Science.gov

Sample records for accurate finished sequence

  1. Sequence finishing and mapping of Drosophila melanogasterheterochromatin

    SciTech Connect

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

    2007-06-15

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

  2. Accurately measuring dynamic coefficient of friction in ultraform finishing

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  3. Finishing The Euchromatic Sequence Of The Human Genome

    SciTech Connect

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

    2004-09-07

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

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

    ScienceCinema

    Fitzsimmons, Michael [LANL

    2016-07-12

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

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

    SciTech Connect

    Fitzsimmons, Michael

    2012-06-01

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

  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. The finished DNA sequence of human chromosome 12.

    PubMed

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

    2006-03-16

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

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

    ScienceCinema

    Yin, Shuangye (Broad Institute)

    2016-07-12

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

  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)

    ScienceCinema

    Athavale, Ajay [Monsanto

    2016-07-12

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

  11. 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.

  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. Accurate and comprehensive sequencing of personal genomes.

    PubMed

    Ajay, Subramanian S; Parker, Stephen C J; Abaan, Hatice Ozel; Fajardo, Karin V Fuentes; Margulies, Elliott H

    2011-09-01

    As whole-genome sequencing becomes commoditized and we begin to sequence and analyze personal genomes for clinical and diagnostic purposes, it is necessary to understand what constitutes a complete sequencing experiment for determining genotypes and detecting single-nucleotide variants. Here, we show that the current recommendation of ∼30× coverage is not adequate to produce genotype calls across a large fraction of the genome with acceptably low error rates. Our results are based on analyses of a clinical sample sequenced on two related Illumina platforms, GAII(x) and HiSeq 2000, to a very high depth (126×). We used these data to establish genotype-calling filters that dramatically increase accuracy. We also empirically determined how the callable portion of the genome varies as a function of the amount of sequence data used. These results help provide a "sequencing guide" for future whole-genome sequencing decisions and metrics by which coverage statistics should be reported.

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

    ScienceCinema

    McMahon, Ben [LANL

    2016-07-12

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

  16. 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.

  17. Accurate whole human genome sequencing using reversible terminator chemistry.

    PubMed

    Bentley, David R; Balasubramanian, Shankar; Swerdlow, Harold P; Smith, Geoffrey P; Milton, John; Brown, Clive G; Hall, Kevin P; Evers, Dirk J; Barnes, Colin L; Bignell, Helen R; Boutell, Jonathan M; Bryant, Jason; Carter, Richard J; Keira Cheetham, R; Cox, Anthony J; Ellis, Darren J; Flatbush, Michael R; Gormley, Niall A; Humphray, Sean J; Irving, Leslie J; Karbelashvili, Mirian S; Kirk, Scott M; Li, Heng; Liu, Xiaohai; Maisinger, Klaus S; Murray, Lisa J; Obradovic, Bojan; Ost, Tobias; Parkinson, Michael L; Pratt, Mark R; Rasolonjatovo, Isabelle M J; Reed, Mark T; Rigatti, Roberto; Rodighiero, Chiara; Ross, Mark T; Sabot, Andrea; Sankar, Subramanian V; Scally, Aylwyn; Schroth, Gary P; Smith, Mark E; Smith, Vincent P; Spiridou, Anastassia; Torrance, Peta E; Tzonev, Svilen S; Vermaas, Eric H; Walter, Klaudia; Wu, Xiaolin; Zhang, Lu; Alam, Mohammed D; Anastasi, Carole; Aniebo, Ify C; Bailey, David M D; Bancarz, Iain R; Banerjee, Saibal; Barbour, Selena G; Baybayan, Primo A; Benoit, Vincent A; Benson, Kevin F; Bevis, Claire; Black, Phillip J; Boodhun, Asha; Brennan, Joe S; Bridgham, John A; Brown, Rob C; Brown, Andrew A; Buermann, Dale H; Bundu, Abass A; Burrows, James C; Carter, Nigel P; Castillo, Nestor; Chiara E Catenazzi, Maria; Chang, Simon; Neil Cooley, R; Crake, Natasha R; Dada, Olubunmi O; Diakoumakos, Konstantinos D; Dominguez-Fernandez, Belen; Earnshaw, David J; Egbujor, Ugonna C; Elmore, David W; Etchin, Sergey S; Ewan, Mark R; Fedurco, Milan; Fraser, Louise J; Fuentes Fajardo, Karin V; Scott Furey, W; George, David; Gietzen, Kimberley J; Goddard, Colin P; Golda, George S; Granieri, Philip A; Green, David E; Gustafson, David L; Hansen, Nancy F; Harnish, Kevin; Haudenschild, Christian D; Heyer, Narinder I; Hims, Matthew M; Ho, Johnny T; Horgan, Adrian M; Hoschler, Katya; Hurwitz, Steve; Ivanov, Denis V; Johnson, Maria Q; James, Terena; Huw Jones, T A; Kang, Gyoung-Dong; Kerelska, Tzvetana H; Kersey, Alan D; Khrebtukova, Irina; Kindwall, Alex P; Kingsbury, Zoya; Kokko-Gonzales, Paula I; Kumar, Anil; Laurent, Marc A; Lawley, Cynthia T; Lee, Sarah E; Lee, Xavier; Liao, Arnold K; Loch, Jennifer A; Lok, Mitch; Luo, Shujun; Mammen, Radhika M; Martin, John W; McCauley, Patrick G; McNitt, Paul; Mehta, Parul; Moon, Keith W; Mullens, Joe W; Newington, Taksina; Ning, Zemin; Ling Ng, Bee; Novo, Sonia M; O'Neill, Michael J; Osborne, Mark A; Osnowski, Andrew; Ostadan, Omead; Paraschos, Lambros L; Pickering, Lea; Pike, Andrew C; Pike, Alger C; Chris Pinkard, D; Pliskin, Daniel P; Podhasky, Joe; Quijano, Victor J; Raczy, Come; Rae, Vicki H; Rawlings, Stephen R; Chiva Rodriguez, Ana; Roe, Phyllida M; Rogers, John; Rogert Bacigalupo, Maria C; Romanov, Nikolai; Romieu, Anthony; Roth, Rithy K; Rourke, Natalie J; Ruediger, Silke T; Rusman, Eli; Sanches-Kuiper, Raquel M; Schenker, Martin R; Seoane, Josefina M; Shaw, Richard J; Shiver, Mitch K; Short, Steven W; Sizto, Ning L; Sluis, Johannes P; Smith, Melanie A; Ernest Sohna Sohna, Jean; Spence, Eric J; Stevens, Kim; Sutton, Neil; Szajkowski, Lukasz; Tregidgo, Carolyn L; Turcatti, Gerardo; Vandevondele, Stephanie; Verhovsky, Yuli; Virk, Selene M; Wakelin, Suzanne; Walcott, Gregory C; Wang, Jingwen; Worsley, Graham J; Yan, Juying; Yau, Ling; Zuerlein, Mike; Rogers, Jane; Mullikin, James C; Hurles, Matthew E; McCooke, Nick J; West, John S; Oaks, Frank L; Lundberg, Peter L; Klenerman, David; Durbin, Richard; Smith, Anthony J

