Science.gov

Sample records for accurate finished sequence

  1. Sequence finishing and mapping of Drosophila melanogasterheterochromatin

    SciTech Connect

    Hoskins, Roger A.; Carlson, Joseph W.; Kennedy, Cameron; Acevedo,David; Evans-Holm, Martha; Frise, Erwin; Wan, Kenneth H.; Park, Soo; Mendez-Lago, Maria; Rossi, Fabrizio; Villasante, Alfredo; Dimitri,Patrizio; Karpen, Gary H.; Celniker, Susan E.

    2007-06-15

    Genome sequences for most metazoans are incomplete due tothe presence of repeated DNA in the pericentromeric heterochromatin. Theheterochromatic regions of D. melanogaster contain 20 Mb of sequenceamenable to mapping, sequence assembly and finishing. Here we describethe generation of 15 Mb of finished or improved heterochromatic sequenceusing available clone resources and assembly and mapping methods. We alsoconstructed a BAC-based physical map that spans approximately 13 Mb ofthe pericentromeric heterochromatin, and a cytogenetic map that positionsapproximately 11 Mb of BAC contigs and sequence scaffolds in specificchromosomal locations. The integrated sequence assembly and maps greatlyimprove our understanding of the structure and composition of this poorlyunderstood fraction of a metazoan genome and provide a framework forfunctional analyses.

  2. Accurately measuring dynamic coefficient of friction in ultraform finishing

    NASA Astrophysics Data System (ADS)

    Briggs, Dennis; Echaves, Samantha; Pidgeon, Brendan; Travis, Nathan; Ellis, Jonathan D.

    2013-09-01

    UltraForm Finishing (UFF) is a deterministic sub-aperture computer numerically controlled grinding and polishing platform designed by OptiPro Systems. UFF is used to grind and polish a variety of optics from simple spherical to fully freeform, and numerous materials from glasses to optical ceramics. The UFF system consists of an abrasive belt around a compliant wheel that rotates and contacts the part to remove material. This work aims to accurately measure the dynamic coefficient of friction (μ), how it changes as a function of belt wear, and how this ultimately affects material removal rates. The coefficient of friction has been examined in terms of contact mechanics and Preston's equation to determine accurate material removal rates. By accurately predicting changes in μ, polishing iterations can be more accurately predicted, reducing the total number of iterations required to meet specifications. We have established an experimental apparatus that can accurately measure μ by measuring triaxial forces during translating loading conditions or while manufacturing the removal spots used to calculate material removal rates. Using this system, we will demonstrate μ measurements for UFF belts during different states of their lifecycle and assess the material removal function from spot diagrams as a function of wear. Ultimately, we will use this system for qualifying belt-wheel-material combinations to develop a spot-morphing model to better predict instantaneous material removal functions.

  3. Finishing The Euchromatic Sequence Of The Human Genome

    SciTech Connect

    Rubin, Edward M.; Lucas, Susan; Richardson, Paul; Rokhsar, Daniel; Pennacchio, Len

    2004-09-07

    The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process.The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers {approx}99% of the euchromatic genome and is accurate to an error rate of {approx}1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number,birth and death. Notably, the human genome seems to encode only20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead.

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

    ScienceCinema

    Fitzsimmons, Michael [LANL

    2016-07-12

    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.

  5. Almost finished: the complete genome sequence of Mycosphaerella graminicola

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mycosphaerella graminicola causes septoria tritici blotch of wheat. An 8.9x shotgun sequence of bread wheat strain IPO323 was generated through the Community Sequencing Program of the U.S. Department of Energy’s Joint Genome Institute (JGI), and was finished at the Stanford Human Genome Center. The ...

  6. Finished Genome Sequence of the Unicellular Cyanobacterium Synechocystis sp. Strain PCC 6714.

    PubMed

    Kopf, Matthias; Klähn, Stephan; Voss, Björn; Stüber, Kurt; Huettel, Bruno; Reinhardt, Richard; Hess, Wolfgang R

    2014-07-31

    Synechocystis sp. strain PCC 6714 is a unicellular cyanobacterium closely related to the popular model organism Synechocystis sp. strain PCC 6803. A combination of PacBio SMRT and Illumina GAIIx data results in a highly accurate finished genome sequence that provides a reliable resource for further comparative analyses.

  7. The finished DNA sequence of human chromosome 12.

    PubMed

    Scherer, Steven E; Muzny, Donna M; Buhay, Christian J; Chen, Rui; Cree, Andrew; Ding, Yan; Dugan-Rocha, Shannon; Gill, Rachel; Gunaratne, Preethi; Harris, R Alan; Hawes, Alicia C; Hernandez, Judith; Hodgson, Anne V; Hume, Jennifer; Jackson, Andrew; Khan, Ziad Mohid; Kovar-Smith, Christie; Lewis, Lora R; Lozado, Ryan J; Metzker, Michael L; Milosavljevic, Aleksandar; Miner, George R; Montgomery, Kate T; Morgan, Margaret B; Nazareth, Lynne V; Scott, Graham; Sodergren, Erica; Song, Xing-Zhi; Steffen, David; Lovering, Ruth C; Wheeler, David A; Worley, Kim C; Yuan, Yi; Zhang, Zhengdong; Adams, Charles Q; Ansari-Lari, M Ali; Ayele, Mulu; Brown, Mary J; Chen, Guan; Chen, Zhijian; Clerc-Blankenburg, Kerstin P; Davis, Clay; Delgado, Oliver; Dinh, Huyen H; Draper, Heather; Gonzalez-Garay, Manuel L; Havlak, Paul; Jackson, Laronda R; Jacob, Leni S; Kelly, Susan H; Li, Li; Li, Zhangwan; Liu, Jing; Liu, Wen; Lu, Jing; Maheshwari, Manjula; Nguyen, Bao-Viet; Okwuonu, Geoffrey O; Pasternak, Shiran; Perez, Lesette M; Plopper, Farah J H; Santibanez, Jireh; Shen, Hua; Tabor, Paul E; Verduzco, Daniel; Waldron, Lenee; Wang, Qiaoyan; Williams, Gabrielle A; Zhang, Jingkun; Zhou, Jianling; Allen, Carlana C; Amin, Anita G; Anyalebechi, Vivian; Bailey, Michael; Barbaria, Joseph A; Bimage, Kesha E; Bryant, Nathaniel P; Burch, Paula E; Burkett, Carrie E; Burrell, Kevin L; Calderon, Eliana; Cardenas, Veronica; Carter, Kelvin; Casias, Kristal; Cavazos, Iracema; Cavazos, Sandra R; Ceasar, Heather; Chacko, Joseph; Chan, Sheryl N; Chavez, Dean; Christopoulos, Constantine; Chu, Joseph; Cockrell, Raynard; Cox, Caroline D; Dang, Michelle; Dathorne, Stephanie R; David, Robert; Davis, Candi Mon'Et; Davy-Carroll, Latarsha; Deshazo, Denise R; Donlin, Jeremy E; D'Souza, Lisa; Eaves, Kristy A; Egan, Amy; Emery-Cohen, Alexandra J; Escotto, Michael; Flagg, Nicole; Forbes, Lisa D; Gabisi, Abdul M; Garza, Melissa; Hamilton, Cerissa; Henderson, Nicholas; Hernandez, Omar; Hines, Sandra; Hogues, Marilyn E; Huang, Mei; Idlebird, DeVincent G; Johnson, Rudy; Jolivet, Angela; Jones, Sally; Kagan, Ryan; King, Laquisha M; Leal, Belita; Lebow, Heather; Lee, Sandra; LeVan, Jaclyn M; Lewis, Lakeshia C; London, Pamela; Lorensuhewa, Lorna M; Loulseged, Hermela; Lovett, Demetria A; Lucier, Alice; Lucier, Raymond L; Ma, Jie; Madu, Renita C; Mapua, Patricia; Martindale, Ashley D; Martinez, Evangelina; Massey, Elizabeth; Mawhiney, Samantha; Meador, Michael G; Mendez, Sylvia; Mercado, Christian; Mercado, Iracema C; Merritt, Christina E; Miner, Zachary L; Minja, Emmanuel; Mitchell, Teresa; Mohabbat, Farida; Mohabbat, Khatera; Montgomery, Baize; Moore, Niki; Morris, Sidney; Munidasa, Mala; Ngo, Robin N; Nguyen, Ngoc B; Nickerson, Elizabeth; Nwaokelemeh, Ogechi O; Nwokenkwo, Stanley; Obregon, Melissa; Oguh, Maryann; Oragunye, Njideka; Oviedo, Rodolfo J; Parish, Bridgette J; Parker, David N; Parrish, Julia; Parks, Kenya L; Paul, Heidie A; Payton, Brett A; Perez, Agapito; Perrin, William; Pickens, Adam; Primus, Eltrick L; Pu, Ling-Ling; Puazo, Maria; Quiles, Miyo M; Quiroz, Juana B; Rabata, Dina; Reeves, Kacy; Ruiz, San Juana; Shao, Hongmei; Sisson, Ida; Sonaike, Titilola; Sorelle, Richard P; Sutton, Angelica E; Svatek, Amanda F; Svetz, Leah Anne; Tamerisa, Kavitha S; Taylor, Tineace R; Teague, Brian; Thomas, Nicole; Thorn, Rachel D; Trejos, Zulma Y; Trevino, Brenda K; Ukegbu, Ogechi N; Urban, Jeremy B; Vasquez, Lydia I; Vera, Virginia A; Villasana, Donna M; Wang, Ling; Ward-Moore, Stephanie; Warren, James T; Wei, Xuehong; White, Flower; Williamson, Angela L; Wleczyk, Regina; Wooden, Hailey S; Wooden, Steven H; Yen, Jennifer; Yoon, Lillienne; Yoon, Vivienne; Zorrilla, Sara E; Nelson, David; Kucherlapati, Raju; Weinstock, George; Gibbs, Richard A

    2006-03-16

    Human chromosome 12 contains more than 1,400 coding genes and 487 loci that have been directly implicated in human disease. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome. Here we present the finished sequence of human chromosome 12, which has been finished to high quality and spans approximately 132 megabases, representing approximately 4.5% of the human genome. Alignment of the human chromosome 12 sequence across vertebrates reveals the origin of individual segments in chicken, and a unique history of rearrangement through rodent and primate lineages. The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents.

  8. Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the "Finished" C. elegans Genome.

    PubMed

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

    2015-06-03

    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.

  9. Obtaining accurate translations from expressed sequence tags.

    PubMed

    Wasmuth, James; Blaxter, Mark

    2009-01-01

    The genomes of an increasing number of species are being investigated through the generation of expressed sequence tags (ESTs). However, ESTs are prone to sequencing errors and typically define incomplete transcripts, making downstream annotation difficult. Annotation would be greatly improved with robust polypeptide translations. Many current solutions for EST translation require a large number of full-length gene sequences for training purposes, a resource that is not available for the majority of EST projects. As part of our ongoing EST programs investigating these "neglected" genomes, we have developed a polypeptide prediction pipeline, prot4EST. It incorporates freely available software to produce final translations that are more accurate than those derived from any single method. We describe how this integrated approach goes a long way to overcoming the deficit in training data.

  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)

    ScienceCinema

    Yin, Shuangye (Broad Institute)

    2016-07-12

    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. 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)

    SciTech Connect

    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.

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

    ScienceCinema

    Athavale, Ajay [Monsanto

    2016-07-12

    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.

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

    SciTech Connect

    Athavale, Ajay

    2012-06-01

    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.

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

    ScienceCinema

    McMahon, Ben [LANL

    2016-07-12

    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.

  15. Optimal arbitrarily accurate composite pulse sequences

    NASA Astrophysics Data System (ADS)

    Low, Guang Hao; Yoder, Theodore J.; Chuang, Isaac L.

    2014-02-01

    Implementing a single-qubit unitary is often hampered by imperfect control. Systematic amplitude errors ɛ, caused by incorrect duration or strength of a pulse, are an especially common problem. But a sequence of imperfect pulses can provide a better implementation of a desired operation, as compared to a single primitive pulse. We find optimal pulse sequences consisting of L primitive π or 2π rotations that suppress such errors to arbitrary order O (ɛn) on arbitrary initial states. Optimality is demonstrated by proving an L =O(n) lower bound and saturating it with L =2n solutions. Closed-form solutions for arbitrary rotation angles are given for n =1,2,3,4. Perturbative solutions for any n are proven for small angles, while arbitrary angle solutions are obtained by analytic continuation up to n =12. The derivation proceeds by a novel algebraic and nonrecursive approach, in which finding amplitude error correcting sequences can be reduced to solving polynomial equations.

  16. Optimal arbitrarily accurate composite pulse sequences

    NASA Astrophysics Data System (ADS)

    Low, Guang Hao; Yoder, Theodore

    2014-03-01

    Implementing a single qubit unitary is often hampered by imperfect control. Systematic amplitude errors ɛ, caused by incorrect duration or strength of a pulse, are an especially common problem. But a sequence of imperfect pulses can provide a better implementation of a desired operation, as compared to a single primitive pulse. We find optimal pulse sequences consisting of L primitive π or 2 π rotations that suppress such errors to arbitrary order (ɛn) on arbitrary initial states. Optimality is demonstrated by proving an L = (n) lower bound and saturating it with L = 2 n solutions. Closed-form solutions for arbitrary rotation angles are given for n = 1 , 2 , 3 , 4 . Perturbative solutions for any n are proven for small angles, while arbitrary angle solutions are obtained by analytic continuation up to n = 12 . The derivation proceeds by a novel algebraic and non-recursive approach, in which finding amplitude error correcting sequences can be reduced to solving polynomial equations.

  17. Standard finishing categories for high-throughput sequencing of viral genomes.

    PubMed

    Ladner, J T; Kuhn, J H; Palacios, G

    2016-04-01

    Viral genome sequencing has become the cornerstone of almost all aspects of virology. In particular, high-throughput, next-generation viral genome sequencing has become an integral part of molecular epidemiological investigations into outbreaks of viral disease, such as the recent outbreaks of Middle Eastern respiratory syndrome, Ebola virus disease and Zika virus infection. Multiple institutes have acquired the expertise and necessary infrastructure to perform such investigations, as evidenced by the accumulation of thousands of novel viral sequences over progressively shorter time periods. The authors recently proposed a nomenclature comprised of five high-throughput sequencing standard categories to describe the quality of determined viral genome sequences. These five categories (standard draft, high quality, coding complete, complete and finished) cover all levels of viral genome finishing and can be applied to sequences determined by any technology platform or assembly technique.

  18. Finished Genome Sequences of Xanthomonas fragariae, the Cause of Bacterial Angular Leaf Spot of Strawberry

    PubMed Central

    Henry, Peter M.

    2016-01-01

    Xanthomonas fragariae is a foliar pathogen of strawberry that is of significant concern to nursery production of strawberry transplants and field production of strawberry fruit. Long-read sequencing was employed to generate finished genomes for two isolates (each with one chromosome and two plasmids) from symptomatic plants in northern California. PMID:27834715

  19. Library preparation for highly accurate population sequencing of RNA viruses

    PubMed Central

    Acevedo, Ashley; Andino, Raul

    2015-01-01

    Circular resequencing (CirSeq) is a novel technique for efficient and highly accurate next-generation sequencing (NGS) of RNA virus populations. The foundation of this approach is the circularization of fragmented viral RNAs, which are then redundantly encoded into tandem repeats by ‘rolling-circle’ reverse transcription. When sequenced, the redundant copies within each read are aligned to derive a consensus sequence of their initial RNA template. This process yields sequencing data with error rates far below the variant frequencies observed for RNA viruses, facilitating ultra-rare variant detection and accurate measurement of low-frequency variants. Although library preparation takes ~5 d, the high-quality data generated by CirSeq simplifies downstream data analysis, making this approach substantially more tractable for experimentalists. PMID:24967624

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

    SciTech Connect

    Campbell, Catherine

    2012-06-01

    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.

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

    ScienceCinema

    Campbell, Catherine [Noblis

    2016-07-12

    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.

  2. Gap Closing/Finishing by Targeted Genomic Region Enrichment and Sequencing

    SciTech Connect

    Singh, Kanwar; Froula, Jeff; Trice, Hope; Pennacchio, Len A.; Chen, Feng

    2010-05-27

    Gap Closing/Finishing of draft genome assemblies is a labor and cost intensive process where several rounds of repetitious amplification and sequencing are required. Here we demonstrate a high throughput procedure where custom primers flanking gaps in draft genomes are designed. Primer libraries containing up to 4,000 unique pairs in independent droplets are merged with a fragmented genomic template. From this millions of picoliter scale droplets are formed, each one being the functional equivalent of an individual PCR reaction. The PCR products are concatenated and sequenced by Illumina which is then assembled and used for gap closure. Here we present an overall experimental strategy, primer design algorithm and initial results.

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

    ScienceCinema

    Crow, John [National Center for Genome Resources

    2016-07-12

    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.

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

    SciTech Connect

    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.

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

    ScienceCinema

    Sexton, David [Baylor

    2016-07-12

    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.

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

    ScienceCinema

    Smith, Todd [PerkinElmer Omics Laboratory

    2016-07-12

    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.

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

    SciTech Connect

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

    SciTech Connect

    Gardner, S N; Lam, M W; Smith, J R; Torres, C L; Slezak, T R

    2004-10-29

    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 is 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{sup -3}-10{sup -5} ({approx} 8x coverage) of target organisms is suitable for DNA signature prediction. Low quality draft with error rates of {approx} 1% (3x to 6x 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.

  9. 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.

  10. Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4.

    PubMed

    Neupane, Saraswoti; Goodwin, Lynne A; Högberg, Nils; Kyrpides, Nikos C; Alström, Sadhna; Bruce, David; Quintana, Beverly; Munk, Christine; Daligault, Hajnalka; Teshima, Hazuki; Davenport, Karen; Reitenga, Krista; Green, Lance; Chain, Patrick; Erkkila, Tracy; Gu, Wei; Zhang, Xiaojing; Xu, Yan; Kunde, Yulia; Chertkov, Olga; Han, James; Han, Cliff; Detter, John C; Ivanova, Natalia; Pati, Amrita; Chen, Amy; Szeto, Ernest; Mavromatis, Kostas; Huntemann, Marcel; Nolan, Matt; Pitluck, Sam; Deshpande, Shweta; Markowitz, Victor; Pagani, Ioanna; Klenk, Hans-Peter; Woyke, Tanja; Finlay, Roger D

    2013-07-30

    Serratia proteamaculans S4 (previously Serratia sp. S4), isolated from the rhizosphere of wild Equisetum sp., has the ability to stimulate plant growth and to suppress the growth of several soil-borne fungal pathogens of economically important crops. Here we present the non-contiguous, finished genome sequence of S. proteamaculans S4, which consists of a 5,324,944 bp circular chromosome and a 129,797 bp circular plasmid. The chromosome contains 5,008 predicted genes while the plasmid comprises 134 predicted genes. In total, 4,993 genes are assigned as protein-coding genes. The genome consists of 22 rRNA genes, 82 tRNA genes and 58 pseudogenes. This genome is a part of the project "Genomics of four rapeseed plant growth-promoting bacteria with antagonistic effect on plant pathogens" awarded through the 2010 DOE-JGI's Community Sequencing Program.

  11. Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4

    PubMed Central

    Goodwin, Lynne A.; Högberg, Nils; Kyrpides, Nikos C.; Alström, Sadhna; Bruce, David; Quintana, Beverly; Munk, Christine; Daligault, Hajnalka; Teshima, Hazuki; Davenport, Karen; Reitenga, Krista; Green, Lance; Chain, Patrick; Erkkila, Tracy; Gu, Wei; Zhang, Xiaojing; Xu, Yan; Kunde, Yulia; Chertkov, Olga; Han, James; Han, Cliff; Detter, John C.; Ivanova, Natalia; Pati, Amrita; Chen, Amy; Szeto, Ernest; Mavromatis, Kostas; Huntemann, Marcel; Nolan, Matt; Pitluck, Sam; Deshpande, Shweta; Markowitz, Victor; Pagani, Ioanna; Klenk, Hans-Peter; Woyke, Tanja; Finlay, Roger D.

    2013-01-01

    Serratia proteamaculans S4 (previously Serratia sp. S4), isolated from the rhizosphere of wild Equisetum sp., has the ability to stimulate plant growth and to suppress the growth of several soil-borne fungal pathogens of economically important crops. Here we present the non-contiguous, finished genome sequence of S. proteamaculans S4, which consists of a 5,324,944 bp circular chromosome and a 129,797 bp circular plasmid. The chromosome contains 5,008 predicted genes while the plasmid comprises 134 predicted genes. In total, 4,993 genes are assigned as protein-coding genes. The genome consists of 22 rRNA genes, 82 tRNA genes and 58 pseudogenes. This genome is a part of the project “Genomics of four rapeseed plant growth-promoting bacteria with antagonistic effect on plant pathogens” awarded through the 2010 DOE-JGI’s Community Sequencing Program. PMID:24501629

  12. 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 [Ken; SNL,

    2016-07-12

    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.

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

    PubMed

    Johnson, Shannon L; Minogue, Timothy D; Teshima, Hazuki; Davenport, Karen W; Shea, April A; Miner, Haven L; Wolcott, Mark J; Chain, Patrick S G

    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).

  14. Finished Genome Sequence of the Highly Multidrug-Resistant Human Urine Isolate Citrobacter freundii Strain SL151

    PubMed Central

    Taitt, Chris R.; Bangura, Umaru; Ansumana, Rashid; Stenger, David A.; Wang, Zheng

    2016-01-01

    Citrobacter freundii is a Gram-negative opportunistic pathogen that is increasingly being recognized as a causative agent of hospital-acquired urinary tract infections and an important reservoir of antimicrobial resistance determinants. In this report, we describe the finished genome sequence of C. freundii strain SL151, a highly multidrug-resistant human urine isolate. PMID:27811104

  15. Finished Genome Sequence of the Highly Multidrug-Resistant Human Urine Isolate Citrobacter freundii Strain SL151.

    PubMed

    Leski, Tomasz A; Taitt, Chris R; Bangura, Umaru; Ansumana, Rashid; Stenger, David A; Wang, Zheng; Vora, Gary J

    2016-11-03

    Citrobacter freundii is a Gram-negative opportunistic pathogen that is increasingly being recognized as a causative agent of hospital-acquired urinary tract infections and an important reservoir of antimicrobial resistance determinants. In this report, we describe the finished genome sequence of C. freundii strain SL151, a highly multidrug-resistant human urine isolate.

  16. 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).

  17. Effect of dietary calcium and phosphorus level sequences on performance, structural soundness and bone characteristics of growing-finishing swine.

    PubMed

    Cera, K R; Mahan, D C

    1988-07-01

    The effects of feeding various dietary Ca:P level sequences on gain and feed efficiency, leg structural soundness and bone indices of growing-finishing swine were evaluated as an incomplete 3 X 3 factorial arrangement of treatments in a split-plot design. A total of 664 pigs were fed one of three total dietary Ca:P levels (.52:.40, .65:.50, .80:.60%) from 19-kg to 56-kg body weights followed by one of three Ca:P levels (.45:.32, .52:.40, .65:.50%) to market weight. The .80:.60% and .65:.50% Ca:P mineral sequence was not evaluated. Diets were formulated to 14.5% crude protein using a corn-soybean meal mixture with proportions of dicalcium phosphate and limestone altered to attain the desired dietary Ca:P levels. Maximum gains occurred at the .65:.50% and .52:.40% Ca:P level during the grower (P less than .01) and finisher (P less than .01) periods, respectively. No grower X finisher phase pig gain or feed intake interaction resulted, providing evidence of no carry-over response on these measurements from the grower to the finisher period. Serum P concentration increased and plateaued at the same dietary Ca:P level, as did rate of gain at both 56-kg and 95-kg body weights. Leg soundness subjectively evaluated at 56-kg and 95-kg body weights revealed no effect of dietary Ca:P level on soundness scores at 56 kg, but at 95-kg body weight, the interaction between grower and finisher diets was significant. Percentage bone ash of the humerus, shaft thickness and bending moment of the femur increased as dietary Ca:P level increased at both 56-kg and 95-kg body weights.(ABSTRACT TRUNCATED AT 250 WORDS)

  18. FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads

    PubMed Central

    Zhang, Gong; Fedyunin, Ivan; Kirchner, Sebastian; Xiao, Chuanle; Valleriani, Angelo; Ignatova, Zoya

    2012-01-01

    The most crucial step in data processing from high-throughput sequencing applications is the accurate and sensitive alignment of the sequencing reads to reference genomes or transcriptomes. The accurate detection of insertions and deletions (indels) and errors introduced by the sequencing platform or by misreading of modified nucleotides is essential for the quantitative processing of the RNA-based sequencing (RNA-Seq) datasets and for the identification of genetic variations and modification patterns. We developed a new, fast and accurate algorithm for nucleic acid sequence analysis, FANSe, with adjustable mismatch allowance settings and ability to handle indels to accurately and quantitatively map millions of reads to small or large reference genomes. It is a seed-based algorithm which uses the whole read information for mapping and high sensitivity and low ambiguity are achieved by using short and non-overlapping reads. Furthermore, FANSe uses hotspot score to prioritize the processing of highly possible matches and implements modified Smith–Watermann refinement with reduced scoring matrix to accelerate the calculation without compromising its sensitivity. The FANSe algorithm stably processes datasets from various sequencing platforms, masked or unmasked and small or large genomes. It shows a remarkable coverage of low-abundance mRNAs which is important for quantitative processing of RNA-Seq datasets. PMID:22379138

  19. FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads.

    PubMed

    Zhang, Gong; Fedyunin, Ivan; Kirchner, Sebastian; Xiao, Chuanle; Valleriani, Angelo; Ignatova, Zoya

    2012-06-01

    The most crucial step in data processing from high-throughput sequencing applications is the accurate and sensitive alignment of the sequencing reads to reference genomes or transcriptomes. The accurate detection of insertions and deletions (indels) and errors introduced by the sequencing platform or by misreading of modified nucleotides is essential for the quantitative processing of the RNA-based sequencing (RNA-Seq) datasets and for the identification of genetic variations and modification patterns. We developed a new, fast and accurate algorithm for nucleic acid sequence analysis, FANSe, with adjustable mismatch allowance settings and ability to handle indels to accurately and quantitatively map millions of reads to small or large reference genomes. It is a seed-based algorithm which uses the whole read information for mapping and high sensitivity and low ambiguity are achieved by using short and non-overlapping reads. Furthermore, FANSe uses hotspot score to prioritize the processing of highly possible matches and implements modified Smith-Watermann refinement with reduced scoring matrix to accelerate the calculation without compromising its sensitivity. The FANSe algorithm stably processes datasets from various sequencing platforms, masked or unmasked and small or large genomes. It shows a remarkable coverage of low-abundance mRNAs which is important for quantitative processing of RNA-Seq datasets.

  20. Analysis of 4,664 high-quality sequence-finished poplar full-length

    SciTech Connect

    Ralph, S.; Gunter, Lee E; Tuskan, Gerald A; Douglas, Carl; Holt, Robert A.; Jones, Steven; Marra, Marco; Bohlmann, J.

    2008-01-01

    The genus Populus includes poplars, aspens and cottonwoods, which will be collectively referred to as poplars hereafter unless otherwise specified. Poplars are the dominant tree species in many forest ecosystems in the Northern Hemisphere and are of substantial economic value in plantation forestry. Poplar has been established as a model system for genomics studies of growth, development, and adaptation of woody perennial plants including secondary xylem formation, dormancy, adaptation to local environments, and biotic interactions. As part of the poplar genome sequencing project and the development of genomic resources for poplar, we have generated a full-length (FL)-cDNA collection using the biotinylated CAP trapper method. We constructed four FLcDNA libraries using RNA from xylem, phloem and cambium, and green shoot tips and leaves from the P. trichocarpa Nisqually-1 genotype, as well as insect-attacked leaves of the P. trichocarpa x P. deltoides hybrid. Following careful selection of candidate cDNA clones, we used a combined strategy of paired end reads and primer walking to generate a set of 4,664 high-accuracy, sequence-verified FLcDNAs, which clustered into 3,990 putative unique genes. Mapping FLcDNAs to the poplar genome sequence combined with BLAST comparisons to previously predicted protein coding sequences in the poplar genome identified 39 FLcDNAs that likely localize to gaps in the current genome sequence assembly. Another 173 FLcDNAs mapped to the genome sequence but were not included among the previously predicted genes in the poplar genome. Comparative sequence analysis against Arabidopsis thaliana and other species in the non-redundant database of GenBank revealed that 11.5% of the poplar FLcDNAs display no significant sequence similarity to other plant proteins. By mapping the poplar FLcDNAs against transcriptome data previously obtained with a 15.5 K cDNA microarray, we identified 153 FLcDNA clones for genes that were differentially expressed in

  1. Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3T)

    SciTech Connect

    Pitluck, Sam; Yasawong, Montri; Held, Brittany; Lapidus, Alla L.; Nolan, Matt; Copeland, A; Lucas, Susan; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Chertkov, Olga; Goodwin, Lynne A.; Tapia, Roxanne; Han, Cliff; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Pukall, Rudiger; Spring, Stefan; Rohde, Manfred; Sikorski, Johannes; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Aminomonas paucivorans Baena et al. 1999 is the type species of the genus Aminomonas, which belongs to the family Synergistaceae. The species is of interest because it is an asaccharolytic chemoorganotrophic bacterium which ferments quite a number of amino acids. This is the first completed genome sequence (with one gap in a rDNA region) of a member of the genus Aminomonas and the third sequence from the family Synergistaceae. The 2,630,120 bp long genome with its 2,433 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  2. 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 [DOE JGI

    2016-07-12

    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.

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

    SciTech Connect

    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.

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

    ScienceCinema

    Lukjancenko, Oksana [Technical University of Denmark

    2016-07-12

    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.

  5. Non-contiguous finished genome sequence and description of Paucisalibacillus algeriensis sp. nov.

    PubMed Central

    Bendjama, Esma; Loucif, Lotfi; Diene, Seydina M.; Michelle, Caroline; Gacemi-Kirane, Djamila; Rolain, Jean-Marc

    2014-01-01

    Paucisalibacillus algeriensis strain EB02T is the type strain of Paucisalibacillus algeriensis sp. nov., a new species within the genus Paucisalibacillus. This strain, whose genome is described here, was isolated from soil sample from the hypersaline lake Ezzemoul Sabkha in northeastern Algeria. Paucisalibacillus algeriensis is a Gram-positive and strictly aerobic bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,006,766 bp long genome (1 chromosome but no plasmid) exhibits a low G+C content of 36% and contains 3,956 protein-coding and 82 RNA genes, including 9 rRNA genes. PMID:25197503

  6. Non-contiguous finished genome sequence and description of Brevibacterium senegalense sp. nov.

    PubMed Central

    Kokcha, Sahare; Ramasamy, Dhamodharan; Lagier, Jean-Christophe; Robert, Catherine; Raoult, Didier

    2012-01-01

    Brevibacterium senegalense strain JC43T sp. nov. is the type strain of Brevibacterium senegalense sp. nov., a new species within the Brevibacterium genus. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. B. senegalense is an aerobic rod-shaped Gram-positive bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,425,960 bp long genome (1 chromosome but no plasmid) contains 3,064 protein-coding and 49 RNA genes. PMID:23408786

  7. Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov.

    PubMed Central

    Hugon, Perrine; Mishra, Ajay Kumar; Lagier, Jean-Christophe; Nguyen, Thi Thien; Couderc, Carine; Raoult, Didier; Fournier, Pierre-Edouard

    2013-01-01

    Brevibacillus massiliensis strain phRT sp. nov. is the type strain of B. massiliensis sp. nov., a new species within the genus Brevibacillus. This strain was isolated from the fecal flora of a woman suffering from morbid obesity. B. massiliensis is a Gram-positive aerobic rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,051,018 bp long genome (1 chromosome but no plasmid) contains 5,051 protein-coding and 84 RNA genes, and exhibits a G+C content of 53.1%. PMID:23961307

  8. Noncontiguous finished genome sequence and description of Weeksella massiliensis sp. nov.

    PubMed Central

    Sankar, S.A.; Lo, C.I.; Fall, B.; Sambe-Ba, B.; Mediannikov, O.; Diallo, I.; Labas, N.; Faye, N.; Wade, B.; Raoult, D.; Fournier, P.-E.; Fenollar, F.

    2015-01-01

    Strain FF8T (= CSUR P860 = DSM 28259) was isolated in Dakar, Senegal, from the urine of a 65-year-old man with acute cystitis. This strain shows a similarity of sequence of 16S rRNA of 98.38% with Weeksella virosa, and its GenBank accession numbers are HG931340 and CCMH00000000. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis had a poor score, ranging from 1.32 to 1.56, that did not allow identification of the bacterium. Using a polyphasic study made of phenotypic and genomic analyses, strain FF8T was a Gram-negative, aerobic rod and a member of the family Flavobacteriaceae. The sequenced genome is 2 562 781 bp with one chromosome but no plasmid. It exhibits a G + C content of 35.9% and contains 2390 protein-coding and 56 RNA genes, including a complete rRNA operon. On the basis of these data, we propose the creation of Weeksella massiliensis sp. nov. PMID:26649182

  9. Non contiguous-finished genome sequence and description of Bacillus jeddahensis sp. nov.

    PubMed

    Bittar, Fadi; Bibi, Fehmida; Ramasamy, Dhamodharan; Lagier, Jean-Christophe; Azhar, Esam I; Jiman-Fatani, Asif A; Al-Ghamdi, Ahmed K; Nguyen, Ti Thien; Yasir, Muhammad; Fournier, Pierre-Edouard; Raoult, Didier

    2015-01-01

    Strain JCE(T) was isolated from the fecal sample of a 24-year-old obese man living in Jeddah, Saudi Arabia. It is an aerobic, Gram-positive, rod-shaped bacterium. This strain exhibits a 16S rRNA nucleotide sequence similarity of 97.5 % with Bacillus niacini, the phylogenetically closest species with standing nomenclature. Moreover, the strain JCE(T) presents many phenotypic differences, when it is compared to other Bacillus species, and shows a low MALDI-TOF Mass Spectrometry score that does not allow any identification. Thus, it is likely that this strain represents a new species. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,762,944 bp long genome (1 chromosome but no plasmid) contains 4,654 protein-coding and 98 RNAs genes, including 92 tRNA genes. The strain JCE(T) differs from most of the other closely Bacillus species by more than 1 % in G + C content. In addition, digital DNA-DNA hybridization values for the genome of the strain JCE(T) against the closest Bacillus genomes range between 19.5 to 28.1, that confirming again its new species status. On the basis of these polyphasic data made of phenotypic and genomic analyses, we propose the creation of Bacillus jeddahensis sp. nov. that contains the strain JCE(T).

  10. Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov.

    PubMed Central

    Lagier, Jean-Christophe; Bibi, Fehmida; Ramasamy, Dhamodharan; Azhar, Esam I.; Robert, Catherine; Yasir, Muhammad; Jiman-Fatani, Asif A.; Alshali, Khalid Z.; Fournier, Pierre-Edouard

    2014-01-01

    Clostridium jeddahense strain JCDT (= CSUR P693 = DSM 27834) is the type strain of C. jeddahense sp. nov. This strain, whose genome is described here, was isolated from the fecal flora of an obese 24 year-old Saudian male (BMI=52 kg/m2). Clostridium jeddahense strain JCDT is an obligate Gram-positive bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,613,503 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 51.95% and contains 3,462 protein-coding and 53 RNA genes, including 4 rRNA genes. PMID:25197479

  11. Non-contiguous finished genome sequence and description of Streptococcus varani sp. nov.

    PubMed Central

    Bakour, S.; Rathored, J.; Lo, C.I.; Mediannikov, O.; Beye, M.; Ehounoud, C.B.; Biagini, P.; Raoult, D.; Fournier, P.-E.; Fenollar, F.

