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. Should the draft chimpanzee sequence be finished?

    PubMed

    Taudien, Stefan; Ebersberger, Ingo; Glöckner, Gernot; Platzer, Matthias

    2006-03-01

    Owing to the availability of genome working drafts (WDs), current comparative-sequence studies are frequently performed on a genome-wide scale. In this article, we appraise the utility of WD sequences in the detection of genomic differences in closely related species. We compared human DNA sequences with draft and high-quality versions of the corresponding chimpanzee loci to reveal the overall high quality of the chimp WD sequence. Nevertheless, a significant proportion of the differences between WD and high-quality sequences we observed can be attributed to sequencing errors in the draft. Although we suggest methods to reduce the number of such false positives efficiently, our study emphasizes the benefit expected from finishing the chimpanzee genome sequence. PMID:16406850

  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

    2013-01-25

    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. 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. PMID:16541075

  7. 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

    2015-01-01

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

  8. 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)

    2013-02-11

    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.

  9. 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.

  10. 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.

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

    ScienceCinema

    Athavale, Ajay [Monsanto

    2013-01-25

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

  12. Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates

    PubMed Central

    2010-01-01

    Background The approaches for shotgun-based sequencing of vertebrate genomes are now well-established, and have resulted in the generation of numerous draft whole-genome sequence assemblies. In contrast, the process of refining those assemblies to improve contiguity and increase accuracy (known as 'sequence finishing') remains tedious, labor-intensive, and expensive. As a result, the vast majority of vertebrate genome sequences generated to date remain at a draft stage. Results To date, our genome sequencing efforts have focused on comparative studies of targeted genomic regions, requiring sequence finishing of large blocks of orthologous sequence (average size 0.5-2 Mb) from various subsets of 75 vertebrates. This experience has provided a unique opportunity to compare the relative effort required to finish shotgun-generated genome sequence assemblies from different species, which we report here. Importantly, we found that the sequence assemblies generated for the same orthologous regions from various vertebrates show substantial variation with respect to misassemblies and, in particular, the frequency and characteristics of sequence gaps. As a consequence, the work required to finish different species' sequences varied greatly. Application of the same standardized methods for finishing provided a novel opportunity to "assay" characteristics of genome sequences among many vertebrate species. It is important to note that many of the problems we have encountered during sequence finishing reflect unique architectural features of a particular vertebrate's genome, which in some cases may have important functional and/or evolutionary implications. Finally, based on our analyses, we have been able to improve our procedures to overcome some of these problems and to increase the overall efficiency of the sequence-finishing process, although significant challenges still remain. Conclusion Our findings have important implications for the eventual finishing of the draft whole

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

    ScienceCinema

    McMahon, Ben [LANL

    2013-01-25

    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.

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

    SciTech Connect

    McMahon, Ben

    2012-06-01

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

  15. Accurate restoration of DNA sequences. Progress report

    SciTech Connect

    Churchill, G.A.

    1994-05-01

    The primary of this project are the development of (1) a general stochastic model for DNA sequencing errors (2) algorithms to restore the original DNA sequence and (3) statistical methods to assess the accuracy of this restoration. A secondary objective is to develop new algorithms for fragment assembly. Initially a stochastic model that assumes errors are independent and uniformly distributed will be developed. Generalizations of the basic model will be developed to account for (1) decay of accuracy along fragments, (2) variable error rates among fragments, (3) sequence dependent errors (e.g. homopolymeric, runs), and (4) strand--specific systematic errors (e.g. compressions). The emphasis of this project will be the development of a theoretical basis for determining sequence accuracy. However, new algorithms are proposed and these will be implemented as software (in the C programming language). This software will be tested using real and simulated data. It will be modular in design and will be made available for distribution to the scientific community.

  16. Finished Annotated Genome Sequence of Burkholderia pseudomallei Strain Bp1651, a Multidrug-Resistant Clinical Isolate

    PubMed Central

    Sue, David; Hakovirta, Janetta; Loparev, Vladimir N.; Knipe, Kristen; Sammons, Scott A.; Ranganathan-Ganakammal, Satishkumar; Changayil, Shankar; Srinivasamoorthy, Ganesh; Weil, Michael R.; Tatusov, Roman L.; Gee, Jay E.; Elrod, Mindy G.; Hoffmaster, Alex R.; Weigel, Linda M.

    2015-01-01

    Burkholderia pseudomallei strain Bp1651, a human isolate, is resistant to all clinically relevant antibiotics. We report here on the finished genome sequence assembly and annotation of the two chromosomes of this strain. This genome sequence may assist in understanding the mechanisms of antimicrobial resistance for this pathogenic species. PMID:26634765

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

    ScienceCinema

    Campbell, Catherine [Noblis

    2013-03-22

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

  18. 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.

  19. 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.

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

    SciTech Connect

    Smith, Todd

    2012-06-01

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

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

    ScienceCinema

    Sexton, David [Baylor

    2013-01-25

    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.

  2. 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

    2013-01-25

    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.

  3. 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.

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

    ScienceCinema

    Smith, Todd [PerkinElmer Omics Laboratory

    2013-01-25

    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.

  5. 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.

  6. 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.

  7. 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. PMID:24501629

  8. 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

  9. 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,

    2013-01-25

    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.

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

    SciTech Connect

    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).

  11. PROMALS web server for accurate multiple protein sequence alignments.

    PubMed

    Pei, Jimin; Kim, Bong-Hyun; Tang, Ming; Grishin, Nick V

    2007-07-01

    Multiple sequence alignments are essential in homology inference, structure modeling, functional prediction and phylogenetic analysis. We developed a web server that constructs multiple protein sequence alignments using PROMALS, a progressive method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS shows higher alignment accuracy than other advanced methods, such as MUMMALS, ProbCons, MAFFT and SPEM. The PROMALS web server takes FASTA format protein sequences as input. The output includes a colored alignment augmented with information about sequence grouping, predicted secondary structures and positional conservation. The PROMALS web server is available at: http://prodata.swmed.edu/promals/ PMID:17452345

  12. Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time sequencing.

    PubMed

    Wibberg, Daniel; Bremges, Andreas; Dammann-Kalinowski, Tanja; Maus, Irena; Igeño, M Isabel; Vogelsang, Ralph; König, Christoph; Luque-Almagro, Víctor M; Roldán, M Dolores; Sczyrba, Alexander; Moreno-Vivián, Conrado; Blasco, Rafael; Pühler, Alfred; Schlüter, Andreas

    2016-08-20

    Pseudomonas pseudoalcaligenes CECT5344 tolerates cyanide and is also able to utilize cyanide and cyano-derivatives as a nitrogen source under alkaline conditions. The strain is considered as candidate for bioremediation of habitats contaminated with cyanide-containing liquid wastes. Information on the genome sequence of the strain CECT5344 became available previously. The P. pseudoalcaligenes CECT5344 genome was now resequenced by applying the single molecule, real-time (SMRT(®)) sequencing technique developed by Pacific Biosciences. The complete and finished genome sequence of the strain consists of a 4,696,984 bp chromosome featuring a GC-content of 62.34%. Comparative analyses between the new and previous versions of the P. pseudoalcaligenes CECT5344 genome sequence revealed additional regions in the new sequence that were missed in the older version. These additional regions mostly represent mobile genetic elements. Moreover, five additional genes predicted to play a role in sulfoxide reduction are present in the newly established genome sequence. The P. pseudoalcaligenes CECT5344 genome sequence is highly related to the genome sequences of different Pseudomonas mendocina strains. Approximately, 70% of all genes are shared between P. pseudoalcaligenes and P. mendocina. In contrast to P. mendocina, putative pathogenicity genes were not identified in the P. pseudoalcaligenes CECT5344 genome. P. pseudoalcaligenes CECT5344 possesses unique genes for nitrilases and mercury resistance proteins that are of importance for survival in habitats contaminated with cyano- and mercury compounds. As an additional feature of the SMRT sequencing technology, the methylome of P. pseudoalcaligenes was established. Six sequence motifs featuring methylated adenine residues (m6A) were identified in the genome. The genome encodes several methyltransferases, some of which may be considered for methylation of the m6A motifs identified. The complete genome sequence of the strain CECT

  13. Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome

    PubMed Central

    Faino, Luigi; Seidl, Michael F.; Datema, Erwin; van den Berg, Grardy C. M.; Janssen, Antoine; Wittenberg, Alexander H. J.

    2015-01-01

    ABSTRACT Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include PacBio-generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete V. dahliae genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully appreciate an organism’s biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes. PMID:26286689

  14. 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

  15. Non-contiguous finished genome sequence and description of Anaerococcus vaginalis

    PubMed Central

    Hugon, Perrine; Mishra, Ajay Kumar; Robert, Catherine; Raoult, Didier; Fournier, Pierre-Edouard

    2012-01-01

    We report the properties of a draft genome sequence of the bacterium Anaerococcus vaginalis strain PH9, a species within the Anaerococcus genus. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. A. vaginalis is an obligate anaerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,048,125-bp long (one chromosome but no plasmid) and contains 2,095 protein-coding and 38 RNA genes, including three rRNA genes. PMID:23407456

  16. 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.

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

    PubMed Central

    2014-01-01

    The Gram-negative, pleomorphic, rod-shaped bacterium Ornithobacterium 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 a turkey in North Carolina in 2006. Its genome consists of a circular chromosome of 2,319,034 bp in length with a total of 2243 protein-coding genes and nine RNA genes. Genome sequences are available for two additional strains of O. rhinotracheale, isolated in 1988 and 1995, the latter described in a companion genome report in this issue of SIGS. The genome sequence of O. rhinotracheale strain H06-030791, a more contemporary isolate, will be of value in establishing core and pan-genomes for O. rhinotracheale and elucidating its evolutionary history. PMID:25780505

  18. 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.

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

    SciTech Connect

    Tremblay, Julien

    2012-06-01

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

  20. 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

    2013-01-25

    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.

  1. 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

    2013-01-25

    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.

  2. 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

  3. Non-contiguous finished genome sequence and description of Paenibacillus gorillae sp. nov.

    PubMed Central

    Keita, Mamadou Bhoye; Padhmananabhan, Roshan; Caputo, Aurélia; Robert, Catherine; Delaporte, Eric; Raoult, Didier; Fournier, Pierre-Edouard; Bittar, Fadi

    2014-01-01

    Strain G1T sp. nov. is the type strain of Paenibacillus gorillae a newly proposed species within the genus Paenibacillus. This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. P. gorillae is a facultative anaerobic, Gram-negative, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,257,967 bp long genome (one chromosome but no plasmid) contains 5,856 protein-coding and 62 RNAs genes, including 60 tRNA genes. PMID:25197481

  4. Non contiguous-finished genome sequence and description of Cellulomonas massiliensis sp. nov.

    PubMed Central

    Lagier, Jean-Christophe; Ramasamy, Dhamodharan; Rivet, Romain; Raoult, Didier; Fournier, Pierre-Edouard

    2012-01-01

    Cellulomonas massiliensis strain JC225T sp. nov. is the type strain of Cellulomonas massiliensis sp., a new species within the genus Cellulomonas. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. C. massiliensis is an aerobic rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,407,283 bp long genome contains 3,083 protein-coding and 48 RNA genes. PMID:23408774

  5. Non-contiguous finished genome sequence and description of Anaerococcus provenciensis sp. nov.

    PubMed Central

    Pagnier, Isabelle; Croce, Olivier; Robert, Catherine; Raoult, Didier; La Scola, Bernard

    2014-01-01

    Anaerococcus provenciensis strain 9402080T sp. nov. is the type strain of A. provenciensis sp. nov., a new species within the genus Anaerococcus. This strain was isolated from a cervical abscess sample. A. provenciensis is a Gram-positive anaerobic cocci. Here, we describe the features of this organism, together with the complete genome sequence and annotation. The 2.26 Mbp long genome contains 2099 protein-coding and 57 RNA genes including 8 rRNA genes and exhibits a G+C content of 33.48%. PMID:25197492

  6. Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov.

    PubMed Central

    Lagier, Jean-Christophe; El Karkouri, Khalid; Nguyen, Thi-Tien; Armougom, Fabrice; Raoult, Didier; Fournier, Pierre-Edouard

    2012-01-01

    Anaerococcus senegalensis strain JC48T sp. nov. is the type strain of A. senegalensis sp. nov. a new species within the genus Anaerococcus. This strain whose genome is described here was isolated from the fecal flora of a healthy patient. A. senegalensis is an obligate anaerobic coccus. Here we describe the features of this organism together with the complete genome sequence and annotation. The 1,790,835 bp long genome (1 chromosome but no plasmid) contains 1,721 protein-coding and 53 RNA genes including 5 rRNA genes PMID:22675604

  7. Non-contiguous finished genome sequence and description of Bacillus massiliogorillae sp. nov.

    PubMed Central

    Keita, Mamadou Bhoye; Diene, Seydina M.; Robert, Catherine; Raoult, Didier; Fournier, Pierre-Edouard; Bittar, Fadi

    2013-01-01

    Strain G2T sp. nov. is the type strain of B. massiliogorillae, a proposed new species within the genus Bacillus. This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. B. massiliogorillae is a facultative anaerobic, Gram-variable, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,431,633 bp long genome (1 chromosome but no plasmid) contains 5,179 protein-coding and 98 RNA genes, including 91 tRNA genes. PMID:24501648

  8. Noncontiguous finished genome sequence and description of Gabonia massiliensis gen. nov., sp. nov.

    PubMed Central

    Mourembou, G.; Rathored, J.; Ndjoyi-Mbiguino, A.; Lekana-Douki, J.B.; Fenollar, F.; Robert, C.; Fournier, P.-E.; Raoult, D.; Lagier, J.C.

    2015-01-01

    Culturomics coupled with taxonogenomics is currently used to isolate and characterize new bacteria. Here we describe the features and complete genome sequence of Gabonia massiliensis strain GM3, an anaerobic Gram negative, non-spore-forming and catalase-positive bacillus isolated from a stool specimen of a healthy Gabonese male youth. Belonging to a new genus called Gabonia, it exhibits a genome of 4 261 752 bp including 37.9% GC content and 3,288 predicted genes. PMID:26862432

  9. Noncontiguous finished genome sequence and description of Gabonia massiliensis gen. nov., sp. nov.

    PubMed

    Mourembou, G; Rathored, J; Ndjoyi-Mbiguino, A; Lekana-Douki, J B; Fenollar, F; Robert, C; Fournier, P-E; Raoult, D; Lagier, J C

    2016-01-01

    Culturomics coupled with taxonogenomics is currently used to isolate and characterize new bacteria. Here we describe the features and complete genome sequence of Gabonia massiliensis strain GM3, an anaerobic Gram negative, non-spore-forming and catalase-positive bacillus isolated from a stool specimen of a healthy Gabonese male youth. Belonging to a new genus called Gabonia, it exhibits a genome of 4 261 752 bp including 37.9% GC content and 3,288 predicted genes. PMID:26862432

  10. Non-contiguous finished genome sequence and description of Bacillus massilioalgeriensis sp. nov.

    PubMed

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

    2014-06-15

    Strain EB01(T) sp. nov. is the type strain of Bacillus massilioalgeriensis, a new species within the genus Bacillus. This strain, whose genome is described here, was isolated from sediment sample of the hypersaline lake Ezzemoul sabkha in northeastern Algeria. B. massilioalgeriensis is a facultative anaerobic Gram-positive bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,269,577 bp long genome contains 5,098 protein-coding and 95 RNA genes, including 12 rRNA genes. PMID:25197482

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

    PubMed

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

    2014-06-15

    Paucisalibacillus algeriensis strain EB02(T) 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

  12. Non-contiguous finished genome sequence of Corynebacterium timonense type strain 5401744T

    PubMed Central

    Robert, Catherine; Raoult, Didier

    2014-01-01

    Corynebacterium timonense strain 5401744T is a member of the genus Corynebacterium which contains Gram-positive bacteria with a high G+C content. It was isolated from the blood of a patient with endocarditis. In this work, we describe a set of features of this organism, together with the complete genome sequence and annotation. The 2,553,575 bp long genome contains 2,401 protein-coding genes and 55 RNA genes, including between 5 and 6 rRNA operons. PMID:25197476

  13. Non-contiguous finished genome sequence and description of Halopiger djelfamassiliensis sp. nov.

    PubMed

    Hassani, Ikram Imene; Robert, Catherine; Michelle, Caroline; Raoult, Didier; Hacène, Hocine; Desnues, Christelle

    2013-10-16

    Halopiger djelfamassiliensis strain IIH2(T) sp. nov. is the type strain of Halopiger djelfamassiliensis sp. nov., a new species within the genus Halopiger. This strain, whose genome is described here, was isolated from evaporitic sediment of the hypersaline Lake Zahrez Gharbi in the Djelfa region (Algeria). H. Djelfamassiliensis is a Gram-negative, polymorphic-shaped and strictly aerobic archaeon. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,771,216 bp long genome-contains 3,761 protein-coding and 51 RNA genes, including 4 rRNA genes. PMID:24501653

  14. Non-contiguous finished genome sequence and description of Halopiger djelfamassiliensis sp. nov.

    PubMed Central

    Hassani, Ikram Imene; Robert, Catherine; Michelle, Caroline; Raoult, Didier; Hacène, Hocine; Desnues, Christelle

    2013-01-01

    Halopiger djelfamassiliensis strain IIH2T sp. nov. is the type strain of Halopiger djelfamassiliensis sp. nov., a new species within the genus Halopiger. This strain, whose genome is described here, was isolated from evaporitic sediment of the hypersaline Lake Zahrez Gharbi in the Djelfa region (Algeria). H. Djelfamassiliensis is a Gram-negative, polymorphic-shaped and strictly aerobic archaeon. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,771,216 bp long genome-contains 3,761 protein-coding and 51 RNA genes, including 4 rRNA genes. PMID:24501653

  15. Non-contiguous finished genome sequence and description of Bacillus massiliogorillae sp. nov.

    PubMed

    Keita, Mamadou Bhoye; Diene, Seydina M; Robert, Catherine; Raoult, Didier; Fournier, Pierre-Edouard; Bittar, Fadi

    2013-10-16

    Strain G2(T) sp. nov. is the type strain of B. massiliogorillae, a proposed new species within the genus Bacillus. This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. B. massiliogorillae is a facultative anaerobic, Gram-variable, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,431,633 bp long genome (1 chromosome but no plasmid) contains 5,179 protein-coding and 98 RNA genes, including 91 tRNA genes. PMID:24501648

  16. Non-contiguous finished genome sequence and description of Paenibacillus gorillae sp. nov.

    PubMed

    Keita, Mamadou Bhoye; Padhmananabhan, Roshan; Caputo, Aurélia; Robert, Catherine; Delaporte, Eric; Raoult, Didier; Fournier, Pierre-Edouard; Bittar, Fadi

    2014-06-15

    Strain G1(T) sp. nov. is the type strain of Paenibacillus gorillae a newly proposed species within the genus Paenibacillus. This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. P. gorillae is a facultative anaerobic, Gram-negative, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,257,967 bp long genome (one chromosome but no plasmid) contains 5,856 protein-coding and 62 RNAs genes, including 60 tRNA genes. PMID:25197481

  17. Non-contiguous finished genome sequence and description of Bacillus massilioalgeriensis sp. nov.

    PubMed Central

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

    2014-01-01

    Strain EB01T sp. nov. is the type strain of Bacillus massilioalgeriensis, a new species within the genus Bacillus. This strain, whose genome is described here, was isolated from sediment sample of the hypersaline lake Ezzemoul sabkha in northeastern Algeria. B. massilioalgeriensis is a facultative anaerobic Gram-positive bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,269,577 bp long genome contains 5,098 protein-coding and 95 RNA genes, including 12 rRNA genes. PMID:25197482

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

    PubMed Central

    Mishra, Ajay Kumar; Edouard, Sophie; Dangui, Nicole Prisca Makaya; Lagier, Jean-Christophe; Caputo, Aurelia; Blanc-Tailleur, Caroline; Ravaux, Isabelle; Raoult, Didier

    2013-01-01

    Nosocomiicoccus massiliensis strain NP2T sp. nov. is the type strain of a new species within the genus Nosocomiicoccus. This strain, whose genome is described here, was isolated from the fecal flora of an AIDS-infected patient living in Marseille, France. N. massiliensis is a Gram-positive aerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,645,244 bp long genome (one chromosome but no plasmid) contains 1,738 protein-coding and 45 RNA genes, including 3 rRNA genes. PMID:24501657

  19. Rapid and accurate identification of microorganisms contaminating cosmetic products based on DNA sequence homology.

    PubMed

    Fujita, Y; Shibayama, H; Suzuki, Y; Karita, S; Takamatsu, S

    2005-12-01

    The aim of this study was to develop rapid and accurate procedures to identify microorganisms contaminating cosmetic products, based on the identity of the nucleotide sequences of the internal transcribed spacer (ITS) region of the ribosomal RNA coding DNA (rDNA). Five types of microorganisms were isolated from the inner portion of lotion bottle caps, skin care lotions, and cleansing gels. The rDNA ITS region of microorganisms was amplified through the use of colony-direct PCR or ordinal PCR using DNA extracts as templates. The nucleotide sequences of the amplified DNA were determined and subjected to homology search of a publicly available DNA database. Thereby, we obtained DNA sequences possessing high similarity with the query sequences from the databases of all the five organisms analyzed. The traditional identification procedure requires expert skills, and a time period of approximately 1 month to identify the microorganisms. On the contrary, 3-7 days were sufficient to complete all the procedures employed in the current method, including isolation and cultivation of organisms, DNA sequencing, and the database homology search. Moreover, it was possible to develop the skills necessary to perform the molecular techniques required for the identification procedures within 1 week. Consequently, the current method is useful for rapid and accurate identification of microorganisms, contaminating cosmetics. PMID:18492168

  20. 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

  1. 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

  2. Non contiguous-finished genome sequence and description of Microbacterium gorillae sp. nov.

    PubMed

    Hadjadj, Linda; Rathored, Jaishriram; Keita, Mamadou Bhoye; Michelle, Caroline; Levasseur, Anthony; Raoult, Didier; Fournier, Pierre-Edouard; Rolain, Jean-Marc; Bittar, Fadi