    2008-11-01

    DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.

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

    PubMed

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

    2016-04-01

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

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

    PubMed

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

    2016-04-01

    Viral genome sequencing has become the cornerstone of almost all aspects of virology. In particular, high-throughput, next-generation viral genome sequencing has become an integral part of molecular epidemiological investigations into outbreaks of viral disease, such as the recent outbreaks of Middle Eastern respiratory syndrome, Ebola virus disease and Zika virus infection. Multiple institutes have acquired the expertise and necessary infrastructure to perform such investigations, as evidenced by the accumulation of thousands of novel viral sequences over progressively shorter time periods. The authors recently proposed a nomenclature comprised of five high-throughput sequencing standard categories to describe the quality of determined viral genome sequences. These five categories (standard draft, high quality, coding complete, complete and finished) cover all levels of viral genome finishing and can be applied to sequences determined by any technology platform or assembly technique. PMID:27217167

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

    PubMed Central

    Acevedo, Ashley; Andino, Raul

    2015-01-01

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

  1. 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.

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

    ScienceCinema

    Campbell, Catherine [Noblis

    2016-07-12

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

  3. 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.

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

    SciTech Connect

    Sexton, David

    2012-06-01

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

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

    ScienceCinema

    Smith, Todd [PerkinElmer Omics Laboratory

    2016-07-12

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

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

    ScienceCinema

    Crow, John [National Center for Genome Resources

    2016-07-12

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

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

    SciTech Connect

    Crow, John

    2012-06-01

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

  8. 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.

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

    ScienceCinema

    Sexton, David [Baylor

    2016-07-12

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

  10. 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.

  11. 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.

  12. 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

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

    ScienceCinema

    Patel, Kamlesh D [Ken; SNL,

    2016-07-12

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

  14. 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)

    SciTech Connect

    Patel, Kamlesh D; SNL,

    2012-06-01

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

  15. GAMOLA: a new local solution for sequence annotation and analyzing draft and finished prokaryotic genomes.

    PubMed

    Altermann, Eric; Klaenhammer, Todd R

    2003-01-01

    Laboratories working with draft phase genomes have specific software needs, such as the unattended processing of hundreds of single scaffolds and subsequent sequence annotation. In addition, it is critical to follow the "movement" and the manual annotation of single open reading frames (ORFs) within the successive sequence updates. Even with finished genomes, regular database updates can lead to significant changes in the annotation of single ORFs. In functional genomics it is important to mine data and identify new genetic targets rapidly and easily. Often there is no need for sophisticated relational databases (RDB) that greatly reduce the system-independent access of the results. Another aspect is the internet dependency of most software packages. If users are working with confidential data, this dependency poses a security issue. GAMOLA was designed to handle the numerous scaffolds and changing contents of draft phase genomes in an automated process and stores the results for each predicted ORF in flatfile databases. In addition, annotation transfers, ORF designation tracking, Blast comparisons, and primer design for whole genome microarrays have been implemented. The software is available under the license of North Carolina State University. A website and a downloadable example are accessible under (http://fsweb2.schaub. ncsu.edu/TRKwebsite/index.htm). PMID:14506845

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

    PubMed

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

    2015-01-01

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

  17. 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).