    2016-01-01

    Strain FF10T (= CSUR P1489 = DSM 100884) was isolated from the oral cavity of a lizard (Varanus niloticus) in Dakar, Senegal. Here we used a polyphasic study including phenotypic and genomic analyses to describe the strain FF10T. Results support strain FF10T being a Gram-positive coccus, facultative anaerobic bacterium, catalase-negative, non-motile and non-spore forming. The sequenced genome counts 2.46 Mb with one chromosome but no plasmid. It exhibits a G+C content of 40.4% and contains 2471 protein-coding and 45 RNA genes. On the basis of these data, we propose the creation of Streptococcus varani sp. nov. PMID:27158513

  12. Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC 139T)

    SciTech Connect

    Land, Miriam L; Held, Brittany; Gronow, Sabine; Abt, Birte; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Mavromatis, K; Pati, Amrita; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Chen, Amy; Palaniappan, Krishna; Hauser, Loren John; Brambilla, Evelyne-Marie; Rohde, Manfred; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2011-01-01

    Bacteroides coprosuis Whitehead et al. 2005 belongs to the genus Bacteroides, which is a member of the family Bacteroidaceae. Members of the genus Bacteroides in general are known as beneficial protectors of animal guts against pathogenic microorganisms, and as contributors to the degradation of complex molecules such as polysaccharides. B. coprosuis itself was isolated from a manure storage pit of a swine facility, but has not yet been found in an animal host. The species is of interest solely because of its isolated phylogenetic location. The genome of B. coprosuis is already the 5th sequenced type strain genome from the genus Bacteroides. The 2,991,798 bp long genome with its 2,461 protein-coding and 78 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  13. Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139T)

    PubMed Central

    Land, Miriam; Held, Brittany; Gronow, Sabine; Abt, Birte; Lucas, Susan; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Chen, Amy; Palaniappan, Krishna; Hauser, Loren; Brambilla, Evelyne-Marie; Rohde, Manfred; Göker, Markus; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lapidus, Alla

    2011-01-01

    Bacteroides coprosuis Whitehead et al. 2005 belongs to the genus Bacteroides, which is a member of the family Bacteroidaceae. Members of the genus Bacteroides in general are known as beneficial protectors of animal guts against pathogenic microorganisms, and as contributors to the degradation of complex molecules such as polysaccharides. B. coprosuis itself was isolated from a manure storage pit of a swine facility, but has not yet been found in an animal host. The species is of interest solely because of its isolated phylogenetic location. The genome of B. coprosuis is already the 5th sequenced type strain genome from the genus Bacteroides. The 2,991,798 bp long genome with its 2,461 protein-coding and 78 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21677860

  14. Accurate whole genome sequencing and haplotyping from10-20 human cells

    PubMed Central

    Peters, Brock A.; Kermani, Bahram G.; Sparks, Andrew B.; Alferov, Oleg; Hong, Peter; Alexeev, Andrei; Jiang, Yuan; Dahl, Fredrik; Tang, Y. Tom; Haas, Juergen; Robasky, Kimberly; Zaranek, Alexander Wait; Lee, Je-Hyuk; Ball, Madeleine Price; Peterson, Joseph E.; Perazich, Helena; Yeung, George; Liu, Jia; Chen, Linsu; Kennemer, Michael I.; Pothuraju, Kaliprasad; Konvicka, Karel; Tsoupko-Sitnikov, Mike; Pant, Krishna P.; Ebert, Jessica C.; Nilsen, Geoffrey B.; Baccash, Jonathan; Halpern, Aaron L.; Church, George M.; Drmanac, Radoje

    2012-01-01

    Recent advances in whole genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context (haplotypes) in which genome variants co-occur in a cost-effective manner. Here we describe a low-cost DNA sequencing and haplotyping process, Long Fragment Read (LFR) technology, similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes. In this study, ten LFR libraries were made using only ~100 pg of human DNA per sample. Up to 97% of the heterozygous single nucleotide variants (SNVs) were assembled into long haplotype contigs. Removal of false positive SNVs not phased by multiple LFR haplotypes resulted in a final genome error rate of 1 in 10 Mb. Cost-effective and accurate genome sequencing and haplotyping from 10-20 human cells, as demonstrated here, will enable comprehensive genetic studies and diverse clinical applications. PMID:22785314

  15. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

    PubMed Central

    Liu, Zongzhi; DeSantis, Todd Z.; Andersen, Gary L.; Knight, Rob

    2008-01-01

    The recent introduction of massively parallel pyrosequencers allows rapid, inexpensive analysis of microbial community composition using 16S ribosomal RNA (rRNA) sequences. However, a major challenge is to design a workflow so that taxonomic information can be accurately and rapidly assigned to each read, so that the composition of each community can be linked back to likely ecological roles played by members of each species, genus, family or phylum. Here, we use three large 16S rRNA datasets to test whether taxonomic information based on the full-length sequences can be recaptured by short reads that simulate the pyrosequencer outputs. We find that different taxonomic assignment methods vary radically in their ability to recapture the taxonomic information in full-length 16S rRNA sequences: most methods are sensitive to the region of the 16S rRNA gene that is targeted for sequencing, but many combinations of methods and rRNA regions produce consistent and accurate results. To process large datasets of partial 16S rRNA sequences obtained from surveys of various microbial communities, including those from human body habitats, we recommend the use of Greengenes or RDP classifier with fragments of at least 250 bases, starting from one of the primers R357, R534, R798, F343 or F517. PMID:18723574

  16. 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).

  17. Flexible, Fast and Accurate Sequence Alignment Profiling on GPGPU with PaSWAS

    PubMed Central

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

    2015-01-01

    Motivation 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. Results 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. PMID:25830241

  18. 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.

  19. 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.

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

    SciTech Connect

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

    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, and 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.

  1. Accurate identification of A-to-I RNA editing in human by transcriptome sequencing.

    PubMed

    Bahn, Jae Hoon; Lee, Jae-Hyung; Li, Gang; Greer, Christopher; Peng, Guangdun; Xiao, Xinshu

    2012-01-01

    RNA editing enhances the diversity of gene products at the post-transcriptional level. Approaches for genome-wide identification of RNA editing face two main challenges: separating true editing sites from false discoveries and accurate estimation of editing levels. We developed an approach to analyze transcriptome sequencing data (RNA-seq) for global identification of RNA editing in cells for which whole-genome sequencing data are available. We applied the method to analyze RNA-seq data of a human glioblastoma cell line, U87MG. Around 10,000 DNA-RNA differences were identified, the majority being putative A-to-I editing sites. These predicted A-to-I events were associated with a low false-discovery rate (∼5%). Moreover, the estimated editing levels from RNA-seq correlated well with those based on traditional clonal sequencing. Our results further facilitated unbiased characterization of the sequence and evolutionary features flanking predicted A-to-I editing sites and discovery of a conserved RNA structural motif that may be functionally relevant to editing. Genes with predicted A-to-I editing were significantly enriched with those known to be involved in cancer, supporting the potential importance of cancer-specific RNA editing. A similar profile of DNA-RNA differences as in U87MG was predicted for another RNA-seq data set obtained from primary breast cancer samples. Remarkably, significant overlap exists between the putative editing sites of the two transcriptomes despite their difference in cell type, cancer type, and genomic backgrounds. Our approach enabled de novo identification of the RNA editome, which sets the stage for further mechanistic studies of this important step of post-transcriptional regulation.

  2. CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra

    NASA Astrophysics Data System (ADS)

    Novák, Jiří; Lemr, Karel; Schug, Kevin A.; Havlíček, Vladimír

    2015-07-01

    Nonribosomal peptides have a wide range of biological and medical applications. Their identification by tandem mass spectrometry remains a challenging task. A new open-source de novo peptide identification engine CycloBranch was developed and successfully applied in identification or detailed characterization of 11 linear, cyclic, branched, and branch-cyclic peptides. CycloBranch is based on annotated building block databases the size of which is defined by the user according to ribosomal or nonribosomal peptide origin. The current number of involved nonisobaric and isobaric building blocks is 287 and 521, respectively. Contrary to all other peptide sequencing tools utilizing either peptide libraries or peptide fragment libraries, CycloBranch represents a true de novo sequencing engine developed for accurate mass spectrometric data. It is a stand-alone and cross-platform application with a graphical and user-friendly interface; it supports mzML, mzXML, mgf, txt, and baf file formats and can be run in parallel on multiple threads. It can be downloaded for free from http://ms.biomed.cas.cz/cyclobranch/, where the User's manual and video tutorials can be found.

  3. PRIMAL: Fast and accurate pedigree-based imputation from sequence data in a founder population.

    PubMed

    Livne, Oren E; Han, Lide; Alkorta-Aranburu, Gorka; Wentworth-Sheilds, William; Abney, Mark; Ober, Carole; Nicolae, Dan L

    2015-03-01

    Founder populations and large pedigrees offer many well-known advantages for genetic mapping studies, including cost-efficient study designs. Here, we describe PRIMAL (PedigRee IMputation ALgorithm), a fast and accurate pedigree-based phasing and imputation algorithm for founder populations. PRIMAL incorporates both existing and original ideas, such as a novel indexing strategy of Identity-By-Descent (IBD) segments based on clique graphs. We were able to impute the genomes of 1,317 South Dakota Hutterites, who had genome-wide genotypes for ~300,000 common single nucleotide variants (SNVs), from 98 whole genome sequences. Using a combination of pedigree-based and LD-based imputation, we were able to assign 87% of genotypes with >99% accuracy over the full range of allele frequencies. Using the IBD cliques we were also able to infer the parental origin of 83% of alleles, and genotypes of deceased recent ancestors for whom no genotype information was available. This imputed data set will enable us to better study the relative contribution of rare and common variants on human phenotypes, as well as parental origin effect of disease risk alleles in >1,000 individuals at minimal cost.

  4. Fast and accurate simulations of diffusion-weighted MRI signals for the evaluation of acquisition sequences

    NASA Astrophysics Data System (ADS)

    Rensonnet, Gaëtan; Jacobs, Damien; Macq, Benoît.; Taquet, Maxime

    2016-03-01

    Diffusion-weighted magnetic resonance imaging (DW-MRI) is a powerful tool to probe the diffusion of water through tissues. Through the application of magnetic gradients of appropriate direction, intensity and duration constituting the acquisition parameters, information can be retrieved about the underlying microstructural organization of the brain. In this context, an important and open question is to determine an optimal sequence of such acquisition parameters for a specific purpose. The use of simulated DW-MRI data for a given microstructural configuration provides a convenient and efficient way to address this problem. We first present a novel hybrid method for the synthetic simulation of DW-MRI signals that combines analytic expressions in simple geometries such as spheres and cylinders and Monte Carlo (MC) simulations elsewhere. Our hybrid method remains valid for any acquisition parameters and provides identical levels of accuracy with a computational time that is 90% shorter than that required by MC simulations for commonly-encountered microstructural configurations. We apply our novel simulation technique to estimate the radius of axons under various noise levels with different acquisition protocols commonly used in the literature. The results of our comparison suggest that protocols favoring a large number of gradient intensities such as a Cube and Sphere (CUSP) imaging provide more accurate radius estimation than conventional single-shell HARDI acquisitions for an identical acquisition time.

  5. Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification

    PubMed Central

    Fu, Yusi; Li, Chunmei; Lu, Sijia; Zhou, Wenxiong; Tang, Fuchou; Xie, X. Sunney; Huang, Yanyi

    2015-01-01

    Whole-genome amplification (WGA) for next-generation sequencing has seen wide applications in biology and medicine when characterization of the genome of a single cell is required. High uniformity and fidelity of WGA is needed to accurately determine genomic variations, such as copy number variations (CNVs) and single-nucleotide variations (SNVs). Prevailing WGA methods have been limited by fluctuation of the amplification yield along the genome, as well as false-positive and -negative errors for SNV identification. Here, we report emulsion WGA (eWGA) to overcome these problems. We divide single-cell genomic DNA into a large number (105) of picoliter aqueous droplets in oil. Containing only a few DNA fragments, each droplet is led to reach saturation of DNA amplification before demulsification such that the differences in amplification gain among the fragments are minimized. We demonstrate the proof-of-principle of eWGA with multiple displacement amplification (MDA), a popular WGA method. This easy-to-operate approach enables simultaneous detection of CNVs and SNVs in an individual human cell, exhibiting significantly improved amplification evenness and accuracy. PMID:26340991

  6. Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification.

    PubMed

    Fu, Yusi; Li, Chunmei; Lu, Sijia; Zhou, Wenxiong; Tang, Fuchou; Xie, X Sunney; Huang, Yanyi

    2015-09-22

    Whole-genome amplification (WGA) for next-generation sequencing has seen wide applications in biology and medicine when characterization of the genome of a single cell is required. High uniformity and fidelity of WGA is needed to accurately determine genomic variations, such as copy number variations (CNVs) and single-nucleotide variations (SNVs). Prevailing WGA methods have been limited by fluctuation of the amplification yield along the genome, as well as false-positive and -negative errors for SNV identification. Here, we report emulsion WGA (eWGA) to overcome these problems. We divide single-cell genomic DNA into a large number (10(5)) of picoliter aqueous droplets in oil. Containing only a few DNA fragments, each droplet is led to reach saturation of DNA amplification before demulsification such that the differences in amplification gain among the fragments are minimized. We demonstrate the proof-of-principle of eWGA with multiple displacement amplification (MDA), a popular WGA method. This easy-to-operate approach enables simultaneous detection of CNVs and SNVs in an individual human cell, exhibiting significantly improved amplification evenness and accuracy.

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

    PubMed

    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/.

  8. Surface finishing

    NASA Technical Reports Server (NTRS)

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

    1980-01-01

    A surface of an article adapted for relative motion with a fluid environment is finished by coating the surface with a fluid adhesive, covering the adhesive with a sheet of flexible film material under tension on the film material whereby the tensioned film material is bonded to the surface by the adhesive.

  9. SiNG-PCRseq: Accurate inter-sequence quantification achieved by spiking-in a neighbor genome for competitive PCR amplicon sequencing.

    PubMed

    Oh, Soo A; Yang, Inchul; Hahn, Yoonsoo; Kang, Yong-Kook; Chung, Sun-Ku; Jeong, Sangkyun

    2015-07-06

    Despite the recent technological advances in DNA quantitation by sequencing, accurate delineation of the quantitative relationship among different DNA sequences is yet to be elaborated due to difficulties in correcting the sequence-specific quantitation biases. We here developed a novel DNA quantitation method via spiking-in a neighbor genome for competitive PCR amplicon sequencing (SiNG-PCRseq). This method utilizes genome-wide chemically equivalent but easily discriminable homologous sequences with a known copy arrangement in the neighbor genome. By comparing the amounts of selected human DNA sequences simultaneously to those of matched sequences in the orangutan genome, we could accurately draw the quantitative relationships for those sequences in the human genome (root-mean-square deviations <0.05). Technical replications of cDNA quantitation performed using different reagents at different time points also resulted in excellent correlations (R(2) > 0.95). The cDNA quantitation using SiNG-PCRseq was highly concordant with the RNA-seq-derived version in inter-sample comparisons (R(2) = 0.88), but relatively discordant in inter-sequence quantitation (R(2) < 0.44), indicating considerable level of sequence-dependent quantitative biases in RNA-seq. Considering the measurement structure explicitly relating the amount of different sequences within a sample, SiNG-PCRseq will facilitate sharing and comparing the quantitation data generated under different spatio-temporal settings.

  10. Graphical contig analyzer for all sequencing platforms (G4ALL): a new stand-alone tool for finishing and draft generation of bacterial genomes

    PubMed Central

    Ramos, Rommel Thiago Jucá; Carneiro, Adriana R; Caracciolo, Pablo H; Azevedo, Vasco; Schneider, Maria Paula C; Barh, Debmalya; Silva, Artur

    2013-01-01

    Genome assembly has always been complicated due to the inherent difficulties of sequencing technologies, as well the computational methods used to process sequences. Although many of the problems for the generation of contigs from reads are well known, especially those involving short reads, the orientation and ordination of contigs in the finishing stages is still very challenging and time consuming, as it requires the manual curation of the contigs to guarantee correct identification them and prevent misassembly. Due to the large numbers of sequences that are produced, especially from the reads produced by next generation sequencers, this process demands considerable manual effort, and there are few software options available to facilitate the process. To address this problem, we have developed the Graphic Contig Analyzer for All Sequencing Platforms (G4ALL): a stand-alone multi-user tool that facilitates the editing of the contigs produced in the assembly process. Besides providing information on the gene products contained in each contig, obtained through a search of the available biological databases, G4ALL produces a scaffold of the genome, based on the overlap of the contigs after curation. Availability The software is available at: http://www.genoma.ufpa.br/rramos/softwares/g4all.xhtml PMID:23888102

  11. Accurate Prediction of the Statistics of Repetitions in Random Sequences: A Case Study in Archaea Genomes

    PubMed Central

    Régnier, Mireille; Chassignet, Philippe

    2016-01-01

    Repetitive patterns in genomic sequences have a great biological significance and also algorithmic implications. Analytic combinatorics allow to derive formula for the expected length of repetitions in a random sequence. Asymptotic results, which generalize previous works on a binary alphabet, are easily computable. Simulations on random sequences show their accuracy. As an application, the sample case of Archaea genomes illustrates how biological sequences may differ from random sequences. PMID:27376057

  12. Fast and Accurate Discovery of Degenerate Linear Motifs in Protein Sequences

    PubMed Central

    Levy, Emmanuel D.; Michnick, Stephen W.

    2014-01-01

    Linear motifs mediate a wide variety of cellular functions, which makes their characterization in protein sequences crucial to understanding cellular systems. However, the short length and degenerate nature of linear motifs make their discovery a difficult problem. Here, we introduce MotifHound, an algorithm particularly suited for the discovery of small and degenerate linear motifs. MotifHound performs an exact and exhaustive enumeration of all motifs present in proteins of interest, including all of their degenerate forms, and scores the overrepresentation of each motif based on its occurrence in proteins of interest relative to a background (e.g., proteome) using the hypergeometric distribution. To assess MotifHound, we benchmarked it together with state-of-the-art algorithms. The benchmark consists of 11,880 sets of proteins from S. cerevisiae; in each set, we artificially spiked-in one motif varying in terms of three key parameters, (i) number of occurrences, (ii) length and (iii) the number of degenerate or “wildcard” positions. The benchmark enabled the evaluation of the impact of these three properties on the performance of the different algorithms. The results showed that MotifHound and SLiMFinder were the most accurate in detecting degenerate linear motifs. Interestingly, MotifHound was 15 to 20 times faster at comparable accuracy and performed best in the discovery of highly degenerate motifs. We complemented the benchmark by an analysis of proteins experimentally shown to bind the FUS1 SH3 domain from S. cerevisiae. Using the full-length protein partners as sole information, MotifHound recapitulated most experimentally determined motifs binding to the FUS1 SH3 domain. Moreover, these motifs exhibited properties typical of SH3 binding peptides, e.g., high intrinsic disorder and evolutionary conservation, despite the fact that none of these properties were used as prior information. MotifHound is available (http://michnick.bcm.umontreal.ca or http

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

    SciTech Connect

    Pati, Amrita; Gronow, Sabine; Lu, Megan; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Mavromatis, K; Mikhailova, Natalia; Huntemann, Marcel; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Detter, J. Chris; Brambilla, Evelyne-Marie; Rohde, Manfred; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Ivanova, N

    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 and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

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

    SciTech Connect

    Brown, Steven D; Nagaraju, Shilpa; Utturkar, Sagar M; De Tissera, Sashini; Segovia, Simón; Mitchell, Wayne; Land, Miriam L; Dassanayake, Asela; Köpke, Michael

    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. Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China

    PubMed Central

    Molnár, István; Li, Xinna; Tang, Ran; Chen, Ming; Wang, Lin; Su, Shiyou; Zhang, Wei; Lin, Min

    2015-01-01

    A novel Gram-negative bacterium, designated ZWT, was isolated from a soil sample of the Western Desert of China, and its phenotypic properties and phylogenetic position were investigated using a polyphasic approach. Growth occurred on TGY medium at 5–42°C with an optimum of 30°C, and at pH 7.0–11.0 with an optimum of pH 9.0. The predominant cellular fatty acids were summed feature 3 (C16:1ω7c/C16:1ω6c or C16:1ω6c/C16:1ω7c) (39.22%), iso-C15:0 (27.91%), iso-C17:0 3OH (15.21%), C16:0 (4.98%), iso-C15:0 3OH (3.03%), C16:0 3OH (5.39%) and C14:0 (1.74%). The major polar lipid of strain ZWT is phosphatidylethanolamine. The only menaquinone observed was MK-7. The GC content of the DNA of strain ZWT is 44.9 mol%. rDNA phylogeny, genome relatedness and chemotaxonomic characteristics all indicate that strain ZWT represents a novel species of the genus Sphingobacterium. We propose the name S. deserti sp. nov., with ZWT (= KCTC 32092T = ACCC 05744T) as the type strain. Whole genome optical mapping and next-generation sequencing was used to derive a finished genome sequence for strain ZWT, consisting of a circular chromosome of 4,615,818 bp in size. The genome of strain ZWT features 3,391 protein-encoding and 48 tRNA-encoding genes. Comparison of the predicted proteome of ZWT with those of other sphingobacteria identified 925 species-unique proteins that may contribute to the adaptation of ZWT to its native, extremely arid and inhospitable environment. As the first finished genome sequence for any Sphingobacterium, our work will serve as a useful reference for subsequent sequencing and mapping efforts for additional strains and species within this genus. PMID:25830331

  16. Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification?

    PubMed

    Muth, Thilo; Renard, Bernhard Y

    2017-03-21

    While peptide identifications in mass spectrometry (MS)-based shotgun proteomics are mostly obtained using database search methods, high-resolution spectrum data from modern MS instruments nowadays offer the prospect of improving the performance of computational de novo peptide sequencing. The major benefit of de novo sequencing is that it does not require a reference database to deduce full-length or partial tag-based peptide sequences directly from experimental tandem mass spectrometry spectra. Although various algorithms have been developed for automated de novo sequencing, the prediction accuracy of proposed solutions has been rarely evaluated in independent benchmarking studies. The main objective of this work is to provide a detailed evaluation on the performance of de novo sequencing algorithms on high-resolution data. For this purpose, we processed four experimental data sets acquired from different instrument types from collision-induced dissociation and higher energy collisional dissociation (HCD) fragmentation mode using the software packages Novor, PEAKS and PepNovo. Moreover, the accuracy of these algorithms is also tested on ground truth data based on simulated spectra generated from peak intensity prediction software. We found that Novor shows the overall best performance compared with PEAKS and PepNovo with respect to the accuracy of correct full peptide, tag-based and single-residue predictions. In addition, the same tool outpaced the commercial competitor PEAKS in terms of running time speedup by factors of around 12-17. Despite around 35% prediction accuracy for complete peptide sequences on HCD data sets, taken as a whole, the evaluated algorithms perform moderately on experimental data but show a significantly better performance on simulated data (up to 84% accuracy). Further, we describe the most frequently occurring de novo sequencing errors and evaluate the influence of missing fragment ion peaks and spectral noise on the accuracy. Finally

  17. 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)

    SciTech Connect

    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.

  18. 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 [DOE JGI

    2016-07-12

    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.

  19. 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.

  20. Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profile.

    PubMed

    Faraggi, Eshel; Kouza, Maksim; Zhou, Yaoqi; Kloczkowski, Andrzej

    2017-01-01

    A fast accessible surface area (ASA) predictor is presented. In this new approach no residue mutation profiles generated by multiple sequence alignments are used as inputs. Instead, we use only single sequence information and global features such as single-residue and two-residue compositions of the chain. The resulting predictor is both highly more efficient than sequence alignment based predictors and of comparable accuracy to them. Introduction of the global inputs significantly helps achieve this comparable accuracy. The predictor, termed ASAquick, is found to perform similarly well for so-called easy and hard cases indicating generalizability and possible usability for de-novo protein structure prediction. The source code and a Linux executables for ASAquick are available from Research and Information Systems at http://mamiris.com and from the Battelle Center for Mathematical Medicine at http://mathmed.org .

  1. Noncontiguous finished genome sequence and description of Virgibacillus massiliensis sp. nov., a moderately halophilic bacterium isolated from human gut

    PubMed Central

    Khelaifia, S.; Croce, O.; Lagier, J.-C.; Robert, C.; Couderc, C.; Di Pinto, F.; Davoust, B.; Djossou, F.; Raoult, D.; Fournier, P.-E.

    2015-01-01

    Strain Vm-5T was isolated from the stool specimen of a 10-year-old Amazonian boy. This bacterium is a Gram-positive, strictly aerobic rod, motile by a polar flagellum. Here we describe its phenotypic characteristics and complete genome sequence. The 4 353 177 bp long genome exhibits a G + C content of 36.87% and contains 4394 protein-coding and 125 predicted RNA genes. Phylogenetically and genetically, strain Vm-c is a member of the genus Virgibacillus but is distinct enough to be classified as a new species. We propose the creation of V. massiliensis sp. nov., whose type strain is strain Vm-5T (CSUR P971 = DSM 28587). PMID:26649181

  2. DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences

    PubMed Central

    2010-01-01

    Background In metagenomic sequence data, majority of sequences/reads originate from new or partially characterized genomes, the corresponding sequences of which are absent in existing reference databases. Since taxonomic assignment of reads is based on their similarity to sequences from known organisms, the presence of reads originating from new organisms poses a major challenge to taxonomic binning methods. The recently published SOrt-ITEMS algorithm uses an elaborate work-flow to assign reads originating from hitherto unknown genomes with significant accuracy and specificity. Nevertheless, a significant proportion of reads still get misclassified. Besides, the use of an alignment-based orthology step (for improving the specificity of assignments) increases the total binning time of SOrt-ITEMS. Results In this paper, we introduce a rapid binning approach called DiScRIBinATE (Distance Score Ratio for Improved Binning And Taxonomic Estimation). DiScRIBinATE replaces the orthology approach of SOrt-ITEMS with a quicker 'alignment-free' approach. We demonstrate that incorporating this approach reduces binning time by half without any loss in the specificity and accuracy of assignments. Besides, a novel reclassification strategy incorporated in DiScRIBinATE results in reducing the overall misclassification rate to around 3 - 7%. This misclassification rate is 1.5 - 3 times lower as compared to that by SOrt-ITEMS, and 3 - 30 times lower as compared to that by MEGAN. Conclusions A significant reduction in binning time, coupled with a superior assignment accuracy (as compared to existing binning methods), indicates the immense applicability of the proposed algorithm in rapidly mapping the taxonomic diversity of large metagenomic samples with high accuracy and specificity. Availability The program is available on request from the authors. PMID:21106121

  3. 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

    2015-10-30

    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.

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

    SciTech Connect

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

    2011-01-01

    Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedo- nobacter, 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 unclassi- fied 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 Ge- nomic Encyclopedia of Bacteria and Archaea project.

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

    PubMed Central

    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

    2011-01-01

    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. PMID:22180814

  6. 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

  7. Sequence features accurately predict genome-wide MeCP2 binding in vivo

    PubMed Central

    Rube, H. Tomas; Lee, Wooje; Hejna, Miroslav; Chen, Huaiyang; Yasui, Dag H.; Hess, John F.; LaSalle, Janine M.; Song, Jun S.; Gong, Qizhi

    2016-01-01

    Methyl-CpG binding protein 2 (MeCP2) is critical for proper brain development and expressed at near-histone levels in neurons, but the mechanism of its genomic localization remains poorly understood. Using high-resolution MeCP2-binding data, we show that DNA sequence features alone can predict binding with 88% accuracy. Integrating MeCP2 binding and DNA methylation in a probabilistic graphical model, we demonstrate that previously reported genome-wide association with methylation is in part due to MeCP2's affinity to GC-rich chromatin, a result replicated using published data. Furthermore, MeCP2 co-localizes with nucleosomes. Finally, MeCP2 binding downstream of promoters correlates with increased expression in Mecp2-deficient neurons. PMID:27008915

  8. Re-ranking sequencing variants in the post-GWAS era for accurate causal variant identification.

    PubMed

    Faye, Laura L; Machiela, Mitchell J; Kraft, Peter; Bull, Shelley B; Sun, Lei

    2013-01-01

    Next generation sequencing has dramatically increased our ability to localize disease-causing variants by providing base-pair level information at costs increasingly feasible for the large sample sizes required to detect complex-trait associations. Yet, identification of causal variants within an established region of association remains a challenge. Counter-intuitively, certain factors that increase power to detect an associated region can decrease power to localize the causal variant. First, combining GWAS with imputation or low coverage sequencing to achieve the large sample sizes required for high power can have the unintended effect of producing differential genotyping error among SNPs. This tends to bias the relative evidence for association toward better genotyped SNPs. Second, re-use of GWAS data for fine-mapping exploits previous findings to ensure genome-wide significance in GWAS-associated regions. However, using GWAS findings to inform fine-mapping analysis can bias evidence away from the causal SNP toward the tag SNP and SNPs in high LD with the tag. Together these factors can reduce power to localize the causal SNP by more than half. Other strategies commonly employed to increase power to detect association, namely increasing sample size and using higher density genotyping arrays, can, in certain common scenarios, actually exacerbate these effects and further decrease power to localize causal variants. We develop a re-ranking procedure that accounts for these adverse effects and substantially improves the accuracy of causal SNP identification, often doubling the probability that the causal SNP is top-ranked. Application to the NCI BPC3 aggressive prostate cancer GWAS with imputation meta-analysis identified a new top SNP at 2 of 3 associated loci and several additional possible causal SNPs at these loci that may have otherwise been overlooked. This method is simple to implement using R scripts provided on the author's website.

  9. Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data.

    PubMed

    Chen, Weizhong; Liu, Yi; Zhu, Shanshan; Green, Christopher D; Wei, Gang; Han, Jing-Dong Jackie

    2014-09-18

    Accurate determination of genome-wide nucleosome positioning can provide important insights into global gene regulation. Here, we describe the development of an improved nucleosome-positioning algorithm-iNPS-which achieves significantly better performance than the widely used NPS package. By determining nucleosome boundaries more precisely and merging or separating shoulder peaks based on local MNase-seq signals, iNPS can unambiguously detect 60% more nucleosomes. The detected nucleosomes display better nucleosome 'widths' and neighbouring centre-centre distance distributions, giving rise to sharper patterns and better phasing of average nucleosome profiles and higher consistency between independent data subsets. In addition to its unique advantage in classifying nucleosomes by shape to reveal their different biological properties, iNPS also achieves higher significance and lower false positive rates than previously published methods. The application of iNPS to T-cell activation data demonstrates a greater ability to facilitate detection of nucleosome repositioning, uncovering additional biological features underlying the activation process.

  10. 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.

  11. Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing

    PubMed Central

    Walters, William A.; Lennon, Niall J.; Bochicchio, James; Krohn, Andrew; Pennanen, Taina

    2016-01-01

    ABSTRACT While high-throughput sequencing methods are revolutionizing fungal ecology, recovering accurate estimates of species richness and abundance has proven elusive. We sought to design internal transcribed spacer (ITS) primers and an Illumina protocol that would maximize coverage of the kingdom Fungi while minimizing nontarget eukaryotes. We inspected alignments of the 5.8S and large subunit (LSU) ribosomal genes and evaluated potential primers using PrimerProspector. We tested the resulting primers using tiered-abundance mock communities and five previously characterized soil samples. We recovered operational taxonomic units (OTUs) belonging to all 8 members in both mock communities, despite DNA abundances spanning 3 orders of magnitude. The expected and observed read counts were strongly correlated (r = 0.94 to 0.97). However, several taxa were consistently over- or underrepresented, likely due to variation in rRNA gene copy numbers. The Illumina data resulted in clustering of soil samples identical to that obtained with Sanger sequence clone library data using different primers. Furthermore, the two methods produced distance matrices with a Mantel correlation of 0.92. Nonfungal sequences comprised less than 0.5% of the soil data set, with most attributable to vascular plants. Our results suggest that high-throughput methods can produce fairly accurate estimates of fungal abundances in complex communities. Further improvements might be achieved through corrections for rRNA copy number and utilization of standardized mock communities. IMPORTANCE Fungi play numerous important roles in the environment. Improvements in sequencing methods are providing revolutionary insights into fungal biodiversity, yet accurate estimates of the number of fungal species (i.e., richness) and their relative abundances in an environmental sample (e.g., soil, roots, water, etc.) remain difficult to obtain. We present improved methods for high-throughput Illumina sequencing of the

  12. Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

    PubMed Central

    Flynn, Jullien M; Brown, Emily A; Chain, Frédéric J J; MacIsaac, Hugh J; Cristescu, Melania E

    2015-01-01

    Metabarcoding has the potential to become a rapid, sensitive, and effective approach for identifying species in complex environmental samples. Accurate molecular identification of species depends on the ability to generate operational taxonomic units (OTUs) that correspond to biological species. Due to the sometimes enormous estimates of biodiversity using this method, there is a great need to test the efficacy of data analysis methods used to derive OTUs. Here, we evaluate the performance of various methods for clustering length variable 18S amplicons from complex samples into OTUs using a mock community and a natural community of zooplankton species. We compare analytic procedures consisting of a combination of (1) stringent and relaxed data filtering, (2) singleton sequences included and removed, (3) three commonly used clustering algorithms (mothur, UCLUST, and UPARSE), and (4) three methods of treating alignment gaps when calculating sequence divergence. Depending on the combination of methods used, the number of OTUs varied by nearly two orders of magnitude for the mock community (60–5068 OTUs) and three orders of magnitude for the natural community (22–22191 OTUs). The use of relaxed filtering and the inclusion of singletons greatly inflated OTU numbers without increasing the ability to recover species. Our results also suggest that the method used to treat gaps when calculating sequence divergence can have a great impact on the number of OTUs. Our findings are particularly relevant to studies that cover taxonomically diverse species and employ markers such as rRNA genes in which length variation is extensive. PMID:26078860

  13. Performing Accurate Rigid Kinematics Measurements from 3D in vivo Image Sequences through Median Consensus Simultaneous Registration.

    PubMed

    Cresson, T; Jacq, J; Burdin, V; Roux, Ch

    2005-01-01

    While focusing at accurate 3D joint kinematics, this paper explores the problem of how to perform a robust rigid registration for a sequence of object surfaces observed using standard 3D medical imaging techniques. Each object instance is assumed to give access to a polyhedral encoding of its boundary. We consider the case where object instances are noised with significant truncations and segmentation errors. The proposed method aims to tackle this problem in a global way, fully exploiting the duality between redundancy and complementarity of the available instances set. The algorithm operates through robust and simultaneous registration of all geometrical instances on a virtual instance accounting for their median consensus. When compared with standard robust techniques, trials reveal significant gains, as much in robustness as in accuracy. The considered applications are mainly focused on generating highly accurate kinematics in relation to the bone structures of the most complex joints - the tarsus and the carpus - for which no alternative examination techniques exist, enabling fine morphological analysis as well as access to internal joint motions.

  14. 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.

  15. 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/.

  16. Agile robotic edge finishing

    SciTech Connect

    Powell, M.

    1996-08-01

    Edge finishing processes have seemed like ideal candidates for automation. Most edge finishing processes are unpleasant, dangerous, tedious, expensive, not repeatable and labor intensive. Estimates place the cost of manual edge finishing processes at 12% of the total cost of fabricating precision parts. For small, high precision parts, the cost of hand finishing may be as high as 305 of the total part cost. Up to 50% of this cost could be saved through automation. This cost estimate includes the direct costs of edge finishing: the machining hours required and the 30% scrap and rework rate after manual finishing. Not included in these estimates are the indirect costs resulting from cumulative trauma disorders and retraining costs caused by the high turnover rate for finishing jobs.. Despite the apparent economic advantages, edge finishing has proven difficult to automate except in low precision and/or high volume production environments. Finishing automation systems have not been deployed successfully in Department of Energy defense programs (DOE/DP) production, A few systems have been attempted but have been subsequently abandoned for traditional edge finishing approaches: scraping, grinding, and filing the edges using modified dental tools and hand held power tools. Edge finishing automation has been an elusive but potentially lucrative production enhancement. The amount of time required for reconfiguring workcells for new parts, the time required to reprogram the workcells to finish new parts, and automation equipment to respond to fixturing errors and part tolerances are the most common reasons cited for eliminating automation as an option for DOE/DP edge finishing applications. Existing automated finishing systems have proven to be economically viable only where setup and reprogramming costs are a negligible fraction of overall production costs.

  17. Multiplexed highly-accurate DNA sequencing of closely-related HIV-1 variants using continuous long reads from single molecule, real-time sequencing.

    PubMed

    Dilernia, Dario A; Chien, Jung-Ting; Monaco, Daniela C; Brown, Michael P S; Ende, Zachary; Deymier, Martin J; Yue, Ling; Paxinos, Ellen E; Allen, Susan; Tirado-Ramos, Alfredo; Hunter, Eric

    2015-11-16

    Single Molecule, Real-Time (SMRT) Sequencing (Pacific Biosciences, Menlo Park, CA, USA) provides the longest continuous DNA sequencing reads currently available. However, the relatively high error rate in the raw read data requires novel analysis methods to deconvolute sequences derived from complex samples. Here, we present a workflow of novel computer algorithms able to reconstruct viral variant genomes present in mixtures with an accuracy of >QV50. This approach relies exclusively on Continuous Long Reads (CLR), which are the raw reads generated during SMRT Sequencing. We successfully implement this workflow for simultaneous sequencing of mixtures containing up to forty different >9 kb HIV-1 full genomes. This was achieved using a single SMRT Cell for each mixture and desktop computing power. This novel approach opens the possibility of solving complex sequencing tasks that currently lack a solution.

  18. Fractal surface finish

    SciTech Connect

    Church, E.L.

