJF- THE 1OMOPOLYMERS AND /,THEIR CUPOLYMERS WITH !IxKL LALEK i.W o D DC BEST AVAILABLE...NATIONAL DEFENCE CANADA DEFENCE RESEARCH ESTABLISHMENT OTTAWA REPORT NO. 804 FLUOROALKYL SILOXANES AS LIQUID-REPELLENT FABRIC FINISHES PART II THE...cent) and cotton as finishes , and the oil and water repellency imparted to these fabrics ascertained by standard tests. In this manner it is possible

  6. Multilocus sequence typing of total-genome-sequenced bacteria.

    PubMed

    Larsen, Mette V; Cosentino, Salvatore; Rasmussen, Simon; Friis, Carsten; Hasman, Henrik; Marvig, Rasmus Lykke; Jelsbak, Lars; Sicheritz-Pontén, Thomas; Ussery, David W; Aarestrup, Frank M; Lund, Ole

    2012-04-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST.

  7. Device accurately measures and records low gas-flow rates

    NASA Technical Reports Server (NTRS)

    Branum, L. W.

    1966-01-01

    Free-floating piston in a vertical column accurately measures and records low gas-flow rates. The system may be calibrated, using an adjustable flow-rate gas supply, a low pressure gage, and a sequence recorder. From the calibration rates, a nomograph may be made for easy reduction. Temperature correction may be added for further accuracy.

  8. Performance evaluation of a dental handpiece in simulation of clinical finishing using a novel 2DOF in vitro apparatus.

    PubMed

    Yin, L; Song, X F; Qu, S F; Huang, T; Mei, J P; Yang, Z Y; Li, J

    2006-11-01

    This paper reports on the performance evaluation of a dental handpiece in simulation of clinical finishing using a novel two-degrees-of-freedom (2DOF) in vitro apparatus. The instrumented apparatus consisted of a two-dimensional computer-controlled coordinate worktable carrying a dental handpiece, a piezoelectric force dynamometer, and a high-speed data acquisition and signal conditioning system for simulating the clinical operations and monitoring the dental finishing processes. The performance of the dental handpiece was experimentally evaluated with respect to rotational speed, torque, and specific finishing energy under the applied clinical finishing conditions. The results show that the rotational speeds of the dental handpiece decreased by increasing either the depth of cut or the feed rate at a constant clinically applied air pressure and water flowrate. They also decreased when increasing both the tangential and normal finishing forces. The specific finishing energy decreased with an increase in either depth of cut or feed rate, while the finishing torque increased as either the depth of cut or the feed rate was increased. Implications of these results were to provide guidance for proper applications of dental handpieces in clinical practice.

  9. MSeq-CNV: accurate detection of Copy Number Variation from Sequencing of Multiple samples.

    PubMed

    Malekpour, Seyed Amir; Pezeshk, Hamid; Sadeghi, Mehdi

    2018-03-05

    Currently a few tools are capable of detecting genome-wide Copy Number Variations (CNVs) based on sequencing of multiple samples. Although aberrations in mate pair insertion sizes provide additional hints for the CNV detection based on multiple samples, the majority of the current tools rely only on the depth of coverage. Here, we propose a new algorithm (MSeq-CNV) which allows detecting common CNVs across multiple samples. MSeq-CNV applies a mixture density for modeling aberrations in depth of coverage and abnormalities in the mate pair insertion sizes. Each component in this mixture density applies a Binomial distribution for modeling the number of mate pairs with aberration in the insertion size and also a Poisson distribution for emitting the read counts, in each genomic position. MSeq-CNV is applied on simulated data and also on real data of six HapMap individuals with high-coverage sequencing, in 1000 Genomes Project. These individuals include a CEU trio of European ancestry and a YRI trio of Nigerian ethnicity. Ancestry of these individuals is studied by clustering the identified CNVs. MSeq-CNV is also applied for detecting CNVs in two samples with low-coverage sequencing in 1000 Genomes Project and six samples form the Simons Genome Diversity Project.

  10. 26. A battery of calender presses at work finishing magazine ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    26. A battery of calender presses at work finishing magazine paper. After the coated paper has been dried and put into rolls, as shown in the preceding pictures, it is brought to the room shown here. A roll is put in the reel at the man's shoulder in the foreground and started through the machine. It passes between the two top rollers and then in and out between the succeeding rollers, until it reaches the bottom. Many tons' pressure have ironed it before it comes out and is rolled up again. This process gives it the finish that the National Geographic must have to maintain its high standard. (p.240.) - Champion-International Paper Company, West bank of Spicket River at Canal Street, Lawrence, Essex County, MA

  11. 40 CFR 141.510 - Is my system subject to the new finished water reservoir requirements?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 24 2013-07-01 2013-07-01 false Is my system subject to the new finished water reservoir requirements? 141.510 Section 141.510 Protection of Environment ENVIRONMENTAL... Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Finished Water Reservoirs § 141.510 Is...

  12. 40 CFR 141.510 - Is my system subject to the new finished water reservoir requirements?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 24 2012-07-01 2012-07-01 false Is my system subject to the new finished water reservoir requirements? 141.510 Section 141.510 Protection of Environment ENVIRONMENTAL... Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Finished Water Reservoirs § 141.510 Is...

  13. Fatty acid metabolism and deposition in subcutaneous adipose tissue of pasture and feedlot finished cattle

    USDA-ARS?s Scientific Manuscript database

    An experiment was conducted to evaluate the effects of pasture finishing versus high-concentrate finishing, over time, on fatty acid metabolism in Angus crossbred (n = 24) steers. Ruminal fluid, serum, and adipose tissue biopsies were obtained on d 0, 28, 84, and 140. Pasture forages and diet ingr...

  14. Finishing/polishing of composite and compomer restoratives: effectiveness of one-step systems.

    PubMed

    Yap, Adrian U J; Yap, S H; Teo, C K; Ng, J J

    2004-01-01

    This study investigated the surface texture of composite (Z100, 3M ESPE) and compomer (F2000, 3M ESPE) restoratives after treatment with different one-step finishing/polishing systems (One-Gloss [OG], Shofu; PoGo [PG], Dentsply; Sof-Lex Brush [SB], 3M ESPE). The surface roughness obtained was compared to that using a matrix strip [MS], a two-step rubber abrasive (CompoSite [CS], Shofu) and a graded abrasive disk (Super Snap [SS], Shofu) system. Eight specimens (3-mm long x 3-mm wide x 2-mm deep) of each material were made according to manufacturer's instructions. With exception of the MS group, all groups were roughened with 320 grit grinding paper using a lapping device prior to finishing/polishing with the different systems. The mean surface roughness (microm) was measured with a profilometer. Data was subjected to ANOVA/Scheffe's tests and independent samples t-test at significance level 0.05. Mean Ra ranged from 0.22 to 0.32 microm for Z100 and 0.45 to 0.68 for F2000. For both materials, the smoothest surfaces were obtained with MS. The roughest surfaces were observed after treatment with SS and OG for Z100 and F2000, respectively. The effectiveness of the finishing/polishing systems was material dependent. The surface finish produced by PG and SB was superior or comparable to that obtained with CS, SS and OG.

  15. Fast and accurate phylogeny reconstruction using filtered spaced-word matches

    PubMed Central

    Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

    2017-01-01

    Abstract Motivation: Word-based or ‘alignment-free’ algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. Results: We propose Filtered Spaced Word Matches (FSWM), a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don’t-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don’t-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don’t-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. Availability and Implementation: The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/ Contact: chris.leimeister@stud.uni-goettingen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28073754

  16. Fast and accurate phylogeny reconstruction using filtered spaced-word matches.

    PubMed

    Leimeister, Chris-André; Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

    2017-04-01

    Word-based or 'alignment-free' algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. We propose Filtered Spaced Word Matches (FSWM) , a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don't-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don't-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don't-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/. chris.leimeister@stud.uni-goettingen.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

  17. UltraForm Finishing (UFF) a 5-axis computer controlled precision optical component grinding and polishing system

    NASA Astrophysics Data System (ADS)

    Bechtold, Michael; Mohring, David; Fess, Edward

    2007-05-01

    OptiPro Systems has developed a new finishing process for the manufacturing of precision optical components. UltraForm Finishing (UFF) has evolved from a tire shaped tool with polishing material on its periphery, to its newest design, which incorporates a precision rubber wheel wrapped with a band of polishing material passing over it. Through our research we have developed a user friendly graphical interface giving the optician a deterministic path for finishing precision optical components. Complex UFF Algorithms combine the removal function and desired depth of removal into a motion controlled tool path which minimizes surface roughness and form errors. The UFF process includes 5 axes of computer controlled motion, (3 linear and 2 rotary) which provide the flexibility for finishing a variety of shapes including spheres, aspheres, and freeform optics. The long arm extension, along with a range of diameters for the "UltraWheel" provides a unique solution for the finishing of steep concave shapes such as ogives and domes. The UltraForm process utilizes, fixed and loose abrasives, in combination with our proprietary "UltraBelts" made of a range of materials such as polyurethane, felt, resin, diamond and others.

  18. Influence of Finishing and Polishing Techniques and Abrasion on Transmittance and Roughness of Composite Resins.

    PubMed

    Carneiro, Pma; Ramos, T M; de Azevedo, C S; de Lima, E; de Souza, Shj; Turbino, M L; Cesar, P F; Matos, A B

    The aim of this study was to evaluate the influence of finishing and polishing systems and toothbrush abrasion on transmittance (T) and surface roughness (Ra) of three composite resins (Filtek Z350 XT, Tetric N-Ceram, and IPS Empress Direct). Eighteen resin disks (10 mm diameter × 2 mm thick) finished by polyester strips had initial surface smoothness recorded, representing phase 1 (P1). Specimens were divided into three groups (n=6) according to the finishing/polishing instrument used (OneGloss, TopGloss, and Sof-Lex) to compose phase 2 samples (P2). Then specimens were subjected to 514 cycles of toothbrush simulation using a toothpaste slurry, with a constant load applied to soft bristles, and were then washed (phase 3=P3). After each phase, the specimens were examined by an optical profiler and spectrophotometer to measure Ra and T. Data were analyzed by analysis of variance, Tukey and Pearson tests. T values were statistically influenced by composite resin ( p=0.000) and phase of measurement ( p=0.000) factors, while the finishing/polishing system used ( p=0.741) did not affect T. On the other hand, Ra values were statistically affected by the factor finishing/polishing system ( p=0.000), but not by composite resin ( p=0.100) and phase of measurement ( p=0.451). Tetric N-Ceram and Empress Direct presented higher values of roughness when polished by OneGloss, while TopGloss and Sof-Lex showed a lower roughness. It can be concluded that composite resins transmitted more light after dental abrasion. Transmittance of composite resins was not modified by the distinct roughness created by finishing/polishing instruments.

  19. DETECTION OF CRYPTOSPORIDIUM OOCYSTS IN SOURCE AND FINISHED WATERS

    EPA Science Inventory

    Numerous waterborne outbreaks of cryptosporidiosis have occurred with the most notable being the 1993 episode in Milwaukee. As a result, the past decade has seen a massive effort expended on the development of methods to detect Cryptosporidium parvum oocysts in source and finish...

  20. 40 CFR 425.30 - Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 31 2012-07-01 2012-07-01 false Applicability; description of the hair... TANNING AND FINISHING POINT SOURCE CATEGORY Hair Save or Pulp, Non-Chrome Tan, Retan-Wet Finish Subcategory § 425.30 Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish...

  1. 40 CFR 425.30 - Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 30 2014-07-01 2014-07-01 false Applicability; description of the hair... TANNING AND FINISHING POINT SOURCE CATEGORY Hair Save or Pulp, Non-Chrome Tan, Retan-Wet Finish Subcategory § 425.30 Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish...

  2. 40 CFR 425.30 - Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 30 2011-07-01 2011-07-01 false Applicability; description of the hair... FINISHING POINT SOURCE CATEGORY Hair Save or Pulp, Non-Chrome Tan, Retan-Wet Finish Subcategory § 425.30 Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish subcategory. The...

  3. 40 CFR 425.30 - Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 31 2013-07-01 2013-07-01 false Applicability; description of the hair... TANNING AND FINISHING POINT SOURCE CATEGORY Hair Save or Pulp, Non-Chrome Tan, Retan-Wet Finish Subcategory § 425.30 Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish...

  4. Sensory quality of beef from different finishing diets.

    PubMed

    Resconi, V C; Campo, M M; Font i Furnols, M; Montossi, F; Sañudo, C

    2010-11-01

    Beef production under different local husbandry systems might have meat sensory quality implications for the marketing of these products abroad. In order to assess the effect of finishing diet systems on beef quality, a trained sensory taste panel assessed meat aged for 20 days from 80 Uruguayan Hereford steers that were finished on one of the following diets: T1=Pasture [4% of animal live weight (LW)], T2=Pasture [3% LW plus concentrate (0.6% LW)], T3=Pasture [3% LW plus concentrate (1.2% LW)], or T4=Concentrate plus hay ad libitum. Beef odour and flavour intensities decreased with an increase in the energy content of the diet. The meat from T2 had the lowest acid flavour and strange odours intensities. In general, steers fed only concentrate plus hay (T4) produced meat that had an inferior sensory quality because they had more pronounced off-flavours and was tougher. Copyright © 2010 The American Meat Science Association. Published by Elsevier Ltd. All rights reserved.

  5. Finish line distinctness and accuracy in 7 intraoral scanners versus conventional impression: an in vitro descriptive comparison.