  18. 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

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  1. 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

  2. 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

  3. 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.

  4. Finished Genome Sequence of the Laboratory Strain Escherichia coli K-12 RV308 (ATCC 31608).

    PubMed

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

    2014-11-20

    Escherichia coli strain K-12 substrain RV308 is an engineered descendant of the K-12 wild-type strain. Like its ancestor, it is an important organism in biotechnological research and is heavily used for the expression of single-chain variable fragments. Here, we report the complete genome sequence of E. coli K-12 RV308 (ATCC 31608).

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

    PubMed

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

    2014-11-20

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

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

    ScienceCinema

    Tremblay, Julien [DOE JGI

    2016-07-12

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

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

    ScienceCinema

    Lukjancenko, Oksana [Technical University of Denmark

    2016-07-12

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

  8. 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.

  9. 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.

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

    PubMed

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

    2012-12-19

    Cellulomonas massiliensis strain JC225(T) 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.

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

    PubMed Central

    Padmanabhan, Roshan; Lagier, Jean-Christophe; Dangui, Nicole Prisca Makaya; Michelle, Caroline; Couderc, Carine; Raoult, Didier; Fournier, Pierre-Edouard

    2013-01-01

    Megasphaera massiliensis strain NP3T sp. nov. is the type strain of Megasphaera massiliensis sp. nov., a new species within the genus Megasphaera. This strain, whose genome is described here, was isolated from the fecal flora of an HIV-infected patient. M. massiliensis is a Gram-negative, obligate anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,661,757 bp long genome (1 chromosome but no plasmid) contains 2,577 protein-coding and 61 RNA genes, including 5 rRNA genes. PMID:24501636

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

    PubMed Central

    Mishra, Ajay Kumar; Lagier, Jean-Christophe; Pfleiderer, Anne; Nguyen, Thi Thien; Caputo, Aurelia; Raoult, Didier; Fournier, Pierre-Edouard

    2013-01-01

    Holdemania massiliensis strain AP2T sp. nov. is the type strain of H. massiliensis sp. nov., a new species within the genus Holdemania. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old French Caucasian female suffering from severe restrictive anorexia nervosa. H. massiliensis is a Gram-positive, anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,795,625 bp-long genome (one chromosome but no plasmid) contains 3,461 protein-coding and 49 RNA genes, including 3 rRNA genes. PMID:24976895

  13. 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

  14. Non-contiguous finished genome sequence and description of Clostridium saudii sp. nov

    PubMed Central

    2014-01-01

    Clostridium saudii strain JCCT sp. nov. is the type strain of C. saudii sp. nov., a new species within the genus Clostridia. This strain, whose genome is described here, was isolated from a fecal sample collected from an obese 24-year-old (body mass index 52 kg/m2) man living in Jeddah, Saudi Arabia. C. saudii is a Gram-positive, anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,653,762 bp long genome contains 3,452 protein-coding and 53 RNA genes, including 4 rRNA genes. PMID:25780501

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

    Enterobacter massiliensis strain JC163T sp. nov. is the type strain of E. massiliensis sp. nov., a new species within the genus Enterobacter. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. E. massiliensis is an aerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,922,247 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 55.1% and contains 4,644 protein-coding and 80 RNA genes, including 5 rRNA genes. PMID:24019988

  19. Non contiguous-finished genome sequence and description of Alistipes obesi sp. nov

    PubMed Central

    Hugon, Perrine; Ramasamy, Dhamodharan; Lagier, Jean-Christophe; Rivet, Romain; Couderc, Carine; Raoult, Didier; Fournier, Pierre-Edouard

    2013-01-01

    Alistipes obesi sp. nov. strain ph8T is the type strain of A. obesi, a new species within the genus Alistipes. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. A. obesi is an obligately anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,162,233 bp long genome (1 chromosome but no plasmid) contains 2,623 protein-coding and 49 RNA genes, including three rRNA genes. PMID:24019990

  20. 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

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

    PubMed Central

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

    2014-01-01

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

  2. 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

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

    PubMed Central

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

    2013-01-01

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

  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 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

  6. CRYSpred: accurate sequence-based protein crystallization propensity prediction using sequence-derived structural characteristics.