    1988-04-15

    Surface finish measurements are usually fitted to models of the finish correlation function which are parametrized in terms of root-mean-square roughnesses, sigma, and correlation lengths, l. Highly finished optical surfaces, however, are frequently better described by fractal models, which involve inverse power-law spectra and are parametrized by spectral strengths, K/sub n/, and spectral indices, n. Analyzing measurements of fractal surfaces in terms of sigma and l gives results which are not intrinsic surface parameters but which depend on the bandwidth parameters of the measurement process used. This paper derives expressions for these pseudoparameters and discusses the errors involved in using them for the characterization and specification of surface finish.

  19. Fractal surface finish

    SciTech Connect

    Church, E.L.

    1988-01-01

    Surface finish measurements are usually fitted to models of the finish correlation function which are parameterized in terms of root-mean-square roughness, sigma, and correlation lengths, l. Highly-finished optical surfaces, however, are frequently better described by fractal models, which involve inverse-power-law spectra and are parameterized by spectral strengths, K/sub n/, and spectral indices, n. Analyzing measurements of fractal surfaces in terms of sigma and l gives results which are not intrinsic surface parameters but which depend on the bandwidth parameters of the measurement process used. This paper derives expressions for these pseudo parameters and discusses the errors involved in using them for the characterization and specification of surface finish. 30 refs., 5 figs., 1 tab.

  20. Sustainable Design of EPA's Campus in Research Triangle Park, NC—Environmental Performance Specifications in Construction Contracts—Section 01450 Sequence of Finishes Installation

    EPA Pesticide Factsheets

    Learn more about the special construction scheduling/sequencing requirements and procedures necessary to assure achievement of designed Indoor Air Quality (IAQ) levels for the completed project required by the EPA IAQ Program.

  1. Accurate Profiling of Gene Expression and Alternative Polyadenylation with Whole Transcriptome Termini Site Sequencing (WTTS-Seq)

    PubMed Central

    Zhou, Xiang; Li, Rui; Michal, Jennifer J.; Wu, Xiao-Lin; Liu, Zhongzhen; Zhao, Hui; Xia, Yin; Du, Weiwei; Wildung, Mark R.; Pouchnik, Derek J.; Harland, Richard M.; Jiang, Zhihua

    2016-01-01

    Construction of next-generation sequencing (NGS) libraries involves RNA manipulation, which often creates noisy, biased, and artifactual data that contribute to errors in transcriptome analysis. In this study, a total of 19 whole transcriptome termini site sequencing (WTTS-seq) and seven RNA sequencing (RNA-seq) libraries were prepared from Xenopus tropicalis adult and embryo samples to determine the most effective library preparation method to maximize transcriptomics investigation. We strongly suggest that appropriate primers/adaptors are designed to inhibit amplification detours and that PCR overamplification is minimized to maximize transcriptome coverage. Furthermore, genome annotation must be improved so that missing data can be recovered. In addition, a complete understanding of sequencing platforms is critical to limit the formation of false-positive results. Technically, the WTTS-seq method enriches both poly(A)+ RNA and complementary DNA, adds 5′- and 3′-adaptors in one step, pursues strand sequencing and mapping, and profiles both gene expression and alternative polyadenylation (APA). Although RNA-seq is cost prohibitive, tends to produce false-positive results, and fails to detect APA diversity and dynamics, its combination with WTTS-seq is necessary to validate transcriptome-wide APA. PMID:27098915

  2. Asymmetric single-strand polymorphism: an accurate and cost-effective method to amplify and sequence allelic variants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We needed to obtain an alternative to conventional cloning to generate high-quality DNA sequences from a variety of nuclear orthologs for phylogenetic studies in potato, to save time and money and to avoid problems typically encountered in cloning. We tested a variety of SSCP protocols to include pu...

  3. RCK: accurate and efficient inference of sequence- and structure-based protein–RNA binding models from RNAcompete data

    PubMed Central

    Orenstein, Yaron; Wang, Yuhao; Berger, Bonnie

    2016-01-01

    Motivation: Protein–RNA interactions, which play vital roles in many processes, are mediated through both RNA sequence and structure. CLIP-based methods, which measure protein–RNA binding in vivo, suffer from experimental noise and systematic biases, whereas in vitro experiments capture a clearer signal of protein RNA-binding. Among them, RNAcompete provides binding affinities of a specific protein to more than 240 000 unstructured RNA probes in one experiment. The computational challenge is to infer RNA structure- and sequence-based binding models from these data. The state-of-the-art in sequence models, Deepbind, does not model structural preferences. RNAcontext models both sequence and structure preferences, but is outperformed by GraphProt. Unfortunately, GraphProt cannot detect structural preferences from RNAcompete data due to the unstructured nature of the data, as noted by its developers, nor can it be tractably run on the full RNACompete dataset. Results: We develop RCK, an efficient, scalable algorithm that infers both sequence and structure preferences based on a new k-mer based model. Remarkably, even though RNAcompete data is designed to be unstructured, RCK can still learn structural preferences from it. RCK significantly outperforms both RNAcontext and Deepbind in in vitro binding prediction for 244 RNAcompete experiments. Moreover, RCK is also faster and uses less memory, which enables scalability. While currently on par with existing methods in in vivo binding prediction on a small scale test, we demonstrate that RCK will increasingly benefit from experimentally measured RNA structure profiles as compared to computationally predicted ones. By running RCK on the entire RNAcompete dataset, we generate and provide as a resource a set of protein–RNA structure-based models on an unprecedented scale. Availability and Implementation: Software and models are freely available at http://rck.csail.mit.edu/ Contact: bab@mit.edu Supplementary information

  4. Accurate Breakpoint Mapping in Apparently Balanced Translocation Families with Discordant Phenotypes Using Whole Genome Mate-Pair Sequencing

    PubMed Central

    Aristidou, Constantia; Koufaris, Costas; Theodosiou, Athina; Bak, Mads; Mehrjouy, Mana M.; Behjati, Farkhondeh; Tanteles, George; Christophidou-Anastasiadou, Violetta; Tommerup, Niels

    2017-01-01

    Familial apparently balanced translocations (ABTs) segregating with discordant phenotypes are extremely challenging for interpretation and counseling due to the scarcity of publications and lack of routine techniques for quick investigation. Recently, next generation sequencing has emerged as an efficacious methodology for precise detection of translocation breakpoints. However, studies so far have mainly focused on de novo translocations. The present study focuses specifically on familial cases in order to shed some light to this diagnostic dilemma. Whole-genome mate-pair sequencing (WG-MPS) was applied to map the breakpoints in nine two-way ABT carriers from four families. Translocation breakpoints and patient-specific structural variants were validated by Sanger sequencing and quantitative Real Time PCR, respectively. Identical sequencing patterns and breakpoints were identified in affected and non-affected members carrying the same translocations. PTCD1, ATP5J2-PTCD1, CADPS2, and STPG1 were disrupted by the translocations in three families, rendering them initially as possible disease candidate genes. However, subsequent mutation screening and structural variant analysis did not reveal any pathogenic mutations or unique variants in the affected individuals that could explain the phenotypic differences between carriers of the same translocations. In conclusion, we suggest that NGS-based methods, such as WG-MPS, can be successfully used for detailed mapping of translocation breakpoints, which can also be used in routine clinical investigation of ABT cases. Unlike de novo translocations, no associations were determined here between familial two-way ABTs and the phenotype of the affected members, in which the presence of cryptic imbalances and complex chromosomal rearrangements has been excluded. Future whole-exome or whole-genome sequencing will potentially reveal unidentified mutations in the patients underlying the discordant phenotypes within each family. In

  5. Identification of metallothionein subisoforms in HPLC using accurate mass and online sequencing by electrospray hybrid linear ion trap-orbital ion trap mass spectrometry.

    PubMed

    Mounicou, Sandra; Ouerdane, Laurent; L'Azou, Béatrice; Passagne, Isabelle; Ohayon-Courtès, Céline; Szpunar, Joanna; Lobinski, Ryszard

    2010-08-15

    A comprehensive approach to the characterization of metallothionein (MT) isoforms based on microbore HPLC with multimodal detection was developed. MTs were separated as Cd(7) complexes, detected by ICP MS and tentatively identified by molecular mass measured with 1-2 ppm accuracy using Orbital ion trap mass spectrometry. The identification was validated by accurate mass of the corresponding apo-MTs after postcolumn acidification and by their sequences acquired online by higher-energy collision dissociation MS/MS. The detection limits down to 10 fmol and 45 fmol could be obtained by ESI MS for apo- and Cd(7)-isoforms, respectively, and were lower than those obtained by ICP MS (100 fmol). The individual MT isoforms could be sequenced at levels as low as 200 fmol with the sequence coverage exceeding 90%. The approach was successfully applied to the identification of MT isoforms induced in a pig kidney cell line (LLC-PK(1)) exposed to CdS nanoparticles.

  6. BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters

    PubMed Central

    Chu, Justin; Sadeghi, Sara; Raymond, Anthony; Jackman, Shaun D.; Nip, Ka Ming; Mar, Richard; Mohamadi, Hamid; Butterfield, Yaron S.; Robertson, A. Gordon; Birol, Inanç

    2014-01-01

    Large datasets can be screened for sequences from a specific organism, quickly and with low memory requirements, by a data structure that supports time- and memory-efficient set membership queries. Bloom filters offer such queries but require that false positives be controlled. We present BioBloom Tools, a Bloom filter-based sequence-screening tool that is faster than BWA, Bowtie 2 (popular alignment algorithms) and FACS (a membership query algorithm). It delivers accuracies comparable with these tools, controls false positives and has low memory requirements. Availability and implementaion: www.bcgsc.ca/platform/bioinfo/software/biobloomtools Contact: cjustin@bcgsc.ca or ibirol@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25143290

  7. Accurate Prediction of Protein Functional Class From Sequence in the Mycobacterium Tuberculosis and Escherichia Coli Genomes Using Data Mining

    PubMed Central

    Karwath, Andreas; Clare, Amanda; Dehaspe, Luc

    2000-01-01

    The analysis of genomics data needs to become as automated as its generation. Here we present a novel data-mining approach to predicting protein functional class from sequence. This method is based on a combination of inductive logic programming clustering and rule learning. We demonstrate the effectiveness of this approach on the M. tuberculosis and E. coli genomes, and identify biologically interpretable rules which predict protein functional class from information only available from the sequence. These rules predict 65% of the ORFs with no assigned function in M. tuberculosis and 24% of those in E. coli, with an estimated accuracy of 60–80% (depending on the level of functional assignment). The rules are founded on a combination of detection of remote homology, convergent evolution and horizontal gene transfer. We identify rules that predict protein functional class even in the absence of detectable sequence or structural homology. These rules give insight into the evolutionary history of M. tuberculosis and E. coli. PMID:11119305

  8. Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes

    PubMed Central

    Lin, Hsin-Hung; Liao, Yu-Chieh

    2016-01-01

    Metagenomics, the application of shotgun sequencing, facilitates the reconstruction of the genomes of individual species from natural environments. A major challenge in the genome recovery domain is to agglomerate or ‘bin’ sequences assembled from metagenomic reads into individual groups. Metagenomic binning without consideration of reference sequences enables the comprehensive discovery of new microbial organisms and aids in the microbial genome reconstruction process. Here we present MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments. We demonstrate the superior performance of MyCC compared to other binning tools including CONCOCT, GroopM, MaxBin and MetaBAT on both synthetic and real human gut communities with a small sample size (one to 11 samples), as well as on a large metagenome dataset (over 250 samples). Moreover, we demonstrate the visualization of metagenomes in MyCC to aid in the reconstruction of genomes from distinct bins. MyCC is freely available at http://sourceforge.net/projects/sb2nhri/files/MyCC/. PMID:27067514

  9. UltraForm finishing

    NASA Astrophysics Data System (ADS)

    Fess, E.; Schoen, J.; Bechtold, M.; Mohring, D.

    2005-05-01

    A new compliant sub-aperture optical finishing technique is being investigated for the removal of mid-spatial frequency artifacts and smoothing of hard polycrystalline infrared ceramics for aspheric applications and conformal shaped optics. The UltraForm concept was developed by OptiPro Systems, Ontario, NY, and is a joint process development effort with the Center for Optics manufacturing (COM). The UltraForm tool is a pressurized, elastomeric bladder in the shape of a toroid. Finishing pads are attached to the periphery, allowing the use of a wide variety of pad materials and abrasive selections. Experimentation has been conducted using both slurry mixes and fixed abrasive pads. The toroidal tool is rotated while the compliant tool is compressed into contact with the surface. Currently this process has specific interest for the finishing of conformal ALON Domes. Also to be discussed will be new versions of the UltraForm Tools which are currently be developed and tested.

  10. A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.

    PubMed

    Zhang, Yuan; Sun, Yanni; Cole, James R

    2014-08-01

    Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, heterogeneous sequence coverage caused by heterogeneous expression or species abundance, similarity between isoforms or homologous genes, and large data size all pose challenges to de novo assembly. As a result, existing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footprint. In this work, we introduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of particular interest to biologists. It addresses the above challenges by conducting family-specific homology search, homology-guided overlap graph construction, and careful graph traversal. It can be applied to both RNA-Seq and metagenomic data. Our experimental results on an Arabidopsis RNA-Seq data set and two metagenomic data sets show that SAT-Assembler has smaller memory usage, comparable or better gene coverage, and lower chimera rate for assembling a set of genes from one or multiple pathways compared with other assembly tools. Moreover, the family-specific design and rapid homology search allow SAT-Assembler to be naturally compatible with parallel computing platforms. The source code of SAT-Assembler is available at https://sourceforge.net/projects/sat-assembler/. The data sets and experimental settings can be found in supplementary material.

  11. Sequencing the Unrearranged Human Immunoglobin

    SciTech Connect

    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

  12. A geometric sequence that accurately describes allowed multiple conductance levels of ion channels: the "three-halves (3/2) rule".

    PubMed Central

    Pollard, J R; Arispe, N; Rojas, E; Pollard, H B

    1994-01-01

    Ion channels can express multiple conductance levels that are not integer multiples of some unitary conductance, and that interconvert among one another. We report here that for 26 different types of multiple conductance channels, all allowed conductance levels can be calculated accurately using the geometric sequence gn = g(o) (3/2)n, where gn is a conductance level and n is an integer > or = 0. We refer to this relationship as the "3/2 Rule," because the value of any term in the sequence of conductances (gn) can be calculated as 3/2 times the value of the preceding term (gn-1). The experimentally determined average value for "3/2" is 1.491 +/- 0.095 (sample size = 37, average +/- SD). We also verify the choice of a 3/2 ratio on the basis of error analysis over the range of ratio values between 1.1 and 2.0. In an independent analysis using Marquardt's algorithm, we further verified the 3/2 ratio and the assignment of specific conductances to specific terms in the geometric sequence. Thus, irrespective of the open time probability, the allowed conductance levels of these channels can be described accurately to within approximately 6%. We anticipate that the "3/2 Rule" will simplify description of multiple conductance channels in a wide variety of biological systems and provide an organizing principle for channel heterogeneity and differential effects of channel blockers. PMID:7524712

  13. Sequencing Intractable DNA to Close Microbial Genomes

    SciTech Connect

    Hurt, Jr., Richard Ashley; Brown, Steven D; Podar, Mircea; Palumbo, Anthony Vito; 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 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 difficult 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. These developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  14. 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…

  15. 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.…

  16. Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the Family Erysipelotrichaceae

    PubMed Central

    Ramasamy, Dhamodharan; Lagier, Jean-Christophe; Nguyen, Thi Tien; Raoult, Didier; Fournier, Pierre-Edouard

    2013-01-01

    Dielma fastidiosa strain JC13T gen. nov., sp. nov. is the type strain of D. fastidiosa gen. nov., sp. nov., the type species of a new genus within the family Erysipelotrichaceae. This strain, whose draft genome is described here, was isolated from the fecal flora of a healthy 16-year-old male Senegalese volunteer. D. fastidiosa is a Gram-negative anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,574,031 bp long genome comprises a 3,556,241-bp chromosome and a 17,790-bp plasmid. The chromosome contains 3,441 protein-coding and 50 RNA genes, including 3 rRNA genes, whereas the plasmid contains 17 protein-coding genes. PMID:23991263

  17. Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features

    NASA Astrophysics Data System (ADS)

    Li, Yuan; Wang, Mingjun; Wang, Huilin; Tan, Hao; Zhang, Ziding; Webb, Geoffrey I.; Song, Jiangning

    2014-07-01

    Lysine acetylation is a reversible post-translational modification, playing an important role in cytokine signaling, transcriptional regulation, and apoptosis. To fully understand acetylation mechanisms, identification of substrates and specific acetylation sites is crucial. Experimental identification is often time-consuming and expensive. Alternative bioinformatics methods are cost-effective and can be used in a high-throughput manner to generate relatively precise predictions. Here we develop a method termed as SSPKA for species-specific lysine acetylation prediction, using random forest classifiers that combine sequence-derived and functional features with two-step feature selection. Feature importance analysis indicates functional features, applied for lysine acetylation site prediction for the first time, significantly improve the predictive performance. We apply the SSPKA model to screen the entire human proteome and identify many high-confidence putative substrates that are not previously identified. The results along with the implemented Java tool, serve as useful resources to elucidate the mechanism of lysine acetylation and facilitate hypothesis-driven experimental design and validation.

  18. Performing accurate joint kinematics from 3-D in vivo image sequences through consensus-driven simultaneous registration.

    PubMed

    Jacq, Jean-José; Cresson, Thierry; Burdin, Valérie; Roux, Christian

    2008-05-01

    This paper addresses the problem of the robust registration of multiple observations of the same object. Such a problem typically arises whenever it becomes necessary to recover the trajectory of an evolving object observed through standard 3-D medical imaging techniques. The instances of the tracked object are assumed to be variously truncated, locally subject to morphological evolutions throughout the sequence, and imprinted with significant segmentation errors as well as significant noise perturbations. The algorithm operates through the robust and simultaneous registration of all surface instances of a given object through median consensus. This operation consists of two interwoven processes set up to work in close collaboration. The first one progressively generates a median and implicit shape computed with respect to current estimations of the registration transformations, while the other refines these transformations with respect to the current estimation of their median shape. When compared with standard robust techniques, tests reveal significant improvements, both in robustness and precision. The algorithm is based on widely-used techniques, and proves highly effective while offering great flexibility of utilization.

  19. 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

  20. Non-contiguous finished genome sequence and description of Sulfurimonas hongkongensis sp. nov., a strictly anaerobic denitrifying, hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from marine sediment.

    PubMed

    Cai, Lin; Shao, Ming-Fei; Zhang, Tong

    2014-06-15

    Here, we report a type strain AST-10 representing a novel species Sulfurimonas hongkongensis within Epsilonproteobacteria, which is involved in marine sedimentary sulfur oxidation and denitrification. Strain AST-10(T) (= DSM 22096(T) = JCM 18418(T)) was isolated from the coastal sediment at the Kai Tak Approach Channel connected to Victoria Harbour in Hong Kong. It grew chemolithoautotrophically using thiosulfate, sulfide or hydrogen as the sole electron donor and nitrate as the electron acceptor under anoxic conditions. It was rod-shaped and grew at 15-35°C (optimum at 30°C), pH 6.5-8.5 (optimum at 7.0-7.5), and 10-60 g L(-1) NaCl (optimum at 30 g L(-1)). Genome sequencing and annotation of strain AST-10(T) showed a 2,302,023 bp genome size, with 34.9% GC content, 2,290 protein-coding genes, and 42 RNA genes, including 3 rRNA genes.

  1. Urolithiasis in finishing pigs.

    PubMed

    Maes, D G D; Vrielinck, J; Millet, S; Janssens, G P J; Deprez, P

    2004-11-01

    Urolithiasis in sows and neonatal pigs is well-known, but information on its occurrence and impact in finishing pigs is sparse. This study reports three outbreaks of urolithiasis in finishing pigs. In one herd, no symptoms were observed, whereas in the other herds the presence of calculi caused obstruction of the urinary tract resulting in death. Using infra-red spectroscopy, the predominant mineral-type found in the uroliths was calcium carbonate (calcite). Only small amounts of calcium oxalate (< 1%) could be detected. A high urinary pH, small abnormalities in the mineral composition of the feed and insufficient drinking water were the most important risk factors identified. To prevent urolithiasis, it is important to ensure adequate water intake, to provide a balanced mineral diet, and to avoid urinary tract infections.

  2. Nanometric Finishing on Biomedical Implants by Abrasive Flow Finishing

    NASA Astrophysics Data System (ADS)

    Subramanian, Kavithaa Thirumalai; Balashanmugam, Natchimuthu; Shashi Kumar, Panaghra Veeraiah

    2016-01-01

    Abrasive flow finishing (AFF) is a non-conventional finishing technique that offers better accuracy, efficiency, consistency, economy in finishing of complex/difficult to machine materials/components and provides the possibility of effective automation as aspired by the manufacturing sector. The present study describes the finishing of a hip joint made of ASTM grade Co-Cr alloy by Abrasive Flow Machining (AFM) process. The major input parameters of the AFF process were optimized for achieving nanometric finishing of the component. The roughness average (Ra) values were recorded during experimentation using surface roughness tester and the results are discussed in detail. The surface finished hip joints were characterized using Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM) and residual stress analysis using X-Ray Diffraction (XRD). The discussion lays emphasis on the significance, efficacy and versatile nature of the AFF process in finishing of bio-medical implants.

  3. A hybrid approach for the automated finishing of bacterial genomes.

    PubMed

    Bashir, Ali; Klammer, Aaron A; 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

    2012-07-01

    Advances in DNA sequencing technology have improved our ability to characterize most genomic diversity. However, accurate resolution of large structural events is challenging because of the short read lengths of second-generation technologies. Third-generation sequencing technologies, which can yield longer multikilobase reads, have the potential to address limitations associated with genome assembly. 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 relevant structure were completely resolved. In separate control assemblies on experimental and simulated data for the canonical N16961 cholera reference strain, we obtained 14 scaffolds of greater than 1 kb for the experimental data and 8 scaffolds of greater than 1 kb for the simulated data, which allowed us to correct several errors in contigs assembled from the short-read data alone. This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly.

  4. Breath-hold Multi-Echo Fast Spin-Echo Pulse Sequence for Accurate R2 Measurement in the Heart and Liver

    PubMed Central

    Kim, Daniel; Jensen, Jens H.; Wu, Ed X.; Sheth, Sujit S.; Brittenham, Gary M.

    2009-01-01

    Measurement of proton transverse relaxation rates (R2) is a generally useful means for quantitative characterization of pathological changes in tissue with a variety of clinical applications. The most widely used R2 measurement method is the Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence but its relatively long scan time requires respiratory gating for chest or body MRI, rendering this approach impractical for comprehensive assessment within a clinically acceptable examination time. The purpose of our study was to develop a breath-hold multi-echo fast spin-echo (FSE) sequence for accurate measurement of R2 in the liver and heart. Phantom experiments and studies of subjects in vivo were performed to compare the FSE data with the corresponding even-echo CPMG data. For pooled data, the R2 measurements were strongly correlated (Pearson correlation coefficient = 0.99) and in excellent agreement (mean difference [CPMG-FSE] = 0.10 s−1; 95% limits of agreement were 1.98 and −1.78 s−1) between the two pulse sequences. PMID:19526516

  5. PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases

    PubMed Central

    Floden, Evan W.; Tommaso, Paolo D.; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

    2016-01-01

    The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. PMID:27106060

  6. Accurate and absolute diffusion measurements of Rhodamine 6G in low-concentration aqueous solutions by the PGSE-WATERGATE sequence

    SciTech Connect

    Majer, G.; Zick, K.

    2015-04-28

    A pulsed field gradient spin-echo nuclear magnetic resonance (NMR) sequence with solvent suppression (PGSE-WATERGATE) was applied to accurately measure the diffusion coefficients of Rhodamine 6G (Rh6G) in low-concentration aqueous solutions. Three samples with Rh6G concentrations of C{sub Rh6G} = 1, 4.5, and 25 μM were investigated. The precise determination of the diffusion coefficients in this low-concentration range was made possible by using a cryogenically cooled NMR probe and by the effective solvent suppression of the PGSE-WATERGATE sequence. The present results bridge the gap between diffusion data measured by fluorescence correlation spectroscopy in the single molecule limit and diffusivities obtained by pulsed field gradient NMR (PFG-NMR) without solvent suppression at higher concentrations. To further extend the concentration range, the diffusion coefficient of Rh6G was also measured on a sample with C{sub Rh6G} = 410 μM by PFG-NMR. The overall concentration dependence of the Rh6G diffusion at 25 °C is discussed in terms of dimerization of the Rh6G molecules. The concentration-dependent monomer/dimer proportion is deduced from the diffusion data.

  7. 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

  8. 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.

  9. Archived neonatal dried blood spot samples can be used for accurate whole genome and exome-targeted next-generation sequencing.

    PubMed

    Hollegaard, Mads Vilhelm; Grauholm, Jonas; Nielsen, Ronni; Grove, Jakob; Mandrup, Susanne; Hougaard, David Michael

    2013-01-01

    Dried blood spot samples (DBSS) have been collected and stored for decades as part of newborn screening programmes worldwide. Representing almost an entire population under a certain age and collected with virtually no bias, the Newborn Screening Biobanks are of immense value in medical studies, for example, to examine the genetics of various disorders. We have previously demonstrated that DNA extracted from a fraction (2×3.2mm discs) of an archived DBSS can be whole genome amplified (wgaDNA) and used for accurate array genotyping. However, until now, it has been uncertain whether wgaDNA from DBSS can be used for accurate whole genome sequencing (WGS) and exome sequencing (WES). This study examined two individuals represented by three different types of samples each: whole-blood (reference samples), 3-year-old DBSS spotted with reference material (refDBSS), and 27- to 29-year-old archived neonatal DBSS (neoDBSS) stored at -20°C in the Danish Newborn Screening Biobank. The reference samples were genotyped using an Illumina Omni2.5M array, and all samples were sequenced on a HighSeq2000 Paired-End flow cell. First, we compared the array single nucleotide polymorphism (SNP) genotype data to the single nucleotide variation (SNV) calls from the WGS and WES SNV calls. We also compared the WGS and WES reference sample SNV calls to the DBSS SNV calls. The overall performance of the archived DBSS was similar to the whole blood reference sample. Plotting the error rates relative to coverage revealed that the error rates of DBSS were similar to that of their reference samples. SNVs called with a coverage<×8 had error rates between 1.5 and 35%, whereas the error rates of SNVs called with a coverage≥8 were <1.5%. In conclusion, the wgaDNA amplified from both new and old neonatal DBSS perform as well as their whole-blood reference samples with regards to error rates, strongly indicating that neonatal DBSS collected shortly after birth and stored for decades comprise an

  10. Advanced cleaning by mass finishing

    NASA Astrophysics Data System (ADS)

    McCoy, M. W.

    1983-10-01

    The effectiveness of vibratory finishing for removing a variety of radioactively contaminated soils was investigated by measuring the radiation levels of the test material, the lining of the vibratory finishing tub, and the media. Many soils including corrosion products, scale, oil, grease and paint were removed from steels, aluminum, polyvinyl chloride, plexiglass, glass and flexible materials such as rubber. Zinc, copper, and lead were not cleaned. Results indicate that vibratory finishing should be an effective cleaning process or a variety of manufacturing operations.

  11. Sequencer-Based Capillary Gel Electrophoresis (SCGE) Targeting the rDNA Internal Transcribed Spacer (ITS) Regions for Accurate Identification of Clinically Important Yeast Species

    PubMed Central

    Chen, Sharon C.-A.; Wang, He; Zhang, Li; Fan, Xin; Xu, Zhi-Peng; Cheng, Jing-Wei; Kong, Fanrong; Zhao, Yu-Pei; Xu, Ying-Chun

    2016-01-01

    Accurate species identification of Candida, Cryptococcus, Trichosporon and other yeast pathogens is important for clinical management. In the present study, we developed and evaluated a yeast species identification scheme by determining the rDNA internal transcribed spacer (ITS) region length types (LTs) using a sequencer-based capillary gel electrophoresis (SCGE) approach. A total of 156 yeast isolates encompassing 32 species were first used to establish a reference SCGE ITS LT database. Evaluation of the ITS LT database was then performed on (i) a separate set of (n = 97) clinical isolates by SCGE, and (ii) 41 isolates of 41 additional yeast species from GenBank by in silico analysis. Of 156 isolates used to build the reference database, 41 ITS LTs were identified, which correctly identified 29 of the 32 (90.6%) species, with the exception of Trichosporon asahii, Trichosporon japonicum and Trichosporon asteroides. In addition, eight of the 32 species revealed different electropherograms and were subtyped into 2–3 different ITS LTs each. Of the 97 test isolates used to evaluate the ITS LT scheme, 96 (99.0%) were correctly identified to species level, with the remaining isolate having a novel ITS LT. Of the additional 41 isolates for in silico analysis, none was misidentified by the ITS LT database except for Trichosporon mucoides whose ITS LT profile was identical to that of Trichosporon dermatis. In conclusion, yeast identification by the present SCGE ITS LT assay is a fast, reproducible and accurate alternative for the identification of clinically important yeasts with the exception of Trichosporon species. PMID:27105313

  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. NICE3 Textile Finishing Process

    SciTech Connect

    Blazek, S.

    1999-01-29

    This new energy-saving approach to fabric finishing can help our domestic textile industry compete in an increasingly competitive global market. Learn how this new technology can lower your maintenance costs and increase your productivity.

  14. Cosmogenic Beryllium Production from Ocean Sediment Sequences Help to Construct Accurate Records of the Geodynamo Variation at the Millennial to Million Year Scale

    NASA Astrophysics Data System (ADS)

    Thouveny, N.; Ménabréaz, L.; Bourles, D. L.; Demory, F.; Guillou, V.; Arnold, M.; Vidal, L.

    2013-12-01

    The possible contribution of the axial precession to the energy of the geodynamo was recently reintroduced by theoretical and experimental studies. It is supported by relative paleointensity stacks and deep sea floor magnetization records documenting series of geomagnetic dipole lows (GDL) with recurrence at periods ranging from 30 to 120 kyr, and intriguing phase relationships with obliquity variations and δ18O records (e.g. Fuller, 2006; Thouveny et al. 2008). Yet, these time-series are presently not precise and complete enough to validate this fundamental and debated relationship. The MAG-ORB project funded by the French "Agence nationale de la Recherche" aims at reconstructing the series of GDL over the last Ma, by coupling -on the very same sedimentary sequences- the reconstructions of paleomagnetic variations, cosmogenic10Be production variations and δ18O isotope variations. Recent results (e.g. Ménabréaz et al., 2012, 2013) demonstrate that 10Be overproduction events are systematically induced by the GDL linked with excursions and reversals -as awaited from the theoretical and empirical non linear inverse relationship established between the magnetic moment value and the penetration rate of cosmic rays and particles. The calibration of the authigenic 10Be/9Be ratio signals using absolute Virtual (axial) Dipole Moment values allowed us to construct 10Be-derived Geomagnetic Dipole Moment records over the last millennium, the last 60 ka and the last Ma, allowing to assess the robustness of the GDL series by a method completely independent from rock and paleo-magnetic methods. These records are comparable with individuals RPI records obtained from the same cores, and with global RPI stacks (e.g. GLOPIS, SINT 800 and PISO-1500). Since the Beryllium atoms are adsorbed on the settling silicate particles, the measured 10Be/9Be ratio signatures of cosmogenic isotope overproductions accurately indicate the exact stratigraphic position of the GDL in the sedimentary

  15. Dimensioning, Tolerancing, and Machine Finishes.

    ERIC Educational Resources Information Center

    Adams, George C.

    Intended for use with the vocational education student interested in technical drawing, this guide provides answers to questions relating to dimensioning and tolerancing machine drawings. It also gives examples of standard dimensioning practices, tolerancing applications, and finish applications. The problems and examples presented are based on…

  16. 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…

  17. 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.

  18. Figure and finish of grazing incidence mirrors

    SciTech Connect

    Takacs, P.Z. ); Church, E.L. . Army Armament Research, Development and Engineering Center)

    1989-08-01

    Great improvement has been made in the past several years in the quality of optical components used in synchrotron radiation (SR) beamlines. Most of this progress has been the result of vastly improved metrology techniques and instrumentation permitting rapid and accurate measurement of the surface finish and figure on grazing incidence optics. A significant theoretical effort has linked the actual performance of components used as x-ray wavelengths to their topological properties as measured by surface profiling instruments. Next-generation advanced light sources will require optical components and systems to have sub-arc second surface figure tolerances. This paper will explore the consequences of these requirements in terms of manufacturing tolerances to see if the present manufacturing state-of-the-art is capable of producing the required surfaces. 15 refs., 14 figs., 2 tabs.

  19. Finishing bacterial genome assemblies with Mix

    PubMed Central

    2013-01-01

    Motivation 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. Methods 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. Results 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. Availability 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/. PMID:24564706

  20. The allele distribution in next-generation sequencing data sets is accurately described as the result of a stochastic branching process.

    PubMed

    Heinrich, Verena; Stange, Jens; Dickhaus, Thorsten; Imkeller, Peter; Krüger, Ulrike; Bauer, Sebastian; Mundlos, Stefan; Robinson, Peter N; Hecht, Jochen; Krawitz, Peter M

    2012-03-01

    With the availability of next-generation sequencing (NGS) technology, it is expected that sequence variants may be called on a genomic scale. Here, we demonstrate that a deeper understanding of the distribution of the variant call frequencies at heterozygous loci in NGS data sets is a prerequisite for sensitive variant detection. We model the crucial steps in an NGS protocol as a stochastic branching process and derive a mathematical framework for the expected distribution of alleles at heterozygous loci before measurement that is sequencing. We confirm our theoretical results by analyzing technical replicates of human exome data and demonstrate that the variance of allele frequencies at heterozygous loci is higher than expected by a simple binomial distribution. Due to this high variance, mutation callers relying on binomial distributed priors are less sensitive for heterozygous variants that deviate strongly from the expected mean frequency. Our results also indicate that error rates can be reduced to a greater degree by technical replicates than by increasing sequencing depth.

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. Accurate measurement of heteronuclear dipolar couplings by phase-alternating R-symmetry (PARS) sequences in magic angle spinning NMR spectroscopy

    SciTech Connect

    Hou, Guangjin E-mail: tpolenov@udel.edu; Lu, Xingyu E-mail: lexvega@comcast.net; Vega, Alexander J. E-mail: lexvega@comcast.net; Polenova, Tatyana E-mail: tpolenov@udel.edu

    2014-09-14

    We report a Phase-Alternating R-Symmetry (PARS) dipolar recoupling scheme for accurate measurement of heteronuclear {sup 1}H-X (X = {sup 13}C, {sup 15}N, {sup 31}P, etc.) dipolar couplings in MAS NMR experiments. It is an improvement of conventional C- and R-symmetry type DIPSHIFT experiments where, in addition to the dipolar interaction, the {sup 1}H CSA interaction persists and thereby introduces considerable errors in the dipolar measurements. In PARS, phase-shifted RN symmetry pulse blocks applied on the {sup 1}H spins combined with π pulses applied on the X spins at the end of each RN block efficiently suppress the effect from {sup 1}H chemical shift anisotropy, while keeping the {sup 1}H-X dipolar couplings intact. Another advantage over conventional DIPSHIFT experiments, which require the signal to be detected in the form of a reduced-intensity Hahn echo, is that the series of π pulses refocuses the X chemical shift and avoids the necessity of echo formation. PARS permits determination of accurate dipolar couplings in a single experiment; it is suitable for a wide range of MAS conditions including both slow and fast MAS frequencies; and it assures dipolar truncation from the remote protons. The performance of PARS is tested on two model systems, [{sup 15}N]-N-acetyl-valine and [U-{sup 13}C,{sup 15}N]-N-formyl-Met-Leu-Phe tripeptide. The application of PARS for site-resolved measurement of accurate {sup 1}H-{sup 15}N dipolar couplings in the context of 3D experiments is presented on U-{sup 13}C,{sup 15}N-enriched dynein light chain protein LC8.

  8. Accurate measurement of heteronuclear dipolar couplings by phase-alternating R-symmetry (PARS) sequences in magic angle spinning NMR spectroscopy.