    PubMed

    Nedelcu, Robert; Olsson, Pontus; Nyström, Ingela; Thor, Andreas

    2018-02-23

    Several studies have evaluated accuracy of intraoral scanners (IOS), but data is lacking regarding variations between IOS systems in the depiction of the critical finish line and the finish line accuracy. The aim of this study was to analyze the level of finish line distinctness (FLD), and finish line accuracy (FLA), in 7 intraoral scanners (IOS) and one conventional impression (IMPR). Furthermore, to assess parameters of resolution, tessellation, topography, and color. A dental model with a crown preparation including supra and subgingival finish line was reference-scanned with an industrial scanner (ATOS), and scanned with seven IOS: 3M, CS3500 and CS3600, DWIO, Omnicam, Planscan and Trios. An IMPR was taken and poured, and the model was scanned with a laboratory scanner. The ATOS scan was cropped at finish line and best-fit aligned for 3D Compare Analysis (Geomagic). Accuracy was visualized, and descriptive analysis was performed. All IOS, except Planscan, had comparable overall accuracy, however, FLD and FLA varied substantially. Trios presented the highest FLD, and with CS3600, the highest FLA. 3M, and DWIO had low overall FLD and low FLA in subgingival areas, whilst Planscan had overall low FLD and FLA, as well as lower general accuracy. IMPR presented high FLD, except in subgingival areas, and high FLA. Trios had the highest resolution by factor 1.6 to 3.1 among IOS, followed by IMPR, DWIO, Omnicam, CS3500, 3M, CS3600 and Planscan. Tessellation was found to be non-uniform except in 3M and DWIO. Topographic variation was found for 3M and Trios, with deviations below +/- 25 μm for Trios. Inclusion of color enhanced the identification of the finish line in Trios, Omnicam and CS3600, but not in Planscan. There were sizeable variations between IOS with both higher and lower FLD and FLA than IMPR. High FLD was more related to high localized finish line resolution and non-uniform tessellation, than to high overall resolution. Topography variations were low

  6. Study on mycoflora of poultry feed ingredients and finished feed in Iran

    PubMed Central

    Ghaemmaghami, Seyed Soheil; Modirsaneii, Mehrdad; Khosravi, Ali Reza; Razzaghi-Abyaneh, Mehdi

    2016-01-01

    Background and Objectives: Unhygienic poultry feedstuffs can lead to nutrient losses and detrimental effect on poultry production and public health. In the present study, mycobiota and colony-forming units per gram in ingredients and finish poultry feed was evaluated with special reference to potentially mycotoxigenic fungi. Materials and Methods: Eighty five samples of corn, soybean meal and poultry finished feed were collected from nine poultry feed factories located in three provinces i.e. Tehran, Alborz and Qom in Iran from October 2014 to January 2015. Samples were cultured on Sabouraud dextrose agar (SDA), Aspergillus flavus and parasiticus agar (AFPA) and dichloran rosebengal chloramphenicol agar (DRBC) and incubated at 28 °C for 7–10 days. Purified fungal colonies were identified by a combination of macro- and microscopic morphological criteria. For determining the rate of fungal contamination, samples were cultured on SDA and colony forming units (CFUs) were calculated. Results: A total of 384 fungal isolates belonging to 7 genera of filamentous fungi and yeasts were obtained from corn (124 isolates), soybean meal (92 isolates), and feed before (72 isolates), and after pelleting (96 isolates). The most prominent fungal isolate in corn, soybean meal and feed before pelleting (feed as mash form) was Fusarium but in feed after pelleting was Aspergillus. Among 5 Aspergillus species isolated, potentially aflatoxigenic A. flavus isolates was predominant in corn (46.6%), soybean meal (72.7%) and poultry finished feed (75%). CFUs results indicated that 9/22 corn samples (40.9%), none of 22 soybean meal samples, 19/41 finished feed (46.3%) were contaminated higher than the standard limit. Conclusions: Our results indicated that corn, soybean meal and finished feed of poultry feed mill are contaminated with various fungal genera by different levels sometimes higher that the standard limits. Contamination with potentially mycotoxigenic fungi especially Aspergillus

  7. How to achieve more accurate comparisons in organ donation activity: time to effectiveness indicators.

    PubMed

    Deulofeu, R; Bodí, M A; Twose, J; López, P

    2010-06-01

    We are used to comparisons of activity using donation or transplantation population (pmp) rates between regions or countries, without a further evaluation of the process. But crude pmp rates do not clearly reflect real transplantation capacity, because organ procurement does not finish with the donation step; it is also necessary to know the utilization of the obtained organs. The objective of this study was to present methods and indicators deemed necessary to evaluate the effectiveness of the process. We have proposed the use of simple definitions and indicators to more accurately measure and compare the effectiveness of the total organ procurement process. To illustrate the use and performance of these indicators, we have presented the donation and transplantation activity in Catalonia from 2002 to 2007.

  8. Accurate identification of RNA editing sites from primitive sequence with deep neural networks.

    PubMed

    Ouyang, Zhangyi; Liu, Feng; Zhao, Chenghui; Ren, Chao; An, Gaole; Mei, Chuan; Bo, Xiaochen; Shu, Wenjie

    2018-04-16

    RNA editing is a post-transcriptional RNA sequence alteration. Current methods have identified editing sites and facilitated research but require sufficient genomic annotations and prior-knowledge-based filtering steps, resulting in a cumbersome, time-consuming identification process. Moreover, these methods have limited generalizability and applicability in species with insufficient genomic annotations or in conditions of limited prior knowledge. We developed DeepRed, a deep learning-based method that identifies RNA editing from primitive RNA sequences without prior-knowledge-based filtering steps or genomic annotations. DeepRed achieved 98.1% and 97.9% area under the curve (AUC) in training and test sets, respectively. We further validated DeepRed using experimentally verified U87 cell RNA-seq data, achieving 97.9% positive predictive value (PPV). We demonstrated that DeepRed offers better prediction accuracy and computational efficiency than current methods with large-scale, mass RNA-seq data. We used DeepRed to assess the impact of multiple factors on editing identification with RNA-seq data from the Association of Biomolecular Resource Facilities and Sequencing Quality Control projects. We explored developmental RNA editing pattern changes during human early embryogenesis and evolutionary patterns in Drosophila species and the primate lineage using DeepRed. Our work illustrates DeepRed's state-of-the-art performance; it may decipher the hidden principles behind RNA editing, making editing detection convenient and effective.

  9. Wean-to-finish feeder space availability effects on nursery and finishing pig performance and total tract digestibility in a commercial setting when feeding dried distillers grains with solubles.

    PubMed

    Weber, E K; Stalder, K J; Patience, J F

    2015-04-01

    The study objectives were to determine nursery phase feeder space allowance effects on pig performance when double stocked and, second, to determine feeder space allowance and dried distillers grains with solubles (DDGS) inclusion level effects on pig performance and nutrient digestibility during the growing-finishing phase. This study was performed on the same group of pigs within a commercial wean-finish system. For the nursery phase, a completely randomized design was used to compare 3 feeder space allowance treatments (2.1, 2.5, and 2.9 cm/pig). A total of 3,720 pigs were randomly allotted to same-sex pens (10 feeders/treatment) housing 62 pigs/pen. Thirty 7-hole, double-sided feeders were utilized in the study. Differing linear feeder space treatments were established by blocking off sections for the nursery and grow-finish portions of this experiment. All pigs were provided equal floor space (0.26 m2/pig). In the grow-finish phase, a total of 1,860 pigs (n = 60 pens) were utilized in a 2 × 3 factorial design with 3 feeder space allowances (4.1, 4.9, or 5.7 cm/pig) and 2 dietary DDGS treatments (30% [D30] or 60% [D60]). Fecal and diet samples were collected and analyzed to estimate apparent total tract digestibility percentage (ATTD %). In the nursery portion of the trial, there was no feeder space treatment effect on ADG, ADFI, or feed efficiency (P > 0.10) from weaning to d 56 postweaning or during any weigh period. In the grow-finish portion of the trial, feeder space allowance and DDGS inclusion level did not affect ADG, ADFI, or feed efficiency (P > 0.05) from d 57 postweaning to market. Pigs fed the D30 diet had greater HCW, percent yield, and loin depth than those on the D60 diet (P < 0.05). Pigs fed the D30 treatment had greater (P < 0.05) ATTD for DM and GE for both collection periods compared with those on the D60 treatment. In summary, feeder space allowance did not impact pig performance during the nursery or grow-finish production phases

  10. Machine finishes balls to high degree of roundness

    NASA Technical Reports Server (NTRS)

    Angele, W.; Hill, J. P., Jr.

    1972-01-01

    Machine was developed to finish ball to roundness within 12.5 nm (half a microinch) from any types of hard material. Grinding and polishing to this tolerance is accomplished by lapping elements on four to six motor-driven spindles. Spindles are adjustably spring-loaded to ensure constant contact pressure on ball and are driven by variable speed electric motors.

  11. IMPLEMENTATION OF THE US ENVIRONMENTAL PROTECTION AGENCY'S METAL FINISHING FACILITY POLLUTION PREVENTION TOOL (MFFP2T)

    EPA Science Inventory

    The United States Environmental Protection Agency has developed a pre-release version of a process simulation tool, the Metal Finishing Facility Pollution Prevention Tool (MFFP2T), for the metal finishing industry. This presentation will provide a demonstration of the current ver...

  12. Accurate detection for a wide range of mutation and editing sites of microRNAs from small RNA high-throughput sequencing profiles

    PubMed Central

    Zheng, Yun; Ji, Bo; Song, Renhua; Wang, Shengpeng; Li, Ting; Zhang, Xiaotuo; Chen, Kun; Li, Tianqing; Li, Jinyan

    2016-01-01

    Various types of mutation and editing (M/E) events in microRNAs (miRNAs) can change the stabilities of pre-miRNAs and/or complementarities between miRNAs and their targets. Small RNA (sRNA) high-throughput sequencing (HTS) profiles can contain many mutated and edited miRNAs. Systematic detection of miRNA mutation and editing sites from the huge volume of sRNA HTS profiles is computationally difficult, as high sensitivity and low false positive rate (FPR) are both required. We propose a novel method (named MiRME) for an accurate and fast detection of miRNA M/E sites using a progressive sequence alignment approach which refines sensitivity and improves FPR step-by-step. From 70 sRNA HTS profiles with over 1.3 billion reads, MiRME has detected thousands of statistically significant M/E sites, including 3′-editing sites, 57 A-to-I editing sites (of which 32 are novel), as well as some putative non-canonical editing sites. We demonstrated that a few non-canonical editing sites were not resulted from mutations in genome by integrating the analysis of genome HTS profiles of two human cell lines, suggesting the existence of new editing types to further diversify the functions of miRNAs. Compared with six existing studies or methods, MiRME has shown much superior performance for the identification and visualization of the M/E sites of miRNAs from the ever-increasing sRNA HTS profiles. PMID:27229138

  13. 218. CURVE ON FINISHED ROAD AT STATION 803+, WITH CAR ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    218. CURVE ON FINISHED ROAD AT STATION 803+, WITH CAR AND CEDAR LAMP POST, 1930 - George Washington Memorial Parkway, Along Potomac River from McLean to Mount Vernon, VA, Mount Vernon, Fairfax County, VA

  14. rpoB Gene Sequencing for Identification of Corynebacterium Species

    PubMed Central

    Khamis, Atieh; Raoult, Didier; La Scola, Bernard

    2004-01-01

    The genus Corynebacterium is a heterogeneous group of species comprising human and animal pathogens and environmental bacteria. It is defined on the basis of several phenotypic characters and the results of DNA-DNA relatedness and, more recently, 16S rRNA gene sequencing. However, the 16S rRNA gene is not polymorphic enough to ensure reliable phylogenetic studies and needs to be completely sequenced for accurate identification. The almost complete rpoB sequences of 56 Corynebacterium species were determined by both PCR and genome walking methods. In all cases the percent similarities between different species were lower than those observed by 16S rRNA gene sequencing, even for those species with degrees of high similarity. Several clusters supported by high bootstrap values were identified. In order to propose a method for strain identification which does not require sequencing of the complete rpoB sequence (approximately 3,500 bp), we identified an area with a high degree of polymorphism, bordered by conserved sequences that can be used as universal primers for PCR amplification and sequencing. The sequence of this fragment (434 to 452 bp) allows accurate species identification and may be used in the future for routine sequence-based identification of Corynebacterium species. PMID:15364970

  15. Antibacterial and anti-inflammatory finishing of cotton by microencapsulation using three marine organisms.

    PubMed

    El-Rafie, H M; El-Rafie, M H; AbdElsalam, H M; El-Sayed, W A

    2016-05-01

    This work is a small effort in the production of an eco-friendly natural based antibacterial and anti-inflammatory finished cotton fabrics using the ethanolic extracts (Ex) of the sea grass Halophila stipulacea (H. stipulacea) and marine macroalgae [Colbomenia sinuosa (C. sinuosa) and Ulva fasciata (U. fasciata)]. The extracts were phytochemically screened for their constituents. These extracts were used to finish cotton fabrics by a variety of methods. Concerning this, fabrics (F) were singly treated with ethanolic extracts (ExF) of these marine organisms by the dip technique and the extract encapsulated with sodium alginate or meypro gum. The encapsulated fabric (EnF) was further finished individually with citric acid (CA), (EnF/CA) and mono-tert-butyl ether of glycerol (MTBG) binder (EnF/Bin) by the pad-dry-cure technique. The fabrics so-finished were evaluated for their antibacterial and anti-inflammatory activities without washing (control) and after different washing cycles. The results obtained showed that, both EnF/CA and EnF/Bin inhibit the bacterial growth by about 90% after 10 washing cycles for both Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus). The anti-inflammatory activity, the potency% reached to 88.3% for the fabric encapsulated with microcapsules of sodium alginate/H. stipulacea sea grass and the EnF/CA. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Effect of Various Finishing Procedures on the Reflectivity (Shine) of Tooth Enamel - An In-vitro Study.

    PubMed

    Patil, Harshal Ashok; Chitko, Shrikant Shrinivas; Kerudi, Veerendra Virupaxappa; Maheshwari, Amit Ratanlal; Patil, Neeraj Suresh; Tekale, Pawankumar Dnyandeo; Gore, Ketan Ashorao; Zope, Amit Ashok

    2016-08-01

    Reflectivity of an object is a good parameter for surface finish. As the patient evaluates finishing as a function of gloss/reflectivity/shine an attempt is made here to evaluate changes in surface finish with custom made reflectometer. The aim of the present study was to study the effect of various procedures during orthodontic treatment on the shine of enamel, using a custom made reflectometer. Sixty one extracted premolars were collected and each tooth was mounted on acrylic block. Reflectivity of the teeth was measured as compared to standard before any procedure. One tooth was kept as standard throughout the study. Sixty teeth were acid etched. Reflectivity was measured on custom made reflectometer and readings recorded. Same procedure was repeated after debonding. Then 60 samples were divided into three groups: Group 1 - Tungsten Carbide, Group 2 - Astropol, Group 3- Sof-Lex disc depending upon the finishing method after debonding and reflectivity was measured. The mean percentage of reflectivity after acid etching was 31.4%, debonding 45.5%, Tungsten carbide bur finishing (Group 1) was 58.3%, Astropol (Group 2) 72.8%, and Sof-Lex disc (Group 3) 84.4% as that to the standard. There was statistically very highly significant (p<0.001) difference in reflectivity restored by the three finishing materials in the study. Thus, the light reflection was better in Group 3> Group 2> Group 1. The primary goal was to restore the enamel to its original state after orthodontic treatment. The methods tested in this study could not restore the original enamel reflectivity.

  17. SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.

    PubMed

    Mariano, Diego C B; Pereira, Felipe L; Aguiar, Edgar L; Oliveira, Letícia C; Benevides, Leandro; Guimarães, Luís C; Folador, Edson L; Sousa, Thiago J; Ghosh, Preetam; Barh, Debmalya; Figueiredo, Henrique C P; Silva, Artur; Ramos, Rommel T J; Azevedo, Vasco A C

    2016-12-15

    The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several

  18. Sequence History Update Tool

    NASA Technical Reports Server (NTRS)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  19. Panel-based Genetic Diagnostic Testing for Inherited Eye Diseases is Highly Accurate and Reproducible and More Sensitive for Variant Detection Than Exome Sequencing

    PubMed Central

    Bujakowska, Kinga M.; Sousa, Maria E.; Fonseca-Kelly, Zoë D.; Taub, Daniel G.; Janessian, Maria; Wang, Dan Yi; Au, Elizabeth D.; Sims, Katherine B.; Sweetser, David A.; Fulton, Anne B.; Liu, Qin; Wiggs, Janey L.; Gai, Xiaowu; Pierce, Eric A.