    PubMed

    Mizianty, Marcin J; Kurgan, Lukasz A

    2012-01-01

    Relatively low success rates of X-ray crystallography, which is the most popular method for solving proteins structures, motivate development of novel methods that support selection of tractable protein targets. This aspect is particularly important in the context of the current structural genomics efforts that allow for a certain degree of flexibility in the target selection. We propose CRYSpred, a novel in-silico crystallization propensity predictor that uses a set of 15 novel features which utilize a broad range of inputs including charge, hydrophobicity, and amino acid composition derived from the protein chain, and the solvent accessibility and disorder predicted from the protein sequence. Our method outperforms seven modern crystallization propensity predictors on three, independent from training dataset, benchmark test datasets. The strong predictive performance offered by the CRYSpred is attributed to the careful design of the features, utilization of the comprehensive set of inputs, and the usage of the Support Vector Machine classifier. The inputs utilized by CRYSpred are well-aligned with the existing rules-of-thumb that are used in the structural genomics studies. PMID:21919861

  7. CRYSpred: accurate sequence-based protein crystallization propensity prediction using sequence-derived structural characteristics.

    PubMed

    Mizianty, Marcin J; Kurgan, Lukasz A

    2012-01-01

    Relatively low success rates of X-ray crystallography, which is the most popular method for solving proteins structures, motivate development of novel methods that support selection of tractable protein targets. This aspect is particularly important in the context of the current structural genomics efforts that allow for a certain degree of flexibility in the target selection. We propose CRYSpred, a novel in-silico crystallization propensity predictor that uses a set of 15 novel features which utilize a broad range of inputs including charge, hydrophobicity, and amino acid composition derived from the protein chain, and the solvent accessibility and disorder predicted from the protein sequence. Our method outperforms seven modern crystallization propensity predictors on three, independent from training dataset, benchmark test datasets. The strong predictive performance offered by the CRYSpred is attributed to the careful design of the features, utilization of the comprehensive set of inputs, and the usage of the Support Vector Machine classifier. The inputs utilized by CRYSpred are well-aligned with the existing rules-of-thumb that are used in the structural genomics studies.

  8. 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.

  9. 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

  10. 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

  11. 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

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

    SciTech Connect

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

    2011-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  14. Non-contiguous finished genome sequence and description of Alistipes ihumii sp. nov.

    PubMed Central

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

    2014-01-01

    Alistipes ihumii strain AP11T sp. nov. is the type strain of A. ihumii sp. nov., a new species within the genus Alistipes. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old French Caucasian female, suffering from a severe restrictive form of anorexia nervosa since the age of 12 years. A. ihumii is a Gram-negative anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,753,264 bp long genome (one chromosome but no plasmid) contains 2,254 protein-coding and 47 RNA genes, including 3 rRNA genes. PMID:25197494

  15. Non contiguous-finished genome sequence and description of Peptoniphilus senegalensis sp. nov.

    PubMed Central

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

    2013-01-01

    Peptoniphilus senegalensis strain JC140T sp. nov., is the type strain of P. senegalensis sp. nov., a new species within the genus Peptoniphilus. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. P. senegalensis strain JC140T is an obligate Gram-positive anaerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,840,641 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 32.2% and contains 1,744 protein-coding and 23 RNA genes, including 3 rRNA genes. PMID:24019986

  16. Non-contiguous finished genome sequence and description of Halopiger goleamassiliensis sp. nov.

    PubMed Central

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

    2013-01-01

    Halopiger goleamassiliensis strain IIH3T sp. nov. is a novel, extremely halophilic archaeon within the genus Halopiger. This strain was isolated from an evaporitic sediment in El Golea Lake, Ghardaïa region (Algeria). The type strain is strain IIH3T. H. goleamassiliensis is moderately thermophilic, neutrophilic, non-motile and coccus-shaped. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,906,923 bp long genome contains 3,854 protein-encoding genes and 49 RNA genes (1 gene is 16S rRNA, 1 gene is 23S rRNA, 3 genes are 5S rRNA, and 44 are tRNA genes). PMID:25197441

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

    PubMed Central

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

    2013-01-01

    Bacillus massilioanorexius strain AP8T sp. nov. is the type strain of B. massilioanorexius sp. nov., a new species within the genus Bacillus. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old Caucasian French female suffering from a severe form of anorexia nervosa since the age of 12 years. B. massilioanorexius is a Gram-positive aerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,616,135 bp long genome (one chromosome but no plasmid) contains 4,432 protein-coding and 87 RNA genes, including 8 rRNA genes. PMID:24501631

  18. Non contiguous-finished genome sequence and description of Bacillus massiliosenegalensis sp. nov.

    PubMed Central

    Ramasamy, Dhamodharan; Lagier, Jean-Christophe; Gorlas, Aurore; Raoult, Didier

    2013-01-01

    Bacillus massiliosenegalensis strain JC6T sp. nov. is the type strain of Bacillus massiliosenegalensis sp. nov., a new species within the genus Bacillus. This strain was isolated from the fecal flora of a healthy Senegalese patient. B. massiliosenegalensis is an aerobic Gram-positive rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,981,278-bp long genome comprises a 4,957,301-bp chromosome and a 23,977-bp plasmid. The chromosome contains 4,925 protein-coding and 72 RNA genes, including 4 rRNA genes. The plasmid contains 29 protein-coding genes. PMID:23991258