    PubMed

    Hou, Guangjin; Lu, Xingyu; Vega, Alexander J; Polenova, Tatyana

    2014-09-14

    We report a Phase-Alternating R-Symmetry (PARS) dipolar recoupling scheme for accurate measurement of heteronuclear (1)H-X (X = (13)C, (15)N, (31)P, etc.) dipolar couplings in MAS NMR experiments. It is an improvement of conventional C- and R-symmetry type DIPSHIFT experiments where, in addition to the dipolar interaction, the (1)H CSA interaction persists and thereby introduces considerable errors in the dipolar measurements. In PARS, phase-shifted RN symmetry pulse blocks applied on the (1)H spins combined with π pulses applied on the X spins at the end of each RN block efficiently suppress the effect from (1)H chemical shift anisotropy, while keeping the (1)H-X dipolar couplings intact. Another advantage over conventional DIPSHIFT experiments, which require the signal to be detected in the form of a reduced-intensity Hahn echo, is that the series of π pulses refocuses the X chemical shift and avoids the necessity of echo formation. PARS permits determination of accurate dipolar couplings in a single experiment; it is suitable for a wide range of MAS conditions including both slow and fast MAS frequencies; and it assures dipolar truncation from the remote protons. The performance of PARS is tested on two model systems, [(15)N]-N-acetyl-valine and [U-(13)C,(15)N]-N-formyl-Met-Leu-Phe tripeptide. The application of PARS for site-resolved measurement of accurate (1)H-(15)N dipolar couplings in the context of 3D experiments is presented on U-(13)C,(15)N-enriched dynein light chain protein LC8.

  9. The Robotic Edge Finishing Laboratory

    SciTech Connect

    Loucks, C.S.; Selleck, C.B.

    1990-08-01

    The Robotic Edge Finishing Laboratory at Sandia National Laboratories is developing four areas of technology required for automated deburring, chamfering, and blending of machined edges: (1) the automatic programming of robot trajectories and deburring processes using information derived from a CAD database, (2) the use of machine vision for locating the workpiece coupled with force control to ensure proper tool contact, (3) robotic deburring, blending, and machining of precision chamfered edges, and (4) in-process automated inspection of the formed edge. The Laboratory, its components, integration, and results from edge finishing experiments to date are described here. Also included is a discussion of the issues regarding implementation of the technology in a production environment. 24 refs., 17 figs.

  10. Ct shift: A novel and accurate real-time PCR quantification model for direct comparison of different nucleic acid sequences and its application for transposon quantifications.

    PubMed

    Kolacsek, Orsolya; Pergel, Enikő; Varga, Nóra; Apáti, Ágota; Orbán, Tamás I

    2017-01-20

    There are numerous applications of quantitative PCR for both diagnostic and basic research. As in many other techniques the basis of quantification is that comparisons are made between different (unknown and known or reference) specimens of the same entity. When the aim is to compare real quantities of different species in samples, one cannot escape their separate precise absolute quantification. We have established a simple and reliable method for this purpose (Ct shift method) which combines the absolute and the relative approach. It requires a plasmid standard containing both sequences of amplicons to be compared (e.g. the target of interest and the endogenous control). It can serve as a reference sample with equal copies of templates for both targets. Using the ΔΔCt formula we can quantify the exact ratio of the two templates in each unknown sample. The Ct shift method has been successfully applied for transposon gene copy measurements, as well as for comparison of different mRNAs in cDNA samples. This study provides the proof of concept and introduces some potential applications of the method; the absolute nature of results even without the need for real reference samples can contribute to the universality of the method and comparability of different studies.

  11. VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing

    PubMed Central

    Medina, Ignacio; De Maria, Alejandro; Bleda, Marta; Salavert, Francisco; Alonso, Roberto; Gonzalez, Cristina Y.; Dopazo, Joaquin

    2012-01-01

    The massive use of Next-Generation Sequencing (NGS) technologies is uncovering an unexpected amount of variability. The functional characterization of such variability, particularly in the most common form of variation found, the Single Nucleotide Variants (SNVs), has become a priority that needs to be addressed in a systematic way. VARIANT (VARIant ANalyis Tool) reports information on the variants found that include consequence type and annotations taken from different databases and repositories (SNPs and variants from dbSNP and 1000 genomes, and disease-related variants from the Genome-Wide Association Study (GWAS) catalog, Online Mendelian Inheritance in Man (OMIM), Catalog of Somatic Mutations in Cancer (COSMIC) mutations, etc). VARIANT also produces a rich variety of annotations that include information on the regulatory (transcription factor or miRNA-binding sites, etc.) or structural roles, or on the selective pressures on the sites affected by the variation. This information allows extending the conventional reports beyond the coding regions and expands the knowledge on the contribution of non-coding or synonymous variants to the phenotype studied. Contrarily to other tools, VARIANT uses a remote database and operates through efficient RESTful Web Services that optimize search and transaction operations. In this way, local problems of installation, update or disk size limitations are overcome without the need of sacrifice speed (thousands of variants are processed per minute). VARIANT is available at: http://variant.bioinfo.cipf.es. PMID:22693211

  12. International innovations in optical finishing

    NASA Astrophysics Data System (ADS)

    Jacobs, Stephen D.

    2004-10-01

    Every few years new polishing technologies attempt to make the transition from the research laboratory into the commercial sector. Success awaits any process that is well controlled and predictable (e.g., deterministic), rapid, capable of smoothing to sub-nm rms roughness levels while removing damage from grinding, affordable, and easily implemented. Applicability to different optical materials and a variety of part sizes and shapes is extremely important, but may not be required for a new technology to succeed in a niche market. This paper reviews six innovations in polishing of precision optics: Canon"s Super-Smooth Polisher (CSSP) that uses a sub-aperture pitch lap - a relatively mature but important base-line technology; Nikon / Osaka University"s RF Plasma Chemical Vaporization Machining (CVM); Epion"s Gas Cluster Ion Beam (GCIB) Process; the IOM University of Leipzig / NTGL Ion Beam Finishing (IBF) Technology; Zeeko"s "Precessions" Process with a sub-aperture section of an inflatable pad; and QED Technology"s Magnetorheological Finishing (MRF) with a magnetic fluid ribbon. The removal mechanism and some recent achievements for each process are discussed.

  13. Megraft: A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Metagenomic libraries represent subsamples of the total DNA found at a study site and offer unprecedented opportunities to study ecological and functional aspects of microbial communities. To examine the depth of the sequencing effort, rarefaction analysis of the ribosomal small sub-unit (SSU/16S/18...

  14. 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.

  15. Evaluation of finishing and polishing techniques on surface roughness of chromium-cobalt castings.

    PubMed

    Aydin, A K

    1991-06-01

    The effect of finishing and polishing techniques on surface roughness of a chromium-cobalt alloy was evaluated by means of a stylus profile instrumentation and scanning electron microscopy. Scanning electron micrographs, surface profile tracings, surface roughness recordings, and statistical analysis of data support the finding that the best surface finish is obtained when sandblasting, hard stone, medium abrasive disk, second sandblasting, electropolishing, hard rubber point, hard felt disk with pumice slurry, and felt disk and soft brush with polishing paste are used progressively. The results of this study indicate that the finishing procedure should be carried out in a logical, systematic sequence of steps.

  16. An improved evaluation of surface finish with a three dimensional tester

    NASA Technical Reports Server (NTRS)

    GRANDADAM; PREBET; RIOUT

    1980-01-01

    The design and programming of an automated three dimensional surface finish tester is described. The device produces a three dimensional image of the microscopic texture of the examined surface. The surface finish tester presents the following advantages over conventional profilometry: (1) more complete exploration of surface texture by successive probe sweeps; (2) automation of measuring and calculating; (3) more accurate representation of the derived parameters; (4) analysis of the degree of homogeneity of the surface; (5) three dimensional graphic representation accurately depicting the state of the surface; (6) detection of local imperfections; and (7) detection of scoring that occurred during machining.

  17. 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 ...

  18. 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....

  19. 25 CFR 301.8 - Finish.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 2 2011-04-01 2011-04-01 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. 25 CFR 301.8 - Finish.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 25 Indians 2 2012-04-01 2012-04-01 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....

  1. 25 CFR 301.8 - Finish.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 25 Indians 2 2014-04-01 2014-04-01 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....

  2. 25 CFR 301.8 - Finish.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 25 Indians 2 2013-04-01 2013-04-01 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....

  3. 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.

  4. FON: From Start to Finish

    NASA Astrophysics Data System (ADS)

    Pakuliak, L. K.; Andruk, V. M.; Golovnia, V. V.; Shatokhina, S. V.; Yizhakevych, O. M.; Ivanov, G. A.; Yatsenko, A. I.; Sergeeva, T. P.

    Almost 40-year history of FON project ended with the creation of the whole northern sky catalog of objects down to B ≤ 16.5m. The idea of 4-fold overlapping of the northern sky with 6 wide-field astrographs has not been realized in full. For historical reasons it has been transformed into the 2-fold overlapping observational program of MAO NAS of Ukraine, resulted in three versions of the multimillion catalog of positions, proper motions, and B-magnitudes of stars. The first version of 1.2 million stars had been finished before the 2000s and is based on the AC object list. The measurements of plates were made by automatic measuring complex PARSEC, specially developed for massive photographic reviews. As the input list was limited by AC objects, the most part of stars on the FON plates remained unmeasured. Principles of workflow organization of such works formed the basis for the further development of the project using the latest IT-technologies. For the creation of the second and the third versions of the catalog, the list of objects was obtained as a result of total digitizing of plates and their image processing. The final third version contains 19.5 million stars and galaxies with the maximum possible for the photographic astrometry accuracy. The collection of plates, obtained in other observatories - participants of the project, are partially safe and can be used for the same astrometric tasks.

  5. The Genome Sequencing Center at NCGR

    SciTech Connect

    Schilkey, Faye

    2010-06-02

    Faye Schilkey from the National Center for Genome Resources discusses NCGR's research, sequencing and analysis experience on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  6. Plutonium finishing plant dangerous waste training plan

    SciTech Connect

    ENTROP, G.E.

    1999-05-24

    This training plan describes general requirements, worker categories, and provides course descriptions for operation of the Plutonium Finish Plant (PFP) waste generation facilities, permitted treatment, storage and disposal (TSD) units, and the 90-Day Accumulation Areas.

  7. 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.

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

    ScienceCinema

    Jenkins, David [EdgeBio

    2016-07-12

    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.

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

    SciTech Connect

    Jenkins, David

    2012-06-01

    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.

  10. Sequencing Technologies Panel at SFAF

    SciTech Connect

    Turner, Steve; Fiske, Haley; Knight, Jim; Rhodes, Michael; Vander Horn, Peter

    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

  11. An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones

    PubMed Central

    Butterfield, Yaron S. N.; Marra, Marco A.; Asano, Jennifer K.; Chan, Susanna Y.; Guin, Ranabir; Krzywinski, Martin I.; Lee, Soo Sen; MacDonald, Kim W. K.; Mathewson, Carrie A.; Olson, Teika E.; Pandoh, Pawan K.; Prabhu, Anna-Liisa; Schnerch, Angelique; Skalska, Ursula; Smailus, Duane E.; Stott, Jeff M.; Tsai, Miranda I.; Yang, George S.; Zuyderduyn, Scott D.; Schein, Jacqueline E.; Jones, Steven J. M.

    2002-01-01

    We describe an efficient high-throughput method for accurate DNA sequencing of entire cDNA clones. Developed as part of our involvement in the Mammalian Gene Collection full-length cDNA sequencing initiative, the method has been used and refined in our laboratory since September 2000. Amenable to large scale projects, we have used the method to generate >7 Mb of accurate sequence from 3695 candidate full-length cDNAs. Sequencing is accomplished through the insertion of Mu transposon into cDNAs, followed by sequencing reactions primed with Mu-specific sequencing primers. Transposon insertion reactions are not performed with individual cDNAs but rather on pools of up to 96 clones. This pooling strategy reduces the number of transposon insertion sequencing libraries that would otherwise be required, reducing the costs and enhancing the efficiency of the transposon library construction procedure. Sequences generated using transposon-specific sequencing primers are assembled to yield the full-length cDNA sequence, with sequence editing and other sequence finishing activities performed as required to resolve sequence ambiguities. Although analysis of the many thousands (22 785) of sequenced Mu transposon insertion events revealed a weak sequence preference for Mu insertion, we observed insertion of the Mu transposon into 1015 of the possible 1024 5mer candidate insertion sites. PMID:12034834

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

    DOE PAGES

    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.

  13. Effect of Burnishing Parameters on Surface Finish

    NASA Astrophysics Data System (ADS)

    Shirsat, Uddhav; Ahuja, Basant; Dhuttargaon, Mukund

    2016-06-01

    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.

  14. UltraForm finishing; Techical Digest

    NASA Astrophysics Data System (ADS)

    Fess, Edward; Schoen, John; Bechtold, Michael; Mohring, D.

    2005-05-01

    A new compliant sub-aperture optical finishing technique is being investigated for the removal of mid-spatial frequency artifacts and smoothing of hard polycrystalline infrared ceramics for aspheric applications and conformal shaped optics. The UltraForm concept was developed by OptiPro Systems, Ontario, NY, and is a joint process development effort with the Center for Optics Manufacturing (COM). The UltraForm tool is a pressurized, elastomeric bladder in the shape of a toroid. Finishing pads are attached to the periphery, allowing the use of a wide variety of pad materials and abrasive selections. Experimentation has been conducted using both slurry mixes and fixed abrasive pads. The toroidal tool is rotated while the compliant tool is compressed into contact with the surface. Currently this process has specific interest for the finishing of conformal ALON domes. Also to be discussed will be new versions of the UltraForm Tool, which are currently being developed and tested.

  15. Accurate inference of local phased ancestry of modern admixed populations.

    PubMed

    Ma, Yamin; Zhao, Jian; Wong, Jian-Syuan; Ma, Li; Li, Wenzhi; Fu, Guoxing; Xu, Wei; Zhang, Kui; Kittles, Rick A; Li, Yun; Song, Qing

    2014-07-23

    Population stratification is a growing concern in genetic-association studies. Averaged ancestry at the genome level (global ancestry) is insufficient for detecting the population substructures and correcting population stratifications in association studies. Local and phase stratification are needed for human genetic studies, but current technologies cannot be applied on the entire genome data due to various technical caveats. Here we developed a novel approach (aMAP, ancestry of Modern Admixed Populations) for inferring local phased ancestry. It took about 3 seconds on a desktop computer to finish a local ancestry analysis for each human genome with 1.4-million SNPs. This method also exhibits the scalability to larger datasets with respect to the number of SNPs, the number of samples, and the size of reference panels. It can detect the lack of the proxy of reference panels. The accuracy was 99.4%. The aMAP software has a capacity for analyzing 6-way admixed individuals. As the biomedical community continues to expand its efforts to increase the representation of diverse populations, and as the number of large whole-genome sequence datasets continues to grow rapidly, there is an increasing demand on rapid and accurate local ancestry analysis in genetics, pharmacogenomics, population genetics, and clinical diagnosis.

  16. Figaro: a novel statistical method for vector sequence removal

    PubMed Central

    White, James Robert; Roberts, Michael; Yorke, James A.; Pop, Mihai

    2009-01-01

    Motivation Sequences produced by automated Sanger sequencing machines frequently contain fragments of the cloning vector on their ends. Software tools currently available for identifying and removing the vector sequence require knowledge of the vector sequence, specific splice sites and any adapter sequences used in the experiment—information often omitted from public databases. Furthermore, the clipping coordinates themselves are missing or incorrectly reported. As an example, within the ~1.24 billion shotgun sequences deposited in the NCBI Trace Archive, as many as ~735 million (~60%) lack vector clipping information. Correct clipping information is essential to scientists attempting to validate, improve and even finish the increasingly large number of genomes released at a ‘draft’ quality level. Results We present here Figaro, a novel software tool for identifying and removing the vector from raw sequence data without prior knowledge of the vector sequence. The vector sequence is automatically inferred by analyzing the frequency of occurrence of short oligo-nucleotides using Poisson statistics. We show that Figaro achieves 99.98% sensitivity when tested on ~1.5 million shotgun reads from Drosophila pseudoobscura. We further explore the impact of accurate vector trimming on the quality of whole-genome assemblies by re-assembling two bacterial genomes from shotgun sequences deposited in the Trace Archive. Designed as a module in large computational pipelines, Figaro is fast, lightweight and flexible. Availability Figaro is released under an open-source license through the AMOS package (http://amos.sourceforge.net/Figaro). PMID:18202027

  17. 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...

  18. 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...

  19. 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...

  20. 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…

  1. 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…

  2. 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.

  3. Comparison of vitality states of finishers and withdrawers in trail running: An enactive and phenomenological perspective

    PubMed Central

    Rochat, Nadège; Hauw, Denis; Antonini Philippe, Roberta; Crettaz von Roten, Fabienne; Seifert, Ludovic

    2017-01-01

    Studies on ultra-endurance suggest that during the races, athletes typically experience three vitality states (i.e., preservation, loss, and revival) at the phenomenological level. Nevertheless, how these states contribute to the management and outcome of performance remains unclear. The aim of this study was to determine whether and how the vitality states experienced by runners and their evolution during a trail race can be used to distinguish finishers from withdrawers. From an enactive and phenomenological framework, we processed enactive interviews and blog posts of race narratives. We distinguished units of meaning, which were grouped into sequences of experience; each sequence was then categorized as one of the three vitality states: state of vitality preservation (SVP), state of vitality loss (SVL) or state of vitality revival (SVR). We analyzed the distribution of these vitality states and their temporal organization at the beginning, in the second and third quarters, and at the end of the races, and we qualitatively characterized runners’ adaptations to SVL. Results showed that finishers completed the race in SVP, with overall significantly more sequences in SVP and significantly fewer sequences in SVL than withdrawers. SVR did not discriminate finishers from withdrawers. The temporal organization of the vitality states showed a significant difference in the emergence of SVP from the second quarter of the race, as well as a significant difference in the emergence of SVL from the third quarter of the race. The analysis of adaptations to SVL confirmed that finishers were more capable of exiting SVL by enacting a preservation world when they felt physical or psychological alerts, whereas withdrawers remained in SVL. Our results showed that finishers and withdrawers did not enact the same phenomenological worlds in the race situation, especially in the organization of vitality adaptations and their relationships to difficulties; the cumulative effect of the

  4. 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

  5. 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

  6. Centrifugal Barrel Finishing Of Turbine-Blade "Fir Trees"

    NASA Technical Reports Server (NTRS)

    Mandel, Johnny L.

    1990-01-01

    Modified centrifugal barrel-finishing machine imparts desired residual compressive stresses to "fir trees" of turbine blades. Centrifugal forces generate compressive stresses, which are transmitted to turbine blades through abrasive slurries in which suspended. Eliminates need for shot peening, rounding of edges and burrs caused by shot peening and, consequently, need for mass finishing operations to remove burrs. Improves surface finish of "fir trees".

  7. 9 CFR 381.309 - Finished product inspection.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... AGENCY ORGANIZATION AND TERMINOLOGY; MANDATORY MEAT AND POULTRY PRODUCTS INSPECTION AND VOLUNTARY... Finished product inspection. (a) Finished product inspections must be handled according to: (1) A HACCP.... (b)-(c) (d) Procedures for finished product inspections where the HACCP plan for thermally...

  8. 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.

  9. Laser Window Surface Finishing and Coating Science

    DTIC Science & Technology

    1975-07-01

    IKlf il fie. r . *ttt\\ mil nlrol’ly h\\ lllm k Itumhvr ■ LasLr windows. Surface finishing, Thin films , Antireflection coatings , 10.6...Zuccaro) During the course of our program it is our objective to prepare antireflection (AR) film coatings for candidate infrared laser window...antireflection coatings under UHV conditions and to compare; these films with (.host- prepared under ordinary vacuum conditions. a. Experimental Results

  10. Agile robotic edge finishing system research

    SciTech Connect

    Powell, M.A.

    1995-07-01

    This paper describes a new project undertaken by Sandia National Laboratories to develop an agile, automated, high-precision edge finishing system. The project has a two-year duration and was initiated in October, 1994. This project involves re-designing and adding additional capabilities to an existing finishing workcell at Sandia; and developing intelligent methods for automating process definition and for controlling finishing processes. The resulting system will serve as a prototype for systems that will be deployed into highly flexible automated production lines. The production systems will be used to produce a wide variety of products with limited production quantities and quick turnaround requirements. The prototype system is designed to allow programming, process definition, fixture re-configuration, and process verification to be performed off-line for new products. CAD/CAM (Computer Aided Design/Computer Aided Manufacturing) models of the part will be used to assist with the automated process development and process control tasks. To achieve Sandia`s performance goals, the system will be employ advanced path planning, burr prediction expert systems, automated process definition, statistical process models in a process database, and a two-level control scheme using hybrid position-force control and fuzzy logic control. In this paper, we discuss the progress and the planned system development under this project.

  11. 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

  12. Acidic magnetorheological finishing of infrared polycrystalline materials

    SciTech Connect

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

    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, 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.

  13. The complete sequence of human chromosome 5

    SciTech Connect

    Schmutz, Jeremy; Martin, Joel; Terry, Astrid; Couronne, Olivier; Grimwood, Jane; Lowry, State; Gordon, Laurie A.; Scott, Duncan; Xie, Gary; Huang, Wayne; Hellsten, Uffe; Tran-Gyamfi, Mary; She, Xinwei; Prabhakar, Shyam; Aerts, Andrea; Altherr, Michael; Bajorek, Eva; Black, Stacey; Branscomb, Elbert; Caoile, Chenier; Challacombe, Jean F.; Chan, Yee Man; Denys, Mirian; Detter, Chris; Escobar, Julio; Flowers, Dave; Fotopulos, Dea; Glavina, Tijana; Gomez, Maria; Gonzales, Eidelyn; Goodstenin, David; Grigoriev, Igor; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Israni, Sanjay; Jett, Jamie; Kadner, Kristen; Kimbal, Heather; Kobayashi, Arthur; Lopez, Frederick; Lou, Yunian; Martinez, Diego; Medina, Catherine; Morgan, Jenna; Nandkeshwar, Richard; Noonan, James P.; Pitluck, Sam; Pollard, Martin; Predki, Paul; Priest, James; Ramirez, Lucia; Rash, Sam; Retterer, James; Rodriguez, Alex; Rogers, Stephanie; Salamov, Asaf; Salazar, Angelica; Thayer, Nina; Tice, Hope; Tsai, Ming; Ustaszewska, Anna; Vo, Nu; Wheeler, Jeremy; Wu, Kevin; Yang, Joan; Dickson, Mark; Cheng, Jan-Fang; Eichler, Evan E.; Olsen, Anne; Pennacchio, Len A.; Rokhsar, Daniel S.; Richardson, Paul; Lucas, Susan M.; Myers, Richard M.; Rubin, Edward M.

    2004-04-15

    Chromosome 5 is one of the largest human chromosomes yet has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding and syntenic conservation with non-mammalian vertebrates, suggesting they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-encoding genes including the protocadherin and interleukin gene families and the first complete versions of each of the large chromosome 5 specific internal duplications. These duplications are very recent evolutionary events and play a likely mechanistic role, since deletions of these regions are the cause of debilitating disorders including spinal muscular atrophy (SMA).

  14. Genome Sequence Databases (Overview): Sequencing and Assembly

    SciTech Connect

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  15. 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.

  16. The DNA Sequence And Comparative Analysis Of Human Chromosome5

    SciTech Connect

    Schmutz, Jeremy; Martin, Joel; Terry, Astrid; Couronne, Olivier; Grimwood, Jane; Lowry, Steve; Gordon, Laurie A.; Scott, Duncan; Xie,Gary; Huang, Wayne; Hellsten, Uffe; Tran-Gyamfi, Mary; She, Xinwei; Prabhakar, Shyam; Aerts, Andrea; Altherr, Michael; Bajorek, Eva; Black,Stacey; Branscomb, Elbert; Caoile, Chenier; Challacombe, Jean F.; Chan,Yee Man; Denys, Mirian; Detter, John C.; Escobar, Julio; Flowers, Dave; Fotopulos, Dea; Glavina, Tijana; Gomez, Maria; Gonzales, Eidelyn; Goodstein, David; Grigoriev, Igor; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Israni, Sanjay; Jett, Jamie; Kadner,Kristen; Kimball, Heather; Kobayashi, Arthur; Lopez, Frederick; Lou,Yunian; Martinez, Diego; Medina, Catherine; Morgan, Jenna; Nandkeshwar,Richard; Noonan, James P.; Pitluck, Sam; Pollard, Martin; Predki, Paul; Priest, James; Ramirez, Lucia; Retterer, James; Rodriguez, Alex; Rogers,Stephanie; Salamov, Asaf; Salazar, Angelica; Thayer, Nina; Tice, Hope; Tsai, Ming; Ustaszewska, Anna; Vo, Nu; Wheeler, Jeremy; Wu, Kevin; Yang,Joan; Dickson, Mark; Cheng, Jan-Fang; Eichler, Evan E.; Olsen, Anne; Pennacchio, Len A.; Rokhsar, Daniel S.; Richardson, Paul; Lucas, SusanM.; Myers, Richard M.; Rubin, Edward M.

    2004-08-01

    Chromosome 5 is one of the largest human chromosomes and contains numerous intrachromosomal duplications, yet it has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding conservation with non-mammalian vertebrates, suggesting that they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-coding genes including the protocadherin and interleukin gene families. We also completely sequenced versions of the large chromosome-5-specific internal duplications. These duplications are very recent evolutionary events and probably have a mechanistic role in human physiological variation, as deletions in these regions are the cause of debilitating disorders including spinal muscular atrophy.

  17. 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

  18. Lineage-specific biology revealed by a finished genome assembly of the mouse.

    PubMed

    Church, Deanna M; Goodstadt, Leo; 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

    2009-05-05

    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.

  19. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  20. Accurate monotone cubic interpolation

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1991-01-01

    Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.

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

    SciTech Connect

    Johnson, Shannon L.; Minogue, Timothy D.; Daligault, Hajnalka E.; Wolcott, Mark J.; Teshima, Hazuki; Coyne, Susan R.; Davenport, Karen W.; Jaissle, James G.; Chain, Patrick S.

    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.

  2. [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.

  3. Sampling considerations for herd-level measurement of faecal Escherichia coli antimicrobial resistance in finisher pigs.

    PubMed Central

    Dunlop, R. H.; McEwen, S. A.; Meek, A. H.; Friendship, R. M.; Black, W. D.; Clarke, R. C.

    1999-01-01

    The objective of this study was to determine the most efficient means of sampling faeces of finisher pigs for accurate and precise farm-level estimates of antimicrobial resistance among faecal Escherichia coli. Resistance to tetracycline and gentamicin of 8250 isolates of E. coli from 55 finisher pigs on one farm was measured with a hydrophobic grid membrane filter method. The between-pig, within-pen component of variance in resistance was large (97.5%), while between-pen, within-room and between-room components were small (2.5% and 0%, respectively). Using these resistance data, the abilities of two sampling strategies to estimate prevalence were modelled with a Monte Carlo 'bootstrap' procedure. Compositing faecal samples from several pigs before testing produced unbiased and precise estimates of prevalence and is simpler technically than individual animal testing. PMID:10459654

  4. 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

  5. Micro-finish hard anodized coatings on aluminum

    SciTech Connect

    Steffani, C.

    1992-03-01

    The production of thin hard anodized coatings on Single Point Diamond Turned (SPDT) 6061-T6 aluminum has been studied. The investigation centered on producing a surface finish of less than 10 microinch after anodizing. By starting with a 2 microinch (AA) surface finish and controlling time, temperature, current density and solution chemistry, coatings with surface finishes of 8 microinch and a thickness of .0003 inch, are obtained. Surface roughness from several anodizing solutions is compared. The operational life of a PTFE sliding seal against a coated cylinder bore is used as verification of finish quality.

  6. EuLoc: a web-server for accurately predict protein subcellular localization in eukaryotes by incorporating various features of sequence segments into the general form of Chou's PseAAC

    NASA Astrophysics Data System (ADS)

    Chang, Tzu-Hao; Wu, Li-Ching; Lee, Tzong-Yi; Chen, Shu-Pin; Huang, Hsien-Da; Horng, Jorng-Tzong

    2013-01-01

    The function of a protein is generally related to its subcellular localization. Therefore, knowing its subcellular localization is helpful in understanding its potential functions and roles in biological processes. This work develops a hybrid method for computationally predicting the subcellular localization of eukaryotic protein. The method is called EuLoc and incorporates the Hidden Markov Model (HMM) method, homology search approach and the support vector machines (SVM) method by fusing several new features into Chou's pseudo-amino acid composition. The proposed SVM module overcomes the shortcoming of the homology search approach in predicting the subcellular localization of a protein which only finds low-homologous or non-homologous sequences in a protein subcellular localization annotated database. The proposed HMM modules overcome the shortcoming of SVM in predicting subcellular localizations using few data on protein sequences. Several features of a protein sequence are considered, including the sequence-based features, the biological features derived from PROSITE, NLSdb and Pfam, the post-transcriptional modification features and others. The overall accuracy and location accuracy of EuLoc are 90.5 and 91.2 %, respectively, revealing a better predictive performance than obtained elsewhere. Although the amounts of data of the various subcellular location groups in benchmark dataset differ markedly, the accuracies of 12 subcellular localizations of EuLoc range from 82.5 to 100 %, indicating that this tool is much more balanced than other tools. EuLoc offers a high, balanced predictive power for each subcellular localization. EuLoc is now available on the web at http://euloc.mbc.nctu.edu.tw/.

  7. EuLoc: a web-server for accurately predict protein subcellular localization in eukaryotes by incorporating various features of sequence segments into the general form of Chou's PseAAC.

    PubMed

    Chang, Tzu-Hao; Wu, Li-Ching; Lee, Tzong-Yi; Chen, Shu-Pin; Huang, Hsien-Da; Horng, Jorng-Tzong

    2013-01-01

    The function of a protein is generally related to its subcellular localization. Therefore, knowing its subcellular localization is helpful in understanding its potential functions and roles in biological processes. This work develops a hybrid method for computationally predicting the subcellular localization of eukaryotic protein. The method is called EuLoc and incorporates the Hidden Markov Model (HMM) method, homology search approach and the support vector machines (SVM) method by fusing several new features into Chou's pseudo-amino acid composition. The proposed SVM module overcomes the shortcoming of the homology search approach in predicting the subcellular localization of a protein which only finds low-homologous or non-homologous sequences in a protein subcellular localization annotated database. The proposed HMM modules overcome the shortcoming of SVM in predicting subcellular localizations using few data on protein sequences. Several features of a protein sequence are considered, including the sequence-based features, the biological features derived from PROSITE, NLSdb and Pfam, the post-transcriptional modification features and others. The overall accuracy and location accuracy of EuLoc are 90.5 and 91.2 %, respectively, revealing a better predictive performance than obtained elsewhere. Although the amounts of data of the various subcellular location groups in benchmark dataset differ markedly, the accuracies of 12 subcellular localizations of EuLoc range from 82.5 to 100 %, indicating that this tool is much more balanced than other tools. EuLoc offers a high, balanced predictive power for each subcellular localization. EuLoc is now available on the web at http://euloc.mbc.nctu.edu.tw/.

  8. [Finishing and detailing, stability and harmony].

    PubMed

    Fourquet, Lucile; Göttle, Magalie; Bounoure, Guy

    2014-03-01

    The finishing and detailing phase, the last stage of active orthodontic treatment, makes it possible to perfect the occlusion, by adhering to criteria defined by various authors and to improve the esthetic result, while achieving the treatment objectives made during the pre-planning phase. The reliability of end of treatment results cannot be ensured without an initial individualized analysis of the risk factors for relapse specific to each patient. It is only after this analysis, that the orthodontist will be able to determine how to comply with these criteria for stability, common in any treatment, and to individually choose and implement reliable procedures. When planning for stability as the treatment objective, orthodontic patients are able to achieve stable alignment. This course of action is the necessary process to help ensure equilibrium and alignment. Eight different methods of alignment, already frequently discussed in the literature, will be described and analyzed in this paper.

  9. Functional finishes of stretch cotton fabrics.

    PubMed

    Ibrahim, N A; Amr, A; Eid, B M; Almetwally, A A; Mourad, M M

    2013-11-06

    Functionalized cotton cellulose/spandex woven fabrics with different structures namely plain (1/1), twill (2/2) and satin were produced. Factors affecting the imparted functional properties such as weave structure and constituents of the finishing formulations including ether or ester cross-linker and catalyst type, silicone-micro-emulsion, water/oil repellent, Ag-NP(,)s and TiO2-NP(,)s were studied. The treated fabrics were found to have easy care property together with one or more of the imparted functional properties such as soft-handle, water/oil repellence, antibacterial, UV-protection and self cleaning. The effectiveness of the imparted properties is not seriously affected even after 10 washing cycles. Surface modifications as well as the composition of certain samples were confirmed by SEM images and EDX spectra. Mode of interactions was also suggested.

  10. 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.

  11. Salmonella infection and immune response in finishing pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Finishing pigs infected with Salmonella pose significant food safety risks by carrying the pathogen into abattoirs. A study was conducted to determine the dynamic of Salmonella infection in finishing pigs, and the immunological alterations that occur in Salmonella-carrier pigs, by longitudinally com...

  12. 16 CFR 1508.7 - Construction and finishing.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Construction and finishing. 1508.7 Section 1508.7 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FEDERAL HAZARDOUS SUBSTANCES ACT REGULATIONS REQUIREMENTS FOR FULL-SIZE BABY CRIBS § 1508.7 Construction and finishing. (a) All wood...

  13. 16 CFR 1508.7 - Construction and finishing.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Construction and finishing. 1508.7 Section 1508.7 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FEDERAL HAZARDOUS SUBSTANCES ACT REGULATIONS REQUIREMENTS FOR FULL-SIZE BABY CRIBS § 1508.7 Construction and finishing. (a) All wood...

  14. 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...

  15. Influence of finishing on the electrochemical properties of dental alloys.

    PubMed

    Kaneko, T; Hattori, M; Hasegawa, K; Yoshinari, M; Kawada, E; Oda, Y

    2000-05-01

    Dental alloy surface finishing procedures of may influence their electrochemical behavior, which is used to evaluate their corrosion resistance. We examined the polarization resistance and potentiodynamic polarization profile of the precious-metal alloys, Type 4 gold alloy and silver-palladium alloy, and the base-metal alloys, nickel-chromium alloy, cobalt-chromium alloy, and CP-titanium. Three types of finishing procedure were examined: mirror-finishing using 0.05 micron alumina particles, polishing using #600 abrasive paper and sandblasting. Dissolution of the alloy elements in 0.9% NaCl solution was also measured and compared with the electrochemical evaluation. The corrosion resistance of the dental alloys was found to relate to finishing as follows: The polarization resistance and potentiodynamic polarization behavior revealed that the corrosion resistance improved in the order of sandblasting, #600-abrasive-paper polishing, and mirror-finishing. While the corrosion potential, critical current density and passive current density varied depending on the type of finishing, the transpassive potential remained unchanged. The influence of finishing on the corrosion resistance of precious-metal alloys was less significant than on that of base-metal alloys. A mirror-finishing specimen was recommended for use in evaluation of the corrosion resistance of various dental alloys.

  16. 30 CFR 18.33 - Finish of surface joints.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Finish of surface joints. 18.33 Section 18.33 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND... Requirements § 18.33 Finish of surface joints. Flat surfaces between bolt holes that form any part of a...

  17. 30 CFR 18.33 - Finish of surface joints.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Finish of surface joints. 18.33 Section 18.33 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND... Requirements § 18.33 Finish of surface joints. Flat surfaces between bolt holes that form any part of a...

  18. 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... Requirements § 18.33 Finish of surface joints. Flat surfaces between bolt holes that form any part of a...

  19. 30 CFR 18.33 - Finish of surface joints.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Finish of surface joints. 18.33 Section 18.33 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND... Requirements § 18.33 Finish of surface joints. Flat surfaces between bolt holes that form any part of a...

  20. 30 CFR 18.33 - Finish of surface joints.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Finish of surface joints. 18.33 Section 18.33 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND... Requirements § 18.33 Finish of surface joints. Flat surfaces between bolt holes that form any part of a...

  1. 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...

  2. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  3. Phosphorus requirement of finishing feedlot calves.

    PubMed

    Erickson, G E; Klopfenstein, T J; Milton, C T; Brink, D; Orth, M W; Whittet, K M

    2002-06-01

    Dietary P supplied to feedlot cattle is important because an inadequate supply will compromise performance, whereas excess P may harm the environment. However, P requirements of feedlot cattle are not well documented. Therefore, 45 steer calves (265.2+/-16.6 kg) were individually fed to determine the P required for gain and bone integrity over a 204-d finishing period. The basal diet consisted of 33.5% high-moisture corn, 30% brewers grits, 20% corn bran, 7.5% cottonseed hulls, 3% tallow, and 6% supplement. Treatments consisted of 0.16 (no supplemental inorganic P), 0.22, 0.28, 0.34, and 0.40% P (DM basis). Supplemental P was provided by monosodium phosphate top-dressed to the daily feed allotment. Blood was sampled every 56 d to assess P status. At slaughter, phalanx and metacarpal bones were collected from the front leg to determine bone ash and assess P resorption from bone. Dry matter intake and ADG did not change linearly (P > 0.86) or quadratically (P > 0.28) due to P treatment. Feed efficiency was not influenced (P > 0.30) by P treatment and averaged 0.169. Plasma inorganic P averaged across d 56 to 204 responded quadratically, with calves fed 0.16% P having the lowest concentration of plasma inorganic P. However, plasma inorganic P concentration (5.7 mg/dL) for steers fed 0.16% P is generally considered adequate. Total bone ash weight was not influenced by dietary P for phalanx (P = 0.19) or metacarpal bones (P = 0.37). Total P intake ranged from 14.2 to 35.5 g/d. The NRC (1996) recommendation for these calves was 18.7 g/d, assuming 68% absorption. Based on performance results, P requirements for finishing calves is < 0.16% of diet DM or 14.2 g/d. Based on these observations, we suggest that typical grain-based feedlot cattle diets do not require supplementation of inorganic mineral P to meet P requirements.