    2016-01-01

    Strain G3(T) (CSUR P207 = DSM 26203) was isolated from the fecal sample of a wild gorilla (Gorilla gorilla subsp gorilla) from Cameroon. It is a Gram-positive, facultative anaerobic short rod. This strain exhibits a 16S rRNA sequence similarity of 98.2 % with Microbacterium thalassium, the closest validly published Microbacterium species and member of the family Microbacteriaceae. Moreover, it shows a low MALDI-TOF-MS score (1.1 to 1.3) that does not allow any identification. Thus, it is likely that this strain represents a new species. Here we describe the phenotypic features of this organism, the complete genome sequence and annotation. The 3,692,770 bp long genome (one chromosome but no plasmid) contains 3,505 protein-coding and 61 RNA genes, including 4 rRNA genes. In addition, digital DNA-DNA hybridization values for the genome of the strain G3(T) against the closest Microbacterium genomes range between 19.7 to 20.5, once again confirming its new status as a new species. On the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we propose the creation of Microbacterium gorillae sp. nov. that contains the strain G3(T). PMID:27087892

  3. Non-contiguous-Finished Genome Sequence and Description of Paenibacillus camerounensis sp. nov.

    PubMed

    Keita, Mamadou Bhoye; Padhmanabhan, Roshan; Robert, Catherine; Delaporte, Eric; Raoult, Didier; Fournier, Pierre-Edouard; Bittar, Fadi

    2016-05-01

    Strain G4(T) was isolated from the stool sample of a wild gorilla (Gorilla gorilla gorilla) from Cameroon. It is a facultative anaerobic, Gram-negative, rod-shaped bacterium. This strain exhibits a 16S rRNA nucleotide sequence similarity of 97.48% with Paenibacillus typhae, the phylogenetically closest species with standing nomenclature. Moreover, the strain G4(T) presents some phenotypic differences when compared to other Paenibacillus 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 characteristics of this organism, complete genome sequence, and annotation. The 6,933,847 bp size genome (1 chromosome but no plasmid) contains 5972 protein-coding genes and 54 RNAs genes, including 44 tRNA genes. In addition, digital DNA-DNA hybridization values for the genome of the strain G4(T) against the closest Paenibacillus genomes range between 19.7 and 22.1, once again confirming its new status as a new species. On the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we propose the creation of Paenibacillus camerounensis sp. nov. that contains the strain G4(T). PMID:26714966

  4. A method for accurate determination of terminal sequences of viral genomic RNA.

    PubMed

    Weng, Z; Xiong, Z

    1995-09-01

    A combination of ligation-anchored PCR and anchored cDNA cloning techniques were used to clone the termini of the saguaro cactus virus (SCV) RNA genome. The terminal sequences of the viral genome were subsequently determined from the clones. The 5' terminus was cloned by ligation-anchored PCR, whereas the 3' terminus was obtained by a technique we term anchored cDNA cloning. In anchored cDNA cloning, an anchor oligonucleotide was prepared by phosphorylation at the 5' end, followed by addition of a dideoxynucleotide at the 3' end to block the free hydroxyl group. The 5' end of the anchor was subsequently ligated to the 3' end of SCV RNA. The anchor-ligated, chimerical viral RNA was then reverse-transcribed into cDNA using a primer complementary to the anchor. The cDNA containing the complete 3'-terminal sequence was converted into ds-cDNA, cloned, and sequenced. Two restriction sites, one within the viral sequence and one within the primer sequence, were used to facilitate cloning. The combination of these techniques proved to be an easy and accurate way to determine the terminal sequences of SCV RNA genome and should be applicable to any other RNA molecules with unknown terminal sequences. PMID:9132274

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

    PubMed

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

    2016-05-01

    Strain FF10(T) (= 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 FF10(T). Results support strain FF10(T) 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

  6. Non-contiguous finished genome sequence and description of Clostridium dakarense sp. nov.

    PubMed Central

    Lo, Cheikh Ibrahima; Mishra, Ajay Kumar; Padhmanabhan, Roshan; Samb, Bissoume; Sow, Amy Gassama; Robert, Catherine; Couderc, Carine; Faye, Ngor; Raoult, Didier; Fournier, Pierre-Edouard; Fenollar, Florence

    2013-01-01

    Clostridium dakarense strain FF1T, is the type strain of Clostridium dakarense sp. nov., a new species within the genus Clostridium. This strain, whose genome is described here, was isolated from the fecal flora of a 4-month-old Senegalese child suffering from gastroenteritis. C. dakarense sp. nov. strain FF1T is an obligate anaerobic Gram-positive bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,735,762 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 27.98% and contains 3,843 protein-coding and 73 RNA genes, including 8 rRNA genes. PMID:24501642

  7. Non-contiguous finished genome sequence and description of Clostridium senegalense sp. nov.

    PubMed Central

    Mishra, Ajay Kumar; Lagier, Jean-Christophe; Robert, Catherine; Raoult, Didier; Fournier, Pierre-Edouard

    2012-01-01

    Clostridium senegalense strain JC122T, is the type strain of Clostridium senegalense sp. nov., a new species within the genus Clostridium. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. C. senegalense strain JC122T is an obligate anaerobic Gram-positive rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,893,008 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 26.8% and contains 3,704 protein-coding and 57 RNA genes, including 6 rRNA genes. PMID:23408737

  8. Noncontiguous finished genome sequence and description of Bacillus testis strain SIT10 sp. nov.

    PubMed

    Cimmino, T; Traore, S I; Valentini, C; le Page, S; Sokhna, C; Diallo, A; Raoult, D; Rolain, J M

    2016-07-01

    Bacillus testis strain SIT10 (= CSUR P1492 = DSMZ 101190) is the new type strain collected from stool from a 2-year-old boy from Senegal during a culturomics study. This Gram-positive bacterium is a facultative anaerobic rod and a member of the Bacillaceae family. We describe here the features of this bacterium, together with the complete genome sequence and annotation. The 3 987 349 bp long genome (one chromosome but no plasmid) with 42.8% GC content contains 4005 protein-coding and 171 sRNA genes, including 19 5S rRNA gene, 15 16S rRNA genes and ten 23S rRNA genes. PMID:27222713

  9. 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

  10. 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.

  11. Noncontiguous finished genome sequence and description of Enterococcus massiliensis sp. nov.

    PubMed

    Le Page, S; Cimmino, T; Togo, A; Million, M; Michelle, C; Khelaifia, S; Lagier, J-C; Raoult, D; Rolain, J-M

    2016-07-01

    Enterococcus massiliensis strain sp. nov. (= CSUR P1927 = DSM 100308) is a new species within the genus Enterococcus. This strain was first isolated from a fresh stool sample of a man during culturomics study of intestinal microflora. Enterococcus massiliensis is a Gram-positive cocci, facultative anaerobic and motile. E. massiliensis is negative for mannitol and positive for β-galactosidase, contrary to E. gallinarum. The complete genome sequence is 2 712 841 bp in length with a GC content of 39.6% and contains 2617 protein-coding genes and 70 RNA genes, including nine rRNA genes. PMID:27330820

  12. Noncontiguous finished genome sequence and description of Necropsobacter massiliensis sp. nov.

    PubMed Central

    Lo, C.I.; Padhamanabhan, R.; Fall, B.; Sambe-Ba, B.; Mediannikov, O.; Nguyen, T.-T.; Prudent, E.; Faye, N.; Wade, B.; Raoult, D.; Fournier, P.-E.; Fenollar, F.

    2015-01-01

    Strain FF6T was isolated from the cervical abscess of a 4-year-old Senegalese boy, in Dakar, Senegal. MALDI-TOF MS did not provide any identification. This strain exhibited a 95.17% 16S rRNA sequence identity with Necropsobacter rosorum. Using a polyphasic study including phenotypic and genomic analyses, strain FF6T was an aero-anaerobic Gram-negative cocobacillus, oxidase positive, and exhibited a genome of 2,493,927 bp (1 chromosome but no plasmid) with a G+C content of 46.2% that coded 2,309 protein-coding and 53 RNA genes. On the basis of these data, we propose the creation of Necropsobacter massiliensis sp. nov. PMID:26587237

  13. Main-Sequence Effective Temperatures from a Revised Mass-Luminosity Relation Based on Accurate Properties

    NASA Astrophysics Data System (ADS)

    Eker, Z.; Soydugan, F.; Soydugan, E.; Bilir, S.; Yaz Gökçe, E.; Steer, I.; Tüysüz, M.; Şenyüz, T.; Demircan, O.

    2015-04-01

    The mass-luminosity (M-L), mass-radius (M-R), and mass-effective temperature (M-{{T}eff}) diagrams for a subset of galactic nearby main-sequence stars with masses and radii accurate to ≤slant 3% and luminosities accurate to ≤slant 30% (268 stars) has led to a putative discovery. Four distinct mass domains have been identified, which we have tentatively associated with low, intermediate, high, and very high mass main-sequence stars, but which nevertheless are clearly separated by three distinct break points at 1.05, 2.4, and 7 {{M}⊙ } within the studied mass range of 0.38-32 {{M}⊙ }. Further, a revised mass-luminosity relation (MLR) is found based on linear fits for each of the mass domains identified. The revised, mass-domain based MLRs, which are classical (L\\propto {{M}α }), are shown to be preferable to a single linear, quadratic, or cubic equation representing an alternative MLR. Stellar radius evolution within the main sequence for stars with M\\gt 1 {{M}⊙ } is clearly evident on the M-R diagram, but it is not clear on the M-{{T}eff} diagram based on published temperatures. Effective temperatures can be calculated directly using the well known Stephan-Boltzmann law by employing the accurately known values of M and R with the newly defined MLRs. With the calculated temperatures, stellar temperature evolution within the main sequence for stars with M\\gt 1 {{M}⊙ } is clearly visible on the M-{{T}eff} diagram. Our study asserts that it is now possible to compute the effective temperature of a main-sequence star with an accuracy of ˜6%, as long as its observed radius error is adequately small (\\lt 1%) and its observed mass error is reasonably small (\\lt 6%).

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

    PubMed Central

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

    2015-01-01

    Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution. PMID:25823460

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

    PubMed

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

    2016-07-01

    High-throughput sequencing (HTS) (next-generation sequencing) of the rearranged Ig and T-cell receptor genes promises to be less expensive and more sensitive than current methods of monitoring minimal residual disease (MRD) in patients with acute lymphoblastic leukemia. However, the adoption of new approaches by clinical laboratories requires careful evaluation of all potential sources of error and the development of strategies to ensure the highest accuracy. Timely and efficient clinical use of HTS platforms will depend on combining multiple samples (multiplexing) in each sequencing run. Here we examine the Ig heavy-chain gene HTS on the Illumina MiSeq platform for MRD. We identify errors associated with multiplexing that could potentially impact the accuracy of MRD analysis. We optimize a strategy that combines high-purity, sequence-optimized oligonucleotides, dual indexing, and an error-aware demultiplexing approach to minimize errors and maximize sensitivity. We present a probability-based, demultiplexing pipeline Error-Aware Demultiplexer that is suitable for all MiSeq strategies and accurately assigns samples to the correct identifier without excessive loss of data. Finally, using controls quantified by digital PCR, we show that HTS-MRD can accurately detect as few as 1 in 10(6) copies of specific leukemic MRD. PMID:27183494

  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). PMID:24599324

  17. An accurate clone-based haplotyping method by overlapping pool sequencing.

    PubMed

    Li, Cheng; Cao, Changchang; Tu, Jing; Sun, Xiao

    2016-07-01

    Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate. PMID:27095193

  18. An accurate clone-based haplotyping method by overlapping pool sequencing

    PubMed Central

    Li, Cheng; Cao, Changchang; Tu, Jing; Sun, Xiao

    2016-01-01

    Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate. PMID:27095193

  19. 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

  20. The scalpel finishing technique: a tooth-friendly way to finish dental composites in anterior teeth.

    PubMed

    Kup, Elaine; Tirlet, Gil; Attal, Jean-Pierre

    2015-01-01

    Optimal results can be obtained on direct restorations by the application of layering procedures that combine the accurate morphological insertion of restorative materials with the knowledge of the optical and mechanical properties of both composite resin and natural hard dental tissue. Even if the finishing procedures on restorations, such as margination (the trimming of margins), are minimized by anatomical layering techniques, finishing can still be highly complicated due to a number of pre-finishing sequences using specific instruments proposed in the literature, which include finishing burs and abrasive discs. Finishing procedures performed with a scalpel on polymerized direct composite restorations can improve the quality of the final sculptured surface by developing natural contours and characteristics and by removing the excess restorative material at the tooth-structure margin. Enhanced movement control and fine fingertip perception of the surface texture while moving the scalpel blade allow the operator to detect and cut the excess composite material during the margination procedure and to refine the final anatomy. Avoiding the use of finishing burs during finishing procedures on direct composite restorations may save adjacent enamel surfaces from abrasive damage. The composite surface and margins may also benefit from using the scalpel finishing technique, considering the potential risk of excess removal and surface crazing that the improper use of finishing burs could cause to composite material. The purpose of this article is to propose and describe the scalpel finishing technique step by step, as well as to briefly discuss the advantages of its application within the limits of a clinical case report. PMID:25874271

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

    PubMed Central

    Burger, Lukas; van Nimwegen, Erik

    2008-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Tang, Yuan-Liang; Kasturi, Rangachar

    1994-01-01

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

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

    PubMed Central

    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. PMID:26751373

  4. 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. PMID:26751373

  5. 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.

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

    PubMed

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

    2013-01-01

    Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are exploited to predict protein structures in conjunction with computational approaches. Here we demonstrate a novel approach, NMRDSP, which can accurately predict the protein shape string based on nuclear magnetic resonance chemical shifts and structural profiles obtained from sequence data. The NMRDSP uses six chemical shifts (HA, H, N, CA, CB and C) and eight elements of structure profiles as features, a non-redundant set (1,003 entries) as the training set, and a conditional random field as a classification algorithm. For an independent testing set (203 entries), we achieved an accuracy of 75.8% for S8 (the eight states accuracy) and 87.8% for S3 (the three states accuracy). This is higher than only using chemical shifts or sequence data, and confirms that the chemical shift and the structure profile are significant features for shape string prediction and their combination prominently improves the accuracy of the predictor. We have constructed the NMRDSP web server and believe it could be employed to provide a solid platform to predict other protein structures and functions. The NMRDSP web server is freely available at http://cal.tongji.edu.cn/NMRDSP/index.jsp. PMID:24376713

  7. NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data

    PubMed Central

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

    2013-01-01

    Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are exploited to predict protein structures in conjunction with computational approaches. Here we demonstrate a novel approach, NMRDSP, which can accurately predict the protein shape string based on nuclear magnetic resonance chemical shifts and structural profiles obtained from sequence data. The NMRDSP uses six chemical shifts (HA, H, N, CA, CB and C) and eight elements of structure profiles as features, a non-redundant set (1,003 entries) as the training set, and a conditional random field as a classification algorithm. For an independent testing set (203 entries), we achieved an accuracy of 75.8% for S8 (the eight states accuracy) and 87.8% for S3 (the three states accuracy). This is higher than only using chemical shifts or sequence data, and confirms that the chemical shift and the structure profile are significant features for shape string prediction and their combination prominently improves the accuracy of the predictor. We have constructed the NMRDSP web server and believe it could be employed to provide a solid platform to predict other protein structures and functions. The NMRDSP web server is freely available at http://cal.tongji.edu.cn/NMRDSP/index.jsp. PMID:24376713

  8. PSIONplus: Accurate Sequence-Based Predictor of Ion Channels and Their Types

    PubMed Central

    Gao, Jianzhao; Cui, Wei; Sheng, Yajun; Ruan, Jishou; Kurgan, Lukasz

    2016-01-01

    Ion channels are a class of membrane proteins that attracts a significant amount of basic research, also being potential drug targets. High-throughput identification of these channels is hampered by the low levels of availability of their structures and an observation that use of sequence similarity offers limited predictive quality. Consequently, several machine learning predictors of ion channels from protein sequences that do not rely on high sequence similarity were developed. However, only one of these methods offers a wide scope by predicting ion channels, their types and four major subtypes of the voltage-gated channels. Moreover, this and other existing predictors utilize relatively simple predictive models that limit their accuracy. We propose a novel and accurate predictor of ion channels, their types and the four subtypes of the voltage-gated channels called PSIONplus. Our method combines a support vector machine model and a sequence similarity search with BLAST. The originality of PSIONplus stems from the use of a more sophisticated machine learning model that for the first time in this area utilizes evolutionary profiles and predicted secondary structure, solvent accessibility and intrinsic disorder. We empirically demonstrate that the evolutionary profiles provide the strongest predictive input among new and previously used input types. We also show that all new types of inputs contribute to the prediction. Results on an independent test dataset reveal that PSIONplus obtains relatively good predictive performance and outperforms existing methods. It secures accuracies of 85.4% and 68.3% for the prediction of ion channels and their types, respectively, and the average accuracy of 96.4% for the discrimination of the four ion channel subtypes. Standalone version of PSIONplus is freely available from https://sourceforge.net/projects/psion/ PMID:27044036

  9. PSIONplus: Accurate Sequence-Based Predictor of Ion Channels and Their Types.

    PubMed

    Gao, Jianzhao; Cui, Wei; Sheng, Yajun; Ruan, Jishou; Kurgan, Lukasz

    2016-01-01

    Ion channels are a class of membrane proteins that attracts a significant amount of basic research, also being potential drug targets. High-throughput identification of these channels is hampered by the low levels of availability of their structures and an observation that use of sequence similarity offers limited predictive quality. Consequently, several machine learning predictors of ion channels from protein sequences that do not rely on high sequence similarity were developed. However, only one of these methods offers a wide scope by predicting ion channels, their types and four major subtypes of the voltage-gated channels. Moreover, this and other existing predictors utilize relatively simple predictive models that limit their accuracy. We propose a novel and accurate predictor of ion channels, their types and the four subtypes of the voltage-gated channels called PSIONplus. Our method combines a support vector machine model and a sequence similarity search with BLAST. The originality of PSIONplus stems from the use of a more sophisticated machine learning model that for the first time in this area utilizes evolutionary profiles and predicted secondary structure, solvent accessibility and intrinsic disorder. We empirically demonstrate that the evolutionary profiles provide the strongest predictive input among new and previously used input types. We also show that all new types of inputs contribute to the prediction. Results on an independent test dataset reveal that PSIONplus obtains relatively good predictive performance and outperforms existing methods. It secures accuracies of 85.4% and 68.3% for the prediction of ion channels and their types, respectively, and the average accuracy of 96.4% for the discrimination of the four ion channel subtypes. Standalone version of PSIONplus is freely available from https://sourceforge.net/projects/psion/. PMID:27044036

  10. 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.

  11. Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting.

    PubMed

    Nguyen, Thuy-Diem; Schmidt, Bertil; Zheng, Zejun; Kwoh, Chee-Keong

    2015-01-01

    De novo clustering is a popular technique to perform taxonomic profiling of a microbial community by grouping 16S rRNA amplicon reads into operational taxonomic units (OTUs). In this work, we introduce a new dendrogram-based OTU clustering pipeline called CRiSPy. The key idea used in CRiSPy to improve clustering accuracy is the application of an anomaly detection technique to obtain a dynamic distance cutoff instead of using the de facto value of 97 percent sequence similarity as in most existing OTU clustering pipelines. This technique works by detecting an abrupt change in the merging heights of a dendrogram. To produce the output dendrograms, CRiSPy employs the OTU hierarchical clustering approach that is computed on a genetic distance matrix derived from an all-against-all read comparison by pairwise sequence alignment. However, most existing dendrogram-based tools have difficulty processing datasets larger than 10,000 unique reads due to high computational complexity. We address this difficulty by developing two efficient algorithms for CRiSPy: a compute-efficient GPU-accelerated parallel algorithm for pairwise distance matrix computation and a memory-efficient hierarchical clustering algorithm. Our experiments on various datasets with distinct attributes show that CRiSPy is able to produce more accurate OTU groupings than most OTU clustering applications. PMID:26451819

  12. 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.

  13. Revisiting binary sequence length requirements to accurately emulate optical transmission systems in highly dispersive regime

    NASA Astrophysics Data System (ADS)

    Grellier, Edouard; Antona, Jean-Christophe; Bononi, Alberto; Bigo, Sébastien

    2008-11-01

    When increasing channel bit rate beyond 10Gb/s or when operating over fiber lines with sparse or no in-line dispersion compensation, Kerr-like non-linear effects can be considered as second order with respect to dispersive effects, because pulse broadening can expand over numerous neighbor pulses, before optical non-linear effects imprint their signature noticeably. To accurately emulate the interactions between pulses in this case, a few studies emphasized that Pseudo- Random Binary Sequences (PRBS) should be used, with exponential dependence of the required PRBS length on bit rate and accumulated dispersion. In this paper, we explain our strategy to numerically estimate the required number of random, noisy bits for Monte-Carlo simulations, and show that it weakly increases in presence of pulse to pulse correlations and commonly tolerated levels of non-linearities (i.e. leading to transmission penalties as high as 1.5dB, for reference BERs of 10-2, 10-3 or 10-5) . Then we determine the actual required PRBS length that yields the same (sufficient) BER accuracy as the MC method. We demonstrate its actual dependence on BER, and show that MC theory provides a reliable upper bound in FEC-assisted, highly dispersive systems.

  14. PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population

    PubMed Central

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

    2015-01-01

    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. PMID:25735005

  15. 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

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

    PubMed

    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

  17. 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/. PMID:26309201

  18. PROMALS3D web server for accurate multiple protein sequence and structure alignments.

    PubMed

    Pei, Jimin; Tang, Ming; Grishin, Nick V

    2008-07-01

    Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/. PMID:18503087

  19. 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

  20. 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.