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

    PubMed Central

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

    2014-01-01

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

  20. Non-contiguous finished genome sequence and description of Corynebacterium jeddahense sp. nov.

    PubMed Central

    Edouard, Sophie; Bibi, Fehmida; Dhamodharan, Ramasamy; Lagier, Jean-Christophe; Azhar, Esam Ibraheen; Robert, Catherine; Caputo, Aurelia; Yasir, Muhammad; Jiman-Fatani, Asif Ahmad; Alawi, Maha; Fournier, Pierre-Edouard; Raoult, Didier

    2014-01-01

    Corynebacterium jeddahense sp. nov., strain JCBT, is the type strain of Corynebacterium jeddahense sp. nov., a new species within the genus Corynebacterium. This strain, whose genome is described here, was isolated from fecal flora of a 24-year-old Saudi male suffering from morbid obesity. Corynebacterium jeddahense is a Gram-positive, facultative anaerobic, nonsporulating bacillus. Here, we describe the features of this bacterium, together with the complete genome sequencing and annotation, and compare it to other member of the genus Corynebacterium. The 2,472,125 bp-long genome (1 chromosome but not plasmid) contains 2,359 protein-coding and 53 RNA genes, including 1 rRNA operon. PMID:25197478

  1. 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

  2. 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

  3. 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

  4. 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%).

  5. Haplotype-assisted accurate non-invasive fetal whole genome recovery through maternal plasma sequencing

    PubMed Central

    2013-01-01

    Background The applications of massively parallel sequencing technology to fetal cell-free DNA (cff-DNA) have brought new insight to non-invasive prenatal diagnosis. However, most previous research based on maternal plasma sequencing has been restricted to fetal aneuploidies. To detect specific parentally inherited mutations, invasive approaches to obtain fetal DNA are the current standard in the clinic because of the experimental complexity and resource consumption of previously reported non-invasive approaches. Methods Here, we present a simple and effective non-invasive method for accurate fetal genome recovery-assisted with parental haplotypes. The parental haplotype were firstly inferred using a combination strategy of trio and unrelated individuals. Assisted with the parental haplotype, we then employed a hidden Markov model to non-invasively recover the fetal genome through maternal plasma sequencing. Results Using a sequence depth of approximately 44X against a an approximate 5.69% cff-DNA concentration, we non-invasively inferred fetal genotype and haplotype under different situations of parental heterozygosity. Our data show that 98.57%, 95.37%, and 98.45% of paternal autosome alleles, maternal autosome alleles, and maternal chromosome X in the fetal haplotypes, respectively, were recovered accurately. Additionally, we obtained efficient coverage or strong linkage of 96.65% of reported Mendelian-disorder genes and 98.90% of complex disease-associated markers. Conclusions Our method provides a useful strategy for non-invasive whole fetal genome recovery. PMID:23445748

  6. 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

  7. FAMSA: Fast and accurate multiple sequence alignment of huge protein families

    PubMed Central

    Deorowicz, Sebastian; Debudaj-Grabysz, Agnieszka; Gudyś, Adam

    2016-01-01

    Rapid development of modern sequencing platforms has contributed to the unprecedented growth of protein families databases. The abundance of sets containing hundreds of thousands of sequences is a formidable challenge for multiple sequence alignment algorithms. The article introduces FAMSA, a new progressive algorithm designed for fast and accurate alignment of thousands of protein sequences. Its features include the utilization of the longest common subsequence measure for determining pairwise similarities, a novel method of evaluating gap costs, and a new iterative refinement scheme. What matters is that its implementation is highly optimized and parallelized to make the most of modern computer platforms. Thanks to the above, quality indicators, i.e. sum-of-pairs and total-column scores, show FAMSA to be superior to competing algorithms, such as Clustal Omega or MAFFT for datasets exceeding a few thousand sequences. Quality does not compromise on time or memory requirements, which are an order of magnitude lower than those in the existing solutions. For example, a family of 415519 sequences was analyzed in less than two hours and required no more than 8 GB of RAM. FAMSA is available for free at http://sun.aei.polsl.pl/REFRESH/famsa. PMID:27670777

  8. 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

  9. 3'READS+, a sensitive and accurate method for 3' end sequencing of polyadenylated RNA.