  4. A Transcript Finishing Initiative for Closing Gaps in the Human Transcriptome

    PubMed Central

    Sogayar, Mari Cleide; Camargo, Anamaria A.

    2004-01-01

    We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms. PMID:15197164

  5. BIOACCESSIBILITY TESTS ACCURATELY ESTIMATE ...

    EPA Pesticide Factsheets

    Hazards of soil-borne Pb to wild birds may be more accurately quantified if the bioavailability of that Pb is known. To better understand the bioavailability of Pb to birds, we measured blood Pb concentrations in Japanese quail (Coturnix japonica) fed diets containing Pb-contaminated soils. Relative bioavailabilities were expressed by comparison with blood Pb concentrations in quail fed a Pb acetate reference diet. Diets containing soil from five Pb-contaminated Superfund sites had relative bioavailabilities from 33%-63%, with a mean of about 50%. Treatment of two of the soils with P significantly reduced the bioavailability of Pb. The bioaccessibility of the Pb in the test soils was then measured in six in vitro tests and regressed on bioavailability. They were: the “Relative Bioavailability Leaching Procedure” (RBALP) at pH 1.5, the same test conducted at pH 2.5, the “Ohio State University In vitro Gastrointestinal” method (OSU IVG), the “Urban Soil Bioaccessible Lead Test”, the modified “Physiologically Based Extraction Test” and the “Waterfowl Physiologically Based Extraction Test.” All regressions had positive slopes. Based on criteria of slope and coefficient of determination, the RBALP pH 2.5 and OSU IVG tests performed very well. Speciation by X-ray absorption spectroscopy demonstrated that, on average, most of the Pb in the sampled soils was sorbed to minerals (30%), bound to organic matter 24%, or present as Pb sulfate 18%. Ad

  6. Application of multilocus sequence analysis (MLSA) for accurate identification of Legionella spp. Isolated from municipal fountains in Chengdu, China, based on 16S rRNA, mip, and rpoB genes.

    PubMed

    Guan, Wang; Xu, Ying; Chen, Da-Li; Xu, Jia-Nan; Tian, Yu; Chen, Jian-Ping

    2012-02-01

    Legionellosis (Legionnaires' disease; LD) is a form of severe pneumonia caused by species of Legionella bacteria. Because inhalation of Legionella-contaminated aerosol is considered the major infection route, routine assessments of potential infection sources such as hot water systems, air-conditioner cooling water, and municipal fountains are of great importance. In this study, we utilized in vitro culture and multilocus sequence analysis (MLSA) targeting 16S rRNA, mip, rpoB, and mip-rpoB concatenation to isolate and identify Legionella spp. from 5 municipal fountains in Chengdu City, Sichuan Province, China. Our results demonstrated that 16S rRNA was useful for initial identification, as it could recognize isolates robustly at the genus level, while the genes mip, rpoB, and mip-rpoB concatenation could confidently discriminate Legionella species. Notably, the three subspecies of L. pneumophila could be distinguished by the analysis based on rpoB. The serotyping result of strain CD-1 was consistent with genetic analysis based on the concatenation of mip and rpoB. Despite regular maintenance and sanitizing methods, 4 of the 5 municipal fountains investigated in this study were positive for Legionella contamination. Thus, regularly scheduled monitoring of municipal fountains is urgently needed as well as vigilant disinfection. Although the application of MLSA for inspection of potential sites of infection in public areas is not standard procedure, further investigations may prove its usefulness.

  7. Surface quality control in diamond abrasive finishing

    NASA Astrophysics Data System (ADS)

    Filatov, Yuriy D.; Sidorko, Volodymyr I.; Filatov, Olexandr Yu.; Yaschuk, Vasil P.; Heisel, Uwe; Storchak, Michael

    2009-06-01

    The paper presents a procedure for measuring laser radiation reflection and scattering coefficients of polished surface. A relation between the scattered light intensity and the polished surface roughness is studied. It is demonstrated that colorimetric characteristics of non-metallic materials can be determined from the light scattering and reflection coefficients. This work has demonstrated a possibility of and created prerequisites for the development of an express method for tentative assessment of polished surface roughness. Of interest is the use of the β(Rz) function for the purposes of quality inspection of polished surfaces of natural and synthetic stone and other non-metallic materials. It was established that the most relevant parameter of roughness, which can be defined by the light reflection is Rz. The Dependency of the reflection factor from parameter of roughness Rz was approximated by formula with inaccuracy 5-10%. Inaccuracy of the determination of roughness Rz has formed 1%. It was shown that method of the surface roughness control using the light reflection factor is the most efficient for surfaces with roughness Rz <0.3 microns, typical for finish diamond-abrasive machining.

  8. Plutonium Finishing Plant safety evaluation report

    SciTech Connect

    Not Available

    1995-01-01

    The Plutonium Finishing Plant (PFP) previously known as the Plutonium Process and Storage Facility, or Z-Plant, was built and put into operation in 1949. Since 1949 PFP has been used for various processing missions, including plutonium purification, oxide production, metal production, parts fabrication, plutonium recovery, and the recovery of americium (Am-241). The PFP has also been used for receipt and large scale storage of plutonium scrap and product materials. The PFP Final Safety Analysis Report (FSAR) was prepared by WHC to document the hazards associated with the facility, present safety analyses of potential accident scenarios, and demonstrate the adequacy of safety class structures, systems, and components (SSCs) and operational safety requirements (OSRs) necessary to eliminate, control, or mitigate the identified hazards. Documented in this Safety Evaluation Report (SER) is DOE`s independent review and evaluation of the PFP FSAR and the basis for approval of the PFP FSAR. The evaluation is presented in a format that parallels the format of the PFP FSAR. As an aid to the reactor, a list of acronyms has been included at the beginning of this report. The DOE review concluded that the risks associated with conducting plutonium handling, processing, and storage operations within PFP facilities, as described in the PFP FSAR, are acceptable, since the accident safety analyses associated with these activities meet the WHC risk acceptance guidelines and DOE safety goals in SEN-35-91.

  9. Metal finishing wastewater pressure filter optimization

    SciTech Connect

    Norford, S.W.; Diener, G.A.; Martin, H.L.

    1992-01-01

    The 300-M Area Liquid Effluent Treatment Facility (LETF) of the Savannah River Site (SRS) is an end-of-pipe industrial wastewater treatment facility, that uses precipitation and filtration which is the EPA Best Available Technology economically achievable for a Metal Finishing and Aluminum Form Industries. The LETF consists of three close-coupled treatment facilities: the Dilute Effluent Treatment Facility (DETF), which uses wastewater equalization, physical/chemical precipitation, flocculation, and filtration; the Chemical Treatment Facility (CTF), which slurries the filter cake generated from the DETF and pumps it to interim-StatuS RCRA storage tanks; and the Interim Treatment/Storage Facility (IT/SF) which stores the waste from the CTF until the waste is stabilized/solidified for permanent disposal, 85% of the stored waste is from past nickel plating and aluminum canning of depleted uranium targets for the SRS nuclear reactors. Waste minimization and filtration efficiency are key to cost effective treatment of the supernate, because the waste filter cake generated is returned to the IT/SF. The DETF has been successfully optimized to achieve maximum efficiency and to minimize waste generation.

  10. Metal finishing wastewater pressure filter optimization

    SciTech Connect

    Norford, S.W.; Diener, G.A.; Martin, H.L.

    1992-12-31

    The 300-M Area Liquid Effluent Treatment Facility (LETF) of the Savannah River Site (SRS) is an end-of-pipe industrial wastewater treatment facility, that uses precipitation and filtration which is the EPA Best Available Technology economically achievable for a Metal Finishing and Aluminum Form Industries. The LETF consists of three close-coupled treatment facilities: the Dilute Effluent Treatment Facility (DETF), which uses wastewater equalization, physical/chemical precipitation, flocculation, and filtration; the Chemical Treatment Facility (CTF), which slurries the filter cake generated from the DETF and pumps it to interim-StatuS RCRA storage tanks; and the Interim Treatment/Storage Facility (IT/SF) which stores the waste from the CTF until the waste is stabilized/solidified for permanent disposal, 85% of the stored waste is from past nickel plating and aluminum canning of depleted uranium targets for the SRS nuclear reactors. Waste minimization and filtration efficiency are key to cost effective treatment of the supernate, because the waste filter cake generated is returned to the IT/SF. The DETF has been successfully optimized to achieve maximum efficiency and to minimize waste generation.

  11. Accurate spectral color measurements

    NASA Astrophysics Data System (ADS)

    Hiltunen, Jouni; Jaeaeskelaeinen, Timo; Parkkinen, Jussi P. S.

    1999-08-01

    Surface color measurement is of importance in a very wide range of industrial applications including paint, paper, printing, photography, textiles, plastics and so on. For a demanding color measurements spectral approach is often needed. One can measure a color spectrum with a spectrophotometer using calibrated standard samples as a reference. Because it is impossible to define absolute color values of a sample, we always work with approximations. The human eye can perceive color difference as small as 0.5 CIELAB units and thus distinguish millions of colors. This 0.5 unit difference should be a goal for the precise color measurements. This limit is not a problem if we only want to measure the color difference of two samples, but if we want to know in a same time exact color coordinate values accuracy problems arise. The values of two instruments can be astonishingly different. The accuracy of the instrument used in color measurement may depend on various errors such as photometric non-linearity, wavelength error, integrating sphere dark level error, integrating sphere error in both specular included and specular excluded modes. Thus the correction formulas should be used to get more accurate results. Another question is how many channels i.e. wavelengths we are using to measure a spectrum. It is obvious that the sampling interval should be short to get more precise results. Furthermore, the result we get is always compromise of measuring time, conditions and cost. Sometimes we have to use portable syste or the shape and the size of samples makes it impossible to use sensitive equipment. In this study a small set of calibrated color tiles measured with the Perkin Elmer Lamda 18 and the Minolta CM-2002 spectrophotometers are compared. In the paper we explain the typical error sources of spectral color measurements, and show which are the accuracy demands a good colorimeter should have.

  12. Automated finishing of diamond turned dies for hard x-ray and EUV optics replication

    NASA Astrophysics Data System (ADS)

    Beaucamp, Anthony T. H.; Namba, Yoshiharu; Freeman, Richard R.

    2012-10-01

    Ultra-precision diamond turning can deliver very accurate form, often less than 100nm P-V. A possible manufacturing method for thin Wolter type-1 mirrors in hard X-ray space telescopes thus involves generating electroless nickel plated mandrels by diamond turning, before coating them with a reflective film and substrate. However, the surface texture after turning falls far short from the requirements of X-ray and EUV applications. The machining marks need to be removed, with hand polishing still widely employed. There is thus a compelling need for automated finishing of turned dies. A two step finishing method is presented that combines fluid jet and precessed bonnet polishing on a common 7-axis CNC platform. This method is capable of finishing diamond turned electroless nickel plated dies down to 0.28nm rms roughness, while deterministically improving form error down to 30nm P-V. The fluid jet polishing process, which consists of pressurizing water and abrasive particles for delivery through a nozzle, has been specially optimized with a newly designed slurry delivery unit and computer simulations, to remove diamond turning marks without introducing another waviness signature. The precessed bonnet polishing method, which consists of an inflated membrane rotated at an angle from the local normal to the surface and controlled by geometrical position relative to the work-piece, is subsequently employed with a novel control algorithm to deliver scratch-free surface roughness down to 0.28 nm rms. The combination of these two deterministic processes to finish aspheric and freeform dies promises to unlock new frontiers in X-ray and EUV optics fabrication.

  13. Accurate taxonomic assignment of short pyrosequencing reads.

    PubMed

    Clemente, José C; Jansson, Jesper; Valiente, Gabriel

    2010-01-01

    Ambiguities in the taxonomy dependent assignment of pyrosequencing reads are usually resolved by mapping each read to the lowest common ancestor in a reference taxonomy of all those sequences that match the read. This conservative approach has the drawback of mapping a read to a possibly large clade that may also contain many sequences not matching the read. A more accurate taxonomic assignment of short reads can be made by mapping each read to the node in the reference taxonomy that provides the best precision and recall. We show that given a suffix array for the sequences in the reference taxonomy, a short read can be mapped to the node of the reference taxonomy with the best combined value of precision and recall in time linear in the size of the taxonomy subtree rooted at the lowest common ancestor of the matching sequences. An accurate taxonomic assignment of short reads can thus be made with about the same efficiency as when mapping each read to the lowest common ancestor of all matching sequences in a reference taxonomy. We demonstrate the effectiveness of our approach on several metagenomic datasets of marine and gut microbiota.

  14. Next-Generation Sequencing Tech Panel ( 7th Annual SFAF Meeting, 2012)

    SciTech Connect

    Rhodes, Michael; Fiske, Haley; Knight, Jim; Turner, Steve (Pacific Biosciences

    2012-06-01

    Representatives from several next-generation sequencer manufacturers take part in a panel discussion at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

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

    ScienceCinema

    Appel, Maryke [Kappa Biosystems

    2016-07-12

    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. Finishing of enamel surfaces after debonding of orthodontic attachments.

    PubMed

    Retief, D H; Denys, F R

    1979-01-01

    The finishing of enamel surfaces after removal of directly bonded attachments is essential. The following procedures are suggested: 1. The bonding of mesh-backed stainless steel brackets with a lightly filled resin system. 2. Debonding of attachments with a direct bonding bracket remover. 3. Removal of the bulk of the remaining resin with a 12-bladed tungsten carbide bur operated at high speed with adequate air cooling. 4. Finishing of the residual resin and underlying enamel with graded polishing discs or Ceramisté wheels used with light pressure and adequate air cooling. 5. Final finishing with a rubber cup and a water slurry of pumice.

  17. An overview of plastic optical fiber end finishers at Fermilab

    SciTech Connect

    Mishina, M.; Lindenmeyer, C.; Korienek, J.

    1993-11-01

    Several years ago the need for equipment to precisely finish the ends of plastic optical fibers was recognized. Many high energy physics experiments use thousands of these fibers which must be polished on one or both ends. A fast, easy-to-operate machine yielding repeatable finishes was needed. Three types of machines were designed and constructed that are in daily use at Fermilab, all finish the fiber ends by flycutting with a diamond tool. Althrough diamond flycutting of plastic is not new, the size and fragility of plastic optical fibers present several challenges.

  18. 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...

  19. 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...

  20. 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

  1. 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

  2. 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

  3. 6. INTERIOR OF BASEMENT UNDER KITCHEN SHOWING FINISHED SECTION. OPEN ...

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

    6. INTERIOR OF BASEMENT UNDER KITCHEN SHOWING FINISHED SECTION. OPEN DOOR TO UNFINISHED SECTION IS VISIBLE AT RIGHT PHOTO CENTER. VIEW TO NORTHWEST. - Rush Creek Hydroelectric System, Worker Cottage, Rush Creek, June Lake, Mono County, CA

  4. Plutonium Finishing Plant (PFP) Dangerous Waste Training Plan

    SciTech Connect

    ENTROP, G.E.

    1999-12-03

    This training plan describes general requirements, worker categories, and provides course descriptions for operation of the plutonium finishing plant (PFP) waste generation facilities, permitted treatment, storage and disposal (TSD) units, and the 90-Day Accumulation Areas.

  5. LARGE DIAMETER WATER TEST MACHINE, TEST FINISHED, PIPE ON ...

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

    LARGE DIAMETER - WATER TEST MACHINE, TEST FINISHED, PIPE ON CAR. - United States Pipe & Foundry Company Plant, Pipe Casting & Testing Area, 2023 St. Louis Avenue at I-20/59, Bessemer, Jefferson County, AL

  6. Environmentally friendly antibacterial cotton textiles finished with siloxane sulfopropylbetaine.

    PubMed

    Chen, Shiguo; Chen, Shaojun; Jiang, Song; Xiong, Meiling; Luo, Junxuan; Tang, Jiaoning; Ge, Zaochuan

    2011-04-01

    This paper reports a novel environmentally friendly antibacterial cotton textile finished with reactive siloxane sulfopropylbetaine(SSPB). The results show that SSPB can be covalently bound onto the cotton textile surface, imparting perdurable antibacterial activity. The textiles finished with SSPB have been investigated systematically from the mechanical properties, thermal stability, hydrophilic properties and antibacterial properties. It is found that the hydrophilicity and breaking strength are improved greatly after the cotton textiles are finished with SSPB. Additionally, the cotton textiles finished with SSPB exhibit good antibacterial activities against gram-positive bacteria Staphylococcus aureus (S.aureus, ATCC 6538), gram-negative bacteria Escherichia coli (E.coli, 8099) and fungi Candida albicans (C.albicans, ATCC 10231). Moreover, SSPB is nonleachable from the textiles, and it does not induce skin stimulation and is nontoxic to animals. Thus, SSPB is ideal candidate for environmentally friendly antibacterial textile applications.

  7. CHARACTERISTICS OF KLEBSIELLA FROM TEXTILE FINISHING PLANT EFFLUENTS

    EPA Science Inventory

    Klebsiella strains are found in abnormally high numbers in a stream receiving wastewater from a textile finishing plant. Representative strains are randomly selected to determine biochemical, serotype, and virulence patterns. All strains conform to the commonly accepted biochemic...

  8. VIEW FROM DOWN STREAM OF ARCH IN ELEVATION. NOTE FINISHED ...

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

    VIEW FROM DOWN STREAM OF ARCH IN ELEVATION. NOTE FINISHED INTERIOR ARCH. SSW BY 205 DEGREES - Chasm Brook Bridge, Spanning Chasm Brook on West Sargent Mountain Carriage Road, Bar Harbor, Hancock County, ME

  9. Specifying the surface finish of x-ray mirrors

    SciTech Connect

    Church, E.L.; Takacs, P.Z.

    1993-12-31

    Our measurements of x-ray mirrors at Brookhaven indicate that the power spectral densities of their finish errors have inverse power-law or fractal forms, rather than being flat at low frequencies as is usually assumed. This paper reviews these data and discusses how this apparent divergent behavior leads to finite but unconventional effects in imaging. Results are then used to develop more rational and realistic surface-finish specifications.

  10. 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

  11. Solder flow over fine line PWB surface finishes

    SciTech Connect

    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 provided 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.

  12. 40 CFR 433.10 - Applicability; description of the metal finishing point source category.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... metal finishing point source category. 433.10 Section 433.10 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS (CONTINUED) METAL FINISHING POINT SOURCE CATEGORY Metal Finishing Subcategory § 433.10 Applicability; description of the metal finishing...

  13. 40 CFR 433.10 - Applicability; description of the metal finishing point source category.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... metal finishing point source category. 433.10 Section 433.10 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS METAL FINISHING POINT SOURCE CATEGORY Metal Finishing Subcategory § 433.10 Applicability; description of the metal finishing point source category....

  14. 40 CFR 433.10 - Applicability; description of the metal finishing point source category.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... metal finishing point source category. 433.10 Section 433.10 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS (CONTINUED) METAL FINISHING POINT SOURCE CATEGORY Metal Finishing Subcategory § 433.10 Applicability; description of the metal finishing...

  15. 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

  16. Evaluation of the polished surface characteristic of cobalt-chrome castings subsequent to various finishing and polishing techniques.

    PubMed

    Ponnanna, A A; Joshi, S M; Bhat, S; Shetty, P

    2001-01-01

    Finishing and Polishing constitutes an essential requisite after the fabrication of removable partial dentures. Improper finishing and polishing of cast framework will adversely affect the quality of functional units of partial dentures due to reduced dimensions. In this study the polished surface characteristic and loss of weight of the casting were evaluated and compared following different finishing and polishing techniques. A total number of thirty test specimens were cast and each surface finishing and polishing technique was carried out with a high speed polishing motor and an electropolishing unit under standardised conditions. Surface roughness was evaluated by means of a surface roughness analyzing instrument, Perthometer. The loss of weight due to the metal lost was observed on a sensitive electronic balance. The results of polishing technique employed with G3 group revealed better surface characteristic. It may be understood that sandblasting causes initial roughness and the sequence of coarse cylindrical abrasive, Black hard rubber polisher (coarse grit-Dentauram), Grey hard rubber polisher (Med-grit-Dentauram), Green hard rubber polisher (Fine-grit-Dentauram), Grey flexible rubber polisher (Fine grit-Renfert), felt buff with pumice slurry and felt buff with green polishing compound (Degussa) produced improved surface in this case. The loss of weight due to metal lost show concern with technique groups G4, G5, G6. It can be avoided by judicious sandblasting and application of proper grit of abrasive agents.

  17. RapTOR: Automated sequencing library preparation and suppression for rapid pathogen characterization ( 7th Annual SFAF Meeting, 2012)

    SciTech Connect

    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.

  18. A rapid whole genome sequencing and analysis system supporting genomic epidemiology (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    FitzGerald, Michael [Broad Institute

    2016-07-12

    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.

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

    ScienceCinema

    Muzny, Donna [Baylor College of Medicine

    2016-07-12

    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.

  20. A rapid whole genome sequencing and analysis system supporting genomic epidemiology (7th Annual SFAF Meeting, 2012)

    SciTech Connect

    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.

  1. RapTOR: Automated sequencing library preparation and suppression for rapid pathogen characterization ( 7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Lane, Todd [SNL

    2016-07-12

    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.

  2. UltraForm finishing process for optical materials

    NASA Astrophysics Data System (ADS)

    Fess, E.; Schoen, J.; Bechtold, M.; Mohring, D.; Bouvier, C.

    2005-09-01

    A new compliant sub-aperture optical finishing technique is being investigated for the removal of mid-spatial frequency artifacts and smoothing of hard polycrystalline infrared ceramics for aspheric applications and conformal shaped optics. The UltraForm concept was developed by OptiPro Systems, Ontario, NY, and is a joint process development effort with the Center for Optics Manufacturing (COM). The latest version of the UltraForm tool "V3" is of a belted design whereby a belt of finishing material is passed over a toroidal elastomeric wheel. Finishing materials used include a wide variety of pad materials and abrasive selections. Experimentation has been conducted using both slurry mixes and fixed abrasive bands. The toroidal wheel is rotated while the compliant tool is compressed into contact with the optical surface. Presented will be the current results in optical glasses and crystalline ceramics such as ALON, Spinel and Polycrystalline Alumina.

  3. 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.

  4. Mid-IR fiber-optic reflectance spectroscopy for identifying the finish on wooden furniture.

    PubMed

    Poli, T; Chiantore, O; Nervo, M; Piccirillo, A

    2011-05-01

    Mid-IR fiber-optic reflectance spectroscopy (FORS) is a totally noninvasive infrared analytical technique allowing the investigation of artworks without the need for any sampling. The development and optimization of this analytical methodology can provide a tool that is capable of supporting conservators during the first steps of their interventions, yielding fast results and dramatically reducing the number of samples needed to identify the materials involved. Furthermore, since reflection IR spectra suffer from important spectral anomalies that complicate accurate spectral interpretation, it is important to characterize known reference materials and substrates in advance. This work aims to verify the possibility of investigating and identifying the most widely used wood finishes by means of fiber-optic (chalcogenide and metal halides) mid-infrared spectroscopy. Two historically widely employed wood finishes (beeswax, shellac) and two modern ones (a hydrogenated hydrocarbon resin and a microcrystalline wax) were investigated in an extended IR range (from 1000 to 6000 cm(-1)) with reflectance spectroscopy and with FORS. The broad spectral response of the MCT detector was exploited in order to include overtones and combination bands from the NIR spectral range in the investigation. The reflectance spectra were compared with those collected in transmission mode in order to highlight modifications to shapes and intensities, to assign absorptions, and finally to select "marker" bands indicating the presence of certain finishing materials, even when applied onto a substrate such as wood, which shows many absorptions in the mid-infrared region. After the characterization, the different products were applied to samples of aged pear wood and investigated with the same techniques in order to check the ability of mid-IR FORS to reveal the presence and composition of the product on the wooden substrate.

  5. Accurate Evaluation of Quantum Integrals

    NASA Technical Reports Server (NTRS)

    Galant, D. C.; Goorvitch, D.; Witteborn, Fred C. (Technical Monitor)

    1995-01-01

    Combining an appropriate finite difference method with Richardson's extrapolation results in a simple, highly accurate numerical method for solving a Schrodinger's equation. Important results are that error estimates are provided, and that one can extrapolate expectation values rather than the wavefunctions to obtain highly accurate expectation values. We discuss the eigenvalues, the error growth in repeated Richardson's extrapolation, and show that the expectation values calculated on a crude mesh can be extrapolated to obtain expectation values of high accuracy.

  6. Automated Sequence Preprocessing in a Large-Scale Sequencing Environment

    PubMed Central

    Wendl, Michael C.; Dear, Simon; Hodgson, Dave; Hillier, LaDeana

    1998-01-01

    A software system for transforming fragments from four-color fluorescence-based gel electrophoresis experiments into assembled sequence is described. It has been developed for large-scale processing of all trace data, including shotgun and finishing reads, regardless of clone origin. Design considerations are discussed in detail, as are programming implementation and graphic tools. The importance of input validation, record tracking, and use of base quality values is emphasized. Several quality analysis metrics are proposed and applied to sample results from recently sequenced clones. Such quantities prove to be a valuable aid in evaluating modifications of sequencing protocol. The system is in full production use at both the Genome Sequencing Center and the Sanger Centre, for which combined weekly production is ∼100,000 sequencing reads per week. PMID:9750196

  7. 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...

  8. 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-full-size baby cribs shall be free from splits, cracks, or other defects that might lead to...

  9. 16 CFR 1509.8 - Construction and finishing.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 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-full-size baby cribs shall be free from splits, cracks, or other defects that might lead to...

  10. Exposure to organic solvents during cosmetic finishing of cars.

    PubMed

    Bråtveit, M; Moen, B E

    2001-09-01

    The objectives of this study were to assess the exposure to organic solvents during degreasing, washing and polishing of cars, and to obtain information about acute health symptoms in car-finishing workers. Fifteen car shops participated in this study, and at these locations 36 workers had car finishing as their main working task. All 36 car-finishing workers and 17 randomly selected office workers from six of these car shops completed questionnaires on acute health symptoms. Personal monitoring of exposure to organic solvents was carried out in three representative shops. The highest exposure levels were found during degreasing of new cars, the median level of aliphatic hydrocarbons (C9-C13) being 22 p.p.m. (range 7-215 p.p.m.). This exposure level represents 50% (range 20-540%) of the Norwegian 8 h limit value for additive factor for these compounds. Only 28% of the workers used gas respirators regularly during this process. Very low exposure levels were detected during washing of second-hand cars and during polishing processes. The present study shows that car-finishing workers are exposed to high levels of organic solvents only for short periods of time. It seems that they are not adequately protected during these periods. However, the presence of acute symptoms was low, i.e. comparable to the prevalences in the reference group.

  11. Graphic Arts: The Press and Finishing Processes. Third Edition.

    ERIC Educational Resources Information Center

    Crummett, Dan

    This document contains teacher and student materials for a course in graphic arts concentrating on printing presses and the finishing process for publications. Seven units of instruction cover the following topics: (1) offset press systems; (2) offset inks and dampening chemistry; (3) offset press operating procedures; (4) preventive maintenance…

  12. Plutonium Finishing Plant assessment of confinement system bypass leakage

    SciTech Connect

    Dick, J.D.

    1996-09-30

    The purpose of this report is to document walk-through`s of the safety class confinement systems at the Plutonium Finishing Plant (PFP). In addition this document outlines the actions taken to assess the confinement system for bypass leakage as well as establishing disposition for discovered deficiencies at the PFP.

  13. 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.

  14. 7 CFR 58.525 - Storage of finished product.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... AGRICULTURAL MARKETING ACT OF 1946 AND THE EGG PRODUCTS INSPECTION ACT (CONTINUED) GRADING AND INSPECTION... distribution and storage prior to sale the product should be maintained at a temperature of 45 °F. or lower... 7 Agriculture 3 2010-01-01 2010-01-01 false Storage of finished product. 58.525 Section...

  15. Early Childhood Education in Eritrea, Proceeding as We Would Finish.

    ERIC Educational Resources Information Center

    Andreoni, Helen

    1997-01-01

    Describes the success of early childhood education programs in Eritrea which are based on the principle "we should proceed in the way we wish to finish." Identifies the social, cultural, and developmental factors an educator must consider. Notes how multilingualism and multiculturalism are of special importance in Eritrean early…

  16. Interior Finishes. Floors, Walls, Ceilings: Performance Criteria. Interim Report.

    ERIC Educational Resources Information Center

    State Univ. Construction Fund, Albany, NY.

    A research program and the testing methods it developed are described, indicating the performance criteria of interior finishes for walls, ceilings and floors. Material exposure criteria are given with the probability of damage ratings for--(1) physical impact, (2) chemical damage, (3) biological, food and water damage. The relationship of…

  17. Crossing the Finish Line: Completing College at America's Public Universities

    ERIC Educational Resources Information Center

    Bowen, William G.; Chingos, Matthew M.; McPherson, Michael S.

    2011-01-01

    The United States has long been a model for accessible, affordable education, as exemplified by the country's public universities. And yet less than 60 percent of the students entering American universities today are graduating. Why is this happening, and what can be done? "Crossing the Finish Line" provides the most detailed exploration…

  18. 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...

  19. 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...

  20. 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,…

  1. Finishing lambs and kids on pasture in Appalachia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Traditional sheep, hair sheep and meat goat industries are growing rapidly in the Appalachian Region, particularly on small farms, to help produce meats for ethnic markets. Numerous forage types and qualities are used in small ruminant finishing systems. With the expansion of non-traditional lamb ...

  2. 21 CFR 106.30 - Finished product evaluation.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 2 2010-04-01 2010-04-01 false Finished product evaluation. 106.30 Section 106.30 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION INFANT FORMULA QUALITY CONTROL PROCEDURES Quality Control Procedures...

  3. 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…

  4. 9 CFR 318.309 - Finished product inspection.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... AGENCY ORGANIZATION AND TERMINOLOGY; MANDATORY MEAT AND POULTRY PRODUCTS INSPECTION AND VOLUNTARY... be handled according to: (1) A HACCP plan for canned product that addresses hazards associated with... this section. (b)-(c) (d) Procedures for handling finished product inspections where the HACCP plan...

  5. Effect of panel alignment and surface finish on bond strength

    SciTech Connect

    Wouters, J.M.; Doe, P.J.; Baker, W.E.

    1991-10-01

    The flexural strength of bonded acrylic is tested as a function of panel alignment and bond surface finish. Bond strength was shown to be highly dependent on both parameters with only a narrow range of values yielding a high strength bond. This study was performed for the heavy water-containing acrylic vessel for the Sudbury Neutrino Observatory detector.

  6. 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…

  7. A survey of grass-finished beef producers in Pennsylvania

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  8. Finishing tooth-colored restorations in vitro: an index of surface alteration and finish-line destruction.

    PubMed

    Schmidlin, Patrick R; Göhring, Till N

    2004-01-01

    Many studies have evaluated the surface characteristics of finishing and polishing instruments on different restorative materials using two- and three-dimensional models based on mechanical and optical techniques. However, only limited data are available regarding the problem of marginal causing detectable surface alterations such as scratches or grooves may also cause marginal damage. This study aimed to correlate the smooth-surface polishing efficacy of different instruments with their potential for destructive effects on restoration margins and enamel finish lines. An index was created that will help to evaluate future polishing instruments and select suitable ones for different clinical situations. A planar inlay system with a 100 microm wide defined gap was simulated in vitro. Pre-fabricated ceramic (n = 40) and composite blocks (n = 40) were connected to bovine enamel without luting material. After standardized pre-polishing, mean surface roughness and marginal quality were assessed using a profilometer and scanning electron microscopy (SEM). Enamel and restorative surfaces were colored, and subsequently prepared using one of 10 different finishing and polishing instruments. Four specimens per instrument and material were evaluated, resulting in eight interfaces for each test group. Surface roughness (Ra) and marginal quality (expressed as the percentage fracture-free margin) were measured and compared statistically using unpaired t-tests and two-way ANOVA, respectively. The level of significance was set at 0.05 Eight-micrometer diamond burs and 40-fluted tungsten carbide finishers produced smoother surfaces and less finishing-line destructions than the other instruments under evaluation. The index values developed will prove helpful in evaluating and selecting appropriate instruments.

  9. Immunological, physiological and behavioral effects of Salmonella enterica carriage and shedding in experimentally infected finishing pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Finishing pigs infected with Salmonella pose significant food safety risks by carrying the pathogen into abattoirs. This study was conducted to determine the dynamic of Salmonella infection in finishing pigs, and associated immunological, physiological, and behavioral alterations, by longitudinally ...

  10. 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

    ... From the Federal Register Online via the Government Publishing Office INTERNATIONAL TRADE COMMISSION Certain Prepregs, Laminates, and Finished Circuit Boards: Notice of Institution of Formal... States after importation of certain prepregs, laminates, and finished circuit boards that...

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

    SciTech Connect

    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

  12. Maize genome sequencing by methylation filtration.

    PubMed

    Palmer, Lance E; Rabinowicz, Pablo D; O'Shaughnessy, Andrew L; Balija, Vivekanand S; Nascimento, Lidia U; Dike, Sujit; de la Bastide, Melissa; Martienssen, Robert A; McCombie, W Richard

    2003-12-19

    Gene enrichment strategies offer an alternative to sequencing large and repetitive genomes such as that of maize. We report the generation and analysis of nearly 100,000 undermethylated (or methylation filtration) maize sequences. Comparison with the rice genome reveals that methylation filtration results in a more comprehensive representation of maize genes than those that result from expressed sequence tags or transposon insertion sites sequences. About 7% of the repetitive DNA is unmethylated and thus selected in our libraries, but potentially active transposons and unmethylated organelle genomes can be identified. Reverse transcription polymerase chain reaction can be used to finish the maize transcriptome.

  13. Effect of Finishing System on Subcutaneous Fat Melting Point and Fatty Acid Composition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Angus-cross steers (n = 69) were used to determine the effect of finishing system on subcutaneous fat melting point and fatty acid composition. Three finishing systems were evaluated: 1) mixed pasture for 134 d [MP], 2) mixed pasture for 93 d and alfalfa for 41 d [AL], or 3) concentrate finishing f...

  14. 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…

  15. 40 CFR 63.5395 - How do I measure the density of a finish?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... must be entered on the finish log for each type of finish applied. You are not required to test the materials that you use, but the Administrator may require a test using EPA Method 24 (or another approved... section for each finish when you perform one of the actions listed in paragraphs (b)(1) and (2) of...

  16. Recognizing Sequences of Sequences

    PubMed Central

    Kiebel, Stefan J.; von Kriegstein, Katharina; Daunizeau, Jean; Friston, Karl J.

    2009-01-01

    The brain's decoding of fast sensory streams is currently impossible to emulate, even approximately, with artificial agents. For example, robust speech recognition is relatively easy for humans but exceptionally difficult for artificial speech recognition systems. In this paper, we propose that recognition can be simplified with an internal model of how sensory input is generated, when formulated in a Bayesian framework. We show that a plausible candidate for an internal or generative model is a hierarchy of ‘stable heteroclinic channels’. This model describes continuous dynamics in the environment as a hierarchy of sequences, where slower sequences cause faster sequences. Under this model, online recognition corresponds to the dynamic decoding of causal sequences, giving a representation of the environment with predictive power on several timescales. We illustrate the ensuing decoding or recognition scheme using synthetic sequences of syllables, where syllables are sequences of phonemes and phonemes are sequences of sound-wave modulations. By presenting anomalous stimuli, we find that the resulting recognition dynamics disclose inference at multiple time scales and are reminiscent of neuronal dynamics seen in the real brain. PMID:19680429

  17. 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

  18. Farmer and Public Attitudes Toward Lamb Finishing Systems.

    PubMed

    Coleman, Grahame; Jongman, Ellen; Greenfield, L; Hemsworth, Paul

    2016-01-01

    To develop research and policy on the welfare of lambs in intensive finishing systems, it is important to understand public and sheep farmers' attitudes. The aim of this research was to identify and compare farmer and community attitudes relevant to the intensification of lamb finishing. The majority of respondents in the community sample expressed concern about all listed welfare issues, but particularly about feedlotting of lambs and the associated confinement. These attitudes correlated with community views on the importance of welfare issues including social contact and freedom to roam. Farmers expressed much lower levels of concern than did the general public except with regard to the health of lambs, disease control, access to shade, and lack of access to clean water.