  1. Finishing Well

    NASA Astrophysics Data System (ADS)

    Riendeau, Diane

    2011-05-01

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

  2. Accurate genetic diagnosis of Finnish pulmonary arterial hypertension patients using oligonucleotide-selective sequencing

    PubMed Central

    Vattulainen, Sanna; Aho, Joonas; Salmenperä, Pertteli; Bruce, Siina; Tallila, Jonna; Gentile, Massimiliano; Sankelo, Marja; Laitinen, Tarja; Koskenvuo, Juha W; Alastalo, Tero-Pekka; Myllykangas, Samuel

    2015-01-01

    The genetic basis of pulmonary arterial hypertension (PAH) among Finnish PAH patients is poorly understood. We adopted a novel-targeted next-generation sequencing (NGS) approach called Oligonucleotide-Selective Sequencing (OS-Seq) and developed a custom data analysis and interpretation pipeline to identify pathogenic base substitutions, insertions, and deletions in seven genes associated with PAH (BMPR2, BMPR1B, ACVRL1, ENG, SMAD9, CAV1, and KCNK3) from Finnish PAH patients. This study represents the first clinical study with OS-Seq technology on patients suffering from a rare genetic disorder. We analyzed DNA samples from 21 Finnish PAH patients, whose BMPR2 and ACVRL1 mutation status had been previously studied using Sanger sequencing. Our sequencing panel covered 100% of the targeted base pairs with >15× sequencing depth. Pathogenic base substitutions were identified in the BMPR2 gene in 29% of the Finnish PAH cases. Two of the pathogenic variant-positive patients had been previously tested negative using Sanger sequencing. No clinically significant variants were identified in the six other PAH genes. Our study validates the use of targeted OS-Seq for genetic diagnostics of PAH and revealed pathogenic variants that had been previously missed using Sanger sequencing. PMID:26247051

  3. SMRT Sequencing for Parallel Analysis of Multiple Targets and Accurate SNP Phasing.

    PubMed

    Guo, Xiaoge; Lehner, Kevin; O'Connell, Karen; Zhang, Jenny; Dave, Sandeep S; Jinks-Robertson, Sue

    2015-12-01

    Single-molecule real-time (SMRT) sequencing generates much longer reads than other widely used next-generation (next-gen) sequencing methods, but its application to whole genome/exome analysis has been limited. Here, we describe the use of SMRT sequencing coupled with barcoding to simultaneously analyze one or a small number of genomic targets derived from multiple sources. In the budding yeast system, SMRT sequencing was used to analyze strand-exchange intermediates generated during mitotic recombination and to analyze genetic changes in a forward mutation assay. The general barcoding-SMRT approach was then extended to diffuse large B-cell lymphoma primary tumors and cell lines, where detected changes agreed with prior Illumina exome sequencing. A distinct advantage afforded by SMRT sequencing over other next-gen methods is that it immediately provides the linkage relationships between SNPs in the target segment sequenced. The strength of our approach for mutation/recombination studies (as well as linkage identification) derives from its inherent computational simplicity coupled with a lack of reliance on sophisticated statistical analyses. PMID:26497143

  4. SMRT Sequencing for Parallel Analysis of Multiple Targets and Accurate SNP Phasing

    PubMed Central

    Guo, Xiaoge; Lehner, Kevin; O’Connell, Karen; Zhang, Jenny; Dave, Sandeep S.; Jinks-Robertson, Sue

    2015-01-01

    Single-molecule real-time (SMRT) sequencing generates much longer reads than other widely used next-generation (next-gen) sequencing methods, but its application to whole genome/exome analysis has been limited. Here, we describe the use of SMRT sequencing coupled with barcoding to simultaneously analyze one or a small number of genomic targets derived from multiple sources. In the budding yeast system, SMRT sequencing was used to analyze strand-exchange intermediates generated during mitotic recombination and to analyze genetic changes in a forward mutation assay. The general barcoding-SMRT approach was then extended to diffuse large B-cell lymphoma primary tumors and cell lines, where detected changes agreed with prior Illumina exome sequencing. A distinct advantage afforded by SMRT sequencing over other next-gen methods is that it immediately provides the linkage relationships between SNPs in the target segment sequenced. The strength of our approach for mutation/recombination studies (as well as linkage identification) derives from its inherent computational simplicity coupled with a lack of reliance on sophisticated statistical analyses. PMID:26497143

  5. Improved Microbe Assembly and Finishing Using 454 8kb Libraries

    SciTech Connect

    Buhay, Christian

    2010-06-03

    Christian Buhay from Baylor College of Medicine's Human Genome Sequencing Center discusses microbial genome finishing strategies on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  6. SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

    PubMed Central

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

    2012-01-01

    Motivation: In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. Results: In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Availability: Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license. Contact: epruesse@mpi-bremen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22556368

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

    PubMed Central

    2014-01-01

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

  8. 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

  9. 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

  10. 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.

  11. Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space.

    PubMed

    Fromer, Menachem; Yanover, Chen

    2009-05-15

    precisely. Examination of the predicted ensembles indicates that, for each structure, the amino acid identity at a majority of positions must be chosen extremely selectively so as to not incur significant energetic penalties. We investigate this high degree of similarity and demonstrate how more diverse near-optimal sequences can be predicted in order to systematically overcome this bottleneck for computational design. Finally, we exploit this in-depth analysis of a collection of the lowest energy sequences to suggest an explanation for previously observed experimental design results. The novel methodologies introduced here accurately portray the sequence space compatible with a protein structure and further supply a scheme to yield heterogeneous low-energy sequences, thus providing a powerful instrument for future work on protein design. PMID:19003998

  12. Woods: A fast and accurate functional annotator and classifier of genomic and metagenomic sequences.

    PubMed

    Sharma, Ashok K; Gupta, Ankit; Kumar, Sanjiv; Dhakan, Darshan B; Sharma, Vineet K

    2015-07-01

    Functional annotation of the gigantic metagenomic data is one of the major time-consuming and computationally demanding tasks, which is currently a bottleneck for the efficient analysis. The commonly used homology-based methods to functionally annotate and classify proteins are extremely slow. Therefore, to achieve faster and accurate functional annotation, we have developed an orthology-based functional classifier 'Woods' by using a combination of machine learning and similarity-based approaches. Woods displayed a precision of 98.79% on independent genomic dataset, 96.66% on simulated metagenomic dataset and >97% on two real metagenomic datasets. In addition, it performed >87 times faster than BLAST on the two real metagenomic datasets. Woods can be used as a highly efficient and accurate classifier with high-throughput capability which facilitates its usability on large metagenomic datasets. PMID:25863333

  13. Rapid and accurate sequencing of the rainbow trout physical map using Illumina technology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rainbow trout (Oncorhynchus mykiss) are the most widely cultivated cold freshwater fish in the world and serve as an important model species for many areas of research. Despite their importance, a reference genome sequence has not yet been generated for rainbow trout due in large part to the complex...

  14. Rapid and accurate sequencing of the rainbow trout physical map using Illumina technology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rainbow trout (Oncorhynchus mykiss) are the most widely cultivated cold freshwater fish in the world and an important model species for many areas of research. Despite their importance, a reference genome sequence has not been generated for rainbow trout due in large part to the complex nature of th...

  15. On Efficient and Accurate Calculation of Significance P-Values for Sequence Kernel Association Testing of Variant Set.

    PubMed

    Wu, Baolin; Guan, Weihua; Pankow, James S

    2016-03-01

    The objective of this paper is to discuss and develop alternative computational methods to accurately and efficiently calculate significance P-values for the commonly used sequence kernel association test (SKAT) and adaptive sum of SKAT and burden test (SKAT-O) for variant set association. We show that the existing software can lead to either conservative or inflated type I errors. We develop alternative and efficient computational algorithms that quickly compute the SKAT P-value and have well-controlled type I errors. In addition, we derive an alternative and simplified formula for calculating the significance P-value of SKAT-O, which sheds light on the development of efficient and accurate numerical algorithms. We implement the proposed methods in the publicly available R package that can be readily used or adapted to large-scale sequencing studies. Given that more and more large-scale exome and whole genome sequencing or re-sequencing studies are being conducted, the proposed methods are practically very important. We conduct extensive numerical studies to investigate the performance of the proposed methods. We further illustrate their usefulness with application to associations between rare exonic variants and fasting glucose levels in the Atherosclerosis Risk in Communities (ARIC) study. PMID:26757198

  16. Rapid and accurate measurement of transverse relaxation times using a single shot multi-echo echo-planar imaging sequence.

    PubMed

    Tyler, Damian J; Moore, Rachel J; Marciani, Luca; Gowland, Penny A

    2004-09-01

    Methods for making rapid and accurate measurements and maps of the transverse relaxation time from a single free induction decay (FID) are proposed. The methods use a multi-echo sequence in combination with B1 insensitive (hyperbolic secant or BIREF2b) refocusing pulses and rapid echo-planar imaging techniques. The results were calibrated against a single spin echo echo-planar imaging sequence using a phantom containing a range of CuSO4 concentrations. The mean percentage absolute difference between the multi-echo and single-echo results was 3% for the multi-echo sequence using the hyperbolic secant refocusing pulse, and 7% for the multi-echo sequence using the BIREF2b refocusing pulse, compared to 13% for a multi-echo sequence using a nonselective sinc refocusing pulse. The use of the sequences in vivo has been demonstrated in studies of gastric function, i.e., the measurement of gastric dilution and monitoring of formation of a raft of alginate polysaccharide within the stomach. PMID:15288145

  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

    2013-01-25

    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. Using complete genome comparisons to identify sequences whose presence accurately predicts clinically important phenotypes.

    PubMed

    Hall, Barry G; Cardenas, Heliodoro; Barlow, Miriam

    2013-01-01

    In clinical settings it is often important to know not just the identity of a microorganism, but also the danger posed by that particular strain. For instance, Escherichia coli can range from being a harmless commensal to being a very dangerous enterohemorrhagic (EHEC) strain. Determining pathogenic phenotypes can be both time consuming and expensive. Here we propose a simple, rapid, and inexpensive method of predicting pathogenic phenotypes on the basis of the presence or absence of short homologous DNA segments in an isolate. Our method compares completely sequenced genomes without the necessity of genome alignments in order to identify the presence or absence of the segments to produce an automatic alignment of the binary string that describes each genome. Analysis of the segment alignment allows identification of those segments whose presence strongly predicts a phenotype. Clinical application of the method requires nothing more that PCR amplification of each of the set of predictive segments. Here we apply the method to identifying EHEC strains of E. coli and to distinguishing E. coli from Shigella. We show in silico that with as few as 8 predictive sequences, if even three of those predictive sequences are amplified the probability of being EHEC or Shigella is >0.99. The method is thus very robust to the occasional amplification failure for spurious reasons. Experimentally, we apply the method to screening a set of 98 isolates to distinguishing E. coli from Shigella, and EHEC from non-EHEC E. coli strains and show that all isolates are correctly identified. PMID:23935901

  20. Non-contiguous finished genome sequence and description of Bacteroides neonati sp. nov., a new species of anaerobic bacterium

    PubMed Central

    Cassir, Nadim; Croce, Olivier; Pagnier, Isabelle; Benamar, Samia; Couderc, Carine; Robert, Catherine; Raoult, Didier; La Scola, Bernard

    2014-01-01

    Bacteroides neonati strain MS4T, is the type strain of Bacteroides neonati sp. nov., a new species within the genus Bacteroides. This strain, whose genome is described here, was isolated from a premature neonate stool sample. B. neonati strain MS4T is an obligate anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5.03 Mbp long genome exhibits a G+C content of 43.53% and contains 4,415 protein-coding and 91 RNA genes, including 9 rRNA genes. PMID:25197464

  1. Non-contiguous finished genome sequence and description of Anaerococcus pacaensis sp. nov., a new species of anaerobic bacterium

    PubMed Central

    Pagnier, Isabelle; Croce, Olivier; Robert, Catherine; Raoult, Didier; La Scola, Bernard

    2013-01-01

    Anaerococcus pacaensis strain 9403502T, is the type strain of Anaerococcus pacaensis sp. nov., a new species within a new genus Anaerococcus. This strain, whose genome is described here, was isolated from a blood sample. A. pacaensis strain 9403502T is an obligate anaerobic Gram-positive coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2.36 Mbp long genome exhibits a G+C content of 35.05% and contains 2,186 protein-coding and 72 RNA genes, including 3 rRNA genes. PMID:24501638

  2. Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp.

    PubMed

    Zhao, S; Tyson, G H; Chen, Y; Li, C; Mukherjee, S; Young, S; Lam, C; Folster, J P; Whichard, J M; McDermott, P F

    2016-01-01

    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

  3. Accurate single-sequence prediction of solvent accessible surface area using local and global features

    PubMed Central

    Faraggi, Eshel; Zhou, Yaoqi; Kloczkowski, Andrzej

    2014-01-01

    We present a new approach for predicting the Accessible Surface Area (ASA) using a General Neural Network (GENN). The novelty of the new approach lies in not using residue mutation profiles generated by multiple sequence alignments as descriptive inputs. Instead we use solely sequential window 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 tested on predicting the ASA of globular proteins and 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 GENN and ASAquick are available from Research and Information Systems at http://mamiris.com, from the SPARKS Lab at http://sparks-lab.org, and from the Battelle Center for Mathematical Medicine at http://mathmed.org. PMID:25204636

  4. Accurate single-sequence prediction of solvent accessible surface area using local and global features.

    PubMed

    Faraggi, Eshel; Zhou, Yaoqi; Kloczkowski, Andrzej

    2014-11-01

    We present a new approach for predicting the Accessible Surface Area (ASA) using a General Neural Network (GENN). The novelty of the new approach lies in not using residue mutation profiles generated by multiple sequence alignments as descriptive inputs. Instead we use solely sequential window 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 tested on predicting the ASA of globular proteins and 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 GENN and ASAquick are available from Research and Information Systems at http://mamiris.com, from the SPARKS Lab at http://sparks-lab.org, and from the Battelle Center for Mathematical Medicine at http://mathmed.org. PMID:25204636

  5. 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

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

    PubMed

    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

  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. 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

    2014-01-01

    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. PMID:25233085

  9. A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences

    PubMed Central

    Sreeskandarajan, Sutharzan; Flowers, Michelle M.; Karro, John E.; Liang, Chun

    2014-01-01

    Summary: Palindromic sequences, or inverted repeats (IRs), in DNA sequences involve important biological processes such as DNA–protein binding, DNA replication and DNA transposition. Development of bioinformatics tools that are capable of accurately detecting perfect IRs can enable genome-wide studies of IR patterns in both prokaryotes and eukaryotes. Different from conventional string-comparison approaches, we propose a novel algorithm that uses a cumulative score system based on a prime number representation of nucleotide bases. We then implemented this algorithm as a MATLAB-based program for perfect IR detection. In comparison with other existing tools, our program demonstrates a high accuracy in detecting nested and overlapping IRs. Availability and implementation: The source code is freely available on (http://bioinfolab.miamioh.edu/bioinfolab/palindrome.php) Contact: liangc@miamioh.edu or karroje@miamioh.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24215021

  10. 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.

  11. 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

  12. 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.

  13. Dixon sequence with superimposed model-based bone compartment provides highly accurate PET/MR attenuation correction of the brain

    PubMed Central

    Koesters, Thomas; Friedman, Kent P.; Fenchel, Matthias; Zhan, Yiqiang; Hermosillo, Gerardo; Babb, James; Jelescu, Ileana O.; Faul, David; Boada, Fernando E.; Shepherd, Timothy M.

    2016-01-01

    Simultaneous PET/MR of the brain is a promising new technology for characterizing patients with suspected cognitive impairment or epilepsy. Unlike CT though, MR signal intensities do not provide a direct correlate to PET photon attenuation correction (AC) and inaccurate radiotracer standard uptake value (SUV) estimation could limit future PET/MR clinical applications. We tested a novel AC method that supplements standard Dixon-based tissue segmentation with a superimposed model-based bone compartment. Methods We directly compared SUV estimation for MR-based AC methods to reference CT AC in 16 patients undergoing same-day, single 18FDG dose PET/CT and PET/MR for suspected neurodegeneration. Three Dixon-based MR AC methods were compared to CT – standard Dixon 4-compartment segmentation alone, Dixon with a superimposed model-based bone compartment, and Dixon with a superimposed bone compartment and linear attenuation correction optimized specifically for brain tissue. The brain was segmented using a 3D T1-weighted volumetric MR sequence and SUV estimations compared to CT AC for whole-image, whole-brain and 91 FreeSurfer-based regions-of-interest. Results Modifying the linear AC value specifically for brain and superimposing a model-based bone compartment reduced whole-brain SUV estimation bias of Dixon-based PET/MR AC by 95% compared to reference CT AC (P < 0.05) – this resulted in a residual −0.3% whole-brain mean SUV bias. Further, brain regional analysis demonstrated only 3 frontal lobe regions with SUV estimation bias of 5% or greater (P < 0.05). These biases appeared to correlate with high individual variability in the frontal bone thickness and pneumatization. Conclusion Bone compartment and linear AC modifications result in a highly accurate MR AC method in subjects with suspected neurodegeneration. This prototype MR AC solution appears equivalent than other recently proposed solutions, and does not require additional MR sequences and scan time. These

  14. 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.

  15. Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design

    PubMed Central

    Field, Helen I; Scollen, Serena A; Luccarini, Craig; Baynes, Caroline; Morrison, Jonathan; Dunning, Alison M; Easton, Douglas F; Pharoah, Paul DP

    2009-01-01

    Background In moderate-throughput SNP genotyping there was a gap in the workflow, between choosing a set of SNPs and submitting their sequences to proprietary assay design software, which was not met by existing software. Retrieval and formatting of sequences flanking each SNP, prior to assay design, becomes rate-limiting for more than about ten SNPs, especially if annotated for repetitive regions and adjacent variations. We routinely process up to 50 SNPs at once. Implementation We created Seq4SNPs, a web-based, walk-away software that can process one to several hundred SNPs given rs numbers as input. It outputs a file of fully annotated sequences formatted for one of three proprietary design softwares: TaqMan's Primer-By-Design FileBuilder, Sequenom's iPLEX or SNPstream's Autoprimer, as well as unannotated fasta sequences. We found genotyping assays to be inhibited by repetitive sequences or the presence of additional variations flanking the SNP under test, and in multiplexes, repetitive sequence flanking one SNP adversely affects multiple assays. Assay design software programs avoid such regions if the input sequences are appropriately annotated, so we used Seq4SNPs to provide suitably annotated input sequences, and improved our genotyping success rate. Adjacent SNPs can also be avoided, by annotating sequences used as input for primer design. Conclusion The accuracy of annotation by Seq4SNPs is significantly better than manual annotation (P < 1e-5). Using Seq4SNPs to incorporate all annotation for additional SNPs and repetitive elements into sequences, for genotyping assay designer software, minimizes assay failure at the design stage, reducing the cost of genotyping. Seq4SNPs provides a rapid route for replacement of poor test SNP sequences. We routinely use this software for assay sequence preparation. Seq4SNPs is available as a service at and , currently for human SNPs, but easily extended to include any species in dbSNP. PMID:19523221

  16. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

    PubMed Central

    DiGuistini, Scott; Liao, Nancy Y; Platt, Darren; Robertson, Gordon; Seidel, Michael; Chan, Simon K; Docking, T Roderick; Birol, Inanc; Holt, Robert A; Hirst, Martin; Mardis, Elaine; Marra, Marco A; Hamelin, Richard C; Bohlmann, Jörg; Breuil, Colette; Jones, Steven JM

    2009-01-01

    Sequencing-by-synthesis technologies can reduce the cost of generating de novo genome assemblies. We report a method for assembling draft genome sequences of eukaryotic organisms that integrates sequence information from different sources, and demonstrate its effectiveness by assembling an approximately 32.5 Mb draft genome sequence for the forest pathogen Grosmannia clavigera, an ascomycete fungus. We also developed a method for assessing draft assemblies using Illumina paired end read data and demonstrate how we are using it to guide future sequence finishing. Our results demonstrate that eukaryotic genome sequences can be accurately assembled by combining Illumina, 454 and Sanger sequence data. PMID:19747388

  17. 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

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

    PubMed

    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

    2016-06-01

    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

  19. 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...

  20. 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

  1. 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

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

    PubMed

    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

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

    PubMed Central

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

    2015-01-01

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

  4. 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

  5. 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.

  6. Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information

    PubMed Central

    Pollastri, Gianluca; Martin, Alberto JM; Mooney, Catherine; Vullo, Alessandro

    2007-01-01

    Background Structural properties of proteins such as secondary structure and solvent accessibility contribute to three-dimensional structure prediction, not only in the ab initio case but also when homology information to known structures is available. Structural properties are also routinely used in protein analysis even when homology is available, largely because homology modelling is lower throughput than, say, secondary structure prediction. Nonetheless, predictors of secondary structure and solvent accessibility are virtually always ab initio. Results Here we develop high-throughput machine learning systems for the prediction of protein secondary structure and solvent accessibility that exploit homology to proteins of known structure, where available, in the form of simple structural frequency profiles extracted from sets of PDB templates. We compare these systems to their state-of-the-art ab initio counterparts, and with a number of baselines in which secondary structures and solvent accessibilities are extracted directly from the templates. We show that structural information from templates greatly improves secondary structure and solvent accessibility prediction quality, and that, on average, the systems significantly enrich the information contained in the templates. For sequence similarity exceeding 30%, secondary structure prediction quality is approximately 90%, close to its theoretical maximum, and 2-class solvent accessibility roughly 85%. Gains are robust with respect to template selection noise, and significant for marginal sequence similarity and for short alignments, supporting the claim that these improved predictions may prove beneficial beyond the case in which clear homology is available. Conclusion The predictive system are publicly available at the address . PMID:17570843

  7. GIbPSs: a toolkit for fast and accurate analyses of genotyping-by-sequencing data without a reference genome.

    PubMed

    Hapke, A; Thiele, D

    2016-07-01

    Genotyping-by-sequencing (GBS) and related methods are increasingly used for studies of non-model organisms from population genetic to phylogenetic scales. We present GIbPSs, a new genotyping toolkit for the analysis of data from various protocols such as RAD, double-digest RAD, GBS, and two-enzyme GBS without a reference genome. GIbPSs can handle paired-end GBS data and is able to assign reads from both strands of a restriction fragment to the same locus. GIbPSs is most suitable for population genetic and phylogeographic analyses. It avoids genotyping errors due to indel variation by identifying and discarding affected loci. GIbPSs creates a genotype database that offers rich functionality for data filtering and export in numerous formats. We performed comparative analyses of simulated and real GBS data with GIbPSs and another program, pyRAD. This program accounts for indel variation by aligning homologous sequences. GIbPSs performed better than pyRAD in several aspects. It required much less computation time and displayed higher genotyping accuracy. GIbPSs retained smaller numbers of loci overall in analyses of real GBS data. It nevertheless delivered more complete genotype matrices with greater locus overlap between individuals and greater numbers of loci sampled in all individuals. PMID:26858004

  8. A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data

    PubMed Central

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

    2014-01-01

    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. PMID:25122209

  9. 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. PMID:25122209

  10. 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

  11. COPS: a sensitive and accurate tool for detecting somatic Copy Number Alterations using short-read sequence data from paired samples.

    PubMed

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

    2012-01-01

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

  12. 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.