    PubMed

    Zheng, Dinghai; Liu, Xiaochuan; Tian, Bin

    2016-10-01

    Sequencing of the 3' end of poly(A)(+) RNA identifies cleavage and polyadenylation sites (pAs) and measures transcript expression. We previously developed a method, 3' region extraction and deep sequencing (3'READS), to address mispriming issues that often plague 3' end sequencing. Here we report a new version, named 3'READS+, which has vastly improved accuracy and sensitivity. Using a special locked nucleic acid oligo to capture poly(A)(+) RNA and to remove the bulk of the poly(A) tail, 3'READS+ generates RNA fragments with an optimal number of terminal A's that balance data quality and detection of genuine pAs. With improved RNA ligation steps for efficiency, the method shows much higher sensitivity (over two orders of magnitude) compared to the previous version. Using 3'READS+, we have uncovered a sizable fraction of previously overlooked pAs located next to or within a stretch of adenylate residues in human genes and more accurately assessed the frequency of alternative cleavage and polyadenylation (APA) in HeLa cells (∼50%). 3'READS+ will be a useful tool to accurately study APA and to analyze gene expression by 3' end counting, especially when the amount of input total RNA is limited. PMID:27512124

  10. 3'READS+, a sensitive and accurate method for 3' end sequencing of polyadenylated RNA.

    PubMed

    Zheng, Dinghai; Liu, Xiaochuan; Tian, Bin

    2016-10-01

    Sequencing of the 3' end of poly(A)(+) RNA identifies cleavage and polyadenylation sites (pAs) and measures transcript expression. We previously developed a method, 3' region extraction and deep sequencing (3'READS), to address mispriming issues that often plague 3' end sequencing. Here we report a new version, named 3'READS+, which has vastly improved accuracy and sensitivity. Using a special locked nucleic acid oligo to capture poly(A)(+) RNA and to remove the bulk of the poly(A) tail, 3'READS+ generates RNA fragments with an optimal number of terminal A's that balance data quality and detection of genuine pAs. With improved RNA ligation steps for efficiency, the method shows much higher sensitivity (over two orders of magnitude) compared to the previous version. Using 3'READS+, we have uncovered a sizable fraction of previously overlooked pAs located next to or within a stretch of adenylate residues in human genes and more accurately assessed the frequency of alternative cleavage and polyadenylation (APA) in HeLa cells (∼50%). 3'READS+ will be a useful tool to accurately study APA and to analyze gene expression by 3' end counting, especially when the amount of input total RNA is limited.

  11. 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.

  12. 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

  13. 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.

  14. HapCompass: A Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data

    PubMed Central

    Aguiar, Derek

    2012-01-01

    Abstract Genome assembly methods produce haplotype phase ambiguous assemblies due to limitations in current sequencing technologies. Determining the haplotype phase of an individual is computationally challenging and experimentally expensive. However, haplotype phase information is crucial in many bioinformatics workflows such as genetic association studies and genomic imputation. Current computational methods of determining haplotype phase from sequence data—known as haplotype assembly—have difficulties producing accurate results for large (1000 genomes-type) data or operate on restricted optimizations that are unrealistic considering modern high-throughput sequencing technologies. We present a novel algorithm, HapCompass, for haplotype assembly of densely sequenced human genome data. The HapCompass algorithm operates on a graph where single nucleotide polymorphisms (SNPs) are nodes and edges are defined by sequence reads and viewed as supporting evidence of co-occurring SNP alleles in a haplotype. In our graph model, haplotype phasings correspond to spanning trees. We define the minimum weighted edge removal optimization on this graph and develop an algorithm based on cycle basis local optimizations for resolving conflicting evidence. We then estimate the amount of sequencing required to produce a complete haplotype assembly of a chromosome. Using these estimates together with metrics borrowed from genome assembly and haplotype phasing, we compare the accuracy of HapCompass, the Genome Analysis ToolKit, and HapCut for 1000 Genomes Project and simulated data. We show that HapCompass performs significantly better for a variety of data and metrics. HapCompass is freely available for download (www.brown.edu/Research/Istrail_Lab/). PMID:22697235

  15. 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

  16. 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

  17. 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.

  18. 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

  19. RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data

    PubMed Central

    Gerritsen, Bram; Pandit, Aridaman; Andeweg, Arno C.; de Boer, Rob J.

    2016-01-01

    Motivation: High Throughput Sequencing (HTS) has enabled researchers to probe the human T cell receptor (TCR) repertoire, which consists of many rare sequences. Distinguishing between true but rare TCR sequences and variants generated by polymerase chain reaction (PCR) and sequencing errors remains a formidable challenge. The conventional approach to handle errors is to remove low quality reads, and/or rare TCR sequences. Such filtering discards a large number of true and often rare TCR sequences. However, accurate identification and quantification of rare TCR sequences is essential for repertoire diversity estimation. Results: We devised a pipeline, called Recover TCR (RTCR), that accurately recovers TCR sequences, including rare TCR sequences, from HTS data (including barcoded data) even at low coverage. RTCR employs a data-driven statistical model to rectify PCR and sequencing errors in an adaptive manner. Using simulations, we demonstrate that RTCR can easily adapt to the error profiles of different types of sequencers and exhibits consistently high recall and high precision even at low coverages where other pipelines perform poorly. Using published real data, we show that RTCR accurately resolves sequencing errors and outperforms all other pipelines. Availability and Implementation: The RTCR pipeline is implemented in Python (v2.7) and C and is freely available at http://uubram.github.io/RTCR/along with documentation and examples of typical usage. Contact: b.gerritsen@uu.nl PMID:27324198

  20. 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.