    2015-01-01

    Purpose Next-generation sequencing (NGS) based methods are being adopted broadly for genetic diagnostic testing, but the performance characteristics of these techniques have not been fully defined with regard to test accuracy and reproducibility. Methods We developed a targeted enrichment and NGS approach for genetic diagnostic testing of patients with inherited eye disorders, including inherited retinal degenerations, optic atrophy and glaucoma. In preparation for providing this Genetic Eye Disease (GEDi) test on a CLIA-certified basis, we performed experiments to measure the sensitivity, specificity, reproducibility as well as the clinical sensitivity of the test. Results The GEDi test is highly reproducible and accurate, with sensitivity and specificity for single nucleotide variant detection of 97.9% and 100%, respectively. The sensitivity for variant detection was notably better than the 88.3% achieved by whole exome sequencing (WES) using the same metrics, due to better coverage of targeted genes in the GEDi test compared to commercially available exome capture sets. Prospective testing of 192 patients with IRDs indicated that the clinical sensitivity of the GEDi test is high, with a diagnostic rate of 51%. Conclusion The data suggest that based on quantified performance metrics, selective targeted enrichment is preferable to WES for genetic diagnostic testing. PMID:25412400

  20. Machining the Integral Impeller and Blisk of Aero-Engines: A Review of Surface Finishing and Strengthening Technologies

    NASA Astrophysics Data System (ADS)

    Fu, Youzhi; Gao, Hang; Wang, Xuanping; Guo, Dongming

    2017-05-01

    The integral impeller and blisk of an aero-engine are high performance parts with complex structure and made of difficult-to-cut materials. The blade surfaces of the integral impeller and blisk are functional surfaces for power transmission, and their surface integrity has significant effects on the aerodynamic efficiency and service life of an aero-engine. Thus, it is indispensable to finish and strengthen the blades before use. This paper presents a comprehensive literature review of studies on finishing and strengthening technologies for the impeller and blisk of aero-engines. The review includes independent and integrated finishing and strengthening technologies and discusses advanced rotational abrasive flow machining with back-pressure used for finishing the integral impeller and blisk. A brief assessment of future research problems and directions is also presented.

  1. Growing-finishing performance and carcass characteristics of pigs fed normal and genetically modified low-phytate corn.

    PubMed

    Spencer, J D; Allee, G L; Sauber, T E

    2000-06-01

    A genetically modified corn hybrid homozygous for the lpa1 allele, containing low phytate (LP), and its nearly isogenic equivalent hybrid (normal) were compared in two experiments with growing-finishing swine. In Exp. 1, 210 barrows (27 kg) were allotted to one of six dietary treatments with two corn hybrids (LP and normal) and three P feeding regimens. There were five replicate pens (seven pigs/pen) per treatment. Treatments consisted of diets that were supplemented with P throughout the growing-finishing period (.2% P and .15% supplemental P during growing and finishing phases, respectively) or only during the growing phase (.2% supplemental P) or that were not supplemented with P throughout the growing-finishing period. Performance at the end of the growing phase was based on a 2 x 2 factorial arrangement of treatments with two corn hybrids and two levels of added P (0 and .2%). This resulted in 10 replicates for the treatments supplemented with .2% P. The finishing phase (73 to 112 kg) was a 2 x 3 factorial arrangement of treatments with the two types of corn and three regimens of added P during the finishing period. Breaking load (BL) and ash of the fourth metacarpal were evaluated from one pig/pen at the end of the growing phase and from all pigs after slaughter. Pigs fed the LP corn diet without added P had greater body weight gain, feed efficiency, BL, and ash content of the fourth metacarpal than pigs fed the normal corn diet without added P. Performance was similar between pigs fed the LP diet without added P and pigs fed LP and normal corn with added P. In Exp. 2, 1,092 gilts (34 kg body weight) were allotted by weight in a commercial facility to one of three treatments: 1) normal corn/soybean meal diet containing .29% and .22% available P during the growing and finishing phases, respectively; 2) LP corn/soybean meal diet with the same available P level as Treatment 1; and 3) same as Treatment 2 for 8 wk, then no inorganic P supplementation during the

  2. THE USEPA'S METAL FINISHING FACILITY RISK SCREENING TOOL (MFFRST)

    EPA Science Inventory

    The US Environmetal ProtectionAgenccy's Metal Finishing
    Facility Risk Screening Tool (MFFRST)

    William M. Barrett Jr, Ph.D. , P.E. ; Paul Harten, Ph.D.1, and Matthew Lorber

    The US Environmental Protection Agency completed the development of the first version of...

  3. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs.

    PubMed

    Saunders, Christopher T; Wong, Wendy S W; Swamy, Sajani; Becq, Jennifer; Murray, Lisa J; Cheetham, R Keira

    2012-07-15

    Whole genome and exome sequencing of matched tumor-normal sample pairs is becoming routine in cancer research. The consequent increased demand for somatic variant analysis of paired samples requires methods specialized to model this problem so as to sensitively call variants at any practical level of tumor impurity. We describe Strelka, a method for somatic SNV and small indel detection from sequencing data of matched tumor-normal samples. The method uses a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. We demonstrate that the method has superior accuracy and sensitivity on impure samples compared with approaches based on either diploid genotype likelihoods or general allele-frequency tests. The Strelka workflow source code is available at ftp://strelka@ftp.illumina.com/. csaunders@illumina.com

  4. Evaluate error correction ability of magnetorheological finishing by smoothing spectral function

    NASA Astrophysics Data System (ADS)

    Wang, Jia; Fan, Bin; Wan, Yongjian; Shi, Chunyan; Zhuo, Bin

    2014-08-01

    Power Spectral Density (PSD) has been entrenched in optics design and manufacturing as a characterization of mid-high spatial frequency (MHSF) errors. Smoothing Spectral Function (SSF) is a newly proposed parameter that based on PSD to evaluate error correction ability of computer controlled optical surfacing (CCOS) technologies. As a typical deterministic and sub-aperture finishing technology based on CCOS, magnetorheological finishing (MRF) leads to MHSF errors inevitably. SSF is employed to research different spatial frequency error correction ability of MRF process. The surface figures and PSD curves of work-piece machined by MRF are presented. By calculating SSF curve, the correction ability of MRF for different spatial frequency errors will be indicated as a normalized numerical value.

  5. Marginal and internal discrepancies of zirconia copings: effects of milling system and finish line design.

    PubMed

    Ribeiro, Isabella Lima Arrais; Campos, Fernanda; Sousa, Rafael Santiago; Alves, Maria Luiza Lima; Rodrigues, Dalton Matos; Souza, Rodrigo Othavio Assuncão; Bottino, Marco Antonio

    2015-01-01

    Discrepancies at the abutment/crown interface can affect the longevity of zirconia restorations. The aim was to evaluate the marginal and internal discrepancies (MD and ID) of zirconia copings manufactured by two milling systems with different finish lines. Three aluminum-master-dies (h = 5.5 mm; Ψ =7.5 mm; 6΀), with different finish lines (large chamfer [LC]; tilted chamfer [TC]; rounded shoulder [RS]) were fabricated. Twenty impressions were made from each master die and poured. Sixty zirconia copings were manufactured and divided according to the factors "finish line" and "milling system" (n = 10): CAD LC = Computer-aided design/computer-aided manufacturing (CAD/CAM) + LC; CAD TC = CAD/CAM + TC; CAD RS = CAD/CAM + RS; MAD LC = manually aided design/manually aided manufacturing (MAD/MAM) + LC; MAD TC = MAD/MAM + TC; and MAD RS = MAD/MAM + RS. For MD analysis, each coping was fixed, and the distance between the external edges of the coping and the edge of the cervical preparation was measured (50 points). Using the same copings, the ID of each coping was evaluated, by the replica technique, at 12 points equally distributed among the regions (n = 10): Ray (R), axial (A), and occlusal (Occl). The measurements were performed by optical microscopy (Χ250). The data (μm) were subjected to parametric and non-parametric statistical analyses. For the MAD/MAM system, the "finish line" (P = 0.0001) affected significantly the MD median values (μm): LC = 251.80 a , RS = 68.40 a and TC = 8.10 b (Dunn's test). For the CAD/CAM system, the median MD values (μm) were not affected by the factor "finish line" (P = 0.4037): LC = 0.82 a , RS = 0.52 a , and TC = 0.89 a . For the ID, it was observed interaction between the finish line types and the region (P = 0.0001) and between region and milling system (P = 0.0031) (RM-ANOVA). The CAD/CAM system presented lower MD values, regardless the finish line. However, the MAD/MAM system showed ID values smaller than those of CAD/CAM.

  6. Effects of the Ion PGM™ Hi-Q™ sequencing chemistry on sequence data quality.

    PubMed

    Churchill, Jennifer D; King, Jonathan L; Chakraborty, Ranajit; Budowle, Bruce

    2016-09-01

    Massively parallel sequencing (MPS) offers substantial improvements over current forensic DNA typing methodologies such as increased resolution, scalability, and throughput. The Ion PGM™ is a promising MPS platform for analysis of forensic biological evidence. The system employs a sequencing-by-synthesis chemistry on a semiconductor chip that measures a pH change due to the release of hydrogen ions as nucleotides are incorporated into the growing DNA strands. However, implementation of MPS into forensic laboratories requires a robust chemistry. Ion Torrent's Hi-Q™ Sequencing Chemistry was evaluated to determine if it could improve on the quality of the generated sequence data in association with selected genetic marker targets. The whole mitochondrial genome and the HID-Ion STR 10-plex panel were sequenced on the Ion PGM™ system with the Ion PGM™ Sequencing 400 Kit and the Ion PGM™ Hi-Q™ Sequencing Kit. Concordance, coverage, strand balance, noise, and deletion ratios were assessed in evaluating the performance of the Ion PGM™ Hi-Q™ Sequencing Kit. The results indicate that reliable, accurate data are generated and that sequencing through homopolymeric regions can be improved with the use of Ion Torrent's Hi-Q™ Sequencing Chemistry. Overall, the quality of the generated sequencing data supports the potential for use of the Ion PGM™ in forensic genetic laboratories.

  7. Sequencing technologies - the next generation.

    PubMed

    Metzker, Michael L

    2010-01-01

    Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalysed the development of next-generation sequencing (NGS) technologies. The inexpensive production of large volumes of sequence data is the primary advantage over conventional methods. Here, I present a technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments. I also outline the broad range of applications for NGS technologies, in addition to providing guidelines for platform selection to address biological questions of interest.

  8. Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes

    PubMed Central

    Shiroguchi, Katsuyuki; Jia, Tony Z.; Sims, Peter A.; Xie, X. Sunney

    2012-01-01

    RNA sequencing (RNA-Seq) is a powerful tool for transcriptome profiling, but is hampered by sequence-dependent bias and inaccuracy at low copy numbers intrinsic to exponential PCR amplification. We developed a simple strategy for mitigating these complications, allowing truly digital RNA-Seq. Following reverse transcription, a large set of barcode sequences is added in excess, and nearly every cDNA molecule is uniquely labeled by random attachment of barcode sequences to both ends. After PCR, we applied paired-end deep sequencing to read the two barcodes and cDNA sequences. Rather than counting the number of reads, RNA abundance is measured based on the number of unique barcode sequences observed for a given cDNA sequence. We optimized the barcodes to be unambiguously identifiable, even in the presence of multiple sequencing errors. This method allows counting with single-copy resolution despite sequence-dependent bias and PCR-amplification noise, and is analogous to digital PCR but amendable to quantifying a whole transcriptome. We demonstrated transcriptome profiling of Escherichia coli with more accurate and reproducible quantification than conventional RNA-Seq. PMID:22232676

  9. Effects of roughage inclusion and particle size on performance and rumination behavior of finishing beef steers

    USDA-ARS?s Scientific Manuscript database

    Roughage is mechanically processed to increase digestibility, and handling and mixing characteristics in finishing diets. Roughage is fed to promote rumen health and decrease digestive upset, but inclusion in finishing diets is limited due to the cost per unit of energy. Rumination behavior may be a...

  10. Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov.

    PubMed Central

    Lagier, Jean-Christophe; Elkarkouri, Khalid; Rivet, Romain; Couderc, Carine; Raoult, Didier; Fournier, Pierre-Edouard

    2013-01-01

    Senegalemassilia anaerobia strain JC110T sp.nov. is the type strain of Senegalemassilia anaerobia gen. nov., sp. nov., the type species of a new genus within the Coriobacteriaceae family, Senegalemassilia gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. S. anaerobia is a Gram-positive anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,383,131 bp long genome contains 1,932 protein-coding and 58 RNA genes. PMID:24019984

  11. Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp.

    PubMed Central

    Tyson, G. H.; Chen, Y.; Li, C.; Mukherjee, S.; Young, S.; Lam, C.; Folster, J. P.; Whichard, J. M.; McDermott, P. F.

    2015-01-01

    The objectives of this study were to identify antimicrobial resistance genotypes for Campylobacter and to evaluate the correlation between resistance phenotypes and genotypes using in vitro antimicrobial susceptibility testing and whole-genome sequencing (WGS). A total of 114 Campylobacter species isolates (82 C. coli and 32 C. jejuni) obtained from 2000 to 2013 from humans, retail meats, and cecal samples from food production animals in the United States as part of the National Antimicrobial Resistance Monitoring System were selected for study. Resistance phenotypes were determined using broth microdilution of nine antimicrobials. Genomic DNA was sequenced using the Illumina MiSeq platform, and resistance genotypes were identified using assembled WGS sequences through blastx analysis. Eighteen resistance genes, including tet(O), blaOXA-61, catA, lnu(C), aph(2″)-Ib, aph(2″)-Ic, aph(2′)-If, aph(2″)-Ig, aph(2″)-Ih, aac(6′)-Ie-aph(2″)-Ia, aac(6′)-Ie-aph(2″)-If, aac(6′)-Im, aadE, sat4, ant(6′), aad9, aph(3′)-Ic, and aph(3′)-IIIa, and mutations in two housekeeping genes (gyrA and 23S rRNA) were identified. There was a high degree of correlation between phenotypic resistance to a given drug and the presence of one or more corresponding resistance genes. Phenotypic and genotypic correlation was 100% for tetracycline, ciprofloxacin/nalidixic acid, and erythromycin, and correlations ranged from 95.4% to 98.7% for gentamicin, azithromycin, clindamycin, and telithromycin. All isolates were susceptible to florfenicol, and no genes associated with florfenicol resistance were detected. There was a strong correlation (99.2%) between resistance genotypes and phenotypes, suggesting that WGS is a reliable indicator of resistance to the nine antimicrobial agents assayed in this study. WGS has the potential to be a powerful tool for antimicrobial resistance surveillance programs. PMID:26519386

  12. Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp.