  13. Accurate Identification of Common Pathogenic Nocardia Species: Evaluation of a Multilocus Sequence Analysis Platform and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

    PubMed

    Xiao, Meng; Pang, Lu; Chen, Sharon C-A; Fan, Xin; Zhang, Li; Li, Hai-Xia; Hou, Xin; Cheng, Jing-Wei; Kong, Fanrong; Zhao, Yu-Pei; Xu, Ying-Chun

    2016-01-01

    Species identification of Nocardia is not straightforward due to rapidly evolving taxonomy, insufficient discriminatory power of conventional phenotypic methods and also of single gene locus analysis including 16S rRNA gene sequencing. Here we evaluated the ability of a 5-locus (16S rRNA, gyrB, secA1, hsp65 and rpoB) multilocus sequence analysis (MLSA) approach as well as that of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in comparison with sequencing of the 5'-end 606 bp partial 16S rRNA gene to provide identification of 25 clinical isolates of Nocardia. The 5'-end 606 bp 16S rRNA gene sequencing successfully assigned 24 of 25 (96%) clinical isolates to species level, namely Nocardia cyriacigeorgica (n = 12, 48%), N. farcinica (n = 9, 36%), N. abscessus (n = 2, 8%) and N. otitidiscaviarum (n = 1, 4%). MLSA showed concordance with 16S rRNA gene sequencing results for the same 24 isolates. However, MLSA was able to identify the remaining isolate as N. wallacei, and clustered N. cyriacigeorgica into three subgroups. None of the clinical isolates were correctly identified to the species level by MALDI-TOF MS analysis using the manufacturer-provided database. A small "in-house" spectral database was established incorporating spectra of five clinical isolates representing the five species identified in this study. After complementation with the "in-house" database, of the remaining 20 isolates, 19 (95%) were correctly identified to species level (score ≥ 2.00) and one (an N. abscessus strain) to genus level (score ≥ 1.70 and < 2.00). In summary, MLSA showed superior discriminatory power compared with the 5'-end 606 bp partial 16S rRNA gene sequencing for species identification of Nocardia. MALDI-TOF MS can provide rapid and accurate identification but is reliant on a robust mass spectra database. PMID:26808813

  14. Surface Finishing for Biomaterials

    NASA Astrophysics Data System (ADS)

    Mizutani, Masayoshi; Komotori, Jun; Nagata, Jin; Katahira, Kazutoshi; Ohmori, Hitoshi

    Conventional biomaterials, such as titanium alloys, require enhanced chemical stability and wear resistance, which are dependent on the quality of the surficial oxide layer. However, it is very difficult to produce a sufficiently homogenous oxide layer by polishing using isolation abrasive alone. In our previous study, we proposed a new electrical grinding method (ELID grinding). The process improves oxide formation on the finished surface, resulting in finished surfaces with very thick and potentially stable oxide layers. In this study, to ensure the fabrication of surface with desirable characteristics for biomaterials, three types of specimens, which were processed with different surface finishing methods were prepared. Processed surfaces were analyzed by using an Energy Dispersive X-ray analyzer (EDX). To measure the thickness of surface oxide layers, detailed observation were performed by using a Transmission Electron Microscope (TEM). Although the ELID ground surface shows a higher value of surface roughness, excellent corrosion resistance was observed as compared with the samples finished by polishing. This is because of the formation of a thick oxide layer on the finished surface by ELID grinding. Consequently, ELID grinding appears to offer significant future promise for use in biomaterials and other engineering components subjected to the corrosion process.

  15. Non-contiguous finished genome sequence and description of Gorillibacterium massiliense gen. nov, sp. nov., a new member of the family Paenibacillaceae

    PubMed Central

    Keita, Mamadou Bhoye; Padhmanabhan, Roshan; Caputo, Aurélia; Robert, Catherine; Delaporte, Eric; Raoult, Didier; Fournier, Pierre-Edouard; Bittar, Fadi

    2014-01-01

    Strain G5T gen. nov., sp. nov. is the type strain of Gorillibacterium massiliense, a newly proposed genus within the family Paenibacillaceae. This strain, whose genome is described here, was isolated in France from a stool sample of a wild Gorilla gorilla subsp. gorilla from Cameroon. G. massiliense is a facultatively anaerobic, Gram negative rod. Here we describe the features of this bacterium, together with the complete genome sequence and annotation. The 5,546,433 bp long genome (1 chromosome but no plasmid) contains 5,145 protein-coding and 76 RNA genes, including 69 tRNA genes. PMID:25197465

  16. Non-contiguous finished genome sequence and description of Fenollaria massiliensis gen. nov., sp. nov., a new genus of anaerobic bacterium

    PubMed Central

    Pagnier, Isabelle; Croce, Olivier; Robert, Catherine; Raoult, Didier; La Scola, Bernard

    2014-01-01

    Fenollaria massiliensis strain 9401234T, is the type strain of Fenollaria massiliensis gen. nov., sp. nov., a new species within a new genus Fenollaria. This strain, whose genome is described here, was isolated from an osteoarticular sample. F. massiliensis strain 9401234T is an obligate anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1.71 Mbp long genome exhibits a G+C content of 34.46% and contains 1,667 protein-coding and 30 RNA genes, including 3 rRNA genes. PMID:25197455

  17. 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

  18. 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…

  19. 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.…

  20. Accurate Identification of Common Pathogenic Nocardia Species: Evaluation of a Multilocus Sequence Analysis Platform and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

    PubMed Central

    Chen, Sharon C-A.; Fan, Xin; Zhang, Li; Li, Hai-Xia; Hou, Xin; Cheng, Jing-Wei; Kong, Fanrong; Zhao, Yu-Pei; Xu, Ying-Chun

    2016-01-01

    Species identification of Nocardia is not straightforward due to rapidly evolving taxonomy, insufficient discriminatory power of conventional phenotypic methods and also of single gene locus analysis including 16S rRNA gene sequencing. Here we evaluated the ability of a 5-locus (16S rRNA, gyrB, secA1, hsp65 and rpoB) multilocus sequence analysis (MLSA) approach as well as that of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in comparison with sequencing of the 5’-end 606 bp partial 16S rRNA gene to provide identification of 25 clinical isolates of Nocardia. The 5’-end 606 bp 16S rRNA gene sequencing successfully assigned 24 of 25 (96%) clinical isolates to species level, namely Nocardia cyriacigeorgica (n = 12, 48%), N. farcinica (n = 9, 36%), N. abscessus (n = 2, 8%) and N. otitidiscaviarum (n = 1, 4%). MLSA showed concordance with 16S rRNA gene sequencing results for the same 24 isolates. However, MLSA was able to identify the remaining isolate as N. wallacei, and clustered N. cyriacigeorgica into three subgroups. None of the clinical isolates were correctly identified to the species level by MALDI-TOF MS analysis using the manufacturer-provided database. A small “in-house” spectral database was established incorporating spectra of five clinical isolates representing the five species identified in this study. After complementation with the “in-house” database, of the remaining 20 isolates, 19 (95%) were correctly identified to species level (score ≥ 2.00) and one (an N. abscessus strain) to genus level (score ≥ 1.70 and < 2.00). In summary, MLSA showed superior discriminatory power compared with the 5’-end 606 bp partial 16S rRNA gene sequencing for species identification of Nocardia. MALDI-TOF MS can provide rapid and accurate identification but is reliant on a robust mass spectra database. PMID:26808813

  1. Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE.

    PubMed

    Riley, Todd R; Lazarovici, Allan; Mann, Richard S; Bussemaker, Harmen J

    2015-01-01

    Transcription factors are crucial regulators of gene expression. Accurate quantitative definition of their intrinsic DNA binding preferences is critical to understanding their biological function. High-throughput in vitro technology has recently been used to deeply probe the DNA binding specificity of hundreds of eukaryotic transcription factors, yet algorithms for analyzing such data have not yet fully matured. Here, we present a general framework (FeatureREDUCE) for building sequence-to-affinity models based on a biophysically interpretable and extensible model of protein-DNA interaction that can account for dependencies between nucleotides within the binding interface or multiple modes of binding. When training on protein binding microarray (PBM) data, we use robust regression and modeling of technology-specific biases to infer specificity models of unprecedented accuracy and precision. We provide quantitative validation of our results by comparing to gold-standard data when available. PMID:26701911

  2. 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

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

    2016-07-01

    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

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

    NASA Astrophysics Data System (ADS)

    Majer, G.; Zick, K.

    2015-04-01

    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 CRh6G = 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 CRh6G = 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.

  4. 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.

  5. 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.

  6. 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

  7. Accurate detection for a wide range of mutation and editing sites of microRNAs from small RNA high-throughput sequencing profiles.

    PubMed

    Zheng, Yun; Ji, Bo; Song, Renhua; Wang, Shengpeng; Li, Ting; Zhang, Xiaotuo; Chen, Kun; Li, Tianqing; Li, Jinyan

    2016-08-19

    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

  8. Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE

    PubMed Central

    Riley, Todd R; Lazarovici, Allan; Mann, Richard S; Bussemaker, Harmen J

    2015-01-01

    Transcription factors are crucial regulators of gene expression. Accurate quantitative definition of their intrinsic DNA binding preferences is critical to understanding their biological function. High-throughput in vitro technology has recently been used to deeply probe the DNA binding specificity of hundreds of eukaryotic transcription factors, yet algorithms for analyzing such data have not yet fully matured. Here, we present a general framework (FeatureREDUCE) for building sequence-to-affinity models based on a biophysically interpretable and extensible model of protein-DNA interaction that can account for dependencies between nucleotides within the binding interface or multiple modes of binding. When training on protein binding microarray (PBM) data, we use robust regression and modeling of technology-specific biases to infer specificity models of unprecedented accuracy and precision. We provide quantitative validation of our results by comparing to gold-standard data when available. DOI: http://dx.doi.org/10.7554/eLife.06397.001 PMID:26701911

  9. 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.

  10. Rapid genome mapping in nano channel array for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Next-generation sequencing (NGS) technologies have enabled high-throughput and low-cost generation of sequence data; however, de novo genome assembly remains a great challenge, particularly for large genomes. NGS short reads are often insufficient to create large contigs that span repeat sequences...

  11. 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

  12. 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.

  13. Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA

    PubMed Central

    Zill, Oliver A.; Sebisanovic, Dragan; Lopez, Rene; Blau, Sibel; Collisson, Eric A.; Divers, Stephen G.; Hoon, Dave S. B.; Kopetz, E. Scott; Lee, Jeeyun; Nikolinakos, Petros G.; Baca, Arthur M.; Kermani, Bahram G.; Eltoukhy, Helmy; Talasaz, AmirAli

    2015-01-01

    Next-generation sequencing of cell-free circulating solid tumor DNA addresses two challenges in contemporary cancer care. First this method of massively parallel and deep sequencing enables assessment of a comprehensive panel of genomic targets from a single sample, and second, it obviates the need for repeat invasive tissue biopsies. Digital SequencingTM is a novel method for high-quality sequencing of circulating tumor DNA simultaneously across a comprehensive panel of over 50 cancer-related genes with a simple blood test. Here we report the analytic and clinical validation of the gene panel. Analytic sensitivity down to 0.1% mutant allele fraction is demonstrated via serial dilution studies of known samples. Near-perfect analytic specificity (> 99.9999%) enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%. We compared digital sequencing of plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive matched samples from five outside centers in patients with stage III-IV solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue. The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%. Digital sequencing of plasma-derived DNA is indicated in advanced cancer patients to prevent repeated invasive biopsies when the initial biopsy is inadequate, unobtainable for genomic testing, or uninformative, or when the patient’s cancer has progressed despite treatment. Its clinical utility is derived from reduction in the costs, complications and delays associated with invasive tissue biopsies for genomic testing. PMID:26474073

  14. Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier

    PubMed Central

    Porter, Teresita M; Gibson, Joel F; Shokralla, Shadi; Baird, Donald J; Golding, G Brian; Hajibabaei, Mehrdad

    2014-01-01

    Current methods to identify unknown insect (class Insecta) cytochrome c oxidase (COI barcode) sequences often rely on thresholds of distances that can be difficult to define, sequence similarity cut-offs, or monophyly. Some of the most commonly used metagenomic classification methods do not provide a measure of confidence for the taxonomic assignments they provide. The aim of this study was to use a naïve Bayesian classifier (Wang et al. Applied and Environmental Microbiology, 2007; 73: 5261) to automate taxonomic assignments for large batches of insect COI sequences such as data obtained from high-throughput environmental sequencing. This method provides rank-flexible taxonomic assignments with an associated bootstrap support value, and it is faster than the blast-based methods commonly used in environmental sequence surveys. We have developed and rigorously tested the performance of three different training sets using leave-one-out cross-validation, two field data sets, and targeted testing of Lepidoptera, Diptera and Mantodea sequences obtained from the Barcode of Life Data system. We found that type I error rates, incorrect taxonomic assignments with a high bootstrap support, were already relatively low but could be lowered further by ensuring that all query taxa are actually present in the reference database. Choosing bootstrap support cut-offs according to query length and summarizing taxonomic assignments to more inclusive ranks can also help to reduce error while retaining the maximum number of assignments. Additionally, we highlight gaps in the taxonomic and geographic representation of insects in public sequence databases that will require further work by taxonomists to improve the quality of assignments generated using any method.

  15. Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA.

    PubMed

    Lanman, Richard B; Mortimer, Stefanie A; Zill, Oliver A; Sebisanovic, Dragan; Lopez, Rene; Blau, Sibel; Collisson, Eric A; Divers, Stephen G; Hoon, Dave S B; Kopetz, E Scott; Lee, Jeeyun; Nikolinakos, Petros G; Baca, Arthur M; Kermani, Bahram G; Eltoukhy, Helmy; Talasaz, AmirAli

    2015-01-01

    Next-generation sequencing of cell-free circulating solid tumor DNA addresses two challenges in contemporary cancer care. First this method of massively parallel and deep sequencing enables assessment of a comprehensive panel of genomic targets from a single sample, and second, it obviates the need for repeat invasive tissue biopsies. Digital Sequencing™ is a novel method for high-quality sequencing of circulating tumor DNA simultaneously across a comprehensive panel of over 50 cancer-related genes with a simple blood test. Here we report the analytic and clinical validation of the gene panel. Analytic sensitivity down to 0.1% mutant allele fraction is demonstrated via serial dilution studies of known samples. Near-perfect analytic specificity (> 99.9999%) enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%. We compared digital sequencing of plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive matched samples from five outside centers in patients with stage III-IV solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue. The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%. Digital sequencing of plasma-derived DNA is indicated in advanced cancer patients to prevent repeated invasive biopsies when the initial biopsy is inadequate, unobtainable for genomic testing, or uninformative, or when the patient's cancer has progressed despite treatment. Its clinical utility is derived from reduction in the costs, complications and delays associated with invasive tissue biopsies for genomic testing. PMID:26474073

  16. Organization of the Bacillus subtilis 168 chromosome between kdg and the attachment site of the SP beta prophage: use of Long Accurate PCR and yeast artificial chromosomes for sequencing.

    PubMed

    Capuano, V; Galleron, N; Pujic, P; Sorokin, A; Ehrlich, S D

    1996-11-01

    Within the Bacillus subtilis genome sequencing project, the region between lysA and ilvA was assigned to our laboratory. In this report we present the sequence of the last 36 kb of this region, between the kdg operon and the attachment site of the SP beta prophage. A two-step strategy was used for the sequencing. In the first step, total chromosomal DNA was cloned in phage M13-based vectors and the clones carrying inserts from the target region were identified by hybridization with a cognate yeast artificial chromosome (YAC) from our collection. Sequencing of the clones allowed us to establish a number of contigs. In the second step the contigs were mapped by Long Accurate (LA) PCR and the remaining gaps closed by sequencing of the PCR products. The level of sequence inaccuracy due to LA PCR errors appeared to be about 1 in 10,000, which does not affect significantly the final sequence quality. This two-step strategy is efficient and we suggest that it can be applied to sequencing of longer chromosomal regions. The 36 kb sequence contains 38 coding sequences (CDSs), 19 of which encode unknown proteins. Seven genetic loci already mapped in this region, xpt, metB, ilvA, ilvD, thyB, dfrA and degR were identified. Eleven CDSs were found to display significant similarities to known proteins from the data banks, suggesting possible functions for some of the novel genes: cspD may encode a cold shock protein; bcsA, the first bacterial homologue of chalcone synthase; exol, a 5' to 3' exonuclease, similar to that of DNA polymerase I of Escherichia coli; and bsaA, a stress-response-associated protein. The protein encoded by yplP has homology with the transcriptional NifA-like regulators. The arrangement of the genes relative to possible promoters and terminators suggests 19 potential transcription units. PMID:8969496

  17. Accurate, rapid and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing

    PubMed Central

    2010-01-01

    Background In the event of biocrimes or infectious disease outbreaks, high-resolution genetic characterization for identifying the agent and attributing it to a specific source can be crucial for an effective response. Until recently, in-depth genetic characterization required expensive and time-consuming Sanger sequencing of a few strains, followed by genotyping of a small number of marker loci in a panel of isolates at or by gel-based approaches such as pulsed field gel electrophoresis, which by necessity ignores most of the genome. Next-generation, massively parallel sequencing (MPS) technology (specifically the Applied Biosystems sequencing by oligonucleotide ligation and detection (SOLiD™) system) is a powerful investigative tool for rapid, cost-effective and parallel microbial whole-genome characterization. Results To demonstrate the utility of MPS for whole-genome typing of monomorphic pathogens, four Bacillus anthracis and four Yersinia pestis strains were sequenced in parallel. Reads were aligned to complete reference genomes, and genomic variations were identified. Resequencing of the B. anthracis Ames ancestor strain detected no false-positive single-nucleotide polymorphisms (SNPs), and mapping of reads to the Sterne strain correctly identified 98% of the 133 SNPs that are not clustered or associated with repeats. Three geographically distinct B. anthracis strains from the A branch lineage were found to have between 352 and 471 SNPs each, relative to the Ames genome, and one strain harbored a genomic amplification. Sequencing of four Y. pestis strains from the Orientalis lineage identified between 20 and 54 SNPs per strain relative to the CO92 genome, with the single Bolivian isolate having approximately twice as many SNPs as the three more closely related North American strains. Coverage plotting also revealed a common deletion in two strains and an amplification in the Bolivian strain that appear to be due to insertion element-mediated recombination

  18. Use of Optical Mapping to Aid in Assembly and Finishing of Human Microbiome Genome Projects

    SciTech Connect

    Wagner, Trevor

    2010-06-03

    Trevor Wagner of OpGen, Inc. discusses the use of optical mapping to validate the assembly of HMP genomes on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

    We report a Phase-Alternating R-Symmetry (PARS) dipolar recoupling scheme for accurate measurement of heteronuclear 1H-X (X = 13C, 15N, 31P, 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 1H CSA interaction persists and thereby introduces considerable errors in the dipolar measurements. In PARS, phase-shifted RN symmetry pulse blocks applied on the 1H spins combined with π pulses applied on the X spins at the end of each RN block efficiently suppress the effect from 1H chemical shift anisotropy, while keeping the 1H-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, [15N]-N-acetyl-valine and [U-13C,15N]-N-formyl-Met-Leu-Phe tripeptide. The application of PARS for site-resolved measurement of accurate 1H-15N dipolar couplings in the context of 3D experiments is presented on U-13C,15N-enriched dynein light chain protein LC8.

  20. 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.

  1. The DNA sequence and biological annotation of human chromosome 1.

    PubMed

    Gregory, S G; Barlow, K F; McLay, K E; Kaul, R; Swarbreck, D; Dunham, A; Scott, C E; Howe, K L; Woodfine, K; Spencer, C C A; Jones, M C; Gillson, C; Searle, S; Zhou, Y; Kokocinski, F; McDonald, L; Evans, R; Phillips, K; Atkinson, A; Cooper, R; Jones, C; Hall, R E; Andrews, T D; Lloyd, C; Ainscough, R; Almeida, J P; Ambrose, K D; Anderson, F; Andrew, R W; Ashwell, R I S; Aubin, K; Babbage, A K; Bagguley, C L; Bailey, J; Beasley, H; Bethel, G; Bird, C P; Bray-Allen, S; Brown, J Y; Brown, A J; Buckley, D; Burton, J; Bye, J; Carder, C; Chapman, J C; Clark, S Y; Clarke, G; Clee, C; Cobley, V; Collier, R E; Corby, N; Coville, G J; Davies, J; Deadman, R; Dunn, M; Earthrowl, M; Ellington, A G; Errington, H; Frankish, A; Frankland, J; French, L; Garner, P; Garnett, J; Gay, L; Ghori, M R J; Gibson, R; Gilby, L M; Gillett, W; Glithero, R J; Grafham, D V; Griffiths, C; Griffiths-Jones, S; Grocock, R; Hammond, S; Harrison, E S I; Hart, E; Haugen, E; Heath, P D; Holmes, S; Holt, K; Howden, P J; Hunt, A R; Hunt, S E; Hunter, G; Isherwood, J; James, R; Johnson, C; Johnson, D; Joy, A; Kay, M; Kershaw, J K; Kibukawa, M; Kimberley, A M; King, A; Knights, A J; Lad, H; Laird, G; Lawlor, S; Leongamornlert, D A; Lloyd, D M; Loveland, J; Lovell, J; Lush, M J; Lyne, R; Martin, S; Mashreghi-Mohammadi, M; Matthews, L; Matthews, N S W; McLaren, S; Milne, S; Mistry, S; Moore, M J F; Nickerson, T; O'Dell, C N; Oliver, K; Palmeiri, A; Palmer, S A; Parker, A; Patel, D; Pearce, A V; Peck, A I; Pelan, S; Phelps, K; Phillimore, B J; Plumb, R; Rajan, J; Raymond, C; Rouse, G; Saenphimmachak, C; Sehra, H K; Sheridan, E; Shownkeen, R; Sims, S; Skuce, C D; Smith, M; Steward, C; Subramanian, S; Sycamore, N; Tracey, A; Tromans, A; Van Helmond, Z; Wall, M; Wallis, J M; White, S; Whitehead, S L; Wilkinson, J E; Willey, D L; Williams, H; Wilming, L; Wray, P W; Wu, Z; Coulson, A; Vaudin, M; Sulston, J E; Durbin, R; Hubbard, T; Wooster, R; Dunham, I; Carter, N P; McVean, G; Ross, M T; Harrow, J; Olson, M V; Beck, S; Rogers, J; Bentley, D R; Banerjee, R; Bryant, S P; Burford, D C; Burrill, W D H; Clegg, S M; Dhami, P; Dovey, O; Faulkner, L M; Gribble, S M; Langford, C F; Pandian, R D; Porter, K M; Prigmore, E

    2006-05-18

    The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome. PMID:16710414

  2. A more accurate relocation of the 2013 M s7.0 Lushan, Sichuan, China, earthquake sequence, and the seismogenic structure analysis

    NASA Astrophysics Data System (ADS)

    Long, F.; Wen, X. Z.; Ruan, X.; Zhao, M.; Yi, G. X.