  1. 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

  2. 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/.

  3. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-09-22

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

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. Effective Temperatures of Selected Main-Sequence Stars with the Most Accurate Parameters

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    In this study we investigate the distributions of the properties of detached double-lined binaries (DBs) in the mass-luminosity, mass-radius, and mass-effective temperature diagrams. We have improved the classical mass-luminosity relation based on the database of DBs by Eker et al. (2014a). Based on the accurate observational data available to us we propose a method for improving the effective temperatures of eclipsing binaries with accurate mass and radius determinations.

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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

  20. Whole-genome optical mapping and finished genome sequence of Sphingobacterium deserti sp. nov., a new species isolated from the Western Desert of China.

    PubMed

    Teng, Chao; Zhou, Zhengfu; 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.

  1. 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

  2. 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

  3. 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

  4. 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.

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

    ScienceCinema

    Peng, Ze [DOE JGI

    2016-07-12

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

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

    PubMed Central

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

    2007-01-01

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

  7. 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

  8. 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

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

    PubMed

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

    2015-11-01

    Strain Vm-5(T) 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-5(T) (CSUR P971 = DSM 28587). PMID:26649181

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

    PubMed Central

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

    2015-01-01

    The objectives of this study were to identify antimicrobial resistance genotypes for Campylobacter and to evaluate the correlation between resistance phenotypes and genotypes using in vitro antimicrobial susceptibility testing and whole-genome sequencing (WGS). A total of 114 Campylobacter species isolates (82 C. coli and 32 C. jejuni) obtained from 2000 to 2013 from humans, retail meats, and cecal samples from food production animals in the United States as part of the National Antimicrobial Resistance Monitoring System were selected for study. Resistance phenotypes were determined using broth microdilution of nine antimicrobials. Genomic DNA was sequenced using the Illumina MiSeq platform, and resistance genotypes were identified using assembled WGS sequences through blastx analysis. Eighteen resistance genes, including tet(O), blaOXA-61, catA, lnu(C), aph(2″)-Ib, aph(2″)-Ic, aph(2′)-If, aph(2″)-Ig, aph(2″)-Ih, aac(6′)-Ie-aph(2″)-Ia, aac(6′)-Ie-aph(2″)-If, aac(6′)-Im, aadE, sat4, ant(6′), aad9, aph(3′)-Ic, and aph(3′)-IIIa, and mutations in two housekeeping genes (gyrA and 23S rRNA) were identified. There was a high degree of correlation between phenotypic resistance to a given drug and the presence of one or more corresponding resistance genes. Phenotypic and genotypic correlation was 100% for tetracycline, ciprofloxacin/nalidixic acid, and erythromycin, and correlations ranged from 95.4% to 98.7% for gentamicin, azithromycin, clindamycin, and telithromycin. All isolates were susceptible to florfenicol, and no genes associated with florfenicol resistance were detected. There was a strong correlation (99.2%) between resistance genotypes and phenotypes, suggesting that WGS is a reliable indicator of resistance to the nine antimicrobial agents assayed in this study. WGS has the potential to be a powerful tool for antimicrobial resistance surveillance programs. PMID:26519386

  11. Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels.

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  13. 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.

  14. 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

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

    NASA Astrophysics Data System (ADS)

    Jiang, Ning

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

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

    PubMed

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

    2009-07-01

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

  17. A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis)

    PubMed Central

    Ralph, Steven G; Chun, Hye Jung E; Kolosova, Natalia; Cooper, Dawn; Oddy, Claire; Ritland, Carol E; Kirkpatrick, Robert; Moore, Richard; Barber, Sarah; Holt, Robert A; Jones, Steven JM; Marra, Marco A; Douglas, Carl J; Ritland, Kermit; Bohlmann, Jörg