    PubMed

    Zhao, S; Tyson, G H; Chen, Y; Li, C; Mukherjee, S; Young, S; Lam, C; Folster, J P; Whichard, J M; McDermott, P F

    2016-01-15

    The objectives of this study were to identify antimicrobial resistance genotypes for Campylobacter and to evaluate the correlation between resistance phenotypes and genotypes using in vitro antimicrobial susceptibility testing and whole-genome sequencing (WGS). A total of 114 Campylobacter species isolates (82 C. coli and 32 C. jejuni) obtained from 2000 to 2013 from humans, retail meats, and cecal samples from food production animals in the United States as part of the National Antimicrobial Resistance Monitoring System were selected for study. Resistance phenotypes were determined using broth microdilution of nine antimicrobials. Genomic DNA was sequenced using the Illumina MiSeq platform, and resistance genotypes were identified using assembled WGS sequences through blastx analysis. Eighteen resistance genes, including tet(O), blaOXA-61, catA, lnu(C), aph(2″)-Ib, aph(2″)-Ic, aph(2')-If, aph(2″)-Ig, aph(2″)-Ih, aac(6')-Ie-aph(2″)-Ia, aac(6')-Ie-aph(2″)-If, aac(6')-Im, aadE, sat4, ant(6'), aad9, aph(3')-Ic, and aph(3')-IIIa, and mutations in two housekeeping genes (gyrA and 23S rRNA) were identified. There was a high degree of correlation between phenotypic resistance to a given drug and the presence of one or more corresponding resistance genes. Phenotypic and genotypic correlation was 100% for tetracycline, ciprofloxacin/nalidixic acid, and erythromycin, and correlations ranged from 95.4% to 98.7% for gentamicin, azithromycin, clindamycin, and telithromycin. All isolates were susceptible to florfenicol, and no genes associated with florfenicol resistance were detected. There was a strong correlation (99.2%) between resistance genotypes and phenotypes, suggesting that WGS is a reliable indicator of resistance to the nine antimicrobial agents assayed in this study. WGS has the potential to be a powerful tool for antimicrobial resistance surveillance programs. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  13. Children's discrimination of vowel sequences

    NASA Astrophysics Data System (ADS)

    Coady, Jeffry A.; Kluender, Keith R.; Evans, Julia

    2003-10-01

    Children's ability to discriminate sequences of steady-state vowels was investigated. Vowels (as in ``beet,'' ``bat,'' ``bought,'' and ``boot'') were synthesized at durations of 40, 80, 160, 320, 640, and 1280 ms. Four different vowel sequences were created by concatenating different orders of vowels for each duration, separated by 10-ms intervening silence. Thus, sequences differed in vowel order and duration (rate). Sequences were 12 s in duration, with amplitude ramped linearly over the first and last 2 s. Sequence pairs included both same (identical sequences) and different trials (sequences with vowels in different orders). Sequences with vowel of equal duration were presented on individual trials. Children aged 7;0 to 10;6 listened to pairs of sequences (with 100 ms between sequences) and responded whether sequences sounded the same or different. Results indicate that children are best able to discriminate sequences of intermediate-duration vowels, typical of conversational speaking rate. Children were less accurate with both shorter and longer vowels. Results are discussed in terms of auditory processing (shortest vowels) and memory (longest vowels). [Research supported by NIDCD DC-05263, DC-04072, and DC-005650.

  14. Occurrence of neonicotinoid insecticides in finished drinking water and fate during drinking water treatment

    USGS Publications Warehouse

    Klarich, Kathryn L.; Pflug, Nicholas C.; DeWald, Eden M.; Hladik, Michelle L.; Kolpin, Dana W.; Cwiertny, David M.; LeFevre, Gergory H.

    2017-01-01

    Neonicotinoid insecticides are widespread in surface waters across the agriculturally-intensive Midwestern US. We report for the first time the presence of three neonicotinoids in finished drinking water and demonstrate their general persistence during conventional water treatment. Periodic tap water grab samples were collected at the University of Iowa over seven weeks in 2016 (May-July) after maize/soy planting. Clothianidin, imidacloprid, and thiamethoxam were ubiquitously detected in finished water samples and ranged from 0.24-57.3 ng/L. Samples collected along the University of Iowa treatment train indicate no apparent removal of clothianidin and imidacloprid, with modest thiamethoxam removal (~50%). In contrast, the concentrations of all neonicotinoids were substantially lower in the Iowa City treatment facility finished water using granular activated carbon (GAC) filtration. Batch experiments investigated potential losses. Thiamethoxam losses are due to base-catalyzed hydrolysis at high pH conditions during lime softening. GAC rapidly and nearly completely removed all three neonicotinoids. Clothianidin is susceptible to reaction with free chlorine and may undergo at least partial transformation during chlorination. Our work provides new insights into the persistence of neonicotinoids and their potential for transformation during water treatment and distribution, while also identifying GAC as an effective management tool to lower neonicotinoid concentrations in finished drinking water.

  15. Complete genome sequence of Yersinia ruckeri str. CSF007-82, etiologic agent of enteric redmouth disease in salmonid fish

    USDA-ARS?s Scientific Manuscript database

    We present the complete, closed and finished chromosomal and extra-chromosomal genome sequences of Y. ruckeri strain CSF007-82, etiologic agent of enteric red mouth disease in salmonid fish. The chromosome is 3,799,036 bp with a G+C content of 47.5% and encodes 3,530 predicted CDS, 7 ribosomal opero...

  16. 40 CFR 425.10 - Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 30 2011-07-01 2011-07-01 false Applicability; description of the hair... POINT SOURCE CATEGORY Hair Pulp, Chrome Tan, Retan-Wet Finish Subcategory § 425.10 Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory. The provisions of this subpart are...

  17. 40 CFR 425.20 - Applicability; description of the hair save, chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 30 2011-07-01 2011-07-01 false Applicability; description of the hair... POINT SOURCE CATEGORY Hair Save, Chrome Tan, Retan-Wet Finish Subcategory § 425.20 Applicability; description of the hair save, chrome tan, retan-wet finish subcategory. The provisions of this subpart are...

  18. Genome sequence of the thermotolerant foodborne pathogen Salmonella enterica serovar Senftenberg ATCC 43845 and phylogenetic analysis of Loci encoding increased protein quality control mechanisms

    USDA-ARS?s Scientific Manuscript database

    Salmonella enterica subsp. enterica bacteria are important foodborne pathogens with major economic impact. Some isolates exhibit increased heat tolerance, a concern for food safety. Analysis of a finished-quality genome sequence of an isolate commonly used in heat resistance studies, S. enterica sub...

  19. Lathe Attachment Finishes Inner Surface of Tubes

    NASA Technical Reports Server (NTRS)

    Lancki, A. J.

    1982-01-01

    Extremely smooth finishes are machined on inside surfaces of tubes by new attachment for a lathe. The relatively inexpensive accessory, called a "microhone," holds a honing stone against workpiece by rigid tangs instead of springs as in conventional honing tools. Inner rod permits adjustment of microhoning stone, while outer tube supports assembly. Outer tube is held between split blocks on lathe toolpost. Microhoning can be done with either microhone or workpiece moving and other member stationary.

  20. Finished Genome Sequence of the Laboratory Strain Escherichia coli K-12 RV308 (ATCC 31608).

    PubMed

    Krempl, Peter M; Mairhofer, Juergen; Striedner, Gerald; Thallinger, Gerhard G

    2014-11-20

    Escherichia coli strain K-12 substrain RV308 is an engineered descendant of the K-12 wild-type strain. Like its ancestor, it is an important organism in biotechnological research and is heavily used for the expression of single-chain variable fragments. Here, we report the complete genome sequence of E. coli K-12 RV308 (ATCC 31608). Copyright © 2014 Krempl et al.

  1. Facilitated sequence counting and assembly by template mutagenesis

    PubMed Central

    Levy, Dan; Wigler, Michael

    2014-01-01

    Presently, inferring the long-range structure of the DNA templates is limited by short read lengths. Accurate template counts suffer from distortions occurring during PCR amplification. We explore the utility of introducing random mutations in identical or nearly identical templates to create distinguishable patterns that are inherited during subsequent copying. We simulate the applications of this process under assumptions of error-free sequencing and perfect mapping, using cytosine deamination as a model for mutation. The simulations demonstrate that within readily achievable conditions of nucleotide conversion and sequence coverage, we can accurately count the number of otherwise identical molecules as well as connect variants separated by long spans of identical sequence. We discuss many potential applications, such as transcript profiling, isoform assembly, haplotype phasing, and de novo genome assembly. PMID:25313059

  2. 40 CFR 463.30 - Applicability; description of the finishing water subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS (CONTINUED) PLASTICS MOLDING AND FORMING POINT SOURCE CATEGORY.... Processes in the finishing water subcategory are processes where water comes in contact with the plastic...

  3. 40 CFR 463.30 - Applicability; description of the finishing water subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS (CONTINUED) PLASTICS MOLDING AND FORMING POINT SOURCE CATEGORY.... Processes in the finishing water subcategory are processes where water comes in contact with the plastic...

  4. 40 CFR 425.10 - Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 29 2010-07-01 2010-07-01 false Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory. 425.10 Section 425.10 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS LEATHER TANNING AND FINISHING POINT SOURCE CATEGORY Hair Pulp, Chrome...

  5. 40 CFR 425.20 - Applicability; description of the hair save, chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 29 2010-07-01 2010-07-01 false Applicability; description of the hair save, chrome tan, retan-wet finish subcategory. 425.20 Section 425.20 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS LEATHER TANNING AND FINISHING POINT SOURCE CATEGORY Hair Save, Chrome Tan,...

  6. 2. DETAIL VIEW OF JOURNAL LATHE, AXLE FINISHING AREA. Grinding ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. DETAIL VIEW OF JOURNAL LATHE, AXLE FINISHING AREA. Grinding bearing diameters on locomotive axle. Norton grinder, 1942 (dated). Melvin Grassmeyer, operator. - Juniata Shops, Machine Shop No. 1, East of Fourth Avenue at Third Street, Altoona, Blair County, PA

  7. 3. DETAIL VIEW OF JOURNAL LATHE, AXLE FINISHING AREA. Grinding ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. DETAIL VIEW OF JOURNAL LATHE, AXLE FINISHING AREA. Grinding bearing diameters on locomotive axle. Norton grinder, 1942 (dated). Melvin Grassmeyer, operator. - Juniata Shops, Machine Shop No. 1, East of Fourth Avenue at Third Street, Altoona, Blair County, PA

  8. DEVELOPMENT OF THE METAL FINISHING FACILITY RISK SCREENING TOOL

    EPA Science Inventory

    Enhancement of the US Environmental Protection Agency's
    Metal Finishing Facility Risk Screening Tool (MFFRST)

    William M. Barrett Jr, Ph.D., P.E. , P.E.; Paul Harten, Ph.D.1, Matt Lorber , Charles Peck , and Steve Schwartz, P.E., Q.E.P.3

    Recently, the US Environ...

  9. A survey of grass-finished beef producers in Pennsylvania

    USDA-ARS?s Scientific Manuscript database

    To meet our goal of quantifying the environmental impacts of grass-finished beef production, data on production practices in Pennsylvania were collected at the farm level via visits and online surveys. Twenty-three responses represented a total of 1,055 animals on 2,155 acres of land. Farms were rel...

  10. Cement Finishing. Pre-Apprenticeship Phase 2 Training. Instructor's Guide.

    ERIC Educational Resources Information Center

    Nama, Joe

    This instructor's guide accompanies the self-paced student training modules on cement finishing, available separately as CE 031 576. Introductory materials include a description of the components of the pre-apprenticeship project, discussion of teacher's role in students' completion of the modules, and scope and contents of Phase 2 training. Each…

  11. GASP: Gapped Ancestral Sequence Prediction for proteins

    PubMed Central

    Edwards, Richard J; Shields, Denis C

    2004-01-01

    Background The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate alignments and phylogenies. Several algorithms exist based on Maximum Parsimony or Maximum Likelihood methods but many current implementations are unable to process residues with gaps, which may represent insertion/deletion (indel) events or sequence fragments. Results Here we present a new algorithm, GASP (Gapped Ancestral Sequence Prediction), for predicting ancestral sequences from phylogenetic trees and the corresponding multiple sequence alignments. Alignments may be of any size and contain gaps. GASP first assigns the positions of gaps in the phylogeny before using a likelihood-based approach centred on amino acid substitution matrices to assign ancestral amino acids. Important outgroup information is used by first working down from the tips of the tree to the root, using descendant data only to assign probabilities, and then working back up from the root to the tips using descendant and outgroup data to make predictions. GASP was tested on a number of simulated datasets based on real phylogenies. Prediction accuracy for ungapped data was similar to three alternative algorithms tested, with GASP performing better in some cases and worse in others. Adding simple insertions and deletions to the simulated data did not have a detrimental effect on GASP accuracy. Conclusions GASP (Gapped Ancestral Sequence Prediction) will predict ancestral sequences from multiple protein alignments of any size. Although not as accurate in all cases as some of the more sophisticated maximum likelihood approaches, it can process a wide range of input phylogenies and will predict ancestral sequences for gapped and ungapped residues alike. PMID:15350199

  12. The Effect of Various Finish Line Configurations on the Marginal Seal and Occlusal Discrepancy of Cast Full Crowns After Cementation - An In-vitro Study

    PubMed Central

    Nemane, Vaishali; Meshram, Suresh

    2015-01-01

    Background The marginal fit of crowns is of clinical importance. It is found that marginal and occlusal discrepancies are commonly increased following cementation. The resistance of cementing materials is a factor that prevents cast restorations from being correctly seated. Different finish lines behave differently in facilitating the escape of the cement. When the escape path of the cement decreases, the crown fails to seat further. Materials and Methods This study was planned with an aim to evaluate the effect of various finish lines on the marginal seal and occlusal seat of full crown preparations. Six stainless steel metal dies were machined to simulate molar crown preparations. The diameter was 10 mm and height was 6mm. The occlusal surface was kept flat and a small circular dimple was machined for reorientation of the wax pattern and metal copings, margins of various designs were machined accurately. The margins prepared were Group A- 900C shoulder, Group B- Rounded shoulder, Group C- 45 degree sloped shoulder, Group D- Chamfer, Group E- Long chamfer, Group F- Feather edge. Full cast metal crowns of base metal alloy were fabricated over the metal dies. Zinc phosphate luting cement was used for the cementation. After twenty four hours, the cemented crown and die assembly were embedded in clear acrylic resin so as to hold the assembly together while sectioning. Twenty four hours later, all the samples were sectioned sagitally. The sectioned halves were focused under a stereomicroscope and the cement spaces were measured to the nearest micron. The cement thickness was measured at two points on the occlusal surface and one at each margin. Results Significant differences were observed in the occlusal seat and marginal seal of all the finish line configurations. The rounded shoulder had the best occlusal seat, followed by 900C shoulder. The occlusal seat and marginal seal afforded by the shoulder finish lines were similar whereas there was a vast difference in the

  13. Effects of winter stocker growth rate and finishing system on: III. Tissue proximate, fatty acid, vitamin, and cholesterol content.