  19. Surface profiling in mating parts by combined nonabrasive finishing

    NASA Astrophysics Data System (ADS)

    Smolentsev, EV; Fedonin, ON; Smolentsev, VP

    2017-02-01

    Nonabrasive finishing of precision mating surfaces in locking devices with the use of a combined erosion-chemical process at the first stage of the processing and with the use of anodic dissolution by alternating low-voltage current at the final stage of a refinement operation till gapless joints obtaining is considered. It is shown that the application of electro-erosion, electrochemical and combined nonabrasive finishing in mating parts opens up a possibility to ensure stable impermeability in locking devices on a macro- and micro-level through the method of a substantiated purpose of technological modes. A procedure is created for the development of such modes, and on their basis technological processes for the obtaining of gapless mating surfaces meeting the performance requirements for locking devices are developed. For this purpose, qualitative devices resistant to hostile environment are manufactured that is urgent for the mechanical engineering including repetition work for the equipment of petrochemical industry, transport and household machinery.

  20. 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.

  1. Effect of longitudinal surface finish on elastohydrodynamic lubrication

    NASA Technical Reports Server (NTRS)

    Dow, T. A.; Kannel, J. W.; Parker, R. J.

    1975-01-01

    The effect of longitudinal-lay surface finish on the elastohydrodynamic film thickness and the percentage of film between rolling disks in contact were evaluated using a rolling disk apparatus. Film thickness was measured by transmitted X-rays, and percentage of film was monitored by an alternating-current continuity circuit. Disk finish was varied on both the crowned upper disk and the cylindrical lower disk. A type-2 ester and a synthetic paraffinic oil were used as lubricants. It was shown that the roughness with longitudinal lay has a deleterious effect on both film thickness and percentage of film. Measured film thicknesses for the two lubricants were comparable at equivalent test conditions. The percentage of film where a change in surface topography was observed was approximately 20 percent for the synthetic paraffinic oil and 10 percent for the type-2 ester.

  2. 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.

  3. Bacterial diversity in a finished compost and vermicompost: differences revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes.

    PubMed

    Fracchia, Letizia; Dohrmann, Anja B; Martinotti, Maria Giovanna; Tebbe, Christoph C

    2006-08-01

    Bacterial communities are important catalysts in the production of composts. Here, it was analysed whether the diversity of bacteria in finished composts is stable and specific for the production process. Single-strand conformation polymorphism (SSCP) based on polymerase chain reaction amplified partial 16S rRNA genes was used to profile and analyse bacterial communities found in total DNA extracted from finished composts. Different batches of compost samples stored over a period of 12 years and a 1-year-old vermicompost were compared to each other. According to digital image analysis, clear differences could be detected between the profiles from compost and vermicompost. Differences between three different periods of compost storage and between replicate vermicompost windrows were only minor. A total of 41 different 16S rRNA genes were identified from the SSCP profiles by DNA sequencing, with the vast majority related to yet-uncultivated bacteria. Sequences retrieved from compost mainly belonged to the phyla Actinobacteria and Firmicutes. In contrast, vermicompost was dominated by bacteria related to uncultured Chloroflexi, Acidobacteria, Bacteroidetes and Gemmatimonadetes. The differences were underscored with specific gene probes and Southern blot hybridizations. The results confirmed that different substrates and composting processes selected for specific bacterial communities in the finished products. The specificity and consistency of the bacterial communities inhabiting the compost materials suggest that cultivation-independent bacterial community analysis is a potentially useful indicator to characterize the quality of finished composts in regard to production processes and effects of storage conditions.

  4. Reflective fiber optic probe for surface finish survey

    NASA Astrophysics Data System (ADS)

    Wawrzyniuk, Leszek

    1995-06-01

    The Report relates to verification of the design of refractive fiber optic probes designed for checking surface finish condition and provides a description of tests on the models of such probes. Presented in the paper are the results of performance tests of a bifurcated probe to the concept of application of a non-random bundle of light guides for identification of surfaces representing different CLA values (0.32, 0.63, 1.25, 2.50 micrometers).

  5. Surface finishing of resin-modified glass ionomer.

    PubMed

    Liporoni, Priscila; Paulillo, Luis Alexandre; Cury, Jaime Aparecido; Dos Santos Dias, Carlos Tadeu; Paradella, Thais Cachute

    2003-01-01

    This study utilized spectrophotometry to evaluate in vitro superficial dye deposition on resin-modified glass ionomer, following different surface finishing and polishing treatments. Materials that were photocured adjacent to the mylar strip produced the surfaces with the lowest mean after superficial staining. A restorative technique without excesses resulted in a smoother surface and prolonged the life of the restoration. The resin-modified glass ionomers tested offer adequate clinical performance.

  6. The Analysis of Metal Finishing Solutions by Ion Chromatography

    DTIC Science & Technology

    1987-08-01

    traditional chemical methods now in use. This report describes procedures for the analysis of solutions for chromium plating, acid finishing, metal...samples and standards must have similar acid -base characteristics. These methods are an improvement to standard methods now in practice and have been...CITED ............................... 195 iv LIST OF TABLES Page Table 1. Ionization Constants of Acids (12) . 29 Table 2. Common Anion Eluents

  7. Marathon finishers and pre-race drop-outs.

    PubMed Central

    Clough, P J; Shepherd, J; Maughan, R J

    1989-01-01

    The purpose of this longitudinal questionnaire study was to investigate the effects of participation or non participation in a marathon race on future running behaviour. The majority (70 per cent) of the participants who intended to run a future marathon actually did so and only 11 per cent stopped running altogether. Fewer of the pre-race drop-outs (31 per cent) who indicated their intention to run a future marathon actually did so (P less than 0.001) and more of them (24 per cent) stopped running altogether (P less than 0.001) compared with the runners in the finishers' sample. These results suggest that the experience of running in a marathon does not negatively influence future running habits. However, failure to run in a race for which an entry has been made may lead to a reduced involvement in running. The present study also examined the reasons for pre-race drop-out. Injury (36 per cent), lack of training (31 per cent) and illness (12 per cent) were the most frequently given reasons for drop-out. Few differences were found between the pre-race drop-outs and the finishers, but the drop-outs did feel that running was less important (P less than 0.001), reported a greater number of longer term injuries (P less than 0.001) and did significantly less training (P less than 0.001) than the finishers. Images p101-a PMID:2605449

  8. Development of laser finishing for non-circular profiles

    SciTech Connect

    Liu, K.W.; Sheng, P.S.

    1995-03-01

    A laser-based technique for finishing of non-circular cylindrical parts is presented. In this process, the frequency characteristics of a desired non-circular shape is extracted from a CAD through a Fast Fourier Transform algorithm and implemented through a CO{sub 2} laser machining system. A galvanometer-based scanner is used in the process to achieve programmable beam trajectories and high-speed finishing. An error estimation scheme can be developed to determine the final dimensional error of the non-circular profile. This process can be selected as both a batch production tool and a rapid prototyping tool based on the designated processing rate and precision. Initial experimental results include the production of two- and three-lobed profiles, as well as definition of part feature using higher-order harmonics, in polymethylmethacrylate (PMMA) with corresponding R{sub a} values of less than 1 {mu}m. The machine tool elements and general procedure for non-circular laser finishing are also presented.

  9. 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.

  10. Analysis of Human mRNAs With the Reference Genome Sequence Reveals Potential Errors, Polymorphisms, and RNA Editing

    PubMed Central

    Furey, Terrence S.; Diekhans, Mark; Lu, Yontao; Graves, Tina A.; Oddy, Lachlan; Randall-Maher, Jennifer; Hillier, LaDeana W.; Wilson, Richard K.; Haussler, David

    2004-01-01

    The NCBI Reference Sequence (RefSeq) project and the NIH Mammalian Gene Collection (MGC) together define a set of ∼30,000 nonredundant human mRNA sequences with identified coding regions representing 17,000 distinct loci. These high-quality mRNA sequences allow for the identification of transcribed regions in the human genome sequence, and many researchers accept them as the correct representation of each defined gene sequence. Computational comparison of these mRNA sequences and the recently published essentially finished human genome sequence reveals several thousand undocumented nonsynonymous substitution and frame shift discrepancies between the two resources. Additional analysis is undertaken to verify that the euchromatic human genome is sufficiently complete—containing nearly the whole mRNA collection, thus allowing for a comprehensive analysis to be undertaken. Many of the discrepancies will prove to be genuine polymorphisms in the human population, somatic cell genomic variants, or examples of RNA editing. It is observed that the genome sequence variant has significant additional support from other mRNAs and ESTs, almost four times more often than does the mRNA variant, suggesting that the genome sequence is more accurate. In ∼15% of these cases, there is substantial support for both variants, suggestive of an undocumented polymorphism. An initial screening against a 24-individual genomic DNA diversity panel verified 60% of a small set of potential single nucleotide polymorphisms from which successful results could be obtained. We also find statistical evidence that a few of these discrepancies are due to RNA editing. Overall, these results suggest that the mRNA collections may contain a substantial number of errors. For current and future mRNA collections, it may be prudent to fully reconcile each genome sequence discrepancy, classifying each as a polymorphism, site of RNA editing or somatic cell variation, or genome sequence error. PMID:15489323

  11. 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.

  12. Noncontiguous finished genome sequence and description of Paenibacillus ihumii sp. nov. strain AT5

    PubMed Central

    Togo, A.H.; Khelaifia, S.; Lagier, J.-C.; Caputo, A.; Robert, C.; Fournier, P.-E.; Maraninchi, M.; Valero, R.; Raoult, D.; Million, M.

    2016-01-01

    Paenibacillus ihumii sp. nov. strain AT5 (= CSUR 1981 = DSM 100664) is the type strain of P. ihumii. This bacterium was isolated from a stool sample from a morbidly obese French patient using the culturomics approach. The genome of this Gram-negative, facultative anaerobic, motile and spore-forming bacillus is 5 924 686 bp long. Genomic analysis identified 253 (5%) of 3812 genes as ORFans and at least 2599 (50.03%) of 5194 orthologous proteins not shared with the closest phylogenetic species. PMID:26958346

  13. Non-contiguous finished genome sequence of Ornithobacterium rhinotracheale strain H06-030791

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Gram-negative pleomorphic rod-shaped bacterium Ornithobacterium rhinotracheale (O. rhinotracheale) is a cause of pneumonia and airsacculitis in poultry. It is a member of the family Flavobacteriaceae of the phylum Bacteroidetes. O. rhinotracheale strain H06-030791 was isolated from the lung of...

  14. Mycosphaerella graminicola sequencing heads towards the first finished genome of a filamentous plant pathogenic fungus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mycosphaerella is one of the largest genera of plant pathogenic fungi with more than 1,000 named species, a few of which cause disease in humans and other vertebrates. The genomes of M. graminicola and M. fijiensis, two of the most economically important pathogens of wheat and banana, respectively, ...

  15. Phenotypic and Genotypic Diversity of Salmonella in Finishing Swine.

    PubMed

    Pires, Alda F A; Funk, Julie A; Habing, Greg G; Bolin, Carole

    2016-04-01

    Salmonella enterica (nontyphoidal) is one of the major causes of foodborne diseases in the United States and worldwide. Molecular typing methods are significant tools used to better understand the transmission and ecology of Salmonella in order to implement pre-harvest control measures. The objectives of this study were to describe the Salmonella genotypes, the distribution of isolate subtypes from different ecological niches (i.e., barn environment, nursery, and individual pigs) and their evolution over time in a longitudinal study conducted in three finishing sites (housing pigs from 10 weeks of age until slaughter at 24-26 weeks of age). Among the 107 Salmonella isolates submitted for pulsed-field gel electrophoresis (PFGE) analysis, there were 25 distinct subtypes. PFGE genotyping results were consistent with the serotype findings. A large number of distinguishable PFGE patterns (i.e., within the same serovar) were observed and different combinations of subtypes were identified within and across sites and cohorts. New subtypes may result of the introduction of new strains, genetic changes, or ongoing transmission of evolved strains within the production system. The same subtypes were detected intermittently during the study period, which suggests the persistence of indistinguishable subtypes in this production system. In addition, this study suggests persistence of the same subtype over several cohorts of pigs and potential residual contamination from the barn. Factors affecting adaptation and transmission of Salmonella within and among ecological systems (e.g., finishing pigs, nursery, and environment) should be further investigated. Understanding genotypic diversity of Salmonella in different ecological niches during pre-harvest may contribute to the development of more targeted and cost effective control programs during nursery and finishing phases.

  16. Polymer micromolds with near optical quality surface finishes

    NASA Astrophysics Data System (ADS)

    Shiu, Pun-Pang; Knopf, George K.; Nikumb, Suwas

    2012-03-01

    Disposable microfluidic systems are used to avoid sample contamination in a variety of medical and environmental monitoring applications. A contactless hot intrusion (HI) process for fabricating reusable polymer micromolds with near "optical quality" surface finishes is described in this paper. A metallic hot intrusion mask with the desired microchannels and related passive components is first machined using a tightly focused beam from a diode-pumped solid-state (DPSS) laser. The polymer mold master is then created by pressing the 2D metallic mask onto a polymethylmethacrylate (PMMA) substrate. Since it is a contactless fabrication process the resultant 3D micro-reliefs have near optical quality surface finishes. Unfortunately, the desired micro-relief dimensions (height and width) are not easily related to the hot intrusion process parameters of pressure, temperature, and time exposure profile. A finite element model is introduced to assist the manufacturing engineer in predicting the behavior of the PMMA substrate material as it deforms under heat and pressure during micromold manufacture. The FEM model assumes that thermo-plastics like PMMA become "rubber like" when heated to a temperature slightly above the glass transition temperature. By controlling the material temperature and maintaining its malleable state, it is possible to use the stress-strain relationship to predict the profile dimensions of the imprinted microfeature. Examples of curved microchannels fabricated using PMMA mold masters are presented to illustrate the proposed methodology and verify the finite element model. In addition, the non-contact formation of the micro-reliefs simplifies the demolding process and helps to preserve the high quality surface finishes.

  17. Durable hydrophobic sol-gel finishing for textiles

    NASA Astrophysics Data System (ADS)

    Vihodceva, S.; Kukle, S.; Bitenieks, J.

    2015-03-01

    The surface of cotton textile was modified to create a water-repellent finishing by depositing a modifying coatings using the sol-gel technique. Treated textiles evaluated using scanning electron microscopy, X-Ray powder diffraction (XRD). The wettability of treated fabrics was characterized by water contact angle and drop test. The results showed that the cotton textile treated with 7.5 wt.% zinc acetate dihydrate sol showed excellent hydrophobic properties, water contact angle could reach 145°C without decreasing after 50 hydrothermal treatment cycles.

  18. Automated edge finishing using an active XY table

    DOEpatents

    Loucks, Clifford S.; Starr, Gregory P.

    1993-01-01

    The disclosure is directed to an apparatus and method for automated edge finishing using hybrid position/force control of an XY table. The disclosure is particularly directed to learning the trajectory of the edge of a workpiece by "guarded moves". Machining is done by controllably moving the XY table, with the workpiece mounted thereon, along the learned trajectory with feedback from a force sensor. Other similar workpieces can be mounted, without a fixture on the XY table, located and the learned trajectory adjusted

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

    NASA Astrophysics Data System (ADS)

    D'Antonio, Peter

    2003-04-01

    Architects and 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. It is currently finding application in many architectural applications, including museums. A recent installation in the New Pinakothek Museum in Munich will be illustrated.

  20. On numerically accurate finite element

    NASA Technical Reports Server (NTRS)

    Nagtegaal, J. C.; Parks, D. M.; Rice, J. R.

    1974-01-01

    A general criterion for testing a mesh with topologically similar repeat units is given, and the analysis shows that only a few conventional element types and arrangements are, or can be made suitable for computations in the fully plastic range. Further, a new variational principle, which can easily and simply be incorporated into an existing finite element program, is presented. This allows accurate computations to be made even for element designs that would not normally be suitable. Numerical results are given for three plane strain problems, namely pure bending of a beam, a thick-walled tube under pressure, and a deep double edge cracked tensile specimen. The effects of various element designs and of the new variational procedure are illustrated. Elastic-plastic computation at finite strain are discussed.

  1. 40 CFR 63.5385 - How do I measure the quantity of finish applied to the leather?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... mass, or density, and volume of each applied finish. (b) Determine the mass of each applied finish with... density and volume of each applied finish according to the criteria listed in paragraphs (c)(1) through (3) of this section: (1) Determine the density of each applied finish in pounds per gallon in...

  2. 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

    ... 40 Protection of Environment 12 2010-07-01 2010-07-01 true Example Logs for Recording Leather... 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...

  3. 40 CFR Figure 1 to Subpart Tttt of... - Example Logs for Recording Leather Finish Use and HAP Content

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 12 2011-07-01 2009-07-01 true Example Logs for Recording Leather... 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...

  4. DNA barcode data accurately assign higher spider taxa.

    PubMed

    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; Kuntner, Matjaž

    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 the

  5. 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

  6. The effect of three finishing systems on four esthetic restorative materials.

    PubMed

    Hoelscher, D C; Neme, A M; Pink, F E; Hughes, P J

    1998-01-01

    Previous studies have investigated the finishing and smoothness of composite and traditional glass-ionomer restorations, but few have included resin-modified glass-ionomer cements or more recent finishing systems. The results of using three different finishing systems (Sof-Lex, Enhance, finishing burs) on two composites (Silux, Prisma TPH), a traditional glass ionomer (Ketac-Fil), and a resin-modified glass ionomer (Fuji II LC) were studied. Sixty samples were condensed into sectioned acrylic tubes, covered with a Mylar matrix plus a glass slide at each surface, then cured as per the manufacturers' instructions. Samples were randomized to three groups of five for each material and testing with a Surfanalyzer 4000 of unfinished samples (cured with Mylar matrix) was done to obtain baseline average surface roughness (Ra). Samples were then finished as per the manufacturers' instructions using polishing disks, abrasive impregnated disks, and finishing burs before further surface testing. Samples finished with burs and with abrasive impregnated disks were further polished using polishing paste (Prisma Gloss) and again tested. Data were analyzed with ANOVA testing and Tukey's HSD pairwise comparison. Initial testing after randomization to groups showed no significant difference in surface roughness (P = 0.24). Two-factor analysis revealed no significant difference between materials (P = 0.34), a significant difference in method of finish (P < or = 0.00), with no significant interaction between type of material and method of finish (P = 0.11). Aluminum oxide disk and impregnated disk systems provided the best finish for microfilled composite and both glass-ionomer materials (P < or = 0.00). No significant difference in method of finish existed with the hybrid composite (P = 0.07). Overall, esthetic restorative material finishing is best accomplished using abrasive impregnated disks or aluminum oxide disks. Finishing burs gave a significantly rougher surface than the

  7. Accurate phylogenetic classification of DNA fragments based onsequence composition

    SciTech Connect

    McHardy, Alice C.; Garcia Martin, Hector; Tsirigos, Aristotelis; Hugenholtz, Philip; Rigoutsos, Isidore

    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 sequence 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.

  8. Thermal oxidation technology ready for tougher paint finishing regs

    SciTech Connect

    Brooks, J.

    1995-04-01

    There is good news and bad news in the air for commercial paint finishers. The bad news is that future local and federal clean-air regulations are almost certain to require control of volatile organic compound emissions from spray booths and drying ovens. The good news is that one of the most effective systems for meeting such requirements also can help cut operations and maintenance costs. There are as many solutions to VOC emissions problems in paint finishing as there are types of paint-spraying facilities. However, despite the range of choices, regenerative thermal oxidation systems are gaining favor among plant managers, for whom performance and maximum application flexibility are key considerations. Compared to other VOC-destruction approaches, RTO systems are more forgiving and reliable. Although RTO systems involve somewhat higher capital investments than alternative approaches, such costs typically are offset by lower long-term fuel and maintenance requirements. In addition, RTO systems can convert pollutants into usable energy sources, helping minimize operating costs of abatement equipment.

  9. 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.

  10. Accurate ab Initio Spin Densities.

    PubMed

    Boguslawski, Katharina; Marti, Konrad H; Legeza, Ors; Reiher, Markus

    2012-06-12

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740].

  11. Deburring and surface finishing: The past ten years and projections for the next ten years

    SciTech Connect

    Gillespie, L.K.

    1990-09-01

    The 1970s were a decade of significant growth in deburring and surface finishing. In the 1980s progress was made in robotic finishing, burr formation models, surface finish measurement, new processes, equipment and tooling. The centers of burr and surface related research changed. The decade of the 1990s will bring greater competition, environmental restrictions, more processes, more automation, and better characterization and simulation of processes.

  12. 40 CFR 410.20 - Applicability; description of the wool finishing subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Wool Finishing Subcategory... are applicable to process wastewater discharges resulting from the following types of textile...

  13. 40 CFR 410.20 - Applicability; description of the wool finishing subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Wool Finishing Subcategory... are applicable to process wastewater discharges resulting from the following types of textile...

  14. 40 CFR 410.20 - Applicability; description of the wool finishing subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Wool Finishing Subcategory... are applicable to process wastewater discharges resulting from the following types of textile...

  15. 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.

  16. 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...

  17. 40 CFR 410.20 - Applicability; description of the wool finishing subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Wool Finishing Subcategory... are applicable to process wastewater discharges resulting from the following types of textile...

  18. 40 CFR 410.60 - Applicability; description of the carpet finishing subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Carpet Finishing... subpart are applicable to process wastewater discharges resulting from the following types of...

  19. An ultra-low surface finish process for 6061-Al mirrors

    NASA Astrophysics Data System (ADS)

    Wamboldt, Leonard; Roy, Brian; Crifasi, Joseph; Stephens, Shane; Hanninen, Derek; Woodard, Kenneth; Felock, Robert; Cunha-Vasconcelos, Sofia; Polczwartek, Stephen; Parenteau, Jeffrey

    2015-05-01

    An ultra-low surface finishing process for 6061 T6 type aluminum has been developed by Corning Incorporated, Specialty Materials Division, and has been successfully applied to mirrors up to 13 inches in diameter. This paper presents finish and figure data achieved from the mirror finishing process. Mirror stability is demonstrated through Pre and post thermal cycle surface figure measurements; temperature range of cycle -55°C to +70°C. As an added benefit, the process enables the use of deterministic finishing and enhances the reflective optics resistance to corrosion. Survivability of the reflective optic is evaluated through extended humidity testing.

  20. Crawling to the finish line: why do endurance runners collapse? Implications for understanding of mechanisms underlying pacing and fatigue.

    PubMed

    St Clair Gibson, Alan; De Koning, Jos J; Thompson, Kevin G; Roberts, William O; Micklewright, Dominic; Raglin, John; Foster, Carl

    2013-06-01

    Effective regulation of pace enables the majority of runners to complete competitive endurance events without mishap. However, some runners do experience exercise-induced collapse associated with postural hypotension, which in rare cases results from life-threatening conditions such as cardiac disorders, cerebral events, heat stroke and hyponatraemia. Despite the experience of either catastrophic system failure or extreme peripheral muscle fatigue, some runners persist in attempting to reach the finish line, and this often results in a sequence of dynamic changes in posture and gait that we have termed the 'Foster collapse positions'. The initial stage involves an unstable gait and the runner assumes the 'Early Foster' collapse position with hips slightly flexed and their head lowered. This unstable gait further degrades into a shuffle referred to as the 'Half Foster' collapse position characterized by hip flexion of approximately 90° with the trunk and head parallel to the ground. At this point, the muscles of postural support and the co-ordination of propulsion begin to be compromised. If the condition worsens, the runner will fall to the ground and assume the 'Full Foster' collapse position, which involves crawling forwards on knees and elbows towards the finish line, with their trunk angled such that the head is at a lower angle than the hips. Upon reaching the finish line, or sometimes before that, the runner may collapse and remain prone until recovering either with or without assistance or medical treatment. The Foster collapse positions are indicative of a final, likely primordial, protective mechanism designed to attenuate postural hypotension, cardiac 'pump' insufficiency or cerebral blood flow deficiency. Continuing to attempt to reach the finish line in this impaired state is also perhaps indicative of a high psychological drive or a variety of neurological and psychological pathologies such as diminished sensitivity to interoceptive feedback

  1. Accurate phylogenetic classification of variable-length DNA fragments.

    PubMed

    McHardy, Alice Carolyn; Martín, Héctor García; Tsirigos, Aristotelis; Hugenholtz, Philip; Rigoutsos, Isidore

    2007-01-01

    Metagenome studies have retrieved vast amounts of sequence data from a variety of environments leading to new discoveries and insights into the uncultured microbial world. Except for very simple communities, the encountered diversity has made fragment assembly and the subsequent analysis a challenging problem. A taxonomic characterization of metagenomic fragments is required for a deeper understanding of shotgun-sequenced microbial communities, but success has mostly been limited to sequences containing phylogenetic marker genes. Here we present PhyloPythia, a composition-based classifier that combines higher-level generic clades from a set of 340 completed genomes with sample-derived population models. Extensive analyses on synthetic and real metagenome data sets showed that PhyloPythia allows the accurate classification of most sequence fragments across all considered taxonomic ranks, even for unknown organisms. The method requires no more than 100 kb of training sequence for the creation of accurate models of sample-specific populations and can assign fragments >or=1 kb with high specificity.

  2. Second floor plan. (Also includes a roof plan and finish ...

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

    Second floor plan. (Also includes a roof plan and finish schedule.) March Air Force Base, Riverside, California, Combat Operations Center, Combat Operations Building. By Moffatt and Nichol, Engineers, 122 West Fifth Street, Long Beach, California; for the Corps of Engineers, U.S. Army, Office of the District Engineer, Los Angeles, California. Drawing no. AW-60-02-03, sheet no. 13, approved March, 1962; specifications no. OCI-62-66; D.O. series AW 1596/13, Rev. "C"; file drawer 1290. Last revised 7 February 1984. Roof plan scale one-sixteenth inch to one foot; second floor plan scale one-eighth inch to one foot. 28.75x41 inches. pencil on paper - March Air Force Base, Strategic Air Command, Combat Operations Center, 5220 Riverside Drive, Moreno Valley, Riverside County, CA

  3. Microencapsulated citronella oil for mosquito repellent finishing of cotton textiles.

    PubMed

    Specos, M M Miró; García, J J; Tornesello, J; Marino, P; Vecchia, M Della; Tesoriero, M V Defain; Hermida, L G

    2010-10-01

    Microcapsules containing citronella essential oil were prepared by complex coacervation and applied to cotton textiles in order to study the repellent efficacy of the obtained fabrics. Citronella released from treated textiles was indirectly monitored by the extractable content of its main components. Repellent activity was assessed by exposure of a human hand and arm covered with the treated textiles to Aedes aegypti mosquitoes. Fabrics treated with microencapsulated citronella presented a higher and longer lasting protection from insects compared to fabrics sprayed with an ethanol solution of the essential oil, assuring a repellent effect higher than 90% for three weeks. Complex coacervation is a simple, low cost, scalable and reproducible method of obtaining encapsulated essential oils for textile application. Repellent textiles were achieved by padding cotton fabrics with microcapsules slurries using a conventional pad-dry method. This methodology requires no additional investment for textile finishing industries, which is a desirable factor in developing countries.

  4. Research on reducing the edge effect in magnetorheological finishing.

    PubMed

    Hu, Hao; Dai, Yifan; Peng, Xiaoqiang; Wang, Jianmin

    2011-03-20

    The edge effect could not be avoided in most optical manufacturing methods based on the theory of computer controlled optical surfacing. The difference between the removal function at the workpiece edge and that inside it is also the primary cause for edge effect in magnetorheological finishing (MRF). The change of physical dimension and removal ratio of the removal function is investigated through experiments. The results demonstrate that the situation is different when MRF "spot" is at the leading edge or at the trailing edge. Two methods for reducing the edge effect are put into practice after analysis of the processing results. One is adopting a small removal function for dealing with the workpiece edge, and the other is utilizing the removal function compensation. The actual processing results show that these two ways are both effective on reducing the edge effect in MRF.

  5. Plutonium Finishing Plant (PFP) HVAC System Component Index

    SciTech Connect

    DIAZ, E.N.

    2000-03-30

    This document lists safety class (SC) and safety significant (SS) components for the Heating Ventilation Air Conditioning (HVAC) and specifies the critical characteristics for Commercial Grade Items (CGI), as required by HNF-PRO-268 and HNF-PRO-18 19. These are the minimum specifications that the equipment must meet in order to properly perform its safety function. There may be several manufacturers or models that meet the critical characteristics for any one item. The Plutonium Finishing Plant (PFP) HVAC System includes sub-systems 25A through 25K. Specific system boundaries and justifications are contained in HNF-SD-CP-SDD-005, ''Definition and Means of Maintaining the Ventilation System Confinement Portion of the PFP Safety Envelope.'' The procurement requirements associated with the system necessitates procurement of some system equipment as Commercial Grade Items in accordance with HNF-PRO-268, ''Control of Purchased Items and Services.''

  6. Antimicrobial-finished textile three-dimensional structures.

    PubMed

    Heide, M; Möhring, U; Hänsel, R; Stoll, M; Wollina, U; Heinig, B

    2006-01-01

    This paper describes the possibilities of antimicrobial finishing of three-dimensional spacer fabrics and its applications, and gives information about the different effects. A research project of the Textilforschungsinstitut Thüringen-Vogtland Greiz is presented in which medical shoe insoles, based on specially manufactured three-dimensional spacer fabrics, made of permanently effective antimicrobial yarns were used for interesting and functional textile products. Furthermore, work of the research institute Forschungsinstitut für Leder und Kunststoffbahnen Freiberg is presented which describes the silver-coating process and application of textile materials using antimicrobial substances. The chemical and mechanical stability is investigated, and proof of the effectiveness is supplied. The results show that in the three-dimensional spacer fabrics both - antimicrobial yarn materials and thin silver films with antimicrobial substances - can achieve an antimicrobial effect, even in low quantities.

  7. Plutonium Finishing Plant. Interim plutonium stabilization engineering study

    SciTech Connect

    Sevigny, G.J.; Gallucci, R.H.; Garrett, S.M.K.; Geeting, J.G.H.; Goheen, R.S.; Molton, P.M.; Templeton, K.J.; Villegas, A.J.; Nass, R.

    1995-08-01

    This report provides the results of an engineering study that evaluated the available technologies for stabilizing the plutonium stored at the Plutonium Finishing Plant located at the hanford Site in southeastern Washington. Further processing of the plutonium may be required to prepare the plutonium for interim (<50 years) storage. Specifically this document provides the current plutonium inventory and characterization, the initial screening process, and the process descriptions and flowsheets of the technologies that passed the initial screening. The conclusions and recommendations also are provided. The information contained in this report will be used to assist in the preparation of the environmental impact statement and to help decision makers determine which is the preferred technology to process the plutonium for interim storage.

  8. Adaptive control of surface finish in automated turning processes

    NASA Astrophysics Data System (ADS)

    García-Plaza, E.; Núñez, P. J.; Martín, A. R.; Sanz, A.

    2012-04-01

    The primary aim of this study was to design and develop an on-line control system of finished surfaces in automated machining process by CNC turning. The control system consisted of two basic phases: during the first phase, surface roughness was monitored through cutting force signals; the second phase involved a closed-loop adaptive control system based on data obtained during the monitoring of the cutting process. The system ensures that surfaces roughness is maintained at optimum values by adjusting the feed rate through communication with the PLC of the CNC machine. A monitoring and adaptive control system has been developed that enables the real-time monitoring of surface roughness during CNC turning operations. The system detects and prevents faults in automated turning processes, and applies corrective measures during the cutting process that raise quality and reliability reducing the need for quality control.

  9. Finishing technologies for processing of optical microelectronic items

    NASA Astrophysics Data System (ADS)

    Muratov, K. R.; Ablyaz, T. R.; Gashev, E. A.; Khanov, A. M.; Varlamov, N. V.

    2016-10-01

    This article discusses comparative studies of the influence of specific pressure and speed of relative motion of tool and item on polishing capacity and quality of processed surface of lithium niobate single crystal. The equation for calculation of total depth of layer destroyed upon finishing and time of polishing required for its removal. Analysis of polishing tool has accounted for strength properties of the polishing material, removal capacity, and quality of processed surface of lithium niobate single crystal. It is experimentally established that upon basic pressure both for woven and unwoven polishers with the highest capacity the lower limit of grain coarseness of polishing suspension is 1/0.5 μm. A reserve of increase in shape accuracy and polishing quality is the use of polishers with equal thickness and structure of working surface.

  10. Genome Sequencing.

    PubMed

    Verma, Mansi; Kulshrestha, Samarth; Puri, Ayush

    2017-01-01

    Genome sequencing is an important step toward correlating genotypes with phenotypic characters. Sequencing technologies are important in many fields in the life sciences, including functional genomics, transcriptomics, oncology, evolutionary biology, forensic sciences, and many more. The era of sequencing has been divided into three generations. First generation sequencing involved sequencing by synthesis (Sanger sequencing) and sequencing by cleavage (Maxam-Gilbert sequencing). Sanger sequencing led to the completion of various genome sequences (including human) and provided the foundation for development of other sequencing technologies. Since then, various techniques have been developed which can overcome some of the limitations of Sanger sequencing. These techniques are collectively known as "Next-generation sequencing" (NGS), and are further classified into second and third generation technologies. Although NGS methods have many advantages in terms of speed, cost, and parallelism, the accuracy and read length of Sanger sequencing is still superior and has confined the use of NGS mainly to resequencing genomes. Consequently, there is a continuing need to develop improved real time sequencing techniques. This chapter reviews some of the options currently available and provides a generic workflow for sequencing a genome.

  11. Effects of varying machine stiffness and contact area in UltraForm Finishing

    NASA Astrophysics Data System (ADS)

    Briggs, Dennis E.; Echaves, Samantha; Pidgeon, Brendan; Travis, Nathan; Ellis, Jonathan D.

    2013-09-01

    UltraForm Finishing (UFF) is a deterministic, subaperture, computer numerically controlled, grinding and polishing platform designed by OptiPro Systems. UFF is used to grind and polish a variety optics from simple spherical to fully freeform, and numerous materials from glasses to optical ceramics. The UFF system consists of an abrasive belt around a compliant wheel that rotates and contacts the part to remove material. This work aims to measure the stiffness variations in the system and how it can affect material removal rates. The stiffness of the entire system is evaluated using a triaxial load cell to measure forces and a capacitance sensor to measure deviations in height. Because the wheel is conformal and elastic, the shapes of contact areas are also of interest. For the scope of this work, the shape of the contact area is estimated via removal spot. The measured forces and removal spot area are directly related to material removal rate through Preston's equation. Using our current testing apparatus, we will demonstrate stiffness measurements and contact areas for a single UFF belt during different states of its lifecycle and assess the material removal function from spot diagrams as a function of wear. This investigation will ultimately allow us to make better estimates of Preston's coefficient and develop spot-morphing models in an effort to more accurately predict instantaneous material removal functions throughout the lifetime of a belt.

  12. Comparison of Wyko and TIS measurements of surface finish

    SciTech Connect

    Church, E.L.; Sanger, G.M.; Takacs, P.Z.

    1987-01-01

    Profile and area measurements of the roughness of a given surface will generally be different since the two measurement techniques are sensitive to different areas of surface-frequency space. This paper explores the magnitudes of these differences by calculating the ratio of rms roughness values, sigma (TIS)/sigma(Wyko), using strawman models of a Wyko profiling microscope and a Talandic integrating scatterometer applied to surfaces having different roughness power spectra. As expected, the results show that this ratio can vary widely about unity, with values depending on the magnification of the objective used in the Wyko microscope and the ''color'' of the surface spectrum. An amazing counter example appears to occur for surfaces having an approximately ''1/theta/sup 2/'' BRDF, or equivalently, a 1/f profile power spectrum - shapes which are frequently observed for non-metallic mirror surfaces. In this case the predicted TIS and Wyko roughness values are essentially identical and independent of the Wyko magnification. This equality, however, comes from a curious mathematical-numerical coincidence and does not mean that these apparently ''universal'' values represent any intrinsic finish parameters of the surface being measured. In fact, if the Wyko data are filtered to remove the contributions from surface wavelengths longer than those included in the TIS measurements in order to more nearly match the instrumental bandwidths, the calculated ratio of measured rms roughness values increases to 1.5 to 5, depending on the Wyko parameters used. These results illustrate the fact that any realistic comparison of profile and area measurements of surface finish requires a knowledge of both the instrumental transfer functions and the form of the power spectrum of the surface being measured. The present paper discusses these issues and provides analytic machinery for the detailed quantitative comparison of profile, TIS and BRDF measurements.

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

    NASA Astrophysics Data System (ADS)

    Barman, Anwesa; Das, Manas

    2016-05-01

    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.