    2015-07-01

    We use a combined earthquake location technique to relocate the M s7.0 Lushan, Sichuan, China, earthquake sequence of April 20, 2013. A stepwise approach, employing three existing location methods (the HYPOINVERSE method, the Minimum 1-D model, and the Double Difference method), is used to improve location precision by iteratively revising the velocity model station corrections, and hypocenter relocations throughout the process. Our stepwise approach has significantly improved the location precision of the Lushan earthquake sequence, yielding hypocenter locations with final errors of 359, 309, and 605 m in the E-W, N-S, and vertical directions, respectively, with average travel time residuals of 0.12 s. Furthermore, we analyzed the seismogenic structure surrounding the Lushan earthquake sequence by combining the results of the relocated hypocenter distribution with new focal mechanism solutions and information from regional geological and geophysical investigations. From our analysis, we conclude that the vast majority of the aftershocks of the Lushan earthquake sequence occurred at depths of 6-9 km, near the front of the southwestern segment of the NE-trending Longmenshan fault zone. Densely aligned hypocenters clearly suggest that the seismogenic structure of the mainshock consists of a set of basal thrust faults dipping to the NW at 40-50°, at a ramp of the deep basal décollement-thrust system at depths of 7-18 km. Focal mechanism solutions suggest that the seismogenic faults have produced almost pure thrusting. At least one SE-dipping back-thrust is also observed within the basement, as indicated by the hypocenter relocations, which points to either a secondary rupture plane during the mainshock or a plane of aftershock slips. A small number of minor events in the Lushan sequence are located at depths of 0-6 km, with a distribution suggesting that the three NE-trending faults with surface traces running through or passing close to the aftershock area are

  3. Sequencing Complex Genomic Regions

    SciTech Connect

    Eichler, Evan

    2009-05-28

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

  4. Sequencing Complex Genomic Regions

    SciTech Connect

    Eichler, Evan

    2009-05-28

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

  5. 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.

  6. 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…

  7. 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

  8. Methods for accurate quantification of LTR-retrotransposon copy number using short-read sequence data: a case study in Sorghum.

    PubMed

    Ramachandran, Dhanushya; Hawkins, Jennifer S

    2016-10-01

    Transposable elements (TEs) are ubiquitous in eukaryotic genomes and their mobility impacts genome structure and function in myriad ways. Because of their abundance, activity, and repetitive nature, the characterization and analysis of TEs remain challenging, particularly from short-read sequencing projects. To overcome this difficulty, we have developed a method that estimates TE copy number from short-read sequences. To test the accuracy of our method, we first performed an in silico analysis of the reference Sorghum bicolor genome, using both reference-based and de novo approaches. The resulting TE copy number estimates were strikingly similar to the annotated numbers. We then tested our method on real short-read data by estimating TE copy numbers in several accessions of S. bicolor and its close relative S. propinquum. Both methods effectively identify and rank similar TE families from highest to lowest abundance. We found that de novo characterization was effective at capturing qualitative variation, but underestimated the abundance of some TE families, specifically families of more ancient origin. Also, interspecific reference-based mapping of S. propinquum reads to the S. bicolor database failed to fully describe TE content in S. propinquum, indicative of recent TE activity leading to changes in the respective repetitive landscapes over very short evolutionary timescales. We conclude that reference-based analyses are best suited for within-species comparisons, while de novo approaches are more reliable for evolutionarily distant comparisons. PMID:27295958

  9. 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...

  10. 7 CFR 29.1017 - Finish.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Finish. 29.1017 Section 29.1017 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Type 92) § 29.1017 Finish. The reflectance factor in color perception. Finish indicates the sheen...

  11. 7 CFR 29.3517 - Finish.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Finish. 29.3517 Section 29.3517 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Type 95) § 29.3517 Finish. The reflectance factor in color perception. Finish indicates the sheen...

  12. 7 CFR 29.2518 - Finish.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Finish. 29.2518 Section 29.2518 Agriculture...-Cured Tobacco (u.s. Types 22, 23, and Foreign Type 96) § 29.2518 Finish. The reflectance factor in color perception. Finish indicates the sheen or shine of the surface of a tobacco leaf. (See chart, § 29.2601.)...

  13. 7 CFR 29.2268 - Finish.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Finish. 29.2268 Section 29.2268 Agriculture... INSPECTION Standards Official Standard Grades for Virginia Fire-Cured Tobacco (u.s. Type 21) § 29.2268 Finish. The reflectance factor in color perception. Finish indicates the sheen or shine of the surface of...

  14. 7 CFR 29.3022 - Finish.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Finish. 29.3022 Section 29.3022 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Finish. The reflectance factor in color perception. Finish indicates the sheen or shine of the surface...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. POLLUTION PREVENTION IN THE METAL FINISHING INDUSTRY

    EPA Science Inventory

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

  1. Glacial retreat between the Late-Glacial and Early Holocene sequences in the Southern French Alps : definition of an accurate pattern by new Cosmic Ray Exposure ages.

    NASA Astrophysics Data System (ADS)

    Cossart, Etienne; Fort, Monique; Bourlès, Didier; Braucher, Régis; Carcaillet, Julien; Perrier, Romain; Siame, Lionel; Gribenski, Natacha

    2010-05-01

    The Southern French Alps, characterized by many climatic influences (oceanic, continental and mediterranean), remain a scientific problem for palaeo-environmental studies. Indeed, the lack of chronological benchmarks hitherto hampered the definition of sequences of glacier variations since the Last Glacial Maximum (LGM), even if a scenario was based upon an extensive fieldwork realized in the Ubaye valley. This scenario was then considered as a regional model by many geomorphologists, but this valley is not necessarily representative of the entire region. Firstly, this valley is the driest area within the Southern French Alps due the sheltering effect of relief against humid fluxes. Secondly, topography (altitudes, slopes and shapes) of the upper part of watersheds are not particularly prone to snow accumulation into the cirques. The established scenario is as follows. Glaciers shrank and decayed between the LGM and the Late-Glacial periods and glaciers were restricted in cirques areas during the Late-Glacial and Holocene glaciations. We try to discuss this model thanks to geomorphic investigations and new chronological benchmarks acquired in Briançonnais area, in the upper part of Durance watershed. The upper part of the Durance watershed was chosen because it corresponds to the accumulation zone of the main glacier of the Southern French Alps during the LGM. Thanks to extensive fieldwork and geomorphic mapping of remnants of past glaciations, and thanks to new chronological data (about 35 cosmic ray exposure -CRE- ages, acquired in 2004 and 2009) we propose here the first absolute scenario established in the very upper part of the catchment. To assess CRE ages, we sampled glacially-polished surfaces, along both longitudinal and transverse valley cross-sections, in order to assess both the retreat of the front and the thinning rate of the glacial tongue. We also paid attention to knobs located at the outlet of glacial cirques, and some morainic ridges. The

  2. 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.

  3. 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...

  4. Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding

    PubMed Central

    Ralph, Steven G; Chun, Hye Jung E; Cooper, Dawn; Kirkpatrick, Robert; Kolosova, Natalia; Gunter, Lee; Tuskan, Gerald A; Douglas, Carl J; Holt, Robert A; Jones, Steven JM; Marra, Marco A; Bohlmann, Jörg

    2008-01-01

    Background 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. Results 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 × 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

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

    PubMed Central

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

    2015-01-01

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

  6. 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.

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

    PubMed

    Eastman, Alexander W; Yuan, Ze-Chun

    2014-01-01

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

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

    PubMed Central

    Eastman, Alexander W.; Yuan, Ze-Chun

    2015-01-01

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

  9. Metal Finishing Facility Risk Screening Tool (Mffrst)

    EPA Science Inventory

    The Metal Finishing Facility Risk Screening Tool (MFFRST) is a user-friendly pc-based computer tool which allows an individual to evaluate the potential exposures and health risks to workers and nearby residents from emissions from individual metal finishing facilities. Emission...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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 ...

  16. 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.

  17. NexGen Production – Sequencing and Analysis

    SciTech Connect

    Muzny, Donna

    2010-06-02

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

  18. 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.

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

    ScienceCinema

    Jenkins, David [EdgeBio

    2013-03-22

    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.

  20. 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

  1. MEETING HAZARDOUS WASTE REQUIREMENTS FOR METAL FINISHERS

    EPA Science Inventory

    This document provides information on the regulations affecting hazardous wastes discharged by metal finishers. opics included are: impact of RCRA regulations on both small and large generators; "delisting" of a specific facility waste from hazardous waste regulation; land dispos...

  2. NCMS PWB Surface Finishes Team project summary

    SciTech Connect

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

    1996-04-01

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

  3. 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.

  4. C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison

    PubMed Central

    Minkin, Ilya; Pham, Hoa; Starostina, Ekaterina; Vyahhi, Nikolay; Pham, Son

    2013-01-01

    We present C-Sibelia, a highly accurate and easy-to-use software tool for comparing two closely related bacterial genomes, which can be presented as either finished sequences or fragmented assemblies. C-Sibelia takes as input two FASTA files and produces: (1) a VCF file containing all identified single nucleotide variations and indels; (2) an XMFA file containing alignment information. The software also produces Circos diagrams visualizing high level genomic architecture for rearrangement analyses. C-Sibelia is a part of the Sibelia comparative genomics suite, which is freely available under the GNU GPL v.2 license at http://sourceforge.net/projects/sibelia-bio. C-Sibelia is compatible with Unix-like operating systems. A web-based version of the software is available at http://etool.me/software/csibelia. PMID:25110578

  5. 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

    2014-01-01

    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. PMID:25052506

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

    DOE PAGESBeta

    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.

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

    PubMed Central

    2013-01-01

    Background The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. Results To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads. Conclusions Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization. PMID:24034426

  8. 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.

  9. 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.

  10. 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).

  11. 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...

  12. 7 CFR 29.3022 - Finish.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Finish. 29.3022 Section 29.3022 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE COMMODITY STANDARDS AND STANDARD CONTAINER REGULATIONS TOBACCO INSPECTION Standards Official Standard...

  13. Pneumonia outbreaks in calves and finishers.

    PubMed

    2016-03-19

    Pneumonia in calves and finishers. Ovarian tumour in a calf . Abortion associated with bovine herpesvirus 1 in a suckler herd. Parasitic gastroenteritis causing illthrift and death in sheep. Outbreaks of acute fasciolosis in sheep. These are among matters discussed in the disease surveillance report for December 2015 from SAC Consulting: Veterinary Services (SAC C VS). PMID:26993450

  14. 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…

  15. Vibratory finishing as a decontamination process

    SciTech Connect

    McCoy, M.W.; Arrowsmith, H.W.; Allen, R.P.

    1980-10-01

    The major objective of this research is to develop vibratory finishing into a large-scale decontamination technique that can economicaly remove transuranic and other surface contamination from large volumes of waste produced by the operation and decommissioning of retired nuclear facilities. The successful development and widespread application of this decontamination technique would substantially reduce the volume of waste requiring expensive geologic disposal. Other benefits include exposure reduction for decontamination personnel and reduced risk of environmental contamination. Laboratory-scale studies showed that vibratory finishing can rapidly reduce the contamination level of transuranic-contaminated stainless steel and Plexiglas to well below the 10-nCi/g limit. The capability of vibratory finishing as a decontamination process was demonstrated on a large scale. The first decontamination demonstration was conducted at the Hanford N-Reactor, where a vibratory finisher was installed to reduce personnel exposure during the summer outage. Items decontaminated included fuel spacers, process-tube end caps, process-tube inserts, pump parts, ball-channel inspection tools and miscellaneous hand tools. A second demonstration is currently being conducted in the decontamination facility at the Hanford 231-Z Building. During this demonstration, transuranic-contaminated material from decommissioned plutonium facilities is being decontaminated to <10 nCi/g to minimize the volume of material that will require geologic disposal. Items that are being decontaminated include entire glove boxes, process-hood structural material and panels, process tanks, process-tank shields, pumps, valves and hand tools used during the decommissioning work.

  16. 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...

  17. 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. PMID:26316452

  18. 27 CFR 19.601 - Finished products records.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... for redistillation; (7) Withdrawn for research, development or testing (including government samples... finished product; and (11) Disposed of as samples of the finished product. (26 U.S.C. 5207)...

  19. 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

  20. GUIDES TO POLLUTION PREVENTION: THE METAL FINISHING INDUSTRY

    EPA Science Inventory

    This guide provides an overview of the major metal finishing processes and operations that generate waste and presents options for minimizing it through source reduction and recycling. etal finishing processes generate various waste streams, including contaminated plating baths, ...

  1. 27 CFR 19.601 - Finished products records.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... and a daily summary record of the kind and quantity of finished products bottled or packaged within... transaction records and a daily summary record of the quantity of finished products bottled or packaged...

  2. 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.

  3. 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.

  4. 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.

  5. Evaluation of interproximal finishing techniques for silver amalgam restorations.

    PubMed

    Bower, C F; Reinhardt, R A; DuBois, L M

    1986-09-01

    In spite of the incidence of recurrent caries and gingival inflammation surrounding the gingival margins of interproximal silver amalgam restorations, little information exists on the efficacy of finishing procedures in this location. This study was intended to evaluate surface smoothness of interproximal silver amalgams using four finishing techniques. Results indicated that surfaces finished using the carve, floss, and finishing strip polish consistently produced a measurably smoother surface (p less than 0.01) than did the other techniques. The use of finishing strips on the gingival margin of Class II silver amalgam restorations shows promise of improving interproximal surface smoothness. PMID:3462385

  6. Grading More Accurately

    ERIC Educational Resources Information Center

    Rom, Mark Carl

    2011-01-01

    Grades matter. College grading systems, however, are often ad hoc and prone to mistakes. This essay focuses on one factor that contributes to high-quality grading systems: grading accuracy (or "efficiency"). I proceed in several steps. First, I discuss the elements of "efficient" (i.e., accurate) grading. Next, I present analytical results…

  7. 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. PMID:22274716

  8. 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.

  9. 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.

  10. 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.

  11. Densified carbonaceous bodies with improved surface finishes

    SciTech Connect

    Hucke, E.E.

    1988-08-02

    A method is described of producing a densified carbonaceous body with a superior surface finish, the method comprising the steps of: impregnating a permeable body composed essentially of a fine grained, isotropic graphite with a liquid impregnant containing furfural or furfural alcohol or a mixture thereof, an acid catalyst, and a pore-forming agent comprising a polyalkylene oxide adduct nonionic surfactant; heating the impregnated, permeable body to a temperature which is sufficiently high to polymerize the impregnant; and then heating the body to a temperature which is sufficiently high to pyrolyze the carbon in the polymerized impregnant.

  12. PLUTONIUM FINISHING PLANT (PFP) STABILIZATION & PACKAGING PROJECT

    SciTech Connect

    GERBER, M.S.

    2004-01-14

    Fluor Hanford is pleased to submit the Plutonium Finishing Plant (PFP) Stabilization and Packaging Project (SPP) for consideration by the Project Management Institute as Project of the Year for 2004. The SPP thermally stabilized and/or packaged nearly 18 metric tons (MT) of plutonium and plutonium-bearing materials left in PFP facilities from 40 years of nuclear weapons production and experimentation. The stabilization of the plutonium-bearing materials substantially reduced the radiological risk to the environment and security concerns regarding the potential for terrorists to acquire the non-stabilized plutonium products for nefarious purposes. The work was done In older facilities which were never designed for the long-term storage of plutonium, and required working with materials that were extremely radioactive, hazardous, pyrophoric, and In some cases completely unique. I n some Instances, one-of-a-kind processes and equipment were designed, installed, and started up. The SPP was completed ahead of schedule, substantially beating all Interim progress milestone dates set by the Defense Nuclear Facilities Safety Board (DNFSB) and in the Hanford Site's Federal Facility Agreement and Consent Order (Tri-Party Agreement or TPA), and finished $1-million under budget.

  13. [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. PMID:2076124

  14. 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

  15. 6. FACTORY BUILDING, WITH FINISHED PRODUCT WAREHOUSE IN RIGHT BACKGROUND. ...

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

    6. FACTORY BUILDING, WITH FINISHED PRODUCT WAREHOUSE IN RIGHT BACKGROUND. VIEW TO NORTHWEST. - Commercial & Industrial Buildings, Maizewood Insulation Company Factory, 275 Salina Street, Dubuque, Dubuque County, IA

  16. Hazardous waste reduction in the metal finishing industry

    SciTech Connect

    Not Available

    1989-01-01

    This study identifies opportunities for waste reduction available to the metal finishing industry and develops a generic audit protocol that can be used by metal finishers to assess their own waste reduction opportunities. The study emphasizes technologies available to metal finishing plants of various sizes. Typically, these shops operate a variety of physical, chemical and electrochemical processes. Chemical processes include degreasing, cleaning, pickling, etching, coating, and electroless plating. Electrochemical processes include plating and anodizing. The study identifies three categories of waste reduction technologies that are available to metal finishers: source reduction, recycling and resource recovery, and alternative treatment.

  17. Review of Capabilities of the ENEPIG Surface Finish

    NASA Astrophysics Data System (ADS)

    Ratzker, Menahem; Pearl, Adam; Osterman, Michael; Pecht, Michael; Milad, George

    2014-11-01

    Surface finishes are used to protect exposed copper metallization in printed circuit boards from oxidation and to provide a solderable surface on which to mount electronic components. While it is true that some people have called electroless nickel electroless palladium immersion gold (ENEPIG) a "universal finish" for a wide range of applications from wire bonding to solder interconnects, this paper provides a review of the current literature on ENEPIG and assesses its overall capabilities compared to other surface finishes. Gaps in understanding the performance of ENEPIG as a printed wiring board surface finish are identified and further testing is recommended.

  18. Accurate measurement of time

    NASA Astrophysics Data System (ADS)

    Itano, Wayne M.; Ramsey, Norman F.

    1993-07-01

    The paper discusses current methods for accurate measurements of time by conventional atomic clocks, with particular attention given to the principles of operation of atomic-beam frequency standards, atomic hydrogen masers, and atomic fountain and to the potential use of strings of trapped mercury ions as a time device more stable than conventional atomic clocks. The areas of application of the ultraprecise and ultrastable time-measuring devices that tax the capacity of modern atomic clocks include radio astronomy and tests of relativity. The paper also discusses practical applications of ultraprecise clocks, such as navigation of space vehicles and pinpointing the exact position of ships and other objects on earth using the GPS.

  19. 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.

  20. Sequencing Centers Panel at SFAF

    SciTech Connect

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

    2010-06-02

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

  1. Genome Sequence of Pseudomonas chlororaphis Strain 189

    PubMed Central

    Town, Jennifer; Audy, Patrice; Boyetchko, Susan M.

    2016-01-01

    Pseudomonas chlororaphis strain 189 is a potent inhibitor of the growth of the potato pathogen Phytophthora infestans. We determined the complete, finished sequence of the 6.8-Mbp genome of this strain, consisting of a single contiguous molecule. Strain 189 is closely related to previously sequenced strains of P. chlororaphis. PMID:27340063

  2. 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.

  3. Sample Prep, Workflow Automation and Nucleic Acid Fractionation for Next Generation Sequencing

    SciTech Connect

    Roskey, Mark

    2010-06-03

    Mark Roskey of Caliper LifeSciences discusses how the company's technologies fit into the next generation sequencing workflow on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

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

    ScienceCinema

    Appel, Maryke [Kappa Biosystems

    2013-03-22

    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.

  5. Functional finishes of stretch cotton fabrics.

    PubMed

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

    2013-11-01

    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. PMID:24053846

  6. Analysis of Metagenomic Sequences: From Megabases to Terabases

    SciTech Connect

    Krypides, Nikos

    2010-06-04

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

  7. LLNL metal finishing and pollution prevention activities with small businesses

    SciTech Connect

    Dini, J.W.; Steffani, C.P.

    1996-07-01

    The Metal Finishing Facility at LLNL has emphasized using environmentally conscious manufacturing principles. Key focus items included minimizing hazardous wastes, minimization of water usage, material and process substitutions, and recycling. Joint efforts with NCAMF (Northern California Association of Metal Finishers), Technic, Inc., EPA, and UC Davis, all directed at pollution prevention, are reviewed.

  8. 27 CFR 19.751 - Records of finished products.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Records of finished products. 19.751 Section 19.751 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE... Account § 19.751 Records of finished products. Each processor shall maintain by proof gallons...

  9. 7 CFR 58.525 - Storage of finished product.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Storage of finished product. 58.525 Section 58.525 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards... Procedures § 58.525 Storage of finished product. Cottage cheese after packaging shall be promptly stored at...

  10. 30 CFR 18.33 - Finish of surface joints.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

  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. INNOVATIVE RINSE-AND-RECOVERY SYSTEM FOR METAL FINISHING PROCESSES

    EPA Science Inventory

    This report describes the feasibility of a rinse-and-recovery system that can be installed in almost any metal finishing line and does not harm the environment because no plating solution exits to the sewer. Most toxic pollutants from metal finishing operations are associated wit...

  13. 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...

  14. 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...

  15. 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...

  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. 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...

  18. 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...

  19. Plutonium finishing plant safety systems and equipment list

    SciTech Connect

    Bergquist, G.G.

    1995-01-06

    The Safety Equipment List (SEL) supports Analysis Report (FSAR), WHC-SD-CP-SAR-021 and the Plutonium Finishing Plant Operational Safety Requirements (OSRs), WHC-SD-CP-OSR-010. The SEL is a breakdown and classification of all Safety Class 1, 2, and 3 equipment, components, or system at the Plutonium Finishing Plant complex.