    PubMed

    Duckett, S K; Neel, J P S; Fontenot, J P; Clapham, W M

    2009-09-01

    Angus-cross steers (n = 198; 270 kg of BW; 8 mo) were used in a 3-yr study to assess the effects of winter stocker growth rate and finishing system on LM proximate, fatty acid, cholesterol, vitamin, and mineral composition. During the winter months (December to April), steers were randomly allotted to 3 stocker growth rates: low (0.23 kg/d), medium (0.45 kg/d), or high (0.68 kg/d). At the completion of the stockering phase, steers were allotted randomly within each stocker growth rate to a high concentrate (CONC) or pasture (PAST) finishing system and finished to an equal time endpoint. Winter stocker growth rate did not alter (P > 0.05) proximate, cholesterol, or vitamin content of the LM. All interactions among winter stocker growth rate and finishing system were nonsignificant, indicating that supplementation systems during winter stocker period did not influence beef composition after finishing on PAST or CONC. Finishing steers on CONC decreased (P < 0.001) moisture content of the LM and increased (P < 0.001) lipid content of the LM. Protein, ash, and cholesterol content of the LM did not differ (P > 0.05) between finishing systems. alpha-Tocopherol and beta-carotene content of the LM were 288 and 54% greater, respectively, for PAST-finished cattle than CONC. B-vitamins, thiamine and riboflavin, were also present in greater (P = 0.001) concentrations for PAST than CONC. Calcium, Mg, and K contents of the LM were greater (P < 0.05) for PAST than CONC. Total fatty acid content of the LM was 49% less for PAST than CONC. Myristoleic, palmitoleic, and oleic acid concentrations were all less (P = 0.001) for PAST than CONC. Trans-10 octadecenoic acid percentage in LM was 97% greater (P = 0.001) for CONC than PAST; conversely, trans-11 vaccenic acid percentage in the LM was 90% greater (P = 0.001) for PAST than CONC. Conjugated linoleic acid, cis-9, trans-11 isomer, percentage was greater (P = 0.001) by 117% for PAST than CONC. Linoleic acid (C18:2) concentration did

  14. Physical and nutritional properties of buffalo meat finished on hay or maize silage-based diets.

    PubMed

    Cifuni, Giulia Francesca; Contò, Michela; Amici, Andrea; Failla, Sebastiana

    2014-04-01

    The current study examines the effect of different finishing diets (hay- vs. maize-silage on meal ration) on carcass quality, physical, chemical and sensory properties, and fatty acid profiles of buffalo meat. Twenty male Italian Mediterranean buffaloes (246 ± 9.00 kg live weight) were distributed at random into two groups at the beginning of the finishing period (368 ± 20 days). The buffaloes were offered two finishing diets: a maize silage (MS) or an alfalfa hay (AH) diet. No significant differences were found between dietary treatments for live and carcass weight. Meat chemical composition was influenced by dietary treatment. A higher fat content was detected in meat from animals finished with MS than AH (P < 0.05). Overall, the data indicated differences between the fatty acid profiles of meat as a consequence of different feeding systems. The higher fat deposition in the MS group resulted in meat with a less favorable fatty acid profile (i.e. a lower polyunsaturated/saturated fatty acid ratio and α-linolenic fatty acid content) in relation to human health compared with meat from animals fed the AH diet. © 2013 Japanese Society of Animal Science.

  15. Combined Advanced Finishing and UV-Laser Conditioning for Producing UV-Damage-Resistant Fused Silica Optics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Menapace, J A; Penetrante, B; Golini, D

    2001-11-01

    Laser induced damage initiation on fused silica optics can limit the lifetime of the components when used in high power UV laser environments. Foe example in inertial confinement fusion research applications, the optics can be exposed to temporal laser pulses of about 3-nsec with average fluences of 8 J/cm{sup 2} and peak fluences between 12 and 15 J/cm{sup 2}. During the past year, we have focused on optimizing the damage performance at a wavelength of 355-nm (3{omega}), 3-nsec pulse length, for optics in this category by examining a variety of finishing technologies with a challenge to improve the laser damagemore » initiation density by at least two orders of magnitude. In this paper, we describe recent advances in improving the 3{omega} damage initiation performance of laboratory-scale zirconium oxide and cerium oxide conventionally finished fused silica optics via application of processes incorporating magnetorheological finishing (MRF), wet chemical etching, and UV laser conditioning. Details of the advanced finishing procedures are described and comparisons are made between the procedures based upon large area 3{omega} damage performance, polishing layer contamination, and optical subsurface damage.« less

  16. Choice of crystal surface finishing for a dual-ended readout depth-of-interaction (DOI) detector.

    PubMed

    Fan, Peng; Ma, Tianyu; Wei, Qingyang; Yao, Rutao; Liu, Yaqiang; Wang, Shi

    2016-02-07

    The objective of this study was to choose the crystal surface finishing for a dual-ended readout (DER) DOI detector. Through Monte Carlo simulations and experimental studies, we evaluated 4 crystal surface finishing options as combinations of crystal surface polishing (diffuse or specular) and reflector (diffuse or specular) options on a DER detector. We also tested one linear and one logarithm DOI calculation algorithm. The figures of merit used were DOI resolution, DOI positioning error, and energy resolution. Both the simulation and experimental results show that (1) choosing a diffuse type in either surface polishing or reflector would improve DOI resolution but degrade energy resolution; (2) crystal surface finishing with a diffuse polishing combined with a specular reflector appears a favorable candidate with a good balance of DOI and energy resolution; and (3) the linear and logarithm DOI calculation algorithms show overall comparable DOI error, and the linear algorithm was better for photon interactions near the ends of the crystal while the logarithm algorithm was better near the center. These results provide useful guidance in DER DOI detector design in choosing the crystal surface finishing and DOI calculation methods.

  17. Management Characteristics of Grass-finished Beef Operations in the Northeast

    USDA-ARS?s Scientific Manuscript database

    An online survey of self-identified grass-finished beef producers was conducted throughout the Northeast region along with several farm visits. Seventy acceptable records from producers in Delaware, Maine, Massachusetts, Maryland, New Hampshire, New Jersey, New York, Pennsylvania, Vermont, and West ...

  18. A Comprehensive Strategy for Accurate Mutation Detection of the Highly Homologous PMS2.

    PubMed

    Li, Jianli; Dai, Hongzheng; Feng, Yanming; Tang, Jia; Chen, Stella; Tian, Xia; Gorman, Elizabeth; Schmitt, Eric S; Hansen, Terah A A; Wang, Jing; Plon, Sharon E; Zhang, Victor Wei; Wong, Lee-Jun C

    2015-09-01

    Germline mutations in the DNA mismatch repair gene PMS2 underlie the cancer susceptibility syndrome, Lynch syndrome. However, accurate molecular testing of PMS2 is complicated by a large number of highly homologous sequences. To establish a comprehensive approach for mutation detection of PMS2, we have designed a strategy combining targeted capture next-generation sequencing (NGS), multiplex ligation-dependent probe amplification, and long-range PCR followed by NGS to simultaneously detect point mutations and copy number changes of PMS2. Exonic deletions (E2 to E9, E5 to E9, E8, E10, E14, and E1 to E15), duplications (E11 to E12), and a nonsense mutation, p.S22*, were identified. Traditional multiplex ligation-dependent probe amplification and Sanger sequencing approaches cannot differentiate the origin of the exonic deletions in the 3' region when PMS2 and PMS2CL share identical sequences as a result of gene conversion. Our approach allows unambiguous identification of mutations in the active gene with a straightforward long-range-PCR/NGS method. Breakpoint analysis of multiple samples revealed that recurrent exon 14 deletions are mediated by homologous Alu sequences. Our comprehensive approach provides a reliable tool for accurate molecular analysis of genes containing multiple copies of highly homologous sequences and should improve PMS2 molecular analysis for patients with Lynch syndrome. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  19. Effect of urea-supplemented diets on the ruminal bacterial and archaeal community composition of finishing bulls.

    PubMed

    Zhou, Zhenming; Meng, Qingxiang; Li, Shengli; Jiang, Lan; Wu, Hao

    2017-08-01

    In this study, we evaluated the effects of urea-supplemented diets on the ruminal bacterial and archaeal communities of finishing bulls using sequencing technology. Eighteen bulls were fed a total mixed ration based on maize silage and concentrate (40:60) and randomly allocated to one of three experimental diets: a basal diet with no urea (UC, 0%), a basal diet supplemented with low urea levels (UL, 0.8% dry matter (DM) basis), and a basal diet supplemented with high urea levels (UH, 2% DM basis). All treatments were iso-nitrogenous (14% crude protein, DM basis) and iso-metabolic energetic (ME = 11.3 MJ/kg, DM basis). After a 12-week feeding trial, DNA was isolated from ruminal samples and used for 16S rRNA gene amplicon sequencing. For bacteria, the most abundant phyla were Firmicutes (44.47%) and Bacteroidetes (41.83%), and the dominant genera were Prevotella (13.17%), Succiniclasticum (4.24%), Butyrivibrio (2.36%), and Ruminococcus (1.93%). Urea supplementation had no effect on most phyla (P > 0.05), while there was a decreasing tendency in phylum TM7 with increasing urea levels (P = 0.0914). Compared to UC, UH had lower abundance of genera Butyrivibrio and Coprococcus (P = 0.0092 and P = 0.0222, respectively). For archaea, the most abundant phylum was Euryarchaeota (99.81% of the sequence reads), and the most abundant genus was Methanobrevibacter (90.87% of the sequence reads). UH increased the abundance of genus Methanobrevibacter and Methanobacterium (P = 0.0299 and P = 0.0007, respectively) and decreased the abundance of vadinCA11 (P = 0.0151). These findings suggest that urea-supplemented diets were associated with a shift in archaeal biodiversity and changes in the bacterial community in the rumen.

  20. Effects of Fiber Finish on Mechanical, Low and High Speed Impact of Glass Fiber Reinforced Composites

    DTIC Science & Technology

    2011-05-12

    For 70 Min Cool Down And De-mold 10Unclassified For Producing Polyester Or Vinyl Ester Composite Specimens Resin Resin Inlet Vacuum Bag Trap Pump Steel...Reinforcement Finish Matrix Fiber Content (%) Hexcel 1581-F12 Heat Burnt (No Finish) PP 71.0 Polyester 70.0 Vinyl ester 66.2 Hexcel 1581-GR Greige ( Starch

  1. 77 FR 39997 - Heavy Forged Hand Tools, Finished or Unfinished, With or Without Handles From the People's...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-06

    ... DEPARTMENT OF COMMERCE International Trade Administration [A-570-803] Heavy Forged Hand Tools... review on heavy forged hand tools, finished or unfinished, with or without handles from the People's..., 2012) (Tianjin v. United States). \\2\\ See Heavy Forged Hand Tools, Finished or Unfinished, With or...

  2. Method and means for producing fluorocarbon finishes on fibrous structures

    NASA Technical Reports Server (NTRS)

    Toy, Madeline S. (Inventor); Stringham, Roger S. (Inventor); Fogg, Lawrence C. (Inventor)

    1981-01-01

    An improved process and apparatus is provided for imparting chemically bonded fluorocarbon finishes to textiles. In the process, the textiles are contacted with a gaseous mixture of fluoroolefins in an inert diluent gas in the presence of ultraviolet light under predetermined conditions.

  3. 78 FR 23591 - Certain Prepregs, Laminates, and Finished Circuit Boards

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-19

    ... INTERNATIONAL TRADE COMMISSION [Investigation No. 337-TA-659 (Enforcement)] Certain Prepregs... United States after importation of certain prepregs, laminates, and finished circuit boards that infringe... prepregs and laminates that are the subject of the investigation or that otherwise infringe, induce, and/or...

  4. Pesticides and their breakdown products in Lake Waxahachie, Texas, and in finished drinking water from the lake

    USGS Publications Warehouse

    Ging, Patricia B.

    2002-01-01

    Since 1991, the U.S. Geological Survey (USGS) National Water-Quality Assessment (NAWQA) Program has collected pesticide data from streams and aquifers throughout the Nation (Gilliom and others, 1995). However, little published information on pesticides in public drinking water is available. The NAWQA Program usually collects data on the sources of drinking water but not on the finished drinking water. Therefore, the U.S. Environmental Protection Agency (USEPA), in conjunction with the NAWQA Program, has initiated a nationwide pilot project to collect information on concentrations of pesticides and their breakdown products in finished drinking water, in source waters such as reservoirs, and in the basins that contribute water to the reservoirs. The pilot project was designed to collect water samples from finished drinking-water supplies and the associated source water from selected reservoirs that receive runoff from a variety of land uses. Lake Waxahachie, in Ellis County in north-central Texas, was chosen to represent a reservoir receiving water that includes runoff from cotton cropland. This fact sheet presents the results of pesticide sampling of source water from Lake Waxahachie and in finished drinking water from the lake. Analyses are compared to indicate differences in pesticide detections and concentrations between lake water and finished drinking water.

  5. In silico segmentations of lentivirus envelope sequences

    PubMed Central

    Boissin-Quillon, Aurélia; Piau, Didier; Leroux, Caroline

    2007-01-01

    Background The gene encoding the envelope of lentiviruses exhibits a considerable plasticity, particularly the region which encodes the surface (SU) glycoprotein. Interestingly, mutations do not appear uniformly along the sequence of SU, but they are clustered in restricted areas, called variable (V) regions, which are interspersed with relatively more stable regions, called constant (C) regions. We look for specific signatures of C/V regions, using hidden Markov models constructed with SU sequences of the equine, human, small ruminant and simian lentiviruses. Results Our models yield clear and accurate delimitations of the C/V regions, when the test set and the training set were made up of sequences of the same lentivirus, but also when they were made up of sequences of different lentiviruses. Interestingly, the models predicted the different regions of lentiviruses such as the bovine and feline lentiviruses, not used in the training set. Models based on composite training sets produce accurate segmentations of sequences of all these lentiviruses. Conclusion Our results suggest that each C/V region has a specific statistical oligonucleotide composition, and that the C (respectively V) regions of one of these lentiviruses are statistically more similar to the C (respectively V) regions of the other lentiviruses, than to the V (respectively C) regions of the same lentivirus. PMID:17376229

  6. The influence of surface finishing methods on touch-sensitive reactions

    NASA Astrophysics Data System (ADS)

    Kukhta, M. S.; Sokolov, A. P.; Krauinsh, P. Y.; Kozlova, A. D.; Bouchard, C.

    2017-02-01

    This paper describes the modern technological development trends in jewelry design. In the jewelry industry, new trends, associated with the introduction of updated non-traditional materials and finishing techniques, are appearing. The existing information-oriented society enhances the visual aesthetics of new jewelry forms, decoration techniques (depth and surface), synthesis of different materials, which, all in all, reveal a bias towards positive effects of visual design. Today, the jewelry industry includes not only traditional techniques, but also such improved techniques as computer-assisted design, 3D-prototyping and other alternatives to produce an updated level of jewelry material processing. The authors present the specific features of ornamental pattern designing, decoration types (depth and surface) and comparative analysis of different approaches in surface finishing. Identifying the appearance or the effect of jewelry is based on proposed evaluation criteria, providing an advanced visual aesthetics basis is predicated on touch-sensitive responses.