  14. 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.

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

    SciTech Connect

    Fiske, Haley; Turner, Steve; Rhodes, Michael; Milos, Patrice; Harkins, Tim

    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

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

    SciTech Connect

    Fiske, Haley; Turner, Steve; Rhodes, Michael; Milos, Patrice; Harkins, Tim

    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

  17. Effect of feeding sodium butyrate in the late finishing period on Salmonella carriage, seroprevalence, and growth of finishing pigs.

    PubMed

    Walia, Kavita; Argüello, Hector; Lynch, Helen; Leonard, Finola C; Grant, Jim; Yearsley, Dermot; Kelly, Sinead; Duffy, Geraldine; Gardiner, Gillian E; Lawlor, Peadar G

    2016-09-01

    Pork is an important source of human salmonellosis and low-cost on-farm control measures may provide a useful element in reducing the prevalence of this pathogen in food. This study investigated the effectiveness of dietary supplementation with sodium butyrate administered to finisher pigs for ∼4-weeks prior to slaughter to control Salmonella shedding on highly contaminated farms. Two trials (A and B) were conducted on two commercial pig farms, which had a history of high Salmonella seroprevalence. In both trials, pens (14 pens of 12 pigs/pen in Trial A and 12 pens of 12-17 pigs/pen in Trial B) were randomly assigned to a control (finisher feed without additive) or a treatment group (the same feed with 3kg sodium butyrate/t) for 24-28days, depending on the trial. Faeces were collected from each pig on days 0, 12 and 24/28, and blood, caecal digesta and ileocaecal/mesenteric lymph nodes were collected from the slaughterhouse. Pigs were weighed at the start and end of the trials, feed intake was recorded, and carcass quality parameters were recorded at slaughter. In Trial A, Salmonella shedding was reduced in the treatment compared to the control group at the end of the trial (30% versus 57% probability of detecting Salmonella in faeces, respectively; p<0.001). This reflected the serology results, with detection of a lower seroprevalence in the treatment compared to the control group using the 20% optical density cut-off (69.5% versus 89%; p=0.001). However, no effect on faecal shedding or seroprevalance was observed in Trial B, which may be explained by the detection of a concomitant infection with Lawsonia intracellularis. No significant differences in Salmonella recovery rates were observed in the caecal digesta or lymph nodes in either trial. Furthermore, feed intake, weight gain, and feed conversion efficiency (FCE) did not differ between groups (p>0.05) in either trial. Numerical improvements in weight gain and FCE were found with sodium butyrate treatment

  18. The DNA sequence and biology of human chromosome 19

    SciTech Connect

    Grimwood, J; Gordon, L A; Olsen, A; Terry, A; Schmutz, J; Lamerdin, J; Hellsten, U; Goodstein, D; Couronne, O; Tran-Gyamfi, M

    2004-04-06

    Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high GC content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in Mendelian disorders, including familial hypercholesterolemia and insulin-resistant diabetes. Nearly one quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.

  19. The DNA sequence and biology of human chromosome 19

    SciTech Connect

    Grimwood, Jane; Gordon, Laurie A.; Olsen, Anne; Terry, Astrid; Schmutz, Jeremy; Lamerdin, Jane; Hellsten, Uffe; Goodstein, David; Couronne, Olivier; Tran-Gyamfi, Mary; Aerts, Andrea; Altherr, Michael; Ashworth, Linda; Bajorek, Eva; Black, Stacey; Branscomb, Elbert; Caenepeel, Sean; Carrano, Anthony; Caoile, Chenier; Chan, Yee Man; Christensen, Mari; Cleland, Catherine A.; Copeland, Alex; Dalin, Eileen; Dehal, Paramvir; Denys, Mirian; Detter, John C.; Escobar, Julio; Flowers, Dave; Fotopulos, Dea; Garcia, Carmen; Georgescu, Anca M.; Glavina, Tijana; Gomez, Maria; Gonzales, Eldelyn; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Ho, Issac; Huang, Wayne; Israni, Sanjay; Jett, Jamie; Kadner, Kristen; Kimball, Heather; Kobayashi, Arthur; Larionov, Vladimer; Leem, Sun-Hee; Lopez, Frederick; Lou, Yunian; Lowry, Steve; Malfatti, Stephanie; Martinez, Diego; McCready, Paula; Medina, Catherine; Morgan, Jenna; Nelson, Kathryn; Nolan, Matt; Ovcharenko, Ivan; Pitluck, Sam; Pollard, Martin; Popkie, Anthony P.; Predki, Paul; Quan, Glenda; Ramirez, Lucia; Rash, Sam; Retterer, James; Rodriguez, Alex; Rogers, Stephanine; Salamov, Asaf; Salazar, Angelica; She, Xinwei; Smith, Doug; Slezak, Tom; Solovyev, Victor; Thayer, Nina; Tice, Hope; Tsai, Ming; Ustaszewska, Anna; Vo, Nu; Wagner, Mark; Wheeler, Jeremy; Wu, Kevin; Xie, Gary; Yang, Joan; Dubchak, Inna; Furey, Terrence S.; DeJong, Pieter; Dickson, Mark; Gordon, David; Eichler, Evan E.; Pennacchio, Len A.; Richardson, Paul; Stubbs, Lisa; Rokhsar, Daniel S.; Myers, Richard M.; Rubin, Edward M.; Lucas, Susan M.

    2003-09-15

    Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G1C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9 percent of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25 percent of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, a nd segments of coding and non-coding conservation with the distant fish species Takifugu.

  20. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2013-07-01 2013-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  1. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2012-07-01 2012-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  2. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  3. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2014-07-01 2014-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  4. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2011-07-01 2011-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  5. Surface treatment and finishing of aluminum and its alloys. Volumes 1 and 2 (5th revised and enlarged edition)

    SciTech Connect

    Sheasby, P.G.; Wernick, S.; Pinner, R.

    1987-01-01

    Currently available technologies for treating and finishing Al and Al-alloy surfaces are surveyed in an introduction and reference handbook. Chapters are devoted to the properties, alloys, and finishes of Al; mechanical treatments and finishes; electrolytic and chemical polishing; chemical cleaning and etching; chemical conversion coatings; theoretical models of anodizing; decorative and protective anodizing; and anodizing in architecture. Also included are: hard anodizing, coloring anodic oxide coatings (AOCs) with dyes and pigments, sealing AOCs, properties and tests of AOCs, plating on Al, organic finishing, vitreous enameling, and effluents from Al-finishing operations. Diagrams, drawings, graphs, photographs, micrographs, and tables of national finish specifications are provided.

  6. 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;...

  7. 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...

  8. 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;...

  9. 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...

  10. 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...

  11. 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 and decorations. (a) Ceilings, linings, and any furring incidental to their installation in...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  13. 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...

  14. Effects of roughage inclusion and particle size on performance and rumination behavior of finishing beef steers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  15. 21 CFR 181.26 - Drying oils as components of finished resins.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ...) shall include: Chinawood oil (tung oil). Dehydrated castor oil. Linseed oil. Tall oil. ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Drying oils as components of finished resins. 181... Prior-Sanctioned Food Ingredients § 181.26 Drying oils as components of finished resins....

  16. 21 CFR 181.26 - Drying oils as components of finished resins.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ...). Dehydrated castor oil. Linseed oil. Tall oil. ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Drying oils as components of finished resins. 181... Drying oils as components of finished resins. Substances classified as drying oils, when migrating...

  17. 21 CFR 181.26 - Drying oils as components of finished resins.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...) shall include: Chinawood oil (tung oil). Dehydrated castor oil. Linseed oil. Tall oil. ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Drying oils as components of finished resins. 181... Prior-Sanctioned Food Ingredients § 181.26 Drying oils as components of finished resins....

  18. 21 CFR 181.26 - Drying oils as components of finished resins.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...) shall include: Chinawood oil (tung oil). Dehydrated castor oil. Linseed oil. Tall oil. ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Drying oils as components of finished resins. 181... Prior-Sanctioned Food Ingredients § 181.26 Drying oils as components of finished resins....

  19. 21 CFR 181.26 - Drying oils as components of finished resins.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ...) shall include: Chinawood oil (tung oil). Dehydrated castor oil. Linseed oil. Tall oil. ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Drying oils as components of finished resins. 181... Prior-Sanctioned Food Ingredients § 181.26 Drying oils as components of finished resins....

  20. Relationship of glucocorticoids and hematological measures with feed intake, growth, and efficiency of finishing beef cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this experiment was to determine the association of glucocorticoids and markers for immune status in finishing beef steers and heifers with DMI, growth, and efficiency. Calves (n = 236) were individually fed a finishing ration for 84 d with BW measured every 21 d. Blood samples we...

  1. 40 CFR 425.90 - Applicability; description of the retan-wet finish-splits 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 retan-wet finish-splits subcategory. 425.90 Section 425.90 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS LEATHER TANNING AND FINISHING POINT...

  2. 40 CFR 425.40 - Applicability; description of the retan-wet finish-sides 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 retan-wet finish-sides subcategory. 425.40 Section 425.40 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS LEATHER TANNING AND FINISHING POINT...

  3. 40 CFR 425.90 - Applicability; description of the retan-wet finish-splits 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 retan-wet finish-splits subcategory. 425.90 Section 425.90 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS LEATHER TANNING AND FINISHING POINT...

  4. 40 CFR 425.40 - Applicability; description of the retan-wet finish-sides 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 retan-wet finish-sides subcategory. 425.40 Section 425.40 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS LEATHER TANNING AND FINISHING POINT...

  5. 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…

  6. 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...

  7. New finishing possibilities for producing durable multifunctional cotton/wool and viscose/wool blended fabrics.

    PubMed

    Ibrahim, N A; El-Zairy, M R; Eid, B M; El-Zairy, E M R; Emam, E M

    2015-03-30

    This research work focuses on the development of a one-bath functional finishing procedure for imparting durable multifunctional properties such as easy care, soft-hand, antibacterial and/or ultra violet (UV) protection to cotton/wool and viscose/wool blends using diverse finishing combinations and formulations. In this study finishing agents such as reactant resin, silicon softeners, 4-hydroxybenzophenone, triclosan, and pigment colorant were selected using magnesium chloride/citric acid as a mixed catalyst and the pad-dry microwave fixation technique. The results reveal that enhancement in the imparted functional properties are governed by type of the finished substrate as well as nature and concentration of finishing formulation components. The finished fabrics still retained high level of functionalities even after 15 consecutive laundering. Surface morphology and composition of selected samples were investigated using scan electron microscope (SEM) and energy-dispersive X-ray spectroscopy (EDX) analysis. The mode of interactions was also investigated. Practical applications for multifunctionlization of cellulose/wool blended fabrics are possible using these sorts of proper finishing formulations and unique finishing application method.

  8. 76 FR 19182 - Petition for Rulemaking-Classification of Polyurethane Foam and Certain Finished Products...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-06

    ... in delivery of dairy products or frozen foods, and in refrigerated freight containers. COSTHA said to... Polyurethane Foam and Certain Finished Products Containing Polyurethane Foam as Hazardous Materials AGENCY... finished products containing polyurethane foam as hazardous material for purposes of transportation...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 40 CFR 141.510 - Is my system subject to the new finished water reservoir requirements?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 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...

  15. 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...

  16. 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...

  17. 40 CFR 141.510 - Is my system subject to the new finished water reservoir requirements?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 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...

  18. 40 CFR 141.511 - What is required of new finished water reservoirs?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...) 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 2014-07-01 2014-07-01 false What is required of new finished...

  19. 40 CFR 141.510 - Is my system subject to the new finished water reservoir requirements?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. "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…

  6. 40 CFR 63.5390 - How do I measure the HAP content of a finish?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... standard. This value must be entered on the finish log for each type of finish applied. You are not required to test the materials that you use, but the Administrator may require a test using EPA Method 311..., but are not limited to, a material safety data sheet (MSDS) or a manufacturer's hazardous...

  7. 40 CFR 63.5390 - How do I measure the HAP content of a finish?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... standard. This value must be entered on the finish log for each type of finish applied. You are not required to test the materials that you use, but the Administrator may require a test using EPA Method 311..., but are not limited to, a material safety data sheet (MSDS) or a manufacturer's hazardous...

  8. 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...

  9. 7 CFR 58.343 - Storage of finished product in coolers.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 3 2011-01-01 2011-01-01 false Storage of finished product in coolers. 58.343 Section... Service 1 Operations and Operating Procedures § 58.343 Storage of finished product in coolers. All products shall be kept under refrigeration at temperatures of 40 °F. or lower after packaging and...

  10. 7 CFR 58.343 - Storage of finished product in coolers.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 3 2012-01-01 2012-01-01 false Storage of finished product in coolers. 58.343 Section... Service 1 Operations and Operating Procedures § 58.343 Storage of finished product in coolers. All products shall be kept under refrigeration at temperatures of 40 °F. or lower after packaging and...

  11. 7 CFR 58.343 - Storage of finished product in coolers.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 3 2014-01-01 2014-01-01 false Storage of finished product in coolers. 58.343 Section... Service 1 Operations and Operating Procedures § 58.343 Storage of finished product in coolers. All products shall be kept under refrigeration at temperatures of 40 °F. or lower after packaging and...

  12. 7 CFR 58.343 - Storage of finished product in coolers.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Storage of finished product in coolers. 58.343 Section... Service 1 Operations and Operating Procedures § 58.343 Storage of finished product in coolers. All products shall be kept under refrigeration at temperatures of 40 °F. or lower after packaging and...

  13. 7 CFR 58.343 - Storage of finished product in coolers.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 3 2013-01-01 2013-01-01 false Storage of finished product in coolers. 58.343 Section... Service 1 Operations and Operating Procedures § 58.343 Storage of finished product in coolers. All products shall be kept under refrigeration at temperatures of 40 °F. or lower after packaging and...

  14. Fundamentals of figure control and fracture-'free' finishing for high aspect ratio laser optics

    SciTech Connect

    Suratwala, Tayyab

    2014-10-01

    The high level objectives of the this work were to: 1) scientifically understand critical phenomena affecting the surface figure during full aperture finishing; 2) utilize these fundamentals to more deterministically control the surface figure during finishing; 3) successfully polish under rogue particle-‘free’ environments during polishing by understanding/preventing key sources of rogue particles.

  15. 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

    ... AGENCY 40 CFR Parts 141 and 142 Long Term 2 Enhanced Surface Water Treatment Rule: Uncovered Finished Water Reservoirs; Public Meeting AGENCY: Environmental Protection Agency (EPA). ACTION: Notice of public..., concerning information that may inform the regulatory review of the uncovered finished water...

  16. Strategies for complete plastid genome sequencing.

    PubMed

    Twyford, Alex D; Ness, Rob W

    2016-10-28

    Plastid sequencing is an essential tool in the study of plant evolution. This high-copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss recent innovations and approaches for de novo plastid assembly that harness genomic tools. We focus on technical developments including low-cost sequence library preparation approaches for genome skimming, enrichment via hybrid baits and methylation-sensitive capture, sequence platforms with higher read outputs and longer read lengths, and automated tools for assembly. These developments allow for a much more streamlined assembly than via conventional short-range PCR. Although newer methods make complete plastid sequencing possible for any land plant or green alga, there are still challenges for producing finished plastomes particularly from herbarium material or from structurally divergent plastids such as those of parasitic plants.

  17. Analysis of Failure to Finish a Race in a Cohort of Thoroughbred Racehorses in New Zealand

    PubMed Central

    Tanner, Jasmine; Rogers, Chris; Bolwell, Charlotte; Cogger, Naomi; Gee, Erica; Mcllwraith, Wayne

    2016-01-01

    Simple Summary Overall, the failure to finish rate in New Zealand, 2.88 per 1000 horse starts (95% CI 2.64–3.12), was lower than international figures for race day catastrophic injury. Racing and environmental variables such as horse experience, race distance and season were associated with failure to finish a race. Catastrophic injury accounted for approximately half the failure to finish events. Jockey falls were positively associated with less experienced jockeys and horses. Abstract The objective was to describe the incidence of failure to finish a race in flat-racing Thoroughbreds in New Zealand as these are summary indicators of falls, injuries and poor performance. Retrospective data on six complete flat racing seasons (n = 188,615 race starts) of all Thoroughbred flat race starts from 1 August 2005 to 31 July 2011 were obtained. The incidence of failure to finish events and binomial exact 95% confidence intervals were calculated per 1000 horse starts. The association between horse-, rider- and race-level variables with the outcomes failure to finish, pulled-up/fell and lost rider were examined with a mixed effects Poisson regression model. A total of 544 horses failed to finish in 188,615 race starts with an overall incidence of 2.88 per 1000 horse starts (95% CI 2.64–3.12). The incidence of failure to finish horses across each race year showed little variability. In the univariable analysis race distance, larger field size, season, and ratings bands showed association with failing to finish a race. The overall failure to finish outcome was associated with season, race distance and ratings bands (horse experience and success ranking criteria). In the multivariable analysis, race distance and ratings bands were associated with horses that pulled-up/fell; season, apprentice allowances and ratings bands were associated with the outcome lost rider. The failure to finish rate was lower than international figures for race day catastrophic injury. Racing and

  18. Carcass and meat quality of finished and non-finished Limousin heifers from alpine livestock systems differing in altitudinal origin of the forage.

    PubMed

    Gangnat, Isabelle D M; Kreuzer, Michael; McCormick, Andrea Clavijo; Leiber, Florian; Berard, Joel

    2016-01-01

    Effects of the alpine origin of the forage and of finishing on carcass and beef quality were quantified by modelling different alpine livestock system alternatives. Thirty-five Limousin heifers, initially weighing 383 ± 45 kg, were fed fresh grass at 400 or 2000 m above sea level, or a 1:1 mixture of alpine grass and lowland grass hay at 2000 m. After 9 weeks, the six heaviest and oldest animals per group were slaughtered. The remaining animals were finished for 8 weeks on a silage-concentrate diet in the lowlands to similar age and body weight as the first slaughtered group. Carcass and meat quality (M. longissimus thoracis) were assessed in various respects. The average daily gains achieved were of about 600 g/d and similar between forage-type groups. Dressing percentage was 53.5% in the alpine and 57.2% in the lowland group. Carcass conformation and fat cover scores did not differ between forage-type groups. The meat from the alpine groups had greater ultimate pH and smaller redness, yellowness and protein contents. Still, these differences were of minor practical relevance. There was no forage-type effect on water-holding capacity and shear force of the meat. The alpine systems enhanced the proportion of α-linolenic acid in intramuscular fat and decreased the levels of some volatile compounds in perirenal fat. Finishing resulted in compensatory growth, especially in the animals previously fed lowland grass. There was a trend for the finished compared with the non-finished groups towards greater carcass fat cover and intramuscular fat content. Additionally, ultimate pH was smaller and cooking loss was greater with than without finishing. Meat colour differences were also observed. Shear force was not affected by finishing. The finished animals had a smaller α-linolenic acid proportion in the intramuscular fat. In conclusion, the forage type had small effects on carcass and meat quality. Finishing did not substantially improve carcass and meat quality. The

  19. 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

  20. Performance and carcass traits of finishing heifers fed crude glycerin.

    PubMed

    Parsons, G L; Shelor, M K; Drouillard, J S

    2009-02-01

    Crossbred heifers (n = 373; 421.6 kg +/- 28.9) were fed finishing diets containing 0, 2, 4, 8, 12, or 16% crude glycerin (DM basis). Diets consisted of steam-flaked corn with 6% alfalfa hay and 1.2% urea and provided 300 mg of monensin, 90 mg of tylosin, and 0.5 mg of melengestrol acetate per animal daily. Cattle were stratified by BW and allocated randomly, within strata, to concrete-surfaced feedlot pens each containing 6 to 7 heifers, with 9 pens per dietary treatment. Cattle were transitioned from the control diet to diets containing increasing proportions of glycerin over a period of 10 d. Cattle had ad libitum access to feed, and diets were delivered once daily throughout the 85-d trial period. As the concentration of glycerin increased, DMI decreased linearly (P < 0.001). Heifers fed 0, 2, 4, 8, 12, and 16% glycerin had ADG of 1.19, 1.34, 1.29, 1.25, 1.17, and 1.03 kg, respectively (linear, P = 0.013; quadratic, P = 0.010). Feeding glycerin had a quadratic effect on G:F, and G:F was optimal when glycerin was fed at 2% of the diet (quadratic, P = 0.046). Glycerin increased the final BW by 12.7, 8.1, and 5.3 kg when fed at 2, 4, and 8% of the diet, respectively, but reduced the final BW by 1.9 and 14.3 kg when included at 12 and 16% of the diet (linear, P = 0.009; quadratic, P = 0.006). Similarly, HCW increased by 8.1, 5.1, and 3.3 kg when glycerin was fed at 2, 4, and 8% of the diet, respectively, but were 1.2 and 9.1 kg less than controls when glycerin was fed at 12 and 16%, respectively (linear, P = 0.009; quadratic, P = 0.006). Longissimus muscle area decreased linearly as glycerin concentrations increased (P < 0.013). Feeding glycerin resulted in linear decreases in subcutaneous fat over the 12th rib and marbling scores (P = 0.045). Glycerin tended to decrease the percentage of cattle grading USDA Choice (P = 0.084) and increase the percentage of cattle grading USDA Select. Adding glycerin to cattle-finishing diets improved BW gain and feed efficiency

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

    ScienceCinema

    Weinstock, George [Washington University

    2016-07-12

    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.

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

    SciTech Connect

    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.

  3. Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome.

    PubMed

    Fitzsimons, Michael S; Novotny, Mark; Lo, Chien-Chi; Dichosa, Armand E K; Yee-Greenbaum, Joyclyn L; Snook, Jeremy P; Gu, Wei; Chertkov, Olga; Davenport, Karen W; McMurry, Kim; Reitenga, Krista G; Daughton, Ashlynn R; He, Jian; Johnson, Shannon L; Gleasner, Cheryl D; Wills, Patti L; Parson-Quintana, Beverly; Chain, Patrick S; Detter, John C; Lasken, Roger S; Han, Cliff S

    2013-05-01

    The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome amplification technique of multiple displacement amplification (MDA). However, MDA from a single chromosome copy suffers from amplification bias and a large loss of specificity from even very small amounts of DNA contamination, which makes assembling a genome difficult and completely finishing a genome impossible except in extraordinary circumstances. Gel microdrop cultivation allows culturing of a diverse microbial community and provides hundreds to thousands of genetically identical cells as input for an MDA reaction. We demonstrate the utility of this approach by comparing sequencing results of gel microdroplets and single cells following MDA. Bias is reduced in the MDA reaction and genome sequencing, and assembly is greatly improved when using gel microdroplets. We acquired multiple near-complete genomes for two bacterial species from human oral and stool microbiome samples. A significant amount of genome diversity, including single nucleotide polymorphisms and genome recombination, is discovered. Gel microdroplets offer a powerful and high-throughput technology for assembling whole genomes from complex samples and for probing the pan-genome of naturally occurring populations.

  4. Finisher and performance trends in female and male mountain ultramarathoners by age group

    PubMed Central

    Rüst, Christoph Alexander; Knechtle, Beat; Eichenberger, Evelyn; Rosemann, Thomas; Lepers, Romuald

    2013-01-01

    Background This study examined changes according to age group in the number of finishers and running times for athletes in female and male mountain ultramarathoners competing in the 78 km Swiss Alpine Marathon, the largest mountain ultramarathon in Europe and held in high alpine terrain. Methods The association between age and performance was investigated using analysis of variance and both single and multilevel regression analyses. Results Between 1998 and 2011, a total of 1,781 women and 12,198 men finished the Swiss Alpine Marathon. The number of female finishers increased (r2 = 0.64, P = 0.001), whereas the number of male finishers (r2 = 0.18, P = 0.15) showed no change. The annual top ten men became older and slower, whereas the annual top ten women became older but not slower. Regarding the number of finishers in the age groups, the number of female finishers decreased in the age group 18–24 years, whereas the number of finishers increased in the age groups 30–34, 40–44, 45–49, 50–54, 55–59, 60–64, and 70–74 years. In the age groups 25–29 and 35–39 years, the number of finishers showed no changes across the years. In the age group 70–74 years, the increase in number of finishers was linear. For all other age groups, the increase was exponential. For men, the number of finishers decreased in the age groups 18–24, 25–29, 30–34, and 35–39 years. In the age groups 40–44, 45–49, 50–54, 55–59, 60–64, 70–74, and 75–79 years, the number of finishers increased. In the age group 40–44 years, the increase was linear. For all other age groups, the increase was exponential. Female finishers in the age group 40–44 years became faster over time. For men, finishers in the age groups 18–24, 25–29, 30–34, 40–44, and 45–49 years became slower. Conclusion The number of women older than 30 years and men older than 40 years increased in the Swiss Alpine Marathon. Performance improved in women aged 40–44 years but

  5. 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 ...

  6. DEMOLITIONS OF THE SAVANNAH RIVER SITE'S CONCENTRATOR AND FINISHING FACILITIES

    SciTech Connect

    Mcdonagh, P; Cathy Sizemore, C

    2007-01-17

    The Savannah River Site (SRS) has produced Special Nuclear Materials (SNMs) starting in the early 1950's to the mid 1970's for the Atomic Energy Commission (AEC) and from the mid 1970's to the present for the Department of Energy (DOE). In that time, over 1,000 facilities have been built in the sixteen (16) operational areas of the eight hundred (800) square kilometer site. Over the years, many of the facilities have been dispositioned by the DOE as inactive. In FY-03, DOE identified two hundred and forty-seven (247) (inactive or soon to be inactive) facilities that required demolition. Demolition work was scheduled to start in FY-04 and be completed in the first quarter of FY-07. Two-hundred and thirty-nine (239) of these facilities have been demolished employing Routine demolition techniques. This presentation reviews and discusses two (2) of the eight (8) Non-Routine demolitions Facilities, 420-D ''The Concentrator Facility'', and 421-D ''The Finishing Facility''.

  7. Vitrified metal finishing wastes I. Composition, density and chemical durability.

    PubMed

    Bingham, P A; Hand, R J

    2005-03-17

    Durable phosphate glasses were formed by vitrifying waste filter cakes from two metal finishing operations. Some melts formed crystalline components during cooling. Compositional analysis of dried, heat treated and vitrified samples was made using energy-dispersive X-ray spectroscopy, X-ray fluorescence spectroscopy, inductively-coupled plasma spectroscopy and Leco induction furnace combustion analysis. Hydrolytic dissolution, measured by an adapted product consistency test, was reduced by up to 3 orders of magnitude upon heat treatment or vitrification, surpassing the performance of borosilicate glass in some cases. This was attributed to the high levels of iron and zinc in the wastes, which greatly improve the durability of phosphate glasses. One of the wastes arose from a metal phosphating process and was particularly suitable for vitrification due to its high P2O5 content and favourable melting behaviour. The other waste, which arose from a number of processes, was less suitable as it had a low P2O5 content and during heating it emitted harmful corrosive gases and underwent violent reactions. Substantial volume reductions were obtained by heat treatment and vitrification of both wastes. Compositions and performances of some vitrified wastes were comparable with those of glasses which are under consideration for the immobilisation of toxic and nuclear wastes.

  8. Survey of the finish characteristics of machined optical surfaces

    SciTech Connect

    Church, E.L.; Takacs, P.Z.

    1984-08-01

    This paper reports the findings of a survey of the finished characteristics of machined optical surfaces. The names, addresses, points of contact and telephone numbers of each of the nine participating suppliers are listed alphabetically. The machining parameters provided by and/or derived from information supplied by the manufacturer are summarized. These parameters include: surface material; machine feeds and speeds; tool-mark spacing (d); tool tip radius (R); and ideal RMS surface roughness computed using the expression (Comments) section includes general remarks about the sample or its measurement. For example: discoloration, scratches, graininess, excrescences, homogeneity. Several measurements were made on each sample at different positions. The present report includes data from one such measurement. For surfaces turned off-center, this position is generally at the center of the sample. For surfaces turned on-center, this position is somewhere near the edge. Data are presented in the form of two pages for each measurement, consisting of two graphs of the surface profile on one page and two graphs of the periodogram on the second page.

  9. Optimum selection of high performance mirror substrates for diamond finishing

    NASA Astrophysics Data System (ADS)

    Woodard, Kenneth S.; Comstock, Lovell E.; Wamboldt, Leonard; Sutherland, James S.

    2016-05-01

    Due to advances in manufacturing processes, the substrate options for high performance diamond machined mirrors are expanding. Fewer compromises have to be made to achieve the needed weight, stiffness and finish while maintaining reasonable costs. In addition to the traditional mirror materials like aluminum and beryllium, there are some less common materials that can now be included in the trade space that fill the cost and performance continuum between wrought aluminum and beryllium mirrors. Aluminum and beryllium, respectively, had been the low cost/fair performance and very high cost/very high performance bounds for substrate selection. These additional substrates provide multiple near net shape blank options and processes, mostly within these bounds, that can be considered in a mirror cost versus performance trade analysis. This paper will include a summary of some advances in manufacturing processes that provide more substrate options for diamond machined mirrors with some sample performance analysis and data. This is merged with the traditional substrate options to illustrate the now larger mirror substrate trade space. Some benchmark structural analysis is provided to back up a generic mirror design trade study.

  10. Classification and storage of wastewater from floor finish removal operations

    SciTech Connect

    Hunt, Charles E.

    1996-05-01

    This study evaluates the wastewater generated from hard surface floor finish removal operations at Lawrence Livermore Laboratory in order to determine if this wastewater is a hazardous waste, either by statistical evaluation, or other measurable regulatory guidelines established in California Regulations. This research also comparatively evaluates the 55 gallon drum and other portable tanks, all less than 1,000 gallons in size in order to determine which is most effective for the management of this waste stream at Lawrence Livermore Laboratory. The statistical methods in SW-846 were found to be scientifically questionable in their application to hazardous waste determination. In this statistical evaluation, the different data transformations discussed in the regulatory guidance document were applied along with the log transformation to the population of 18 samples from 55 gallon drums. Although this statistical evaluation proved awkward in its application, once the data is collected and organized on a spreadsheet this statistical analysis can be an effective tool which can aid the environmental manager in the hazardous waste classification process.

  11. Wear analysis and finishing of bioceramic implant surfaces.

    PubMed

    Denkena, Berend; Reichstein, Martin; van der Meer, Marijke; Ostermeier, Sven; Hurschler, Christof

    2008-01-01

    A primary cause for revision operations of joint replacements is the implant loosening, due to immune reactions resulting from the agglomeration of polyethylene wear debris. Motivated by the successful application of bioceramic materials in hip joint prostheses, a trend towards the development of hard implant materials has occurred. Nonetheless in the area of total knee arthroplasty (TKA), modern efforts have still utilized polyethylene as the tibial-inlay joint component. The use of bioceramic hard-hard-pairings for total knee arthroplasty has been prevented by the complex kinematics and geometries required. Ceramics cannot cope with non-uniform loads, which suggests the need for new designs appropriate to the material. Furthermore, biomechanical requirements should be considered. A rolling-gliding wear simulator, which reproduces the movements and stresses of the knee joint on specimens of simplified geometry, has therefore been developed. High-precision machining processes for free formed bioceramic surfaces, with suitable grinding and polishing tools which adjust to constantly changing contact conditions, are essential. The goal is to put automated finishing in one clamping with five simultaneous controlled axes into practice. The developed manufacturing technologies will allow the advantageous bioceramic materials to be applied and accepted for more complex joint replacements such as knee prostheses.

  12. Laser-chemical finishing of micro forming tools

    NASA Astrophysics Data System (ADS)

    Stephen, Andreas; Gerhard, Christoph; Vollertsen, Frank

    2011-03-01

    In this contribution, we report on a laser-chemical removal method for precise machining of micro forming tools. Thereby, a focused machining laser beam is guided coaxially to an etchant jet stream. Since the material removal is caused by laser-induced chemical reactions using this method, machining is achieved at low laser powers. Hence, material stressing involving micro cracks and further parasitic effects can be avoided. Due to these advantages, this method offers a suitable technique for the finishing of precision micro tools. Several experiments have been performed at rotary swaging jaws made of Stellite 21 in order to chamfer the edged transition section between the operating sphere and the tool flank. The influence of both different laser powers and work piece traverse speeds has been investigated. For this purpose, several parallel laser paths were applied along the edged transition section when varying the process parameters. Here, the incident laser beam is subjected to different angles of incidence. Due to reflection effects, the process parameters have to be matched with respect to the particular angle of incidence during the machining. In this vein, the edged transition section of rotary swaging jaws was chamfered at radii in the range of 120 μm.

  13. Fire hazard analysis for Plutonium Finishing Plant complex

    SciTech Connect

    MCKINNIS, D.L.

    1999-02-23

    A fire hazards analysis (FHA) was performed for the Plutonium Finishing Plant (PFP) Complex at the Department of Energy (DOE) Hanford site. The scope of the FHA focuses on the nuclear facilities/structures in the Complex. The analysis was conducted in accordance with RLID 5480.7, [DOE Directive RLID 5480.7, 1/17/94] and DOE Order 5480.7A, ''Fire Protection'' [DOE Order 5480.7A, 2/17/93] and addresses each of the sixteen principle elements outlined in paragraph 9.a(3) of the Order. The elements are addressed in terms of the fire protection objectives stated in paragraph 4 of DOE 5480.7A. In addition, the FHA also complies with WHC-CM-4-41, Fire Protection Program Manual, Section 3.4 [1994] and WHC-SD-GN-FHA-30001, Rev. 0 [WHC, 1994]. Objectives of the FHA are to determine: (1) the fire hazards that expose the PFP facilities, or that are inherent in the building operations, (2) the adequacy of the fire safety features currently located in the PFP Complex, and (3) the degree of compliance of the facility with specific fire safety provisions in DOE orders, related engineering codes, and standards.

  14. Prophylometric and SEM analyses of four different finishing methods

    PubMed Central

    CHIODERA, G.; CERUTTI, F.; CERUTTI, A.; PUTIGNANO, A.; MANGANI, F.

    2013-01-01

    Summary Adhesion is the pivot of the modern restorative dentistry. Inlays, onlays and veneers have become a valid alternative to the traditional prosthetic treatments even in the rehabilitation of extremely damaged teeth, allowing a consistent saving of sound tooth tissues. Composite resins and dental adhesive are continously investigated and improved, nevertheless the optimization of the tooth-adhesive interface has to be considered: in fact, the long-term stability of adhesion between tooth and composite material depends on the treatment of the amelo-dentinal surfaces. This study investigated the quality of the occlusal walls of a cavity prepared to receive an inlay and finished with four different systems: thin and extra-thin diamond coated burs, a 12-blades carbide burs and a diamond-coated tip driven by sonic instrument. Consequently, prophylometric and SEM analyses were performed on the samples. The average roughness values recorded by the prophylometer were expressed by the parameters Ra and RZ: there is a correspondence between the numeric values and the pictures of the SEM. The results show a better quality (low roughness values) of the surface treated with multi-blade burs, followed by the this and extra-thin diamond coated burs. The 25 micron diamond-coated tip of the sonic instrument obtains the roughest surface and a sensibly higher amount of smear layer than the other tested systems. PMID:23741601

  15. Factors influencing dust exposure: finishing activities in drywall construction.

    PubMed

    Simmons, Catherine E; Jones, Rachael M; Boelter, Fred W

    2011-05-01

    Sanding drywall joint compound is a dusty construction activity. We studied potential factors influencing exposure to respirable and total dust for sanders and bystanders in the area of drywall joint compound finishing in 17 test events within a room-scale isolation chamber. We found the air change rate to be negatively correlated with dust C(twa) both in the sander's personal breathing zone and surrounding area. We could not conclude that sanding tool type systematically influences dust C(twa), but the use of 80-grit abrasive was associated with the highest dust C(twa). We found respirable dusts were uniformly dispersed 1-8.2 m from sanding activities at a fixed location. As anticipated, both respirable and total dust C(twa) in the sander's personal breathing zone are higher than in the surrounding area. The respirable fraction of the total dust mass C(twa) was greater in the surrounding area than in the sander's personal breathing zone. Respirable dust concentrations measured in real time increased over the duration of sanding, exhibiting a temporal trend that is similar to that predicted by the well-mixed box model with contaminant removal by mechanical ventilation only, and continuous emission. Dust concentrations returned to pre-activity (background) levels 2-4 hr after cessation of the sanding activity.