  20. Multifunctional finishing of cellulosic/polyester blended fabrics.

    PubMed

    Ibrahim, N A; Eid, B M; Youssef, M A; Ibrahim, H M; Ameen, H A; Salah, A M

    2013-09-12

    Innovative/efficient finishing systems for imparting multi-functional properties to cotton/polyester and viscose/polyester blends were developed. Factors affecting the extent of functionalization including type and concentration of the nano-hybrid, i.e. silver nanoparticles/polyvinyl pyrolidone hybrid (Ag-NP's/PVP) or zinc oxide nanoparticles/hyperbranched polyamide-amine hybrid (ZnO-NP's/HBPAA), concentration of Basic Blue 9, or chitosan and sequence of treatment using citric acid as cross-linker were reported. Loading of β-CD, with its hydrophobic cavities, onto the cross-linked substrates and subsequent treatment with Neem-oil, Lavender-oil or 4-hydroxybenzophenone was also studied. The obtained products exhibit a remarkable easy care, antibacterial and/or UV-blocking functional properties. The improvement in the imparted properties and durability to wash is governed by type and amount of loaded active ingredients. Mode of interactions was suggested, and surface modifications together with composition of selected samples were also confirmed by SEM images and EDX spectra. PMID:23911516

  1. 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

  2. Protein sources for finishing calves as affected by management system.

    PubMed

    Sindt, M H; Stock, R A; Klopfenstein, T J; Vieselmeyer, B A

    1993-03-01

    Two beef production systems were evaluated in conjunction with an evaluation of escape protein sources for finishing calves. Two hundred forty crossbred steers and 80 crossbred heifer calves (BW = 267 +/- 2 kg) were split into two groups: 1) control, finished (207 d) after a 3-wk feedlot adjustment period and 2) grazing cornstalks for 74 d after a 3-wk feedlot adjustment period, then finished (164 d). Finishing treatments were sources and proportions of supplemental CP: 1) urea 100%; 2) soybean meal (SBM) 100%; 3) blood meal (BM) 50%, urea 50%; 4) feather meal (FTH) 50%, urea 50%; 5) SBM 50%, FTH 25%, urea 25%; 6) SBM 25%, FTH 38%, urea 37%; 7) FTH 25%, BM 25%, urea 50%, and 8) FTH 38%, BM 13%, urea 50%. Treatments 1 to 8 were fed in dry-rolled corn (DRC)-based diets. Treatments 9 and 10 were supplement Treatments 1 and 7 fed in diets based on high-moisture corn. Calves finished after a 74-d period of grazing cornstalks consumed more feed (P < .01) and gained faster (P < .01) but were less efficient (P < .05) than calves finished directly after weaning. Although not statistically different, calves finished after grazing cornstalks and supplemented with natural protein in the feedlot were 7% more efficient than calves supplemented with urea alone. Efficiency of calves finished directly after weaning was similar for calves supplemented with natural protein or urea alone. Supplementing SBM/FTH/urea or BM/FTH/urea improved feed efficiency compared with supplementing FTH/urea alone. These data suggest that allowing calves to graze cornstalks before finishing is a possible management option, but this system may require more metabolizable protein in the finishing diet to maximize feed efficiency if the calves are expressing compensatory growth. PMID:8463161

  3. Effect of forage species during finishing on growth rate, final weight and carcass parameters from pasture finished cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In 2005 and 2006, angus-crossbred steers (n = 72) were used to compare growth rate, final weight and carcass parameters from pasture-finished cattle grazing cool-season mixed (MP), alfalfa (AL), or pearl millet (PM) pastures during the final 44 d of finishing. Steers were harvested on the same dates...

  4. Analysis and accurate quantification of CpG methylation by MALDI mass spectrometry

    PubMed Central

    Tost, Jörg; Schatz, Philipp; Schuster, Matthias; Berlin, Kurt; Gut, Ivo Glynne

    2003-01-01

    As the DNA sequence of the human genome is now nearly finished, the main task of genome research is to elucidate gene function and regulation. DNA methylation is of particular importance for gene regulation and is strongly implicated in the development of cancer. Even minor changes in the degree of methylation can have severe consequences. An accurate quantification of the methylation status at any given position of the genome is a powerful diagnostic indicator. Here we present the first assay for the analysis and precise quantification of methylation on CpG positions in simplex and multiplex reactions based on matrix-assisted laser desorption/ ionisation mass spectrometry detection. Calibration curves for CpGs in two genes were established and an algorithm was developed to account for systematic fluctuations. Regression analysis gave R2 ≥ 0.99 and standard deviation around 2% for the different positions. The limit of detection was ∼5% for the minor isomer. Calibrations showed no significant differences when carried out as simplex or multiplex analyses. All variable parameters were thoroughly investigated, several paraffin-embedded tissue biopsies were analysed and results were verified by established methods like analysis of cloned material. Mass spectrometric results were also compared to chip hybridisation. PMID:12711695

  5. 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.

  6. Developments in the finishing of domes and conformal optics

    NASA Astrophysics Data System (ADS)

    Shorey, Aric B.; Kordonski, William; Tracy, Justin; Tricard, Marc

    2007-04-01

    The final finish and characterization of windows and domes presents a number of difficult challenges. Furthermore, there is a desire to incorporate conformal shapes into next generation imaging and surveillance systems to provide significant advantages in overall component performance. Unfortunately, their constantly changing curvature and steep slopes make fabrication of such shapes incompatible with most conventional polishing and metrology solutions. Two novel types of polishing technology, Magnetorheological Finishing (MRF®) and Magnetorheological Jet (MR Jet TM), along with metrology provided by the Sub-aperture Stitching Interferometer (SSI®) have several unique attributes that give them advantages in enhancing fabrication of hemispherical domes and even conformal shapes. The advantages that MRF brings to the precision finishing of a wide range of shapes such as flats, spheres (including hemispheres), cylinders, aspheres and even freeform optics, has been well documented. The recently developed MR Jet process provides additional benefits, particularly in the finishing the inside of steep concave domes and other irregular shapes. Combining these technologies with metrology techniques, such as the SSI, provides a solution for finishing current and future windows and domes. Recent exciting developments in the finishing of such shapes with these technologies will be presented. These include new advances such as the ability to use the SSI to characterize a range of shapes such as domes and aspheres, as well as progress in using MRF and MR Jet for finishing conventional and conformal windows and domes.

  7. 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.

  8. Optimizing parameters for magnetorheological finishing supersmooth surface

    NASA Astrophysics Data System (ADS)

    Cheng, Haobo; Feng, Zhijing; Wang, Yingwei

    2005-02-01

    This paper presents a reasonable approach to this issue, i.e., computer controlled magnetorheological finishing (MRF). In MRF, magnetically stiffened magnetorheological (MR) abrasive fluid flows through a preset converging gap that is formed by a workpiece surface and a moving rigid wall, to create precise material removal and polishing. Tsinghua University recently completed a project with MRF technology, in which a 66 mm diameter, f/5 parabolic mirror was polished to the shape accuracy of λ/17 RMS (λ=632.8nm) and the surface roughness of 1.22 nm Ra. This was done on a home made novel aspheric computer controlled manufacturing system. It is a three-axis, self-rotating wheel machine, the polishing tool is driven with one motor through a belt. This paper presents the manufacturing and testing processes, including establish the mathematics model of MRF optics on the basis of Preston equation, profiler test and relative coefficients, i.e., pressure between workpiece and tool, velocity of MR fluid in polishing spot, tolerance control of geometrical parameters such as radius of curvature and conic constant also been analyzed in the paper. Experiments were carried out on the features of MRF. The results indicated that the required convergent speed, surface roughness could be achieved with high efficiency.

  9. Protein requirements of finishing paca (Cuniculus paca).

    PubMed

    Nogueira-Filho, Sérgio Luiz Gama; Bastos, Ivanise da Hora; Mendes, Alcester; Nogueira, Selene Siqueira da Cunha

    2016-06-01

    We conducted a nitrogen balance digestion trial to determine the crude protein requirements of paca (Cuniculus paca) during the last growth phase. In a 4 × 4 Latin square design, four young captive male pacas, aged 5 months, were fed four isoenergetic diets containing four different levels of nitrogen (N) (11.3, 16.6, 21.4, and 26.6 g N/kg of dry matter). After 15 days of adaptation, we collected all feces and urine for five consecutive days. By regression analysis between N intake and N in feces and urine, the metabolic fecal nitrogen (MFN = 4.2 g/kg of dry matter intake) and daily endogenous urinary N (EUN = 91.6 mg/kg(0.75)) were determined. Likewise, by regression analyses between nitrogen intake and nitrogen retention [NR = N intake-(fecal N + urine N)], we estimated the daily requirement of 280.5 mg N/kg(0.75). Therefore, a minimum of 55 g crude protein per kilogram dry matter and 13 MJ/kg of digestible energy are required by finishing paca on unrestricted diets. Such values are similar to those of other wild frugivores and below those of growing rabbits. The data confirm that farmers overfeed protein, and similar growth can be more economically achieved on lower protein diets. PMID:27026234

  10. Shear Stress in Magnetorheological FInishing for Glasses

    SciTech Connect

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

    2009-04-28

    We report in situ, simultaneous measurements of both drag and normal forces in magnetorheological finishing (MRF) for what is believed to be the first time, using a spot taking machine (STM) as a test bed to take MRF spots on stationary parts. The measurements are carried out over the entire area where material is being removed, i.e., the projected area of the MRF removal function/spot on the part surface, using a dual force sensor. This approach experimentally addresses the mechanisms governing material removal in MRF for optical glasses in terms of the hydrodynamic pressure and shear stress, applied by the hydrodynamic flow of magnetorheological fluid at the gap between the part surface and the STM wheel. This work demonstrates that the volumetric removal rate shows a positive linear dependence on shear stress. Shear stress exhibits a positive linear dependence on a material figure of merit that depends upon Young’s modulus, fracture toughness, and hardness. A modified Preston’s equation is proposed that better estimates MRF material removal rate for optical glasses by incorporating mechanical properties, shear stress, and velocity.

  11. Shear stress in magnetorheological finishing for glasses.

    PubMed

    Miao, Chunlin; Shafrir, Shai N; Lambropoulos, John C; Mici, Joni; Jacobs, Stephen D

    2009-05-01

    We report in situ, simultaneous measurements of both drag and normal forces in magnetorheological finishing (MRF) for what is believed to be the first time, using a spot taking machine (STM) as a test bed to take MRF spots on stationary parts. The measurements are carried out over the entire area where material is being removed, i.e., the projected area of the MRF removal function/spot on the part surface, using a dual force sensor. This approach experimentally addresses the mechanisms governing material removal in MRF for optical glasses in terms of the hydrodynamic pressure and shear stress, applied by the hydrodynamic flow of magnetorheological fluid at the gap between the part surface and the STM wheel. This work demonstrates that the volumetric removal rate shows a positive linear dependence on shear stress. Shear stress exhibits a positive linear dependence on a material figure of merit that depends upon Young's modulus, fracture toughness, and hardness. A modified Preston's equation is proposed that better estimates MRF material removal rate for optical glasses by incorporating mechanical properties, shear stress, and velocity. PMID:19412219

  12. [Drag-out in metal finishing industries].

    PubMed

    Laforest, V; Piatyszek, E; Mojaat, W; Bourgois, J

    2005-10-01

    Currently, environmental regulations induce industrialists to implement source reduction techniques in order to comply with the prevention principle toward sustainable development. The project PIPSI (PIlotage Propre des Systèmes Industriels/industrial system dean piloting) financing by Rhone-Alps Region is carried out with the aim to contribute to this objective. The study presented in this article concerns the pollution transfer in a metal finishing treatment line in order to minimise the environmental impact obtained notably with the pollution balance. Drag-out and draining phenomena have been particularly studied. Results obtained showed that a 10 seconds of draining reduced drag-out from 65 to 85% in terms of pieces design. Moreover, during the experiments, 5 drag-out levels were identified by medium values from 26 to 1700 ml m(-2). So that, either a piece can be associated to a level or knowing the piece drag-out level, it is possible to evaluate its medium drag-out value. Then the pollution balance will be obtained more easily. PMID:16342539

  13. Automatic tool path generation for finish machining

    SciTech Connect

    Kwok, Kwan S.; Loucks, C.S.; Driessen, B.J.

    1997-03-01

    A system for automatic tool path generation was developed at Sandia National Laboratories for finish machining operations. The system consists of a commercially available 5-axis milling machine controlled by Sandia developed software. This system was used to remove overspray on cast turbine blades. A laser-based, structured-light sensor, mounted on a tool holder, is used to collect 3D data points around the surface of the turbine blade. Using the digitized model of the blade, a tool path is generated which will drive a 0.375 inch diameter CBN grinding pin around the tip of the blade. A fuzzified digital filter was developed to properly eliminate false sensor readings caused by burrs, holes and overspray. The digital filter was found to successfully generate the correct tool path for a blade with intentionally scanned holes and defects. The fuzzified filter improved the computation efficiency by a factor of 25. For application to general parts, an adaptive scanning algorithm was developed and presented with simulation results. A right pyramid and an ellipsoid were scanned successfully with the adaptive algorithm.

  14. 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.

  15. 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.

  16. 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...

  17. 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...

  18. 40 CFR 425.90 - Applicability; description of the retan-wet finish-splits subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

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

  19. 40 CFR 425.90 - Applicability; description of the retan-wet finish-splits subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

  20. 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.

  1. 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. PMID:21417413

  2. TREATMENT OF METAL FINISHING WASTES BY SULFIDE PRECIPITATION

    EPA Science Inventory

    This project involved precipitating heavy metals normally present in metal finishing wastewaters by a novel process which employs ferrous sulfide addition (Sulfex), as well as by conventional treatment using calcium hydroxide for comparison purposes. These studies consisted of la...

  3. Large planer for finishing smooth, flat surfaces of large pieces ...

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

    Large planer for finishing smooth, flat surfaces of large pieces of metal; in operating condition and used for public demonstrations. - Thomas A. Edison Laboratories, Building No. 5, Main Street & Lakeside Avenue, West Orange, Essex County, NJ

  4. 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

  5. 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

  6. 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...

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

    ScienceCinema

    Muzny, Donna [Baylor College of Medicine

    2013-03-22

    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.

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

    ScienceCinema

    FitzGerald, Michael [Broad Institute

    2013-02-12

    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.

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

    ScienceCinema

    Lane, Todd [SNL

    2013-02-11

    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.

  10. 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.

  11. 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.

  12. 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

  13. Comparative Evaluation of the Efficiency of Four Ceramic Finishing Systems

    PubMed Central

    Aravind, Prasad; Razak, P Abdul; Francis, P G; Issac, Johnson K; Shanoj, R P; Sasikumar, T P

    2013-01-01

    Aim: To compare the effect of four different finishing systems and diamond paste on ceramic roughness with the objectives of evaluating the roughness of ceramic surface of prepared specimens after abrasion, finishing and polishing. Materials & Methods: A total of 50 test specimens were fabricated in the form of discs of diameter 13mm and 0.6mm thickness. Test specimens were then randomly distributed into five groups of 10 and coded. All the test specimens were then abraded with 125μm diamond in unidirectional motion to create surface roughness that will simulate occlusal or incisal correction. The values were recorded and the specimens were then finished using the various finishing systems. multiple range tests by Duncan's procedure. One way Anova was used to calculate the p-value Results:After fini shing, the Ra,Rq,Rz and Rt values showed a tendency to decline to levels much inferior to the values obtained after the preparation of the specimens. Ra values of group III specimens were slightly higher and the increase was significant. The highest Rt value [5.29] obtained after polishing is below the lowest roughness values [7.42] obtained after finishing the specimens. Conclusions: Finishing and polishing procedures have a significant role in reducing the roughness of ceramics.Following abrasion with diamond point to simulate clinical adjustment the roughness values doubled when compared to the initial reading.Ra, Rq,Rz and Rt values suggest that Sof lex is the most efficient of all the systems tested followed by auto glazing.After the final diamond paste polishing, sof lex group specimens showed the best finish and auto glazed specimens showed a value almost as equal to the so flex group. How to cite this article: Aravind P, Razak PA, Francis PG, Issac JK, Shanoj RP, Sasikumar TP. Comparative Evaluation of the Efficiency of Four Ceramics Finishing Systems. J Int Oral Health 2013; 5(5):59-64. PMID:24324306

  14. Prevalence of clinical signs of disease in Danish finisher pigs.

    PubMed

    Petersen, H H; Nielsen, E O; Hassing, A-G; Ersbøll, A K; Nielsen, J P

    2008-03-22

    Between December 1999 and February 2001, two visits, eight weeks apart, were made to 90 herds of Danish finisher pigs. The prevalence of clinical signs was recorded by three veterinary technicians from the Danish Bacon and Meat Council according to a standardised procedure; they had been trained and their observations were monitored and validated before and during the study. A total of 154,347 finisher pigs were examined and 22,136 clinical signs were recorded. Vices accounted for 43 per cent of the signs. The highest mean prevalence was observed for ear necrosis (4.44 per cent), followed by respiratory signs (2.17 per cent), lameness (1.92 per cent), other skin diseases (1.73 per cent), tail bites (1.26 per cent), umbilical hernia (0.78 per cent), flank bites (0.52 per cent), diarrhoea (0.27 per cent), respiratory distress (0.12 per cent), atrophic rhinitis (0.10 per cent), recumbency (0.09 per cent) and central nervous disease (0.05 per cent). The prevalence of atrophic rhinitis was higher in conventional herds than in specific pathogen-free herds. The prevalence of clinical signs of atrophic rhinitis was higher among finishers weighing 51 to 75 kg than among finishers weighing up to 50 kg, and the prevalence of respiratory signs was higher among finishers weighing 51 to 75 kg then among finishers weighing 76 to 100 kg. PMID:18359931

  15. 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.

  16. 40 CFR 463.30 - Applicability; description of the finishing water subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... finishing water subcategory. 463.30 Section 463.30 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Finishing Water Subcategory § 463.30 Applicability; description of the finishing water subcategory. This subpart applies to discharges of pollutants from processes in the finishing water subcategory to waters...

  17. Deterministic precision finishing of domes and conformal optics

    NASA Astrophysics Data System (ADS)

    Shorey, Aric; Kordonski, William; Tricard, Marc

    2005-05-01

    In order to enhance missile performance, future window and dome designs will incorporate shapes with improved aerodynamic performance compared with the more traditional flats and spheres. Due to their constantly changing curvature and steep slopes, these shapes are incompatible with most conventional polishing and metrology solutions. Two types of a novel polishing technology, Magnetorheological Finishing (MRF®) and Magnetorheological (MR) Jet, could enable cost-effective manufacturing of free-form optical surfaces. MRF, a deterministic sub-aperture magnetically assisted polishing method, has been developed to overcome many of the fundamental limitations of traditional finishing. MRF has demonstrated the ability to produce complex optical surfaces with accuracies better than 30 nm peak-to-valley (PV) and surface micro-roughness less than 1 nm rms on a wide variety of optical glasses, single crystals, and glass-ceramics. The polishing tool in MRF perfectly conforms to the optical surface making it well suited for finishing this class of optics. A newly developed magnetically assisted finishing method MR JetTM, addresses the challenge of finishing the inside of steep concave domes and other irregular shapes. An applied magnetic field coupled with the properties of the MR fluid allow for stable removal rate with stand-off distances of tens of centimeters. Surface figure and roughness values similar to traditional MRF have been demonstrated. Combining these technologies with metrology techniques, such as Sub-aperture Stitching Interferometer (SSI®) and Asphere Stitching Interferometer (ASI®), enable higher precision finishing of the windows and domes today, as well as the finishing of future conformal designs.

  18. 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

  19. 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

  20. NNLOPS accurate associated HW production

    NASA Astrophysics Data System (ADS)

    Astill, William; Bizon, Wojciech; Re, Emanuele; Zanderighi, Giulia

    2016-06-01

    We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross section Working Group.

  1. Decoding the human genome sequence.

    PubMed

    Bentley, D R

    2000-10-01

    The year 2000 is marked by the production of the sequence of the human genome. A 'working draft' of high quality sequence covering 90% of the genome has been determined and a quarter is in finished form, including the first two completed chromosomes. All sequence data from the project is made freely available to the community via the Internet, for further analysis and exploitation. The challenge which lies ahead is to decipher the information. Knowledge of the human genome sequence will enable us to understand how the genetic information determines the development, structure and function of the human body. We will be able to explore how variations within our DNA sequence cause disease, how they affect our interaction with our environment and ultimately to develop new and effective ways to improve human health. PMID:11005789

  2. How to accurately bypass damage

    PubMed Central

    Broyde, Suse; Patel, Dinshaw J.

    2016-01-01

    Ultraviolet radiation can cause cancer through DNA damage — specifically, by linking adjacent thymine bases. Crystal structures show how the enzyme DNA polymerase η accurately bypasses such lesions, offering protection. PMID:20577203

  3. Accurate Evaluation of Quantum Integrals

    NASA Technical Reports Server (NTRS)

    Galant, David C.; Goorvitch, D.

    1994-01-01

    Combining an appropriate finite difference method with Richardson's extrapolation results in a simple, highly accurate numerical method for solving a Schr\\"{o}dinger'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.

  4. Magnetorheological finishing (MRF) in commercial precision optics manufacturing

    NASA Astrophysics Data System (ADS)

    Golini, Donald; Kordonski, William I.; Dumas, Paul; Hogan, Stephen J.

    1999-11-01

    Finish polishing of highly precise optical surfaces is one of the most promising uses of magnetic fluids. We have taken the concept of magnetorheological finishing (MRF) from the laboratory to the optical fabrication shop floor. A commercial, computer numerically controlled (CNC) MRF machine, the Q22, has recently come on-line in optics companies to produce precision flat, spherical and aspheric optical components. MRF is a sub-aperture lap process that requires no specialized tooling, because the magnetically-stiffened abrasive fluid conforms to the local curvature of any arbitrarily shaped workpiece. MRF eliminates subsurface damage, smoothes rms microroughness to less than 1 nm, and corrects p-v surface figure errors to (lambda) /20 in minutes. Here the basic details of the MRF process are reviewed. MR fluid performance for soft and hard materials, the removal of asymmetric grinding errors and diamond turning marks, and examples of batch finishing of glass aspheres are also described.

  5. 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

    2016-06-01

    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.

  6. Analytical methods for the characterization of surface finishing in bricks.

    PubMed

    Nardini, I; Zendri, E; Biscontin, G; Brunetin, A

    2006-09-01

    The recent restoration works of Santo Stefano Church Façade (XV century) in Venice have shown traces variously saved of different kind of surface finishes. These finishes were found on the brick's surface both in the masonry and in the decorative elements. Different brick's surface and decorative tile samples were investigated using several techniques: optical microscopy, scanning electron-microscopy, thermal analysis, infrared spectroscopy and reflectance Fourier transform infrared microspectroscopy. The evaluation of the reached results was used to understand the decorative techniques and to recognize the material employed. PMID:17723684

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

    SciTech Connect

    Green, Eric

    2009-05-27

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

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

    SciTech Connect

    Green, Eric

    2009-05-27

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

  9. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  11. 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.

  12. 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...

  13. Introduction to Concrete Finishing. Instructor Edition. Introduction to Construction Series.

    ERIC Educational Resources Information Center

    Oklahoma State Dept. of Vocational and Technical Education, Stillwater. Curriculum and Instructional Materials Center.