  7. Method and system for processing optical elements using magnetorheological finishing

    DOEpatents

    Menapace, Joseph Arthur; Schaffers, Kathleen Irene; Bayramian, Andrew James; Molander, William A

    2012-09-18

    A method of finishing an optical element includes mounting the optical element in an optical mount having a plurality of fiducials overlapping with the optical element and obtaining a first metrology map for the optical element and the plurality of fiducials. The method also includes obtaining a second metrology map for the optical element without the plurality of fiducials, forming a difference map between the first metrology map and the second metrology map, and aligning the first metrology map and the second metrology map. The method further includes placing mathematical fiducials onto the second metrology map using the difference map to form a third metrology map and associating the third metrology map to the optical element. Moreover, the method includes mounting the optical element in the fixture in an MRF tool, positioning the optical element in the fixture; removing the plurality of fiducials, and finishing the optical element.

  8. Accurate Simulation and Detection of Coevolution Signals in Multiple Sequence Alignments

    PubMed Central

    Ackerman, Sharon H.; Tillier, Elisabeth R.; Gatti, Domenico L.

    2012-01-01

    Background While the conserved positions of a multiple sequence alignment (MSA) are clearly of interest, non-conserved positions can also be important because, for example, destabilizing effects at one position can be compensated by stabilizing effects at another position. Different methods have been developed to recognize the evolutionary relationship between amino acid sites, and to disentangle functional/structural dependencies from historical/phylogenetic ones. Methodology/Principal Findings We have used two complementary approaches to test the efficacy of these methods. In the first approach, we have used a new program, MSAvolve, for the in silico evolution of MSAs, which records a detailed history of all covarying positions, and builds a global coevolution matrix as the accumulated sum of individual matrices for the positions forced to co-vary, the recombinant coevolution, and the stochastic coevolution. We have simulated over 1600 MSAs for 8 protein families, which reflect sequences of different sizes and proteins with widely different functions. The calculated coevolution matrices were compared with the coevolution matrices obtained for the same evolved MSAs with different coevolution detection methods. In a second approach we have evaluated the capacity of the different methods to predict close contacts in the representative X-ray structures of an additional 150 protein families using only experimental MSAs. Conclusions/Significance Methods based on the identification of global correlations between pairs were found to be generally superior to methods based only on local correlations in their capacity to identify coevolving residues using either simulated or experimental MSAs. However, the significant variability in the performance of different methods with different proteins suggests that the simulation of MSAs that replicate the statistical properties of the experimental MSA can be a valuable tool to identify the coevolution detection method that is most

  9. Electromigration Failure Mechanism in Sn-Cu Solder Alloys with OSP Cu Surface Finish

    NASA Astrophysics Data System (ADS)

    Chu, Ming-Hui; Liang, S. W.; Chen, Chih; Huang, Annie T.

    2012-09-01

    Organic solderable preservative (OSP) has been adopted as the Cu substrate surface finish in flip-chip solder joints for many years. In this study, the electromigration behavior of lead-free Sn-Cu solder alloys with thin-film under bump metallization and OSP surface finish was investigated. The results showed that severe damage occurred on the substrate side (cathode side), whereas the damage on the chip side (cathode side) was not severe. The damage on the substrate side included void formation, copper dissolution, and formation of intermetallic compounds (IMCs). The OSP Cu interface on the substrate side became the weakest point in the solder joint even when thin-film metallization was used on the chip side. Three-dimensional simulations were employed to investigate the current density distribution in the area between the OSP Cu surface finish and the solder. The results indicated that the current density was higher along the periphery of the bonding area between the solder and the Cu pad, consistent with the area of IMC and void formation in our experimental results.

  10. Optical mapping and its potential for large-scale sequencing projects.

    PubMed

    Aston, C; Mishra, B; Schwartz, D C

    1999-07-01

    Physical mapping has been rediscovered as an important component of large-scale sequencing projects. Restriction maps provide landmark sequences at defined intervals, and high-resolution restriction maps can be assembled from ensembles of single molecules by optical means. Such optical maps can be constructed from both large-insert clones and genomic DNA, and are used as a scaffold for accurately aligning sequence contigs generated by shotgun sequencing.

  11. Effects of surface-finishing protocols on the roughness, color change, and translucency of different ceramic systems.

    PubMed

    Akar, Gülcan Coşkun; Pekkan, Gürel; Çal, Ebru; Eskitaşçıoğlu, Gürcan; Özcan, Mutlu

    2014-08-01

    Surface-finishing protocols have a mechanical impact on ceramic surfaces that could eventually affect surface topography and light scattering. An optimum protocol is needed to avoid damaging the optical properties of ceramics. The purpose of this study was to determine the effects of different surface-finishing protocols on the surface roughness, color change, and translucency of ceramic and metal ceramic restorations. Standardized disk-shaped specimens (1.5 × 10 mm, n=128) were fabricated from 3 different ceramic core materials (aluminum oxide [Al2O3]-AL, zirconium oxide [ZrO2]-ZR, lithium disilicate [Li2Si2O5]-LIT), veneered (V) with dentin ceramics (n=32 per group), and placed in the following groups: ALV, ZRV, and LITV. The metal ceramic group acted as the control (n=32). Four different surface-finishing methods were tested. Airborne-particle abrasion with 50 μm Al2O3, polishing with adjustment kit, polishing with adjustment kit plus diamond polishing paste, and autoglazing (n=8 subgroup) were applied on the veneering ceramics. The specimens were analyzed with a profilometer for surface roughness, and color change and translucency were measured with a clinical spectrophotometer. Statistical analyses were performed with 1-way ANOVA and the Tukey honest significant difference tests (α=.05). Specimens treated with the airborne particle abrasion method showed significantly higher mean profilometer for surface roughness values in all groups (P<.05). The polishing with adjustment kit and autoglazing methods revealed statistically similar surface roughness values in all groups (P>.05). With the diamond polishing paste method, lower surface roughness values were achieved in the ZRV and metal ceramic groups acted as the control groups. Different surface-finishing methods affected the color change of the ceramic systems, except for ZRV. Surface-finishing protocols significantly affected the translucency values of the ALV, LITV, and metal ceramic groups (P<.05). No

  12. Military Curriculum Materials for Vocational and Technical Education. Builders School, Finish Carpentry I. Classroom Course 3-10.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. National Center for Research in Vocational Education.

    Adapted from military service training materials, this publication contains course materials for teaching finish carpentry, both in the classroom and through practical experience. Students completing this short course will be able to finish carpentry projects involving wallboard, plywood panel, composition floor tile, and acoustical ceiling tile.…

  13. 77 FR 2031 - Tapered Roller Bearings and Parts Thereof, Finished and Unfinished From the People's Republic of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-13

    ... Parts Thereof, Finished and Unfinished From the People's Republic of China: Extension of the Time Limit..., International Trade Administration, U.S. Department of Commerce, 14th Street and Constitution Avenue NW..., finished and unfinished from the People's Republic of China. See Tapered Roller Bearings and Parts Thereof...

  14. Entomopathogen ID: a curated sequence resource for entomopathogenic fungi

    USDA-ARS?s Scientific Manuscript database

    We report the development of a publicly accessible, curated database of Hypocrealean entomopathogenic fungi sequence data. The goal is to provide a platform for users to easily access sequence data from reference strains. The database can be used to accurately identify unknown entomopathogenic fungi...

  15. Carpentry and Finishing Procedures. Building Maintenance. Module II. Instructor's Guide.

    ERIC Educational Resources Information Center

    Hawk, Sam; Brunk, Art

    This curriculum guide, keyed to the building maintenance competency profile developed by industry and education professionals, provides three units on carpentry and finishing procedures. The first unit, Exterior Carpentry, contains the following lessons: carpentry safety procedures, ladder and scaffolding safety, door installation/repair,…

  16. Material removal in magnetorheological finishing of optics.

    PubMed

    Kordonski, William; Gorodkin, Sergei

    2011-05-10

    A concept of material removal based on the principle of conservation of particles momentum in a binary suspension is applied to analyze material removal in magnetorheological finishing and magnetorheological jet processes widely used in precision optics fabrication. According to this concept, a load for surface indentation by abrasive particles is provided at their interaction near the wall with heavier basic (magnetic) particles, which fluctuate (due to collision) in the shear flow of concentrated suspension. The model is in good qualitative and quantitative agreement with experimental results.

  17. Whole-exome/genome sequencing and genomics.

    PubMed

    Grody, Wayne W; Thompson, Barry H; Hudgins, Louanne

    2013-12-01

    As medical genetics has progressed from a descriptive entity to one focused on the functional relationship between genes and clinical disorders, emphasis has been placed on genomics. Genomics, a subelement of genetics, is the study of the genome, the sum total of all the genes of an organism. The human genome, which is contained in the 23 pairs of nuclear chromosomes and in the mitochondrial DNA of each cell, comprises >6 billion nucleotides of genetic code. There are some 23,000 protein-coding genes, a surprisingly small fraction of the total genetic material, with the remainder composed of noncoding DNA, regulatory sequences, and introns. The Human Genome Project, launched in 1990, produced a draft of the genome in 2001 and then a finished sequence in 2003, on the 50th anniversary of the initial publication of Watson and Crick's paper on the double-helical structure of DNA. Since then, this mass of genetic information has been translated at an ever-increasing pace into useable knowledge applicable to clinical medicine. The recent advent of massively parallel DNA sequencing (also known as shotgun, high-throughput, and next-generation sequencing) has brought whole-genome analysis into the clinic for the first time, and most of the current applications are directed at children with congenital conditions that are undiagnosable by using standard genetic tests for single-gene disorders. Thus, pediatricians must become familiar with this technology, what it can and cannot offer, and its technical and ethical challenges. Here, we address the concepts of human genomic analysis and its clinical applicability for primary care providers.

  18. 76 FR 69241 - Tapered Roller Bearings and Parts Thereof, Finished or Unfinished, From the People's Republic of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-08

    ... Parts Thereof, Finished or Unfinished, From the People's Republic of China: Extension of Time Limit for... and parts thereof, finished or unfinished, (``TRBs'') from the People's Republic of China (``PRC... Revocation in Part, 75 FR 44224 (July 28, 2010). On July 13, 2011, the Department published the preliminary...

  19. Machine Learned Replacement of N-Labels for Basecalled Sequences in DNA Barcoding.

    PubMed

    Ma, Eddie Y T; Ratnasingham, Sujeevan; Kremer, Stefan C

    2018-01-01

    This study presents a machine learning method that increases the number of identified bases in Sanger Sequencing. The system post-processes a KB basecalled chromatogram. It selects a recoverable subset of N-labels in the KB-called chromatogram to replace with basecalls (A,C,G,T). An N-label correction is defined given an additional read of the same sequence, and a human finished sequence. Corrections are added to the dataset when an alignment determines the additional read and human agree on the identity of the N-label. KB must also rate the replacement with quality value of in the additional read. Corrections are only available during system training. Developing the system, nearly 850,000 N-labels are obtained from Barcode of Life Datasystems, the premier database of genetic markers called DNA Barcodes. Increasing the number of correct bases improves reference sequence reliability, increases sequence identification accuracy, and assures analysis correctness. Keeping with barcoding standards, our system maintains an error rate of percent. Our system only applies corrections when it estimates low rate of error. Tested on this data, our automation selects and recovers: 79 percent of N-labels from COI (animal barcode); 80 percent from matK and rbcL (plant barcodes); and 58 percent from non-protein-coding sequences (across eukaryotes).

  20. Percent recoveries of anthropogenic organic compounds with and without the addition of ascorbic acid to preserve finished-water samples containing free chlorine, 2004-10

    USGS Publications Warehouse

    Valder, Joshua F.; Delzer, Gregory C.; Bender, David A.; Price, Curtis V.

    2011-01-01

    This report presents finished-water matrix-spike recoveries of 270 anthropogenic organic compounds with and without the addition of ascorbic acid to preserve water samples containing free chlorine. Percent recoveries were calculated using analytical results from a study conducted during 2004-10 for the National Water-Quality Assessment (NAWQA) Program of the U.S. Geological Survey (USGS). The study was intended to characterize the effect of quenching on finished-water matrix-spike recoveries and to better understand the potential oxidation and transformation of 270 anthropogenic organic compounds. The anthropogenic organic compounds studied include those on analytical schedules 1433, 2003, 2033, 2060, 2020, and 4024 of the USGS National Water Quality Laboratory. Three types of samples were collected from 34 NAWQA locations across the Nation: (1) quenched finished-water samples (not spiked), (2) quenched finished-water matrix-spike samples, and (3) nonquenched finished-water matrix-spike samples. Percent recoveries of anthropogenic organic compounds in quenched and nonquenched finished-water matrix-spike samples are presented. Comparisons of percent recoveries between quenched and nonquenched spiked samples can be used to show how quenching affects finished-water samples. A maximum of 18 surface-water and 34 groundwater quenched finished-water matrix-spike samples paired with nonquenched finished-water matrix-spike samples were analyzed. Percent recoveries for the study are presented in two ways: (1) finished-water matrix-spike samples supplied by surface-water or groundwater, and (2) by use (or source) group category for surface-water and groundwater supplies. Graphical representations of percent recoveries for the quenched and nonquenched finished-water matrix-spike samples also are presented.

  1. Discriminative prediction of mammalian enhancers from DNA sequence

    PubMed Central

    Lee, Dongwon; Karchin, Rachel; Beer, Michael A.

    2011-01-01

    Accurately predicting regulatory sequences and enhancers in entire genomes is an important but difficult problem, especially in large vertebrate genomes. With the advent of ChIP-seq technology, experimental detection of genome-wide EP300/CREBBP bound regions provides a powerful platform to develop predictive tools for regulatory sequences and to study their sequence properties. Here, we develop a support vector machine (SVM) framework which can accurately identify EP300-bound enhancers using only genomic sequence and an unbiased set of general sequence features. Moreover, we find that the predictive sequence features identified by the SVM classifier reveal biologically relevant sequence elements enriched in the enhancers, but we also identify other features that are significantly depleted in enhancers. The predictive sequence features are evolutionarily conserved and spatially clustered, providing further support of their functional significance. Although our SVM is trained on experimental data, we also predict novel enhancers and show that these putative enhancers are significantly enriched in both ChIP-seq signal and DNase I hypersensitivity signal in the mouse brain and are located near relevant genes. Finally, we present results of comparisons between other EP300/CREBBP data sets using our SVM and uncover sequence elements enriched and/or depleted in the different classes of enhancers. Many of these sequence features play a role in specifying tissue-specific or developmental-stage-specific enhancer activity, but our results indicate that some features operate in a general or tissue-independent manner. In addition to providing a high confidence list of enhancer targets for subsequent experimental investigation, these results contribute to our understanding of the general sequence structure of vertebrate enhancers. PMID:21875935

  2. Additive manufacturing of reflective optics: evaluating finishing methods

    NASA Astrophysics Data System (ADS)

    Leuteritz, G.; Lachmayer, R.