  16. Roughness Analysis on Composite Materials (Microfilled, Nanofilled and Silorane) After Different Finishing and Polishing Procedures

    PubMed Central

    Pettini, Francesco; Corsalini, Massimo; Savino, Maria Grazia; Stefanachi, Gianluca; Venere, Daniela Di; Pappalettere, Carmine; Monno, Giuseppe; Boccaccio, Antonio

    2015-01-01

    The finishing and polishing of composite materials affect the restoration lifespan. The market shows a variety of finishing and polishing procedures and the choice among them is conditioned by different factors such as the resulting surface roughness. In the present study, 156 samples were realized with three composite materials, -microfilled, nanofilled and silorane-, and treated with different finishing and polishing procedures. Profilometric analyses were carried out on the samples’ surface, the measured roughness values were submitted to statistical analysis. A complete factorial plan was drawn up and two-way analysis of variance (ANOVA) was carried out to investigate whether the following factors affect the values of roughness: (i) material; (ii) polishing/finishing procedure. Tukey post-hoc test was also conducted to evaluate any statistically significant differences between the material/procedure combinations. The results show that the tested materials do not affect the resulting surface quality but roughness values depend on the finishing/polishing procedure adopted. The procedures that involve: (a) the finishing with medium Sof-Lex discs and (b) the finishing with two tungsten carbide multi-blade milling cutters Q series and UF series are those that allow the lowest values of roughness to be obtained. PMID:26734113

  17. 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.

  18. 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.

  19. Effect of interior surface finish on the break-up of commercial shaped charge liners

    SciTech Connect

    Baker, E L; Schwartz, A J

    1999-08-11

    A series of experiments aimed at understanding the influence of the liner interior surface finish on the break-up of shaped charge jets has been completed. The experiments used a standard 81-mm shaped charge design, loaded with LX-14 high explosive; incorporating high-precision copper shaped charged liners. The results indicate that a significant reduction of jet break-up time occurs between a surface finish of 99.30 microinches and 375.65 microinches. Surface finishes of 4.78, 44.54 and 99.30 microinches produced significantly better ductility and associated break-up times than the 375.65-microinch finish. The baseline production process high-precision liners were measured to have an average surface finish of 44.54 microinches. The results show that for the shaped charge warhead geometry and explosive combination investigated, some care must be taken in respect to surface finish, but that very fine surface finishes do not significantly improve the jet ductility and associated break-up times.

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 77 FR 52682 - Tapered Roller Bearings and Parts Thereof, Finished and Unfinished, From the People's Republic of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-30

    ... International Trade Administration Tapered Roller Bearings and Parts Thereof, Finished and Unfinished, From the... the antidumping duty order on tapered roller bearings and parts thereof, finished and unfinished... should the order be revoked.\\2\\ \\2\\ See Tapered Roller Bearings and Parts Thereof, Finished...

  7. 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...

  8. 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

    ... International Trade Administration Tapered Roller Bearings and Parts Thereof, Finished and Unfinished From the... shipper review of the antidumping duty order on tapered roller bearings and parts thereof, finished and unfinished from the People's Republic of China. See Tapered Roller Bearings and Parts Thereof, Finished...

  9. 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

    ... International Trade Administration Heavy Forged Hand Tools, Finished or Unfinished, With or Without Handles From... and is amending the final results of the antidumping duty review on heavy forged hand tools, finished... Heavy Forged Hand Tools, Finished or Unfinished, With or Without Handles, From the People's Republic...

  10. 40 CFR Figure 1 to Subpart Tttt of... - Example Logs for Recording Leather Finish Use and HAP Content

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 13 2013-07-01 2012-07-01 true Example Logs for Recording Leather... Leather Finishing Operations Pt. 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...

  11. 40 CFR Figure 1 to Subpart Tttt of... - Example Logs for Recording Leather Finish Use and HAP Content

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 13 2014-07-01 2014-07-01 false Example Logs for Recording Leather... Leather Finishing Operations Pt. 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...

  12. 40 CFR Figure 1 to Subpart Tttt of... - Example Logs for Recording Leather Finish Use and HAP Content

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 13 2012-07-01 2012-07-01 false Example Logs for Recording Leather... Leather Finishing Operations Pt. 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...

  13. 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.

  14. Effects of Tooth Coating Material and Finishing Agent on Bleached Enamel Surfaces by KTP Laser

    PubMed Central

    Kameda, Ayumi; Masuda, Yoshiko Murakami; Teruo, Toko; Yamada, Yoshishige; Kimura, Yuichi; Tamaki, Yukimichi; Miyazaki, Takashi

    2013-01-01

    Objective: The purpose of this study was to evaluate the effect of tooth coating material and finishing agent on bleached enamel surfaces after using KTP laser with 27% hydrogen peroxide. Background data: There have been few reports on the effects of tooth coating materials and finishing agents after bleaching. Methods: After 40 crowns of human extracted maxillary incisors were bleached by KTP laser, bleached enamels were finished with fluoride only or both of fluoride and nano-hydroxyapatite as a finishing agent. After application(s) of fluoride and/or finishing agent, the enamel surfaces were divided into 2 groups, which were covered with the coating material or without coating material. After application of coating materials, all specimens were kept for 2 weeks at 37°C of 100% humidity. After removing the coating material, color changing was measured and enamel surfaces were examined by scanning electron microscopy (SEM). Results: SEM observation of enamel surfaces treated the fluoride gel, finishing agent and coating material showed the most flattered surface compared to other groups. By measuring the color changing, few color changing was observed on the enamel surfaces treated the fluoride gel, finishing agents and coating material. Conclusion: These results suggested that applications of fluoride gel, finishing agent and coating material made the enamel-surfaces flattered and kept effects of bleaching, could prevent the re-coloration. After applications of fluoride gel and finishing agent, covering the bleached-enamel surfaces with the coating material enhanced the keeping whiteness. It would give the patients satisfaction of whiteness. PMID:24155557

  15. Multifunctional finishing of cotton using chitosan extracted from bio-waste.

    PubMed

    Teli, M D; Sheikh, Javed; Bhavsar, Parag

    2013-03-01

    In the current work, chitosan extracted from waste shrimp shells was used in finishing formulation for cotton fabric, along with DMDHEU and other chemicals, imparting multiple performance characteristics such as wrinkle free, antibacterial and flame retardant properties. The finished fabrics were evaluated for textile properties like tensile strength, bending length, yellowness index and functional properties like crease recovery angle, antibacterial activity and flame retardancy and also for the ecological properties like formaldehyde release. The finished fabric showed excellent crease recovery, antibacterial property and flame retardancy which were retained to a moderate extent even after 20 washes. Besides formaldehyde scavenging action, chitosan clearly showed its positive role in imparting multifunctional properties to cotton.

  16. Identification of kinematic errors of five-axis machine tool trunnion axis from finished test piece

    NASA Astrophysics Data System (ADS)

    Zhang, Ya; Fu, Jianzhong; Chen, Zichen

    2014-09-01

    Compared with the traditional non-cutting measurement, machining tests can more accurately reflect the kinematic errors of five-axis machine tools in the actual machining process for the users. However, measurement and calculation of the machining tests in the literature are quite difficult and time-consuming. A new method of the machining tests for the trunnion axis of five-axis machine tool is proposed. Firstly, a simple mathematical model of the cradle-type five-axis machine tool was established by optimizing the coordinate system settings based on robot kinematics. Then, the machining tests based on error-sensitive directions were proposed to identify the kinematic errors of the trunnion axis of cradle-type five-axis machine tool. By adopting the error-sensitive vectors in the matrix calculation, the functional relationship equations between the machining errors of the test piece in the error-sensitive directions and the kinematic errors of C-axis and A-axis of five-axis machine tool rotary table was established based on the model of the kinematic errors. According to our previous work, the kinematic errors of C-axis can be treated as the known quantities, and the kinematic errors of A-axis can be obtained from the equations. This method was tested in Mikron UCP600 vertical machining center. The machining errors in the error-sensitive directions can be obtained by CMM inspection from the finished test piece to identify the kinematic errors of five-axis machine tool trunnion axis. Experimental results demonstrated that the proposed method can reduce the complexity, cost, and the time consumed substantially, and has a wider applicability. This paper proposes a new method of the machining tests for the trunnion axis of five-axis machine tool.

  17. Sequencing technologies and genome sequencing.

    PubMed

    Pareek, Chandra Shekhar; Smoczynski, Rafal; Tretyn, Andrzej

    2011-11-01

    The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. In the relatively short time frame since 2005, the HT-NGS technologies are revolutionizing the human and animal genome researches by analysis of chromatin immunoprecipitation coupled to DNA microarray (ChIP-chip) or sequencing (ChIP-seq), RNA sequencing (RNA-seq), whole genome genotyping, genome wide structural variation, de novo assembling and re-assembling of genome, mutation detection and carrier screening, detection of inherited disorders and complex human diseases, DNA library preparation, paired ends and genomic captures, sequencing of mitochondrial genome and personal genomics. In this review, we addressed the important features of HT-NGS like, first generation DNA sequencers, birth of HT-NGS, second generation HT-NGS platforms, third generation HT-NGS platforms: including single molecule Heliscope™, SMRT™ and RNAP sequencers, Nanopore, Archon Genomics X PRIZE foundation, comparison of second and third HT-NGS platforms, applications, advances and future perspectives of sequencing technologies on human and animal genome research.

  18. Analysis of the influence of electrolyte on surface finish in electropolished stainless steel

    NASA Astrophysics Data System (ADS)

    Hernando, M.; Núñez, P. J.; García, E.; Trujillo, R.

    2012-04-01

    Electropolishing is a surface finishing process of metals and alloys that enhances brilliant surface finishes with low surface roughness values. The most widely used electrolytes for the electropolishing of stainless steel are varying concentrations of phosphoric and sulphuric acid, and occasionally additives such as chromic acid. The objective of this study was to assess the performance of three commonly used industrial electrolytes in terms of the surface finish of electropolished stainless steel AISI 316L. Each electrolyte had varying sulphuric-phosphoric acid combinations with or without chromic acid. The following electropolishing conditions were assessed: current density, bath temperature, electropolishing time, and initial surface texture. The results revealed that adding chromic acid to the electrolyte did not significantly enhance surface finish, and electropolishing ranges were quite similar for all three electrolytes.

  19. 40 CFR 410.70 - Applicability; description of the stock and yarn finishing subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... following types of textile mills: Stock or yarn dyeing or finishing, which may include any or all of the following unit operations and processes: Cleaning, scouring, bleaching, mercerizing, dyeing and...

  20. 40 CFR 410.70 - Applicability; description of the stock and yarn finishing subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... following types of textile mills: Stock or yarn dyeing or finishing, which may include any or all of the following unit operations and processes: Cleaning, scouring, bleaching, mercerizing, dyeing and...

  1. 40 CFR 410.70 - Applicability; description of the stock and yarn finishing subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... following types of textile mills: Stock or yarn dyeing or finishing, which may include any or all of the following unit operations and processes: Cleaning, scouring, bleaching, mercerizing, dyeing and...

  2. 40 CFR 410.70 - Applicability; description of the stock and yarn finishing subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... following types of textile mills: Stock or yarn dyeing or finishing, which may include any or all of the following unit operations and processes: Cleaning, scouring, bleaching, mercerizing, dyeing and...

  3. 40 CFR 410.70 - Applicability; description of the stock and yarn finishing subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... following types of textile mills: Stock or yarn dyeing or finishing, which may include any or all of the following unit operations and processes: Cleaning, scouring, bleaching, mercerizing, dyeing and...

  4. EPA requires Southern California metal finishers to stop illegal hazardous waste releases, wastewater discharges

    EPA Pesticide Factsheets

    LOS ANGELES -- The U.S. Environmental Protection Agency announced today the resolution of a series of enforcement actions at five Southern California metal finishing companies which will collectively pay more than $223,700 in civil penalties for haz

  5. 40 CFR 410.40 - Applicability; description of the woven fabric finishing subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Woven... following types of textile mills: woven fabric finishers, which may include any or all of the following...

  6. BLISS 4HIGH, SINGLE STAND FINISHING (TEMPER) MILL FOR LIGHTGAUGE PRODUCTS ...

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

    BLISS 4-HIGH, SINGLE STAND FINISHING (TEMPER) MILL FOR LIGHT-GAUGE PRODUCTS UP TO 26" WIDE. KNOWN AS THE #47 MILL, THIS REVERSING MILL WAS INSTALLED IN 1981. - American Brass Foundry, 70 Sayre Street, Buffalo, Erie County, NY

  7. EVALUATING IN VITRO INFECTIVITY FOR MEASURING UV DISINFECTION OF CRYPTOSPORIDIUM PARVUM OOCYSTS IN FINISHED WATER

    EPA Science Inventory

    UV technology to inactivate Cryptosporidium parvum oocysts has become well established in the US. The challenge now is to effectively demonstrate UV reactor performance and disinfection capacity with various finished water matrices and under different operational conditions. In s...

  8. FINAL REPORT FOR VERIFICATION OF THE METAL FINISHING FACILITY POLLUTION PREVENTION TOOL (MFFPPT)

    EPA Science Inventory

    The United States Environmental Protection Agency (USEPA) has prepared a computer process simulation package for the metal finishing industry that enables users to predict process outputs based upon process inputs and other operating conditions. This report documents the developm...

  9. Study for Reduction of Outgassing Property of Adsorbed Water Gas for Improved Surface Finished Titanium Material

    NASA Astrophysics Data System (ADS)

    Takeda, Masatoshi; Kurisu, Hiroki; Uchida, Takashi; Yamamoto, Setsuo; Ishizawa, Katsunobu; Nomura, Takeru; Eda, Takahiro; Murashige, Nobuyuki

    This paper addresses the development of the surface finishing for a titanium material and the study for the reduction of outgassing property of adsorbed water (H2O) molecules. Developed surface finishing is composed of the buffing for the reduction of the surface roughness and improved chemical polishing for the thick surface oxide layer compared with the chemical polishing so far. The surface roughness of the surface finished titanium material is reduced 35% and the thickness of the surface oxide layer increases by 30%. The total amount of thermal desorbed H2O gas for the new surface finished titanium is reduced 30%. It is considered that the origin for the decrease of the amount of desorption H2O gas is the reduction of the adsorption sites due to the decrease of the surface roughness and the reduction of adsorption energy of H2O gas due to the strong surface oxidation for a titanium material.

  10. CONTROL OF CHELATOR-BASED UPSETS IN SURFACE FINISHING SHOP WASTE WATER TREATMENT SYSTEMS

    EPA Science Inventory

    Actual surface finishing shop examples are used to illustrate the use of process chemistry understanding and analyses to identify immediate, interim and permanent response options for industrial waste water treatment plant (IWTP) upset problems caused by chelating agents. There i...

  11. Study on surface finish of AISI 2080 steel based on the Taguchi method

    NASA Astrophysics Data System (ADS)

    Yalcinkaya, S.; Şahin, Y.

    2017-02-01

    Surface finish and dimensional accuracy play a vital role in manufacturing engineering applications. Grinding is one of the most important methods for producing a better surface quality. This paper describes a study of the influences of cutting parameters such as table speed, depth of cut and feed rate on surface finish of AISI 2080 steels, based on the Taguchi (L27) method. The experimental results showed that the table speed was the machining parameter, which had a greater effect on the surface finish, followed by depth of cut, whereas feed rate showed no significant effect. Analysis of variance indicated that a better surface finish was obtained at 190 m/min speed, 0.003 mm depth of cut and 0.08 mm/rev feed rate.

  12. 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.

  13. Scanning electron microscopic evaluation of finishing techniques on IRM and EBA retrofillings.

    PubMed

    Fitzpatrick, E L; Steiman, H R

    1997-07-01

    Various techniques have been advocated for finishing retrofilling materials. This study evaluated marginal interfaces between tooth structure and the retrofilling material following three techniques of finishing IRM and EBA. This interface was evaluated for the presence of flash and for adaptation to the prepared canal walls. Thirty-one teeth were divided into six groups of five and one control. The teeth were instrumented to a minimum of a 35 K-file, obturated with gutta-percha, resected perpendicular to their long axes and ultrasonically prepared to receive a retrofilling. The teeth were filled with either IRM or EBA cement and finished by ball burnishing, burnishing with a moistened cotton pellet, or with a carbide finishing bur in a high-speed handpiece with air/water spray. Photomicrographs were made and examined by four evaluators. Retrofillings finished with a finishing bur displayed significantly better marginal adaptation and little evidence of flash when compared to the other techniques (p < 0.05). There were no significant differences between ball burnished or moistened cotton pellet techniques or between retrofilling materials used in this study (p < 0.05).

  14. Effect of Finishing Time on Microleakage at the Composite-Repair Interface

    PubMed Central

    Shafiei, Fereshteh; Berahman, Nazanin; Niazi, Elmira

    2016-01-01

    Background: Repair is a conservative treatment of defective composite restoration. Sealing the repair interface is a critical factor to achieve successful repaired restorations. Objective: The aim of this study was to evaluatethe effect of three finishing times on the microleakage at the composite-repair interface. Method: Eighty composite specimens (Z250) were made and aged for eight weeks in water. They were randomly divided into four groups. In the control group, repairing was done with no surface treatment and using bonding agent. In groups 2 to 4, the specimens were repaired following roughening, etching and use of Adper Single Bond, and finished immediately, after 20 minutes and after 24 hours, respectively. After thermocycling, the microleakage at the repair interface was assessed using dye-penetration technique. The results were analyzed using Kruskal-Wallis and Mann-Whitney tests (α=0.05). Results: There was a significant difference among the four groups (P<0.001). The control group with the highest leakage showed a significant difference with the other groups (P<0.05). Immediate finishing showed a significantly higher leakage compared to 20-minute and 24-hour delayed finishing time (P<0.001). The two latter groups had no difference. Conclusion: Immediate finishing of the repaired restorations negatively affect the sealing at the repair interface, while 20-minute and 24-hour delayed finishing had no adverse effect on the interface sealing. PMID:27733876

  15. From mapping to sequencing, post-sequencing and beyond.

    PubMed

    Sasaki, Takuji; Matsumoto, Takashi; Antonio, Baltazar A; Nagamura, Yoshiaki

    2005-01-01

    The Rice Genome Research Program (RGP) in Japan has been collaborating with the international community in elucidating a complete high-quality sequence of the rice genome. As the pioneer in large-scale analysis of the rice genome, the RGP has successfully established the fundamental tools for genome research such as a genetic map, a yeast artificial chromosome (YAC)-based physical map, a transcript map and a phage P1 artificial chromosome (PAC)/bacterial artificial chromosome (BAC) sequence-ready physical map, which serve as common resources for genome sequencing. Among the 12 rice chromosomes, the RGP is in charge of sequencing six chromosomes covering 52% of the 390 Mb total length of the genome. The contribution of the RGP to the realization of decoding the rice genome sequence with high accuracy and deciphering the genetic information in the genome will have a great impact in understanding the biology of the rice plant that provides a major food source for almost half of the world's population. A high-quality draft sequence (phase 2) was completed in December 2002. Since then, much of the finished quality sequence (phase 3) has become available in public databases. With the completion of sequencing in December 2004, it is expected that the genome sequence would facilitate innovative research in functional and applied genomics. A map-based genome sequence is indispensable for further improvement of current rice varieties and for development of novel varieties carrying agronomically important traits such as high yield potential and tolerance to both biotic and abiotic stresses. In addition to genome sequencing, various related projects have been initiated to generate valuable resources, which could serve as indispensable tools in clarifying the structure and function of the rice genome. These resources have been made available to the scientific community through the Rice Genome Resource Center (RGRC) of the National Institute of Agrobiological Sciences (NIAS) to

  16. Pharmaceuticals, hormones and bisphenol A in untreated source and finished drinking water in Ontario, Canada--occurrence and treatment efficiency.

    PubMed

    Kleywegt, Sonya; Pileggi, Vince; Yang, Paul; Hao, Chunyan; Zhao, Xiaoming; Rocks, Carline; Thach, Serei; Cheung, Patrick; Whitehead, Brian

    2011-03-15

    The Ontario Ministry of the Environment (MOE) conducted a survey in 2006 on emerging organic contaminants (EOCs) which included pharmaceuticals, hormones and bisphenol A (BPA). The survey collected 258 samples over a 16 month period from selected source waters and 17 drinking water systems (DWSs), and analyzed them for 48 EOCs using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and isotope dilution mass spectrometry (IDMS) for the highest precision and accuracy of analytical data possible. 27 of the 48 target EOCs were detected in source water, finished drinking water, or both. DWSs using river and lake source water accounted for>90% detections. Of the 27 EOCs found, we also reported the first detection of two antibiotics roxithromycin and enrofloxacin in environmental samples. The most frequently detected compounds (≥ 10%) in finished drinking water were carbamazepine (CBZ), gemfibrozil (GFB), ibuprofen (IBU), and BPA; with their concentrations accurately determined by using IDMS and calculated to be 4 to 10 times lower than those measured in the source water. Comparison of plant specific data allowed us to determine removal efficiency (RE) of these four most frequently detected compounds in Ontario DWSs. The RE of CBZ was determined to be from 71 to 93% for DWSs using granulated activated carbon (GAC); and was 75% for DWSs using GAC followed by ultraviolet irradiation (UV). The observed RE of GFB was between 44 and 55% in DWSs using GAC and increased to 82% when GAC was followed by UV. The use of GAC or GAC followed by UV provided an RE improvement of BPA from 80 to 99%. These detected concentration levels are well below the predicted no effect concentration or total allowable concentration reported in the literature. Additional targeted, site specific comparative research is required to fully assess the effectiveness of Ontario DWSs to remove particular compounds of concern.

  17. Demolitions of the Savannah River Site's concentrator and finishing facilities

    SciTech Connect

    McDonagh, Paul

    2008-01-15

    The Savannah River Site (SRS) has produced Special Nuclear Materials (SNMs) starting in the early 1950's to the mid 1970's for the Atomic Energy Commission (AEC) and from the mid 1970's to the present for the Department of Energy (DOE). In that time, over 1,000 facilities have been built in the sixteen operational areas of the eight hundred square kilometer site. Over the years, many of the facilities have been dispositioned by the DOE as inactive. In FY-03, DOE identified two hundred and forty-seven (inactive or soon to be inactive) facilities that required demolition. Demolition work was scheduled to start in FY-04 and be completed in the first quarter of FY-07. Two-hundred and thirty-nine of these facilities have been demolished employing Routine demolition techniques. This presentation reviews and discusses two of the eight Non-Routine demolitions Facilities, 420-D 'The Concentrator Facility', and 421-D 'The Finishing Facility'. Facilities 420-D and 421-D were toppled by attaching rigging from the structural steel building frame to bulldozers and toppling the facilities over. The greatest advantage of this method is that it employs equipment that is on hand at SRS, saving time on locating and leasing offsite equipment as well as operator training. In addition, although the toppled structure does not land in the original facilities footprint, it does land in a contained area that is easily barricaded to prevent access during the operation. There are several disadvantages. First, there must be adequate area for the structure to topple into. Also if the wire rope size required to topple the structure is larger than two in., the ropes become extremely difficult to work with. Lastly, the yield strength of steel members is guaranteed by the manufacturer as a minimum strength, so its ultimate strength is unknown. This requires extremely conservative specifications sizing the bulldozers and any rigging equipment employed. Two hundred and forty-seven facilities have

  18. Surface finish and subsurface damage in polycrystalline optical materials

    NASA Astrophysics Data System (ADS)

    Shafrir, Shai Negev

    We measure and describe surface microstructure and subsurface damage (SSD) induced by microgrinding of hard metals and hard ceramics used in optical applications. We examine grinding of ceramic materials with bonded abrasives, and, specifically, deterministic microgrinding (DMG). DMG, at fixed nominal infeed rate and with bound diamond abrasive tools, is the preferred technique for optical fabrication of ceramic materials. In DMG material removal is by microcracking. DMG provides cost effective high manufacturing rates, while attaining higher strength and performance, i.e., low level of subsurface damage (SSD). A wide range of heterogeneous materials of interest to the optics industry were studied in this work. These materials include: A binderless tungsten carbide, nonmagnetic Ni-based tungsten carbides, magnetic Co-based tungsten carbides, and, in addition, other hard optical ceramics, such as aluminum oxynitride (Al23O27N5/ALON), polycrystalline alumina (Al2O3/PCA), and chemical vapor deposited (CVD) silicon carbide (Si4C/SiC). These materials are all commercially available. We demonstrate that spots taken with magnetorheological finishing (MRF) platforms can be used for estimating SSD depth induced by the grinding process. Surface morphology was characterized using various microscopy techniques, such as: contact interferometer, noncontact white light interferometer, light microscopy, scanning electron microscopy (SEM), and atomic force microscopy (AFM). The evolution of surface roughness with the amount of material removed by the MRF process, as measured within the spot deepest point of penetration, can be divided into two stages. In the first stage the induced damaged layer and associated SSD from microgrinding are removed, reaching a low surface roughness value. In the second stage we observe interaction between the MRF process and the material's microstructure as MRF exposes the subsurface without introducing new damage. Line scans taken parallel to the MR

  19. Genome-Wide Sequence Comparison of Centromeric Regions and BAC-Landing on Chromosomes Provide New Insights into Centromere Evolution Among Wheat, Brachypodium, and Rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As an emerging model system, the nearly finished sequence of Brachypodium distachyon will provide new insights into comparative and functional genomics of grass species. However, centromeres of B. distachyon are unlikely to be sequenced and assembled precisely similar to many other sequenced organis...

  20. Mill profiler machines soft materials accurately

    NASA Technical Reports Server (NTRS)

    Rauschl, J. A.

    1966-01-01

    Mill profiler machines bevels, slots, and grooves in soft materials, such as styrofoam phenolic-filled cores, to any desired thickness. A single operator can accurately control cutting depths in contour or straight line work.

  1. Mulan: Multiple-Sequence Local Alignment and Visualization for Studying Function and Evolution

    SciTech Connect

    Ovcharenko, I; Loots, G; Giardine, B; Hou, M; Ma, J; Hardison, R; Stubbs, L; Miller, W

    2004-07-14

    Multiple sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes and detecting functional regulatory elements. With a growing number of partly or fully sequenced vertebrate genomes, effective tools for performing multiple comparisons are required to accurately and efficiently assist biological discoveries. Here we introduce Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the tba multi-aligner program for rapid identification of local sequence conservation and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA. Local multiple alignments computed by Mulan ensure reliable representation of short-and large-scale genomic rearrangements in distant organisms. Mulan allows for interactive modification of critical conservation parameters to differentially predict conserved regions in comparisons of both closely and distantly related species. We illustrate the uses and applications of the Mulan tool through multi-species comparisons of the GATA3 gene locus and the identification of elements that are conserved differently in avians than in other genomes allowing speculation on the evolution of birds. Source code for the aligners and the aligner-evaluation software can be freely downloaded from http://bio.cse.psu.edu/.

  2. Dna Sequencing

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  3. 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

  4. Complete genome sequence of Coriobacteriaceae Strain 68-1-3, a novel mucus- degrading isolate from the swine intestinal tract

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A novel Coriobacteriaceae bacterium (Strain 68-1-3) was isolated from the ileum of the swine intestinal tract using a selective mucus-based medium. Here we present the finished genome sequence for the swine commensal, totaling 1.97 Mb in size. Genome-wide differences and low 16S rRNA gene sequence ...

  5. Genomic Sequencing of Orientia tsutsugamushi Strain Karp, an Assembly Comparable to the Genome Size of the Strain Ikeda

    PubMed Central

    Liao, Hsiao-Mei; Chao, Chien-Chung; Lei, Haiyan; Li, Bingjie; Tsai, Shien; Hung, Guo-Chiuan

    2016-01-01

    Orientia tsutsugamushi, an intracellular bacterium, belongs to the family Rickettsiaceae. This study presents the draft genome sequence of strain Karp, with 2.0 Mb as the size of the completed genome. This nearly finished draft genome sequence was annotated with the RAST server and the contents compared to those of the other strains. PMID:27540052

  6. Accurate genome relative abundance estimation based on shotgun metagenomic reads.

    PubMed

    Xia, Li C; Cram, Jacob A; Chen, Ting; Fuhrman, Jed A; Sun, Fengzhu

    2011-01-01

    Accurate estimation of microbial community composition based on metagenomic sequencing data is fundamental for subsequent metagenomics analysis. Prevalent estimation methods are mainly based on directly summarizing alignment results or its variants; often result in biased and/or unstable estimates. We have developed a unified probabilistic framework (named GRAMMy) by explicitly modeling read assignment ambiguities, genome size biases and read distributions along the genomes. Maximum likelihood method is employed to compute Genome Relative Abundance of microbial communities using the Mixture Model theory (GRAMMy). GRAMMy has been demonstrated to give estimates that are accurate and robust across both simulated and real read benchmark datasets. We applied GRAMMy to a collection of 34 metagenomic read sets from four metagenomics projects and identified 99 frequent species (minimally 0.5% abundant in at least 50% of the data-sets) in the human gut samples. Our results show substantial improvements over previous studies, such as adjusting the over-estimated abundance for Bacteroides species for human gut samples, by providing a new reference-based strategy for metagenomic sample comparisons. GRAMMy can be used flexibly with many read assignment tools (mapping, alignment or composition-based) even with low-sensitivity mapping results from huge short-read datasets. It will be increasingly useful as an accurate and robust tool for abundance estimation with the growing size of read sets and the expanding database of reference genomes.

  7. Fundamental studies of tin whiskering in microelectronics finishes

    NASA Astrophysics Data System (ADS)

    Pinol, Lesly Agnes

    Common electronics materials, such as tin, copper, steel, and brass, are ambient reactive under common use conditions, and as such are prone to corrosion. During the early 1940s, reports of failures due to electrical shorting of components caused by 'whisker' (i.e., filamentary surface protrusion) growth on many surface types---including the aforementioned metals---began to emerge. Lead alloying of tin (3--10% by weight, typically in the eutectic proportion) eliminated whiskering risk for decades, until the July 2006 adoption of the Restriction of Hazardous Substances (RoHS) directive was issued by the European Union. This directive, which has since been adopted by California and parts of China, severely restricted the use of lead (<1000 ppm) in all electrical and electronics equipment being placed on the EU market, imposing the need for developing reliable new "lead-free" alternatives to SnPb. In spite of the abundance of modern-day anecdotes chronicling whisker-related failures in satellites, nuclear power stations, missiles, pacemakers, and spacecraft navigation equipment, pure tin finishes are still increasingly being employed today, and the root cause(s) of tin whiskering remains elusive. This work describes a series of structured experiments exploring the fundamental relationships between the incidence of tin whiskering (as dependent variable) and numerous independent variables. These variables included deposition method (electroplating, electroless plating, template-based electrochemical synthesis, and various physical vapor deposition techniques, including resistive evaporation, electron beam evaporation, and sputtering), the inclusion of microparticles and organic contamination, the effects of sample geometry, and nanostructuring. Key findings pertain to correlations between sample geometry and whisker propensity, and also to the stress evolution across a series of 4"-diameter silicon wafers of varying thicknesses with respect to the degree of post

  8. Rapid Polymer Sequencer

    NASA Technical Reports Server (NTRS)

    Stolc, Viktor (Inventor); Brock, Mathew W. (Inventor)

    2011-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal or transverse direction at the tip, a polymer sequence is passed through the tip, and a change in an electrical current signal is measured as each polymer component passes through the tip. Each measured change in electrical current signals is compared with a database of reference signals, with each reference signal identified with a polymer component, to identify the unknown polymer component. The tip preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  9. 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.

  10. 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.

  11. 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.

  12. Antimicrobial resistance of Salmonella enterica isolates from apparently healthy and clinically ill finishing pigs in Spain.

    PubMed

    García-Feliz, C; Collazos, J A; Carvajal, A; Herrera, S; Echeita, M A; Rubio, P

    2008-05-01

    This study was the first conducted in Spain to evaluate the occurrence of antimicrobial resistance and multi-resistance in Salmonella isolates recovered from finishing pigs from Spanish swine farms distributed over the whole country. For this purpose, 290 Salmonella isolates recovered from apparently healthy finishing pigs in a farm-based cross-sectional study and 192 Salmonella isolates recovered from faecal samples of finishing pigs suffering from diarrhoea were investigated. Resistance to a panel of 17 antimicrobials was determined using a broth microdilution technique. Resistance was a common finding and was detected in 90.3% of the Salmonella isolates from apparently healthy finishing pigs and 95.3% of the Salmonella isolates from clinically diseased finishing pigs. Resistance was particularly high among isolates of serogroup B and serovars Typhimurium and its monophasic variant S. 4,5,12:i:-. Higher frequencies of resistance were found to tetracycline, sulphamethoxazole, streptomycin, spectinomycin, ampicillin, chloramphenicol and trimethoprim-sulphamethoxazole. Less than 10% of the isolates were resistant to amoxicillin/clavulanic acid, neomycin, cephalotin, apramycin and gentamicin. Resistance to ciprofloxacin, colistin and ceftiofur was rare (under 1%). Multi-resistance, defined as resistance to four or more drugs, was detected in more than 50% of the isolates. Although multi-resistance was particularly frequent among isolates of S. Typhimurium, it was also high among other serovars as Bredeney and the S. Typhimurium monophasic variant. 4,5,12:i:-.

  13. 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.

  14. Combining heterogeneous data sources for accurate functional annotation of proteins

    PubMed Central

    2013-01-01

    Combining heterogeneous sources of data is essential for accurate prediction of protein function. The task is complicated by the fact that while sequence-based features can be readily compared across species, most other data are species-specific. In this paper, we present a multi-view extension to GOstruct, a structured-output framework for function annotation of proteins. The extended framework can learn from disparate data sources, with each data source provided to the framework in the form of a kernel. Our empirical results demonstrate that the multi-view framework is able to utilize all available information, yielding better performance than sequence-based models trained across species and models trained from collections of data within a given species. This version of GOstruct participated in the recent Critical Assessment of Functional Annotations (CAFA) challenge; since then we have significantly improved the natural language processing component of the method, which now provides performance that is on par with that provided by sequence information. The GOstruct framework is available for download at http://strut.sourceforge.net. PMID:23514123

  15. Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700.

    PubMed

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

    2009-07-01

    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.

  16. Accurate pointing of tungsten welding electrodes

    NASA Technical Reports Server (NTRS)

    Ziegelmeier, P.

    1971-01-01

    Thoriated-tungsten is pointed accurately and quickly by using sodium nitrite. Point produced is smooth and no effort is necessary to hold the tungsten rod concentric. The chemically produced point can be used several times longer than ground points. This method reduces time and cost of preparing tungsten electrodes.

  17. 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

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

    PubMed

    Hoskins, Roger A; Carlson, Joseph W; Wan, Kenneth H; Park, Soo; Mendez, Ivonne; Galle, Samuel E; Booth, Benjamin W; Pfeiffer, Barret D; George, Reed A; Svirskas, Robert; Krzywinski, Martin; Schein, Jacqueline; Accardo, Maria Carmela; Damia, Elisabetta; Messina, Giovanni; Méndez-Lago, María; de Pablos, Beatriz; Demakova, Olga V; Andreyeva, Evgeniya N; Boldyreva, Lidiya V; Marra, Marco; Carvalho, A Bernardo; Dimitri, Patrizio; Villasante, Alfredo; Zhimulev, Igor F; Rubin, Gerald M; Karpen, Gary H; Celniker, Susan E

    2015-03-01

    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 and 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. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.

  19. Permanent flame retardant finishing of textiles by allyl-functionalized polyphosphazenes.

    PubMed

    Mayer-Gall, Thomas; Knittel, Dierk; Gutmann, Jochen S; Opwis, Klaus

    2015-05-13

    Despite their excellent flame retardant properties, polyphosphazenes are currently not used as flame retardant agents for textile finishing, because a permanent fixation on the substrate surface has failed so far. Here, we present the successful synthesis and characterization of a noncombustible and foam-forming polyphosphazene derivative, that can be immobilized durably on cotton and different cotton/polyester blended fabrics using photoinduced grafting reactions. The flame retardant properties are improved, a higher limiting oxygen index is found, and the modified textiles pass several standardized flammability tests. As flame retardant mechanism a synergistic effect between the immobilized polyphosphazene and the textile substrate was observed. The polyphosphazene finishing induces an earlier decomposition of the material with a reduced mass loss in thermogravimetric analysis. The decomposition of cotton and polyester leads to the formation of phosphorus oxynitride, which forms a protecting barrier layer on the fiber surface. In addition, the permanence of the flame retardant finishing was proven by laundry and abrasion tests.

  20. Improvements in Sand Mold/Core Technology: Effects on Casting Finish

    SciTech Connect

    Prof. John J. Lannutti; Prof. Carroll E. Mobley

    2005-08-30

    In this study, the development and impact of density gradients on metal castings were investigated using sand molds/cores from both industry and from in-house production. In spite of the size of the castings market, almost no quantitative information about density variation within the molds/cores themselves is available. In particular, a predictive understanding of how structure and binder content/chemistry/mixing contribute to the final surface finish of these products does not exist. In this program we attempted to bridge this gap by working directly with domestic companies in examining the issues of surface finish and thermal reclamation costs resulting from the use of sand molds/cores. We show that these can be substantially reduced by the development of an in-depth understanding of density variations that correlate to surface finish. Our experimental tools and our experience with them made us uniquely qualified to achieve technical progress.