    This instructor's guide contains the materials required to teach a competency-based introductory course in concrete finishing to students who have chosen to explore careers in construction. The following topics are covered in the course's three instructional units: concrete materials, concrete tools, and applied skills. Each unit contains some or…

  14. 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…

  15. Machine finishes balls to high degree of roundness

    NASA Technical Reports Server (NTRS)

    Angele, W.; Hill, J. P., Jr.

    1972-01-01

    Machine was developed to finish ball to roundness within 12.5 nm (half a microinch) from any types of hard material. Grinding and polishing to this tolerance is accomplished by lapping elements on four to six motor-driven spindles. Spindles are adjustably spring-loaded to ensure constant contact pressure on ball and are driven by variable speed electric motors.

  16. 71. September 1913 "No. 113. Some of the finished bitulithic ...

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

    71. September 1913 "No. 113. Some of the finished bitulithic or bituminous macadam road after being sanded and rolled, in the foreground. In the middle distance men are applying oil to incomplete section. In the far distance, roller is working on foundation course." - Crater Lake National Park Roads, Klamath Falls, Klamath County, OR

  17. 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...

  18. 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,…

  19. 1. The finished hull of a 180 is launched in ...

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

    1. The finished hull of a 180 is launched in Duluth, Minnesota. Note the men holding onto the rail and riding the vessel during its launch. - U.S. Coast Guard Buoy Tenders, 180' Class, U.S. Coast Guard Headquarters, 2100 Second Street Southwest, Washington, District of Columbia, DC

  20. 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…

  1. TREATMENT OF METAL FINISHING WASTES BY USE OF FERROUS SULFIDE

    EPA Science Inventory

    This demonstration was performed to study the operation, performance and economics of a new sulfide precipitation process ('Sulfex'TN), for treating metal finishing wastewaters. The study was performed by Holley Carburetor Division of Colt Industries, with assistance from the Per...

  2. 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...

  3. DEVELOPMENT OF THE METAL FINISHING FACILITY RISK SCREENING TOOL (MFFRST)

    EPA Science Inventory

    Recently the US EPA completed the development of the first version of the Metal Finishing Facility Risk Screening Tool (MFFRST) and has made this product available to the general public. MFFRST calculates the air emissions from a metal plating line and determines the risk to bot...

  4. 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 ever of…

  5. SOURCE ASSESSMENT: COTTON AND SYNTHETIC WOVEN FABRIC FINISHING

    EPA Science Inventory

    The report gives reliable data to enable EPA to determine the need for developing control technology for air and water pollution emissions from cotton and synthetic woven fabric finishing plants. The data supplements that in an earlier state-of-the-art report on the same subject ...

  6. 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…

  7. 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...

  8. 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 ...

  9. LEATHER TANNING AND FINISHING WASTE MANAGEMENT RESEARCH AND DEVELOPMENT PROGRAM

    EPA Science Inventory

    Reviewed herein is the waste management research and development program for the leather tanning and finishing industry. Emphasis is placed on the Environmental Protection Agency's (EPA) role, both past and present, and major developments over the past few years outside EPA, incl...

  10. EFFECT OF VENTILATION ON EMISSION RATES OF WOOD FINISHING MATERIALS

    EPA Science Inventory

    The paper gives results from EPA studies on the effect of ventilation (air changes per hour) and material loading on the emission rate for selected organics and total measured organics from three wood finishing materials (stain, polyurethane, and wax). The data are analyzed to sh...

  11. Manipulating Mechanics and Chemistry in Precision Optics Finishing

    SciTech Connect

    Jacobs, S.D.

    2007-05-30

    Deterministic processing is critical to modern precision optics finishing. Put simply, determinism is the ability to predict an outcome before carrying out an activity. With the availability of computer numerically controlled (CNC) equipment and sophisticated software algorithms, it is now possible to grind and polish optics from a variety of materials to surface shape accuracies of ~20 nm peak-to-valley (p-v), with surface roughness values (measured on white light interferometers over 250 um x 350 um areas) to sub-nm root-mean-square (rms) levels. In the grinding phase the capability now exists to estimate removal rates, surface roughness, and the depth of subsurface damage (SSD) for a previously unprocessed material, knowing its Young's modulus, hardness, and fracture toughness. An understanding of how chemistry aids in the abrasive-driven removal of material from the surface during polishing is also critical, Recent polishing process research reveals the importance of chemistry, specifically slurry pH, for preventing particle agglomeration in order to achieve smooth surface finishes with conventional pad or pitch laps. New sub-aperture polishing processes like magnetorheoogical finishing (MRF) can smooth and shape flat, spherical, aspheric and free-form surfaces within a few process iterations. Difficult to finish optical materials like soft polymer polymethyl methacrylate, microstructured polycrystalline zinc sulfide, and water soluble single-crystal potassium dihydrogen phosphate (KDP) can be finished with MRF. The key is the systematic alteration of MR fluid chemistry and mechanics (i.e. the abrasive) to match the unique physical properties of each workpiece.

  12. Improvement of figure and finish of diamond turned surfaces with magneto-rheological finishing (MRF)

    NASA Astrophysics Data System (ADS)

    Dumas, Paul; Golini, Don; Tricard, Marc

    2005-05-01

    Single Point Diamond Turning (SPDT) has been a cost effective technique to achieve the required figure and roughness specification on a wide range of infrared (IR) optics. SPDT is one of the few technologies that can efficiently generate aspherical surfaces, and as recent developments such as fast-tool servos mature, "free-form" surfaces are becoming feasible as well. Optical end-user requirements for a wide range of industries are continuing to tighten, driven, for example by multi-spectral systems that require good performance at shorter wavelengths in addition to IR. In many cases, specified shape tolerances can exceed SPDT capabilities. Additionally, SPDT typically leaves "turning marks" (affecting micro-roughness) that can be detrimental to performance. In some cases, surface integrity (e.g. sub-surface damage) can also be of concern. Magneto-Rheological Finishing (MRF®) has the proven ability to simultaneously improve roughness, figure, and surface integrity in a fast and cost effective manner. MRF is a deterministic, sub-aperture polishing technology, and is typically employed as the last manufacturing step. MRF can deterministically remove from tens of nanometers to microns worth of material, while efficiently "converging" to the specified requirements. Conversely, SPDT has proven to be very effective in removing the hundreds of microns (if not mm) sometimes required to "pre-shape" an aspheric surface before its final polish. After a brief introduction of MRF, this paper will discuss how SPDT and MRF processes can complement one another very effectively. Examples of MRF results on a wide range of IR materials will be presented.

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

    PubMed

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

    2016-05-01

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

  14. 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 ...

  15. 40 CFR 63.5390 - How do I measure the HAP content of a finish?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... determine the HAP content of a finish, the reference method is EPA Method 311 of appendix A of 40 CFR part... (CONTINUED) National Emission Standards for Hazardous Air Pollutants for Leather Finishing Operations...

  16. 40 CFR 63.5390 - How do I measure the HAP content of a finish?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... the HAP content of a finish, the reference method is EPA Method 311 of appendix A of 40 CFR part 63... National Emission Standards for Hazardous Air Pollutants for Leather Finishing Operations Testing...

  17. 40 CFR 63.5390 - How do I measure the HAP content of a finish?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... determine the HAP content of a finish, the reference method is EPA Method 311 of appendix A of 40 CFR part... (CONTINUED) National Emission Standards for Hazardous Air Pollutants for Leather Finishing Operations...

  18. 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.

  19. 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...

  20. 21 CFR 820.80 - Receiving, in-process, and finished device acceptance.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Receiving, in-process, and finished device...-process, and finished device acceptance. (a) General. Each manufacturer shall establish and maintain... acceptance activities. Each manufacturer shall establish and maintain procedures for finished...

  1. 40 CFR 425.40 - Applicability; description of the retan-wet finish-sides subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 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 SOURCE CATEGORY Retan-Wet Finish-Sides Subcategory § 425.40 Applicability; description of the retan-wet...

  2. 40 CFR 63.1347 - Standards for raw and finish mills.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

  3. 40 CFR 429.130 - Applicability; description of the finishing subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... finishing subcategory. 429.130 Section 429.130 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TIMBER PRODUCTS PROCESSING POINT SOURCE CATEGORY Finishing Subcategory § 429.130 Applicability; description of the finishing subcategory. This subpart applies...

  4. 7 CFR 58.344 - Storage of finished product in freezer.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Storage of finished product in freezer. 58.344 Section... Service 1 Operations and Operating Procedures § 58.344 Storage of finished product in freezer. (a) Sharp..., if necessary, at a later time. Requirements for Finished Products Bearing USDA...

  5. 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... Commandant. (b) Bulkheads, linings and ceilings may be covered by a combustible interior finish provided...

  6. EFFECTS OF FORAGE SPECIES ON RIB COMPOSITION, COLOR, AND PALATABILITY IN FORAGE-FINISHED BEEF

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Forty-seven Angus-crossbred steers were used to evaluate the effects of forage species grazed in the last 41 d of the finishing period on rib composition, color, and palatability in forage-finished beef and compared to traditional high concentrate finished. Steers grazed naturalized pastures (bluegr...

  7. 40 CFR 141.511 - What is required of new finished water reservoirs?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... reservoirs? 141.511 Section 141.511 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... Disinfection-Systems Serving Fewer Than 10,000 People Finished Water Reservoirs § 141.511 What is required of new finished water reservoirs? If your system begins construction of a finished water reservoir on...

  8. 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... Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Finished Water Reservoirs § 141.510 Is my system subject to the new finished water reservoir requirements? All subpart H systems which...

  9. 40 CFR 141.511 - What is required of new finished water reservoirs?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... reservoirs? 141.511 Section 141.511 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... Disinfection-Systems Serving Fewer Than 10,000 People Finished Water Reservoirs § 141.511 What is required of new finished water reservoirs? If your system begins construction of a finished water reservoir on...

  10. 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... Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Finished Water Reservoirs § 141.510 Is my system subject to the new finished water reservoir requirements? All subpart H systems which...

  11. 40 CFR 141.511 - What is required of new finished water reservoirs?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... reservoirs? 141.511 Section 141.511 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... Disinfection-Systems Serving Fewer Than 10,000 People Finished Water Reservoirs § 141.511 What is required of new finished water reservoirs? If your system begins construction of a finished water reservoir on...

  12. 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... Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Finished Water Reservoirs § 141.510 Is my system subject to the new finished water reservoir requirements? All subpart H systems which...

  13. THE EFFECTS OF RACTOPAMINE ON BEHAVIOR AND PHYSIOLOGY OF FINISHING PIGS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study aimed to examine the effects of ractopamine (RAC) on behavior and physiology of pigs during handling and transport. Twenty-four groups of 3 finishing pigs were randomly assigned to one of two treatments, four weeks prior to slaughter; 1) finishing feed plus RAC (9ppm), 2) finishing feed a...

  14. Influence of Finishing/Polishing Procedures on the Surface Texture of Two Resin Composites

    PubMed Central

    Kameyama, Atsushi; Nakazawa, Taeko; Haruyama, Akiko; Haruyama, Chikahiro; Hosaka, Makoto; Hirai, Yoshito

    2008-01-01

    This study compared surface roughness and gloss produced by different finishing/polishing procedures for two resin composites, Clearfil AP-X (AP-X) and Estelite Σ (ES). A total of 70 composite discs (n=35 for each resin composite) were prepared and divided at random into seven finishing/polishing groups (n=5): glass-pressed control; using a super-fine-grit diamond bur (SF); using CompoMaster (CM) after SF-finishing (SF+CM); using White Point (WP) after SF-finishing (SF+WP); using CM after SF+WP-finishing (SF+WP+CM); using Stainbuster (SB) after SF-finishing (SF+SB); and using CM after SF+SB-finishing (SF+SB+CM). After the finishing/polishing procedures, average surface roughness (Ra) and surface gloss (Gs(60°)) of all specimens were assessed with a surface profilometer and specimen gloss meter, respectively. Glass-pressed controls for both AP-X and ES composites showed the best surface finish in terms of both Ra and Gs(60°). SF-finishing produced the roughest surface and led to almost complete loss of gloss. While additional polishing with CM reduced Ra and increased Gs(60°), the additional finishing effect of WP or SB between SF-finishing and CM-polishing was not found for either AP-X or ES. PMID:19088883

  15. 40 CFR 410.50 - Applicability; description of the knit fabric finishing subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... fabric finishing subcategory. 410.50 Section 410.50 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Knit Fabric Finishing Subcategory § 410.50 Applicability; description of the knit fabric finishing subcategory....

  16. 40 CFR 410.40 - Applicability; description of the woven fabric finishing subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... fabric finishing subcategory. 410.40 Section 410.40 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Woven Fabric Finishing Subcategory § 410.40 Applicability; description of the woven fabric finishing subcategory....

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

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 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. Substances classified as drying oils, when migrating from food-packaging material (as components of finished...

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

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 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. Substances classified as drying oils, when migrating from food-packaging material (as components of finished...

  19. 21 CFR 820.80 - Receiving, in-process, and finished device acceptance.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Receiving, in-process, and finished device...-process, and finished device acceptance. (a) General. Each manufacturer shall establish and maintain... acceptance activities. Each manufacturer shall establish and maintain procedures for finished...

  20. 21 CFR 820.80 - Receiving, in-process, and finished device acceptance.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Receiving, in-process, and finished device...-process, and finished device acceptance. (a) General. Each manufacturer shall establish and maintain... acceptance activities. Each manufacturer shall establish and maintain procedures for finished...

  1. 21 CFR 820.80 - Receiving, in-process, and finished device acceptance.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Receiving, in-process, and finished device...-process, and finished device acceptance. (a) General. Each manufacturer shall establish and maintain... acceptance activities. Each manufacturer shall establish and maintain procedures for finished...

  2. 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... SOURCE CATEGORY Coating or Finishing of Asbestos Textiles Subcategory § 427.80 Applicability; description of the coating or finishing of asbestos textiles subcategory. The provisions of this subpart...

  3. Painting and Finishing in the Home; Construction 7-9--Prevocational: 5846.07.

    ERIC Educational Resources Information Center

    Dade County Public Schools, Miami, FL.

    The beginning course provides students with the various techniques and supplies necessary for finishing and refinishing in the home and for home furnishings. Course content includes goals, specific objectives, orientation, selecting tools, equipment, finishes, finishing problems, and maintenance and safety. Also incorporated are consumer…

  4. 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…

  5. Laser-assisted pre-finishing of optical ceramic materials

    NASA Astrophysics Data System (ADS)

    Rozzi, Jay C.; Clavier, Odile H.; Barton, Michael D.

    2007-04-01

    At Creare, we are developing a laser-assisted, pre-finishing system that enables the single-point diamond turning of super-hard ceramics into hemispheres, ogives, and other shapes that are ready for final optical finishing. Currently, super-hard ceramic materials cannot be affordably processed due to the low material removal rates and the high amount of sub-surface damage associated with current processes. Our innovation uses a low-power, far-infrared laser to heat, but not ablate, a thin layer of material prior to its removal. By heating the ceramic material, plastic-like deformation at the cutting edge is fostered by high-temperature dislocation motion. In doing so, the cutting forces are reduced which enables attendant reductions in tool wear, surface and sub-surface damage, and processing time. Our paper will summarize the development of our innovation, describe the process, discuss the machine tool, and review the latest results.

  6. 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

  7. Method and system for processing optical elements using magnetorheological finishing

    DOEpatents

    Menapace, Joseph Arthur; Schaffers, Kathleen Irene; Bayramian, Andrew James; Molander, William A

    2012-09-18

    A method of finishing an optical element includes mounting the optical element in an optical mount having a plurality of fiducials overlapping with the optical element and obtaining a first metrology map for the optical element and the plurality of fiducials. The method also includes obtaining a second metrology map for the optical element without the plurality of fiducials, forming a difference map between the first metrology map and the second metrology map, and aligning the first metrology map and the second metrology map. The method further includes placing mathematical fiducials onto the second metrology map using the difference map to form a third metrology map and associating the third metrology map to the optical element. Moreover, the method includes mounting the optical element in the fixture in an MRF tool, positioning the optical element in the fixture; removing the plurality of fiducials, and finishing the optical element.

  8. 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. PMID:26882113

  9. Sensory quality of beef from different finishing diets.

    PubMed

    Resconi, V C; Campo, M M; Font i Furnols, M; Montossi, F; Sañudo, C

    2010-11-01

    Beef production under different local husbandry systems might have meat sensory quality implications for the marketing of these products abroad. In order to assess the effect of finishing diet systems on beef quality, a trained sensory taste panel assessed meat aged for 20 days from 80 Uruguayan Hereford steers that were finished on one of the following diets: T1=Pasture [4% of animal live weight (LW)], T2=Pasture [3% LW plus concentrate (0.6% LW)], T3=Pasture [3% LW plus concentrate (1.2% LW)], or T4=Concentrate plus hay ad libitum. Beef odour and flavour intensities decreased with an increase in the energy content of the diet. The meat from T2 had the lowest acid flavour and strange odours intensities. In general, steers fed only concentrate plus hay (T4) produced meat that had an inferior sensory quality because they had more pronounced off-flavours and was tougher. PMID:20696533

  10. 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).

  11. Predicting the molecular complexity of sequencing libraries.

    PubMed

    Daley, Timothy; Smith, Andrew D

    2013-04-01

    Predicting the molecular complexity of a genomic sequencing library is a critical but difficult problem in modern sequencing applications. Methods to determine how deeply to sequence to achieve complete coverage or to predict the benefits of additional sequencing are lacking. We introduce an empirical bayesian method to accurately characterize the molecular complexity of a DNA sample for almost any sequencing application on the basis of limited preliminary sequencing. PMID:23435259

  12. 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.

  13. Finishes and furnishings: considerations for critical care environments.

    PubMed

    Chambers, Misty; Bowman, Ken L

    2011-01-01

    When selecting finishes and furnishings within a critical care unit, multiple factors can ultimately affect patient outcomes, impact costs, and contribute to operational efficiencies. First, consider the culture of the regional location, operations of the specific facility, and the recent focus on patient-centered care. The intention is to create an appropriate familiarity and comfort level with the environment for the patient and family. Second, safety and infection control are of utmost concern, particularly for the critical care patient with limited mobility. The planning and design team must be acutely aware of the regulations and guidelines of various governing agencies, local codes, and best design practices that can directly affect choices of finishes and furnishings. Flooring, wall, and window finishes, lighting, art and color, as well as furniture and fabric selection should be considered. Issues to address include maintenance, durability, sustainability, infection control, aesthetics, safety, wayfinding, and acoustics. Balancing these issues with comfort, patient and staff satisfaction, accommodations for an aging population, increasing bariatric needs, efficient operations, and avoidance of "never events" requires team collaboration and communication, knowledge of product advancements, a keen awareness of how environmental stimuli are perceived, and utilization of the best available evidence to make informed design decisions. PMID:21921717

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. Predict amine solution properties accurately

    SciTech Connect

    Cheng, S.; Meisen, A.; Chakma, A.

    1996-02-01

    Improved process design begins with using accurate physical property data. Especially in the preliminary design stage, physical property data such as density viscosity, thermal conductivity and specific heat can affect the overall performance of absorbers, heat exchangers, reboilers and pump. These properties can also influence temperature profiles in heat transfer equipment and thus control or affect the rate of amine breakdown. Aqueous-amine solution physical property data are available in graphical form. However, it is not convenient to use with computer-based calculations. Developed equations allow improved correlations of derived physical property estimates with published data. Expressions are given which can be used to estimate physical properties of methyldiethanolamine (MDEA), monoethanolamine (MEA) and diglycolamine (DGA) solutions.

  19. Accurate thickness measurement of graphene

    NASA Astrophysics Data System (ADS)

    Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.

    2016-03-01

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  20. A novel approach to sequence validating protein expression clones with automated decision making

    PubMed Central

    Taycher, Elena; Rolfs, Andreas; Hu, Yanhui; Zuo, Dongmei; Mohr, Stephanie E; Williamson, Janice; LaBaer, Joshua

    2007-01-01

    Background Whereas the molecular assembly of protein expression clones is readily automated and routinely accomplished in high throughput, sequence verification of these clones is still largely performed manually, an arduous and time consuming process. The ultimate goal of validation is to determine if a given plasmid clone matches its reference sequence sufficiently to be "acceptable" for use in protein expression experiments. Given the accelerating increase in availability of tens of thousands of unverified clones, there is a strong demand for rapid, efficient and accurate software that automates clone validation. Results We have developed an Automated Clone Evaluation (ACE) system – the first comprehensive, multi-platform, web-based plasmid sequence verification software package. ACE automates the clone verification process by defining each clone sequence as a list of multidimensional discrepancy objects, each describing a difference between the clone and its expected sequence including the resulting polypeptide consequences. To evaluate clones automatically, this list can be compared against user acceptance criteria that specify the allowable number of discrepancies of each type. This strategy allows users to re-evaluate the same set of clones against different acceptance criteria as needed for use in other experiments. ACE manages the entire sequence validation process including contig management, identifying and annotating discrepancies, determining if discrepancies correspond to polymorphisms and clone finishing. Designed to manage thousands of clones simultaneously, ACE maintains a relational database to store information about clones at various completion stages, project processing parameters and acceptance criteria. In a direct comparison, the automated analysis by ACE took less time and was more accurate than a manual analysis of a 93 gene clone set. Conclusion ACE was designed to facilitate high throughput clone sequence verification projects. The

  1. Noncontiguous finished genome sequence and description of Kallipyga gabonensis sp. nov.

    PubMed Central

    Mourembou, G.; Rathored, J.; Lekana-Douki, J.B.; Ndjoyi-Mbiguino, A.; Fenollar, F.; Michelle, C.; Fournier, P.-E.; Raoult, D.; Lagier, J.-C.

    2015-01-01

    Taxonogenomics coupled with culturomics promotes the isolation and characterization of bacteria. Kallipyga gabonensis sp. nov. strain GM4 is a strictly anaerobic, Gram-positive, and non motile coccus isolated from the stool of a Gabonese male teenager. The genome is 1,621,211 bp long with 50.01% G+C content and two scaffolds. Of the 1,536 predicted genes, 1,475 were protein-coding genes and 61 were RNA genes. A total of 931 genes were assigned a putative function, and 79 genes were identified as ORFans. PMID:26862430

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

    PubMed

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

    2016-03-01

    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

  3. 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

  4. 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...