    2018-02-01

    Individually shaped light distributions become more and more important in lighting technologies and thus the importance of additively manufactured reflectors increases significantly. The vast field of applications ranges from automotive lighting to medical imaging and bolsters the statement. However, the surfaces of additively manufactured reflectors suffer from insufficient optical properties even when manufactured using optimized process parameters for the Selective Laser Melting (SLM) process. Therefore post-process treatments of reflectors are necessary in order to further enhance their optical quality. This work concentrates on the effectiveness of post-process procedures for reflective optics. Based on already optimized aluminum reflectors, which are manufactured with a SLM machine, the parts are differently machined after the SLM process. Selected finishing methods like laser polishing, sputtering or sand blasting are applied and their effects quantified and compared. The post-process procedures are investigated on their impact on surface roughness and reflectance as well as geometrical precision. For each finishing method a demonstrator will be created and compared to a fully milled sample and among themselves. Ultimately, guidelines are developed in order to figure out the optimal treatment of additively manufactured reflectors regarding their optical and geometrical properties. Simulations of the light distributions will be validated with the developed demonstrators.

  3. Heterosis for meat quality and fatty acid profiles in crosses among Bos indicus and Bos taurus finished on pasture or grain.

    PubMed

    Gama, L T; Bressan, M C; Rodrigues, E C; Rossato, L V; Moreira, O C; Alves, S P; Bessa, R J B

    2013-01-01

    Physicochemical properties and fatty acid profiles of meat from Bos indicus, Bos taurus and crossbred B. taurus×B. indicus bullocks (n=216), finished on pasture or grain, were used to estimate the effects of heterosis. Meat quality and fatty acid profiles generally benefited with crossbreeding, but the advantages from heterosis differed among finishing systems. The Warner-Bratzler shear-force in fresh and aged meat was reduced due to heterosis in pasture-finishing, but the effect was minor under grain-finishing. With pasture-finishing, heterosis caused an increase of 5% in CLA concentration, but few other changes in fatty acid profiles. In grain-finishing, heterosis caused a reduction in intramuscular fat and cholesterol, increased amounts of PUFA, n-6 fatty acids and PUFA/SFA ratio, and a decline in atherogenic index. The Δ(9) desaturase estimated activity in crossbreds showed a behavior close to B. indicus, suggesting the existence of few loci and a dominance genetic effect on enzymes involved in fatty acid synthesis and metabolism. Copyright © 2012 Elsevier Ltd. All rights reserved.

  4. RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA

    PubMed Central

    Wright, Imogen A.; Travers, Simon A.

    2014-01-01

    The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. PMID:24861618

  5. DEVELOPMENT OF THE METAL FINISHING FACILITY RISK SCREENING TOOL (MFFRST)

    EPA Science Inventory

    Recently the US EPA completed the development of the first version of the Metal Finishing Facility Risk Screening Tool (MFFRST) and has made this product available to the general public. MFFRST calculates the air emissions from a metal plating line and determines the risk to bot...

  6. 78 FR 34985 - Tapered Roller Bearings and Parts Thereof, Finished and Unfinished From the People's Republic of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-11

    ... Parts Thereof, Finished and Unfinished From the People's Republic of China: Rescission, in Part, of... parts thereof, finished and unfinished (TRBs) from the People's Republic of China (PRC) covering the... section 771(9)(A) of the Act, as amended, Dana Off Highway Products, LLC, for the company Timken de Mexico...

  7. Analyzing and improving surface texture by dual-rotation magnetorheological finishing

    NASA Astrophysics Data System (ADS)

    Wang, Yuyue; Zhang, Yun; Feng, Zhijing

    2016-01-01

    The main advantages of magnetorheological finishing (MRF) are its high convergence rate of surface error, the ability of polishing aspheric surfaces and nearly no subsurface damage. However, common MRF produces directional surface texture due to the constant flow direction of the magnetorheological (MR) polishing fluid. This paper studies the mechanism of surface texture formation by texture modeling. Dual-rotation magnetorheological finishing (DRMRF) is presented to suppress directional surface texture after analyzing the results of the texture model for common MRF. The results of the surface texture model for DRMRF and the proposed quantitative method based on mathematical statistics indicate the effective suppression of directional surface texture. An experimental setup is developed and experiments show directional surface texture and no directional surface texture in common MRF and DRMRF, respectively. As a result, the surface roughness of DRMRF is 0.578 nm (root-mean-square value) which is lower than 1.109 nm in common MRF.

  8. The influence of cervical finish line, internal relief, and cement type on the cervical adaptation of metal crowns.

    PubMed

    Bottino, Marco Antonio; Valandro, Luiz Felipe; Buso, Leonardo; Ozcan, Mutlu

    2007-01-01

    The aim of this investigation was to evaluate the cervical adaptation of metal crowns under several conditions, namely (1) variations in the cervical finish line of the preparation, (2) application of internal relief inside the crowns, and (3) cementation using different luting materials. One hundred eighty stainless-steel master dies were prepared simulating full crown preparations: 60 in chamfer (CH), 60 in 135-degree shoulder (OB), and 60 in rounded shoulder (OR). The finish lines were machined at approximate dimensions of a molar tooth preparation (height: 5.5 mm; cervical diameter: 8 mm; occlusal diameter: 6.4 mm; taper degree: 6; and cervical finish line width: 0.8 mm). One hundred eighty corresponding copings with the same finish lines were fabricated. A 30-Microm internal relief was machined 0.5 mm above the cervical finish line in 90 of these copings. The fit of the die and the coping was measured from all specimens (L0) prior to cementation using an optical microscope. After manipulation of the 3 types of cements (zinc phosphate, glass-ionomer, and resin cement), the coping was luted on the corresponding standard master die under 5-kgf loading for 4 minutes. Vertical discrepancy was again measured (L1), and the difference between L1 and L0 indicated the cervical adaptation. Significant influence of the finish line, cement type, and internal relief was observed on the cervical adaptation (P <.001). The CH type of cervical finish line resulted in the best cervical adaptation of the metal crowns regardless of the cement type either with or without internal relief (36.6 +/- 3 to 100.8 +/- 4 Microm) (3-way analysis of variance and Tukey's test, a = .05). The use of glass-ionomer cement resulted in the least cervical discrepancy (36.6 +/- 3 to 115 +/- 4 Microm) than those of other cements (45.2 +/- 4 to 130.3 +/- 2 Microm) in all conditions. The best cervical adaptation was achieved with the chamfer type of finish line. The internal relief improved the marginal

  9. 75 FR 9391 - Tapered Roller Bearings and Parts Thereof, Finished or Unfinished, from the People's Republic of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-02

    ... Parts Thereof, Finished or Unfinished, from the People's Republic of China: Extension of Time Limit for... review of the antidumping duty order on tapered roller bearings and parts thereof, finished or unfinished... March 9, 2010. Statutory Time Limits Section 751(a)(3)(A) of the Tariff Act of 1930, as amended (``the...

  10. The association between measurements of antimicrobial use and resistance in the faeces microbiota of finisher batches.

    PubMed

    Andersen, V D; DE Knegt, L V; Munk, P; Jensen, M S; Agersø, Y; Aarestrup, F M; Vigre, H

    2017-10-01

    The objectives were to present three approaches for calculating antimicrobial (AM) use in pigs that take into account the rearing period and rearing site, and to study the association between these measurements and phenotypical resistance and abundance of resistance genes in faeces samples from 10 finisher batches. The AM use was calculated relative to the rearing period of the batches as (i) 'Finisher Unit Exposure' at unit level, (ii) 'Lifetime Exposure' at batch level and (iii) 'Herd Exposure' at herd level. A significant effect on the occurrence of tetracycline resistance measured by cultivation was identified for Lifetime Exposure for the AM class: tetracycline. Furthermore, for Lifetime Exposure for the AM classes: macrolide, broad-spectrum penicillin, sulfonamide and tetracycline use as well as Herd Unit Exposure for the AM classes: aminoglycoside, lincosamide and tetracycline use, a significant effect was observed on the occurrence of genes coding for the AM resistance classes: aminoglycoside, lincosamide, macrolide, β-lactam, sulfonamide and tetracycline. No effect was observed for Finisher Unit Exposure. Overall, the study shows that Lifetime Exposure is an efficient measurement of AM use in finisher batches, and has a significant effect on the occurrence of resistance, measured either by cultivation or metagenomics.

  11. 7 CFR 58.344 - Storage of finished product in freezer.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... maintained at −10 °F. or lower and shall be equipped to provide sufficient high velocity, air circulation for rapid freezing. After the products have been completely frozen, they may be transferred to a freezer..., if necessary, at a later time. Requirements for Finished Products Bearing USDA Official...

  12. 7 CFR 58.344 - Storage of finished product in freezer.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... maintained at −10 °F. or lower and shall be equipped to provide sufficient high velocity, air circulation for rapid freezing. After the products have been completely frozen, they may be transferred to a freezer..., if necessary, at a later time. Requirements for Finished Products Bearing USDA Official...

  13. 7 CFR 58.344 - Storage of finished product in freezer.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... maintained at −10 °F. or lower and shall be equipped to provide sufficient high velocity, air circulation for rapid freezing. After the products have been completely frozen, they may be transferred to a freezer..., if necessary, at a later time. Requirements for Finished Products Bearing USDA Official...

  14. 7 CFR 58.344 - Storage of finished product in freezer.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... maintained at −10 °F. or lower and shall be equipped to provide sufficient high velocity, air circulation for rapid freezing. After the products have been completely frozen, they may be transferred to a freezer..., if necessary, at a later time. Requirements for Finished Products Bearing USDA Official...

  15. 7 CFR 58.344 - Storage of finished product in freezer.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... maintained at −10 °F. or lower and shall be equipped to provide sufficient high velocity, air circulation for rapid freezing. After the products have been completely frozen, they may be transferred to a freezer..., if necessary, at a later time. Requirements for Finished Products Bearing USDA Official...

  16. Robust temporal alignment of multimodal cardiac sequences

    NASA Astrophysics Data System (ADS)

    Perissinotto, Andrea; Queirós, Sandro; Morais, Pedro; Baptista, Maria J.; Monaghan, Mark; Rodrigues, Nuno F.; D'hooge, Jan; Vilaça, João. L.; Barbosa, Daniel

    2015-03-01

    Given the dynamic nature of cardiac function, correct temporal alignment of pre-operative models and intraoperative images is crucial for augmented reality in cardiac image-guided interventions. As such, the current study focuses on the development of an image-based strategy for temporal alignment of multimodal cardiac imaging sequences, such as cine Magnetic Resonance Imaging (MRI) or 3D Ultrasound (US). First, we derive a robust, modality-independent signal from the image sequences, estimated by computing the normalized cross-correlation between each frame in the temporal sequence and the end-diastolic frame. This signal is a resembler for the left-ventricle (LV) volume curve over time, whose variation indicates different temporal landmarks of the cardiac cycle. We then perform the temporal alignment of these surrogate signals derived from MRI and US sequences of the same patient through Dynamic Time Warping (DTW), allowing to synchronize both sequences. The proposed framework was evaluated in 98 patients, which have undergone both 3D+t MRI and US scans. The end-systolic frame could be accurately estimated as the minimum of the image-derived surrogate signal, presenting a relative error of 1.6 +/- 1.9% and 4.0 +/- 4.2% for the MRI and US sequences, respectively, thus supporting its association with key temporal instants of the cardiac cycle. The use of DTW reduces the desynchronization of the cardiac events in MRI and US sequences, allowing to temporally align multimodal cardiac imaging sequences. Overall, a generic, fast and accurate method for temporal synchronization of MRI and US sequences of the same patient was introduced. This approach could be straightforwardly used for the correct temporal alignment of pre-operative MRI information and intra-operative US images.

  17. Relationship between influence function accuracy and polishing quality in magnetorheological finishing

    NASA Astrophysics Data System (ADS)

    Schinhaerl, Markus; Schneider, Florian; Rascher, Rolf; Vogt, Christian; Sperber, Peter

    2010-10-01

    Magnetorheological finishing is a typical commercial application of a computer-controlled polishing process in the manufacturing of precision optical surfaces. Precise knowledge of the material removal characteristic of the polishing tool (influence function) is essential for controlling the material removal on the workpiece surface by the dwell time method. Results from the testing series with magnetorheological finishing have shown that a deviation of only 5% between the actual material removal characteristic of the polishing tool and that represented by the influence function caused a considerable reduction in the polishing quality. The paper discusses reasons for inaccuracies in the influence function and the effects on the polishing quality. The generic results of this research serve for the development of improved polishing strategies, and may be used in alternative applications of computer-controlled polishing processes that quantify the material removal characteristic by influence functions.

  18. [Factors of the rapid startup for nitrosation in sequencing batch reactor].

    PubMed

    Li, Dong; Tao, Xiao-Xiao; Li, Zhan; Wang, Jun-An; Zhang, Jie

    2011-08-01

    The approach and factors for realizing the rapid startup of nitrosation were researched at the low level of dissolved oxygen (DO) in sequencing batch reactor (SBR). The main parameters of the reactor were controlled as follows: DO were 0.15-0.40 mg/L, pH values kept from 7.52 to 8.30, temperature maintained at 22.3-27.1 degrees C, and time of aeration was 8 hours. The purpose of rapid startup for nitrosation was achieved after 57 cycles (36 d) with the alternative influent of high and low ammonium wastewater (the mean values were 245.28 mg/L and 58.08 mg/L respectively) in a SBR, and the nitrosation rate was even 100%. Factors of accumulation of nitrite were investigated and the effects of DO and pH were analyzed during the startup for nitrosation. The results showed that it could improve the efficiency of nitrosation when DO concentration was increased appropriately. The activity of nitrite oxidizing bacteria (NOB) was recovered gradually when DO was higher than 0.72 mg/L. The key factor of controlling nitrosation reaction was the concentration of free ammonia (FA), while the final factor was the concentration of DO. pH was a desired controlling parameter to show the end of nitrification in a SBR cycle, while DO concentration did not indicate the finishing of SBR nitrification accurately because it increased rapidly before ammonia nitrogen was oxidized absolutely.

  19. Corrosion of RoHS-Compliant Surface Finishes in Corrosive Mixed Flowing Gas Environments

    NASA Astrophysics Data System (ADS)

    Hannigan, K.; Reid, M.; Collins, M. N.; Dalton, E.; Xu, C.; Wright, B.; Demirkan, K.; Opila, R. L.; Reents, W. D.; Franey, J. P.; Fleming, D. A.; Punch, J.