  5. Noncontiguous finished genome sequence and description of Kallipyga gabonensis sp. nov.

    PubMed

    Mourembou, G; Rathored, J; Lekana-Douki, J B; Ndjoyi-Mbiguino, A; Fenollar, F; Michelle, C; Fournier, P-E; Raoult, D; Lagier, J-C

    2016-01-01

    Taxonogenomics coupled with culturomics promotes the isolation and characterization of bacteria. Kallipyga gabonensis sp. nov. strain GM4 is a strictly anaerobic, Gram-positive, and non motile coccus isolated from the stool of a Gabonese male teenager. The genome is 1,621,211 bp long with 50.01% G+C content and two scaffolds. Of the 1,536 predicted genes, 1,475 were protein-coding genes and 61 were RNA genes. A total of 931 genes were assigned a putative function, and 79 genes were identified as ORFans. PMID:26862430

  6. 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, ...

  7. Accurate ab Initio Spin Densities

    PubMed Central

    2012-01-01

    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]. PMID:22707921

  8. 40 CFR 63.5385 - How do I measure the quantity of finish applied to the leather?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... density, and volume of each applied finish. (b) Determine the mass of each applied finish with a scale... finishing operations must be weighed or have a predetermined weight. (c) Determine the density and volume of...: (1) Determine the density of each applied finish in pounds per gallon in accordance with §...

  9. 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...

  10. 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. PMID:26977814

  11. 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.

  12. 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

  13. STS-92 crew members finish emergency egress training

    NASA Technical Reports Server (NTRS)

    2000-01-01

    STS-92 Mission Specialists (left to right) Peter J.K. '''Jeff''' Wisoff, Leroy Chiao, Koichi Wakata of Japan and William S. McArthur Jr. finish emergency egress training in the slidewire baskets behind them. The training is part of Terminal Countdown Demonstration Test activities that also include a simulated countdown. STS-92 is scheduled to launch Oct. 5 at 9:38 p.m. EDT on the fifth flight to the International Space Station. It will carry two elements of the Space Station, the Integrated Truss Structure Z1 and the third Pressurized Mating Adapter. The mission is also the 100th flight in the Shuttle program.

  14. 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

  15. Radioactive solid waste handling at the Plutonium Finishing Plant

    SciTech Connect

    Manthos, E.J.

    1990-05-01

    The Plutonium Finishing Plant is located on the Hanford Site in the southeast section of Washington State. It has been in operation since 1949. The mission of the plant is to produce plutonium metal and related products for the US Department of Energy defense programs. Solid transuranic, low-level, and mixed wastes are generated at the plant, the radioactive contaminants in the waste being primarily alpha emitting. This paper discusses present waste-handling methods at the plant and recent changes that were made to improve waste characterization. 2 refs.

  16. 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.

  17. 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.

  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. Research on error control and compensation in magnetorheological finishing.

    PubMed

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

    2011-07-01

    Although magnetorheological finishing (MRF) is a deterministic finishing technology, the machining results always fall short of simulation precision in the actual process, and it cannot meet the precision requirements just through a single treatment but after several iterations. We investigate the reasons for this problem through simulations and experiments. Through controlling and compensating the chief errors in the manufacturing procedure, such as removal function calculation error, positioning error of the removal function, and dynamic performance limitation of the CNC machine, the residual error convergence ratio (ratio of figure error before and after processing) in a single process is obviously increased, and higher figure precision is achieved. Finally, an improved technical process is presented based on these researches, and the verification experiment is accomplished on the experimental device we developed. The part is a circular plane mirror of fused silica material, and the surface figure error is improved from the initial λ/5 [peak-to-valley (PV) λ=632.8 nm], λ/30 [root-mean-square (rms)] to the final λ/40 (PV), λ/330 (rms) just through one iteration in 4.4 min. Results show that a higher convergence ratio and processing precision can be obtained by adopting error control and compensation techniques in MRF. PMID:21743536

  20. Specification And Control Of Surface Finish: Empiricism Versus Dogmatism

    NASA Astrophysics Data System (ADS)

    Stout, K. J.; Obray, C.; Jungles, J.

    1985-06-01

    This paper reviews the development of the analysis of surface finish from the early attempts in the 1930s to the present day. The development of parameters used in surface analysis is shown in context with the instrumental techniques available at the time, and it is argued that characterization based on graphical and experimental convenience has influenced industrial practice. As the requirements of manufacture and functional performance have been stretched by advancing technology, many industrialists have been forced to accept the fact that existing specification practices are limited and have sought alternative descriptions based on well-established techniques; but these techniques themselves are limited, their suitability to in-process measurement being practically nonexistent. It is shown that attempts have been made recently to develop optical methods of assessing surface finish using traditional parameters such as Ra. This paper suggests that it may be time to look toward a new form of specification that is more suited to assessment by optical transducers, and some methods of assessment are proposed. To support this view, a simple low-cost device is discussed that can be calibrated to give Ra but that also presents information in a more relevant empirical way that may be more valid than the existing parameter specification.

  1. Antimicrobial finish of textiles by chitosan UV-curing.

    PubMed

    Ferrero, Franco; Periolatto, Monica

    2012-06-01

    The purpose of this research work was to develop a textile finish based on the radical UV-curing of chitosan on textiles to confer antimicrobial properties. Chitosan is a biopolymer with unique properties such as biodegradability, non-toxicity, antimicrobial activity. In this work cotton or silk fabrics and synthetic filter fabrics were impregnated with an acid solution of chitosan added of the photoinitiator in the proper amount and cured at room temperature by exposure to UV lamp. Process conditions such as percentage add-on, dilution, chitosan-fabric contact time, irradiation time and power, were optimized. The antimicrobial activity of finished fabrics was tested according to ASTM E 2149-01 standard test performed with Escherichia Coli ATCC 8739. Moreover dyeing test with Turquoise Telon dye were carried out to evaluate the treatment homogeneity while the amino group content was determined by ninhydrin assay. Moreover on cotton and silk fabrics the treatment fastness to domestic laundering was tested, according to UNI EN ISO105-C01. Obtained results showed a strong antimicrobial activity conferred by the treatment, homogeneous on fabric surface. It is evident already at low add-on, without affecting the hand properties of natural fabrics and the filtration characteristics of the synthetic filter fabrics. Finally, washing fastness was better for samples prepared with a better penetration of chitosan inside the fibers. PMID:22905533

  2. Finishing the family meal. The interactional organisation of satiety.

    PubMed

    Laurier, Eric; Wiggins, Sally

    2011-02-01

    This paper provides an extended review of psychological, sociological and interactional research on mealtimes and satiety (fullness), arguing for a focus on how fullness and finishing a meal is interactionally achieved. Drawing on three specimen data fragments from contrasting family settings, routinely used resources for pursuing completion and expressing satiety are described. We show how checks on completion are tailored to children according to their age, the intimate knowledge family members have of one another and attuned to contingencies, such as, whether there is a further course to be offered. Equally, that in teaching children how to eat together with others, the family also transmits and transforms all manner of other eating practices such as how to comply, or not, with requests to finish. A central aim of the article is to complement the many studies of satiety that have explained its physiological aspects by providing the familial logics that are expressed in bringing the meal to a close. We offer a suggestive analysis, based on conversation analytic principles, to illustrate our argument and to provide a starting point for further work in this field. Where bodies of work have previously used mealtimes as a convenient setting for accessing other social practices, this article turns its focus back toward the tasks of dining together. PMID:21095211

  3. 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.

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 40 CFR 410.60 - Applicability; description of the carpet finishing subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 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...

  9. 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...

  10. 40 CFR 410.60 - Applicability; description of the carpet finishing subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 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...

  11. 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...

  12. 40 CFR 410.60 - Applicability; description of the carpet finishing subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 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...

  13. 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.

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. Accurate Mass Measurements in Proteomics

    SciTech Connect

    Liu, Tao; Belov, Mikhail E.; Jaitly, Navdeep; Qian, Weijun; Smith, Richard D.

    2007-08-01

    proteins can also be extensively modified by PTMs26-31 or by their interactions with other biomolecules or small molecules.32,33 Thus, it is highly desirable that proteins, the primary functional macromolecules involved in almost all biological activities, can be studied directly and systematically to determine their diverse properties and interplay. Such proteome-wide analysis is expected to provide a wealth of biological information, such as sequence, quantity, PTMs, interactions, activities, subcellular distribution and structure of proteins, which is critical to the comprehensive understanding of the biological systems. However, the de novo analysis of proteins isolated from cells, tissues or bodily fluids poses significant challenges due to the tremendous complexity and depth of the proteome, which necessitates high-throughput and highly sensitive analytical techniques. It is therefore not surprising that mass spectrometry (MS) has become an indispensable technology for proteome analysis.

  20. Repetitive Sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Repetitive sequences, or repeats, account for a substantial portion of the eukaryotic genomes. These sequences include very different types of DNA with respect to mode of origin, function, structure, and genomic distribution. Two large families of repetitive sequences can be readily recognized, ta...

  1. 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.

  2. Overview of the manufacturing sequence of the Advanced Solid Rocket Motor

    NASA Technical Reports Server (NTRS)

    Chapman, John S.; Nix, Michael B.

    1992-01-01

    The manufacturing sequence of NASA's new Advanced Solid Rocket Motor, developed as a replacement of the Space Shuttle's existing Redesigned Solid Rocket Motor, is overviewed. Special attention is given to the case preparation, the propellant mix/cast, the nondestructuve evaluation, the motor finishing, and the refurbishment. The fabrication sequences of the case, the nozzle, and the igniter are described.

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

    ScienceCinema

    Weinstock, George [Washington University

    2013-03-22

    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.

  4. 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.

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

    PubMed

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

    2016-01-01

    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 environmental variables were associated with failure to finish a race highlighting the multifactorial nature of race-day events. Further investigation of risk factors for failure to finish is required to better understand the reasons for a low failure to finish rate in Thoroughbred flat races in New Zealand. PMID:27231944

  6. Influence of finishing by burnishing on surface characteristics

    NASA Astrophysics Data System (ADS)

    Saï, W. Bouzid; Lebrun, J. L.

    2003-02-01

    The aim of this study was to analyze the evolution of residual stresses, microhardness, and roughness in relation to the finishing process. The x-ray diffraction (XRD) technique was used to determine the residual stresses, which were measured from the surface to the bottom of the machined workpiece. Processes that were studied included turning, grinding, and burnishing. Burnishing was done on a surface that was initially turned, or turned and then ground. A duplex stainless steel was used in this study. This material belongs to a high-strength stainless steel family with high corrosion resistance properties. We noted that the burnishing process produces the best quality of the surface when compared with turning or grinding.

  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. 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. PMID:20673937

  9. Removal rate model for magnetorheological finishing of glass.

    PubMed

    Degroote, Jessica E; Marino, Anne E; Wilson, John P; Bishop, Amy L; Lambropoulos, John C; Jacobs, Stephen D

    2007-11-10

    Magnetorheological finishing (MRF) is a deterministic subaperture polishing process. The process uses a magnetorheological (MR) fluid that consists of micrometer-sized, spherical, magnetic carbonyl iron (CI) particles, nonmagnetic polishing abrasives, water, and stabilizers. Material removal occurs when the CI and nonmagnetic polishing abrasives shear material off the surface being polished. We introduce a new MRF material removal rate model for glass. This model contains terms for the near surface mechanical properties of glass, drag force, polishing abrasive size and concentration, chemical durability of the glass, MR fluid pH, and the glass composition. We introduce quantitative chemical predictors for the first time, to the best of our knowledge, into an MRF removal rate model. We validate individual terms in our model separately and then combine all of the terms to show the whole MRF material removal model compared with experimental data. All of our experimental data were obtained using nanodiamond MR fluids and a set of six optical glasses. PMID:17994145

  10. Removal Rate Model for Magnetorheological Finishing of Glass

    SciTech Connect

    DeGroote, J.E.; Marino, A.E.; WIlson, J.P.; Bishop, A.L.; Lambropoulos, J.C.; Jacobs, S.D.

    2007-11-14

    Magnetorheological finishing (MRF) is a deterministic subaperture polishing process. The process uses a magntorheological (MR) fluid that consists of micrometer-sized, spherical, magnetic carbonyl iron (CI) particles, nonmagnetic polishing abrasives, water, and stabilizers. Material removal occurs when the CI and nonmagnetic polishing abrasives shear material off the surface being polished. We introduce a new MRF material removal rate model for glass. This model contains terms for the near surface mechanical properties of glass, drag force, polishing abrasive size and concentration, chemical durability of the glass, MR fluid pH, and the glass composition. We introduce quantitative chemical predictors for the first time, to the best of our knowledge, into an MRF removal rate model. We validate individual terms in our model separately and then combine all of the terms to show the whole MRF material removal model compared with experimental data. All of our experimental data were obtained using nanodiamond MR fluids and a set of six optical glasses.

  11. Analysis of thermal sources in a magnetorheological finishing (MRF) process

    NASA Astrophysics Data System (ADS)

    Geiss, Andreas; Schinhaerl, Markus; Pitschke, Elmar; Rascher, Rolf; Sperber, Peter

    2005-09-01

    Magnetorheological finishing (MRF) is a computer controlled polishing (CCP) technique for high quality surfaces. The process uses a magnetorheological fluid which stiffens in a magnetic field and thus acts as the polishing tool. At the University of Applied Sciences Deggendorf thermal sources in a MRF polishing unit have been analysed using an infrared camera. The result of the research is a warming of the fluid in the fluid conditioner caused by the mixer motor. The existing cooling is therefore essential, in order to ensure a constant polishing tool characteristic during polishing runs. A new fluid conditioner, which was developed at the University of Applied Sciences Deggendorf, with the aim of an extended fluid lifetime may be used without cooling, because an increase of the fluid temperature in the conditioner could not been detected. Furthermore, a warming of the workpiece during the polishing process was not ascertainable.

  12. 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

  13. 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.

  14. 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

  15. Automated correction of genome sequence errors

    PubMed Central

    Gajer, Pawel; Schatz, Michael; Salzberg, Steven L.

    2004-01-01

    By using information from an assembly of a genome, a new program called AutoEditor significantly improves base calling accuracy over that achieved by previous algorithms. This in turn improves the overall accuracy of genome sequences and facilitates the use of these sequences for polymorphism discovery. We describe the algorithm and its application in a large set of recent genome sequencing projects. The number of erroneous base calls in these projects was reduced by 80%. In an analysis of over one million corrections, we found that AutoEditor made just one error per 8828 corrections. By substantially increasing the accuracy of base calling, AutoEditor can dramatically accelerate the process of finishing genomes, which involves closing all gaps and ensuring minimum quality standards for the final sequence. It also greatly improves our ability to discover single nucleotide polymorphisms (SNPs) between closely related strains and isolates of the same species. PMID:14744981

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

    Code of Federal Regulations, 2010 CFR

    2010-04-01

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

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

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... finished water reservoir requirements? 141.510 Section 141.510 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Finished Water Reservoirs § 141.510...

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

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 22 2010-07-01 2010-07-01 false What is required of new finished water...) 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...

  19. SUMMARY REPORT: CONTROL AND TREATMENT TECHNOLOGY FOR THE METAL FINISHING INDUSTRY: ION EXCHANGE

    EPA Science Inventory

    This Technology Transfer ummary Report is one of a series of reports that summarizes a pollution control technology for the metal finishing industry. he 45-page report is intended to promote an understanding of the use of ion exchange in the metal finishing industry. The sections...

  20. 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...

  1. 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 58.343 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING... Service 1 Operations and Operating Procedures § 58.343 Storage of finished product in coolers....

  2. Influence of Finishing Systems on Hydrophilic and Lipophilic Oxygen Radical Absorbance Capacity (ORAC) in Beef

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We studied the effect of finishing systems (alfalfa, pearl millet, natural pasture and high concentrate diet) on hydrophilic and lipophilic antioxidants in beef sample using oxygen radical absorbance capacity (ORAC). Finishing system had little impact on hydrophilic ORAC, but affected lipophilic OR...

  3. Minimum 10-year Survival of Kerboull Cemented Stems According to Surface Finish

    PubMed Central

    Baqué, François; Lefevre, Nicolas; Kerboull, Marcel

    2008-01-01

    The optimal surface finish for a cemented THA stem is still debated. We hypothesized surface finish would influence survival of Kerboull cemented hip arthroplasties and a matte finish would have lower survival. We reviewed survival of 433 total hip arthroplasties in 395 patients: 284 consecutive patients (310 hips) were enrolled in a prospective, randomized study of polished (165 hips) or matte finish stems (145 hips) and compared to a historical series of satin stems (123 hips) in 111 patients. The satin and matte finish implants had similar geometry but the polished was quadrangular rather than oval. Finish roughnesses were: polished (radius, 0.04 μm), satin (radius, 0.9 μm), and matte (radius, 1.7 μm). The mean age of the patients at the time of the index arthroplasty was 63.6 years. The survival rate at 13 years, using radiographic loosening as the end point, was 97.3% ± 2.6% for polished stems, 97.1% ± 2.1% for satin stems, and 78.9% ± 5.8% for matte stems. The data suggest survival of Kerboull stems was higher with a polished or satin surface finish than with a matte finish. Level of Evidence: Level II, therapeutic study. See the Guidelines for Authors for a complete description of levels of evidence. PMID:18196414

  4. A system response to an outbreak of enzootic pneumonia in grow/finish pigs.

    PubMed

    Bargen, Leeanne E

    2004-10-01

    A Mycoplasma hyopneumoniae-negative commercial swine production system broke with enzootic pneumonia at their grow/finish site in southern Manitoba in October, 2003. System responses included feed medication, depopulation, delayed shipment of pigs to the infected site, vaccination of at risk sow herds, and disinfection when grow/finish site depopulation was completed. PMID:15532888

  5. 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...

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

    ERIC Educational Resources Information Center

    Alberta Advanced Education, 2005

    2005-01-01

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

  7. 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

    ..., Arizona (``Isola'') on October 6, 2008, and supplemented on October 28, 2008. 73 FR 66919 (November 12... 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...

  8. Relationship between residual feed intake, performance, and carcass parameters of pasture finished cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In 2009 and 2010, Angus-crossbred steers (n = 39) were used to evaluate the relationship between residual feed intake (RFI), pasture-finishing performance and carcass parameters. During RFI determinations prior to pasture finishing initiation in mid-April, animals were fed an alfalfa hay cube diet....

  9. 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...

  10. THE EFFECTS OF RACTOPAMINE ON BEHAVIOR AND PHYSIOLOGY OF FINISHING PIGS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objectives of this study were to examine the effects of ractopamine (RAC) on behavior and physiology of pigs during handling and transport. Twenty-four groups of 3 gilts were randomly assigned to one of two treatments, four weeks prior to slaughter; 1) finishing feed plus RAC (10 ppm), 2) finish...

  11. 40 CFR 63.5395 - How do I measure the density of a finish?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

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

  12. 40 CFR 63.5395 - How do I measure the density of a finish?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

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

  13. 40 CFR 63.5395 - How do I measure the density of a finish?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

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

  14. 40 CFR 63.5395 - How do I measure the density of a finish?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

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

    Code of Federal Regulations, 2014 CFR

    2014-07-01

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

  16. 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...

  17. 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. PMID:25563959

  18. Effects of winter stocker growth rate and finishing system on: I. Animal performance and carcass characteristics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Angus-crossbred steers (n = 216) were used in a three-year study to assess the effects of winter stocker growth rate and finishing system on finishing performance and carcass characteristics. During winter months (December to April) steers were randomly allotted to three stocker growth rates: low (...

  19. 21 CFR 820.80 - Receiving, in-process, and finished device acceptance.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Receiving, in-process, and finished device acceptance. 820.80 Section 820.80 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES QUALITY SYSTEM REGULATION Acceptance Activities § 820.80 Receiving, in-process, and finished device...

  20. 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 58.343 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING... Service 1 Operations and Operating Procedures § 58.343 Storage of finished product in coolers....

  1. 40 CFR 63.5390 - How do I measure the HAP content of a finish?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... the HAP content of a finish, the reference method is EPA Method 311 of appendix A of 40 CFR part 63... analysis by EPA Method 311 are different from the HAP content determined by another means, the EPA Method... content analysis as determined in paragraph (a) of this section for each finish when you perform one...

  2. 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…

  3. 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...

  4. 40 CFR 410.50 - Applicability; description of the knit fabric finishing subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 30 2012-07-01 2012-07-01 false Applicability; description of the knit fabric finishing subcategory. 410.50 Section 410.50 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Knit Fabric Finishing Subcategory § 410.50...

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

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 29 2014-07-01 2012-07-01 true Applicability; description of the woven fabric finishing subcategory. 410.40 Section 410.40 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Woven Fabric Finishing Subcategory § 410.40...

  6. 40 CFR 410.40 - Applicability; description of the woven fabric finishing subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 30 2012-07-01 2012-07-01 false Applicability; description of the woven fabric finishing subcategory. 410.40 Section 410.40 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Woven Fabric Finishing Subcategory §...

  7. 40 CFR 410.50 - Applicability; description of the knit fabric finishing subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 29 2014-07-01 2012-07-01 true Applicability; description of the knit fabric finishing subcategory. 410.50 Section 410.50 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Knit Fabric Finishing Subcategory § 410.50...

  8. 40 CFR 463.30 - Applicability; description of the finishing water 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 finishing water subcategory. 463.30 Section 463.30 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS (CONTINUED) PLASTICS MOLDING AND FORMING POINT SOURCE CATEGORY Finishing Water Subcategory §...

  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. 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...

  12. 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...

  13. 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...

  14. 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;...

  15. Accurate pose estimation using single marker single camera calibration system

    NASA Astrophysics Data System (ADS)

    Pati, Sarthak; Erat, Okan; Wang, Lejing; Weidert, Simon; Euler, Ekkehard; Navab, Nassir; Fallavollita, Pascal

    2013-03-01

    Visual marker based tracking is one of the most widely used tracking techniques in Augmented Reality (AR) applications. Generally, multiple square markers are needed to perform robust and accurate tracking. Various marker based methods for calibrating relative marker poses have already been proposed. However, the calibration accuracy of these methods relies on the order of the image sequence and pre-evaluation of pose-estimation errors, making the method offline. Several studies have shown that the accuracy of pose estimation for an individual square marker depends on camera distance and viewing angle. We propose a method to accurately model the error in the estimated pose and translation of a camera using a single marker via an online method based on the Scaled Unscented Transform (SUT). Thus, the pose estimation for each marker can be estimated with highly accurate calibration results independent of the order of image sequences compared to cases when this knowledge is not used. This removes the need for having multiple markers and an offline estimation system to calculate camera pose in an AR application.

  16. 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

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

    PubMed Central

    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.

    2013-01-01

    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. PMID:23493677

  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. 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 ...