    2012-03-01

    Recently, the corrosion resistance of printed wiring board (PWB) finishes has generated considerable interest due to field failures observed in various parts of the world. This study investigates the corrosion issues associated with the different lead-free PWB surface finishes. Corrosion products on various PWB surface finishes generated in mixed flowing gas (MFG) environments were studied, and analysis techniques such as scanning electron microscopy, energy-dispersive x-ray, x-ray diffraction, focused ion beam, and scanning Auger microscopy were used to quantify the corrosion layer thickness and determine the composition of corrosion products. The corrosion on organic solderability preservative samples shows similar corrosion products to bare copper and is mainly due to direct attack of copper traces by corrosive gases. The corrosion on electroless nickel immersion gold occurs primarily through the porosity in the film and is accelerated by the galvanic potential between gold and copper; similar results were observed on immersion silver. Immersion tin shows excellent corrosion resistance due to its inherent corrosion resistance in the MFG environment as well as the opposite galvanic potential between tin and copper compared with gold or silver and copper.

  20. 40 CFR 410.60 - Applicability; description of the carpet finishing subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 28 2010-07-01 2010-07-01 true Applicability; description of the carpet finishing subcategory. 410.60 Section 410.60 Protection of Environment ENVIRONMENTAL PROTECTION..., carbonizing, fulling, dyeing, printing, resin treatment, waterproofing, flameproofing, soil repellency...

  1. Usefulness of food chain information provided by Dutch finishing pig producers to control antibiotic residues in pork.

    PubMed

    van Wagenberg, Coen P A; Backus, Gé B C; van der Vorst, Jack G A J; Urlings, Bert A P

    2012-11-01

    The EU prescribes that food business operators must use food chain information to assist in food safety control. This study analyses usefulness of food chain information about antibiotic usage covering the 60-day period prior to delivery of pigs to slaughter in the control of antibiotic residues in pork. A dataset with 479 test results for antibiotic residues in tissue samples of finishing pigs delivered to a Dutch slaughter company was linked to information provided by pig producers about antibiotic usage in these finishing pigs. Results show that twice as many producers reported using antibiotics in the group of 82 producers with antibiotic residues (11.0%) compared to the group without antibiotic residues (5.5%) (p=0.0686). For 89% of consignments with a finishing pig with antibiotic residues, the producer reported 'did not use antibiotics'. Food chain information about antibiotic usage provided by Dutch pig producers was no guarantee for absence of antibiotic residues in delivered finishing pigs. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. The effects of finishing diet and postmortem ageing on the eating quality of the M. longissimus thoracis of electrically stimulated Brahman steer carcasses.

    PubMed

    Bruce, H L; Stark, J L; Beilken, S L

    2004-06-01

    Beef from cattle finished on grass will be of similar quality to that from cattle finished on grain when their carcasses are processed using best practice protocols. To test this hypothesis, carcasses of twenty Brahman steers, finished to 400 kg live weight on either Buffel grass pasture (n=10) or grain (n=10), were electrically stimulated with 400 V for 50 s 45 min postmortem, and their beef quality assessed 1 and 14 days postmortem. Hot weight, rump subcutaneous fat thickness and animal rate of growth in the 205 days preceding slaughter were recorded for each carcass as potential influences on beef quality. Quality of the M. longissimus thoracis (LT) at 1 and 14 days postmortem was evaluated using peak Warner-Bratzler shear force, compression, pH, cooking loss and taste panel acceptability, as well as by moisture and crude fat contents measured at 1 day postmortem. Results showed that steers finished on pasture grew the slowest and had the least subcutaneous fat at the same carcass weight. LT from carcasses of steers finished on pasture also had the shortest mean sarcomere lengths, suggesting these muscles may have been cold-affected, but there was no effect of diet on peak shear force. LT from carcasses of steers finished on pasture had the highest mean compression value, possibly because of increased collagen cross-linking associated with slow growth or increased exercise. Ageing significantly decreased LT peak shear force and compression values and increased cooking loss, L (∗), a (∗) and b (∗) values. Taste panellists rated the aged, grass-finished beef the most tender and the best quality; however, the taste panel in this study may have favoured LT from grass-finished steers because it was significantly juicier than LT from the grain-finished steer carcasses. These results indicated that carcass composition and processing conditions interact to exert a greater effect on LT toughness and sensory acceptability than finishing diet. Ageing LT from steers

  3. Introduction to Concrete Finishing. Instructor Edition. Introduction to Construction Series.

    ERIC Educational Resources Information Center

    Oklahoma State Dept. of Vocational and Technical Education, Stillwater. Curriculum and Instructional Materials Center.

    This instructor's guide contains the materials required to teach a competency-based introductory course in concrete finishing to students who have chosen to explore careers in construction. The following topics are covered in the course's three instructional units: concrete materials, concrete tools, and applied skills. Each unit contains some or…

  4. 21 CFR 212.70 - What controls and acceptance criteria must I have for my finished PET drug products?

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... for my finished PET drug products? 212.70 Section 212.70 Food and Drugs FOOD AND DRUG ADMINISTRATION... What controls and acceptance criteria must I have for my finished PET drug products? (a) Specifications. You must establish specifications for each PET drug product, including criteria for determining...

  5. SORBENTS FOR FLUORIDE, METAL FINISHING, AND PETROLEUM SLUDGE LEACHATE CONTAMINANT CONTROL

    EPA Science Inventory

    This report covers the initial laboratory studies carried out to identify the most promising sorbents that may be used to significantly reduce the concentration of measurable contaminant in calcium fluoride sludge leachate, metal finishing sludge leachate, and petroleum sludge le...

  6. Understanding and reduction of defects on finished EUV masks

    NASA Astrophysics Data System (ADS)

    Liang, Ted; Sanchez, Peter; Zhang, Guojing; Shu, Emily; Nagpal, Rajesh; Stivers, Alan

    2005-05-01

    To reduce the risk of EUV lithography adaptation for the 32nm technology node in 2009, Intel has operated a EUV mask Pilot Line since early 2004. The Pilot Line integrates all the necessary process modules including common tool sets shared with current photomask production as well as EUV specific tools. This integrated endeavor ensures a comprehensive understanding of any issues, and development of solutions for the eventual fabrication of defect-free EUV masks. Two enabling modules for "defect-free" masks are pattern inspection and repair, which have been integrated into the Pilot Line. This is the first time we are able to look at real defects originated from multilayer blanks and patterning process on finished masks over entire mask area. In this paper, we describe our efforts in the qualification of DUV pattern inspection and electron beam mask repair tools for Pilot Line operation, including inspection tool sensitivity, defect classification and characterization, and defect repair. We will discuss the origins of each of the five classes of defects as seen by DUV pattern inspection tool on finished masks, and present solutions of eliminating and mitigating them.

  7. Simple chained guide trees give high-quality protein multiple sequence alignments

    PubMed Central

    Boyce, Kieran; Sievers, Fabian; Higgins, Desmond G.

    2014-01-01

    Guide trees are used to decide the order of sequence alignment in the progressive multiple sequence alignment heuristic. These guide trees are often the limiting factor in making large alignments, and considerable effort has been expended over the years in making these quickly or accurately. In this article we show that, at least for protein families with large numbers of sequences that can be benchmarked with known structures, simple chained guide trees give the most accurate alignments. These also happen to be the fastest and simplest guide trees to construct, computationally. Such guide trees have a striking effect on the accuracy of alignments produced by some of the most widely used alignment packages. There is a marked increase in accuracy and a marked decrease in computational time, once the number of sequences goes much above a few hundred. This is true, even if the order of sequences in the guide tree is random. PMID:25002495

  8. Sequencing, annotation and comparative analysis of nine BACs of giant panda (Ailuropoda melanoleuca).

    PubMed

    Zheng, Yang; Cai, Jing; Li, JianWen; Li, Bo; Lin, Runmao; Tian, Feng; Wang, XiaoLing; Wang, Jun

    2010-01-01

    A 10-fold BAC library for giant panda was constructed and nine BACs were selected to generate finish sequences. These BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of giant panda newly generated by the Illumina GA sequencing technology. Complete sanger sequencing, assembly, annotation and comparative analysis were carried out on the selected BACs of a joint length 878 kb. Homologue search and de novo prediction methods were used to annotate genes and repeats. Twelve protein coding genes were predicted, seven of which could be functionally annotated. The seven genes have an average gene size of about 41 kb, an average coding size of about 1.2 kb and an average exon number of 6 per gene. Besides, seven tRNA genes were found. About 27 percent of the BAC sequence is composed of repeats. A phylogenetic tree was constructed using neighbor-join algorithm across five species, including giant panda, human, dog, cat and mouse, which reconfirms dog as the most related species to giant panda. Our results provide detailed sequence and structure information for new genes and repeats of giant panda, which will be helpful for further studies on the giant panda.

  9. Surface finish of resin-modified and highly viscous glass ionomer cements produced by new one-step systems.

    PubMed

    Yap, Adrian U J; Ng, J J; Yap, S H; Teo, C K

    2004-01-01

    This study investigated the surface finish of resin-modified (Fuji II LC, GC) and highly viscous (Fuji IX GP Fast, GC) glass ionomer cements after treatment with three one-step finishing/polishing systems (One-Gloss [OG], Shofu; Pogo [PG], Dentsply; Sof-Lex Brush [SB], 3M-ESPE). The surface roughness obtained was compared to that using a matrix strip [MS], a two-step rubber abrasive (CompoSite [CS], Shofu) and a graded abrasive disk (Super Snap [SS], Shofu) system. Eight specimens (3-mm long x 3-mm wide x 2-mm deep) of each material were made for the various treatment groups. With the exception of the MS group, all groups were roughened with 320 grit grinding paper using a lapping device prior to finishing/polishing with the different systems. The mean surface roughness (microm) was measured with a profilometer. Data was subjected to ANOVA/Scheffe's tests at significance level 0.05. Mean Ra ranged from 0.13 to 1.04 microm for Fuji II LC and 0.14 to 0.81 for Fuji IX GP. For both materials, the smoothest surface was obtained with MS and the roughest with OG. Depending on the materials, the surface finish produced by PG and SB was superior or comparable to that obtained with CS and SS. The effectiveness of one-step systems, when used to finish/polish resin-modified and highly viscous glass ionomer cements, is product dependent.

  10. RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA.

    PubMed

    Wright, Imogen A; Travers, Simon A

    2014-07-01

    The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. SURFACE FINISHES ON STAINLESS STEEL REDUCE BACTERIAL ATTACHMENT AND EARLY BIOFILM FORMATION: SCANNING ELECTRON AND ATOMIC FORCE MICROSCOPY STUDY

    EPA Science Inventory

    Three common finishing treatments of stainless steel that are used for equipment during poultry processing were tested for resistance to bacterial contamination. Methods were developed to measure attached bacteria and to identify factors that make surface finishes susceptible or ...

  12. 21 CFR 212.70 - What controls and acceptance criteria must I have for my finished PET drug products?

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... for my finished PET drug products? 212.70 Section 212.70 Food and Drugs FOOD AND DRUG ADMINISTRATION... acceptance criteria must I have for my finished PET drug products? (a) Specifications. You must establish specifications for each PET drug product, including criteria for determining identity, strength, quality, purity...

  13. 21 CFR 212.70 - What controls and acceptance criteria must I have for my finished PET drug products?

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... for my finished PET drug products? 212.70 Section 212.70 Food and Drugs FOOD AND DRUG ADMINISTRATION... acceptance criteria must I have for my finished PET drug products? (a) Specifications. You must establish specifications for each PET drug product, including criteria for determining identity, strength, quality, purity...

  14. 21 CFR 212.70 - What controls and acceptance criteria must I have for my finished PET drug products?

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... for my finished PET drug products? 212.70 Section 212.70 Food and Drugs FOOD AND DRUG ADMINISTRATION... acceptance criteria must I have for my finished PET drug products? (a) Specifications. You must establish specifications for each PET drug product, including criteria for determining identity, strength, quality, purity...

  15. 21 CFR 212.70 - What controls and acceptance criteria must I have for my finished PET drug products?

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... for my finished PET drug products? 212.70 Section 212.70 Food and Drugs FOOD AND DRUG ADMINISTRATION... acceptance criteria must I have for my finished PET drug products? (a) Specifications. You must establish specifications for each PET drug product, including criteria for determining identity, strength, quality, purity...

  16. Final progress report, Construction of a genome-wide highly characterized clone resource for genome sequencing

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nierman, William C.

    At TIGR, the human Bacterial Artificial Chromosome (BAC) end sequencing and trimming were with an overall sequencing success rate of 65%. CalTech human BAC libraries A, B, C and D as well as Roswell Park Cancer Institute's library RPCI-11 were used. To date, we have generated >300,000 end sequences from >186,000 human BAC clones with an average read length {approx}460 bp for a total of 141 Mb covering {approx}4.7% of the genome. Over sixty percent of the clones have BAC end sequences (BESs) from both ends representing over five-fold coverage of the genome by the paired-end clones. The average phredmore » Q20 length is {approx}400 bp. This high accuracy makes our BESs match the human finished sequences with an average identity of 99% and a match length of 450 bp, and a frequency of one match per 12.8 kb contig sequence. Our sample tracking has ensured a clone tracking accuracy of >90%, which gives researchers a high confidence in (1) retrieving the right clone from the BA C libraries based on the sequence matches; and (2) building a minimum tiling path of sequence-ready clones across the genome and genome assembly scaffolds.« less

  17. Rheological properties of magnetorheological fluid and its finishing application on large aperture BK7 glass

    NASA Astrophysics Data System (ADS)

    Wang, C.; Wei, Q. L.; Huang, W.; Luo, Q.; He, J. G.; Tang, G. P.

    2013-07-01

    The CeO2 nanoparticles with modified surface and mean sizes distribution during 107.0 nm - 127.7 nm are used as abrasive in magnetorheological finishing (MRF) fluid. The slow rotation dispersion without shearing thinning is better than fast emulsification dispersion. Steady D-shaped finishing spots and high quality precise processing surface with PV=0.1λ, GRMS=0.002λ/cm, Rq=0.83 nm are obtained on a 435 mm x 435 mm BK7 glass under self-developed MRF apparatus.

  18. DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

    PubMed

    Kelly, Steven; Maini, Philip K

    2013-01-01

    The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

  19. Protein Structure Determination using Metagenome sequence data

    PubMed Central

    Ovchinnikov, Sergey; Park, Hahnbeom; Varghese, Neha; Huang, Po-Ssu; Pavlopoulos, Georgios A.; Kim, David E.; Kamisetty, Hetunandan; Kyrpides, Nikos C.; Baker, David

    2017-01-01

    Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families, and that metagenome sequence data more than triples the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact based structure matching and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the PDB. This approach provides the representative models for large protein families originally envisioned as the goal of the protein structure initiative at a fraction of the cost. PMID:28104891

  20. 71. September 1913 "No. 113. Some of the finished bitulithic ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    71. September 1913 "No. 113. Some of the finished bitulithic or bituminous macadam road after being sanded and rolled, in the foreground. In the middle distance men are applying oil to incomplete section. In the far distance, roller is working on foundation course." - Crater Lake National Park Roads, Klamath Falls, Klamath County, OR