    2008-01-01

    Background Members of the pine family (Pinaceae), especially species of spruce (Picea spp.) and pine (Pinus spp.), dominate many of the world's temperate and boreal forests. These conifer forests are of critical importance for global ecosystem stability and biodiversity. They also provide the majority of the world's wood and fiber supply and serve as a renewable resource for other industrial biomaterials. In contrast to angiosperms, functional and comparative genomics research on conifers, or other gymnosperms, is limited by the lack of a relevant reference genome sequence. Sequence-finished full-length (FL)cDNAs and large collections of expressed sequence tags (ESTs) are essential for gene discovery, functional genomics, and for future efforts of conifer genome annotation. Results As part of a conifer genomics program to characterize defense against insects and adaptation to local environments, and to discover genes for the production of biomaterials, we developed 20 standard, normalized or full-length enriched cDNA libraries from Sitka spruce (P. sitchensis), white spruce (P. glauca), and interior spruce (P. glauca-engelmannii complex). We sequenced and analyzed 206,875 3'- or 5'-end ESTs from these libraries, and developed a resource of 6,464 high-quality sequence-finished FLcDNAs from Sitka spruce. Clustering and assembly of 147,146 3'-end ESTs resulted in 19,941 contigs and 26,804 singletons, representing 46,745 putative unique transcripts (PUTs). The 6,464 FLcDNAs were all obtained from a single Sitka spruce genotype and represent 5,718 PUTs. Conclusion This paper provides detailed annotation and quality assessment of a large EST and FLcDNA resource for spruce. The 6,464 Sitka spruce FLcDNAs represent the third largest sequence-verified FLcDNA resource for any plant species, behind only rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana), and the only substantial FLcDNA resource for a gymnosperm. Our emphasis on capturing FLcDNAs and ESTs from c

  18. 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

  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. High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure.

    PubMed

    Darby, B J; Todd, T C; Herman, M A

    2013-11-01

    Nematodes are abundant consumers in grassland soils, but more sensitive and specific methods of enumeration are needed to improve our understanding of how different nematode species affect, and are affected by, ecosystem processes. High-throughput amplicon sequencing is used to enumerate microbial and invertebrate communities at a high level of taxonomic resolution, but the method requires validation against traditional specimen-based morphological identifications. To investigate the consistency between these approaches, we enumerated nematodes from a 25-year field experiment using both morphological and molecular identification techniques in order to determine the long-term effects of annual burning and nitrogen enrichment on soil nematode communities. Family-level frequencies based on amplicon sequencing were not initially consistent with specimen-based counts, but correction for differences in rRNA gene copy number using a genetic algorithm improved quantitative accuracy. Multivariate analysis of corrected sequence-based abundances of nematode families was consistent with, but not identical to, analysis of specimen-based counts. In both cases, herbivores, fungivores and predator/omnivores generally were more abundant in burned than nonburned plots, while bacterivores generally were more abundant in nonburned or nitrogen-enriched plots. Discriminate analysis of sequence-based abundances identified putative indicator species representing each trophic group. We conclude that high-throughput amplicon sequencing can be a valuable method for characterizing nematode communities at high taxonomic resolution as long as rRNA gene copy number variation is accounted for and accurate sequence databases are available. PMID:24103081

  1. High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure.

    PubMed

    Darby, B J; Todd, T C; Herman, M A

    2013-11-01

    Nematodes are abundant consumers in grassland soils, but more sensitive and specific methods of enumeration are needed to improve our understanding of how different nematode species affect, and are affected by, ecosystem processes. High-throughput amplicon sequencing is used to enumerate microbial and invertebrate communities at a high level of taxonomic resolution, but the method requires validation against traditional specimen-based morphological identifications. To investigate the consistency between these approaches, we enumerated nematodes from a 25-year field experiment using both morphological and molecular identification techniques in order to determine the long-term effects of annual burning and nitrogen enrichment on soil nematode communities. Family-level frequencies based on amplicon sequencing were not initially consistent with specimen-based counts, but correction for differences in rRNA gene copy number using a genetic algorithm improved quantitative accuracy. Multivariate analysis of corrected sequence-based abundances of nematode families was consistent with, but not identical to, analysis of specimen-based counts. In both cases, herbivores, fungivores and predator/omnivores generally were more abundant in burned than nonburned plots, while bacterivores generally were more abundant in nonburned or nitrogen-enriched plots. Discriminate analysis of sequence-based abundances identified putative indicator species representing each trophic group. We conclude that high-throughput amplicon sequencing can be a valuable method for characterizing nematode communities at high taxonomic resolution as long as rRNA gene copy number variation is accounted for and accurate sequence databases are available.

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

    PubMed Central

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

    2014-01-01

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

  3. Accurate variant detection across non-amplified and whole genome amplified DNA using targeted next generation sequencing

    PubMed Central

    2012-01-01

    Background Many hypothesis-driven genetic studies require the ability to comprehensively and efficiently target specific regions of the genome to detect sequence variations. Often, sample availability is limited requiring the use of whole genome amplification (WGA). We evaluated a high-throughput microdroplet-based PCR approach in combination with next generation sequencing (NGS) to target 384 discrete exons from 373 genes involved in cancer. In our evaluation, we compared the performance of six non-amplified gDNA samples from two HapMap family trios. Three of these samples were also preamplified by WGA and evaluated. We tested sample pooling or multiplexing strategies at different stages of the tested targeted NGS (T-NGS) workflow. Results The results demonstrated comparable sequence performance between non-amplified and preamplified samples and between different indexing strategies [sequence specificity of 66.0% ± 3.4%, uniformity (coverage at 0.2× of the mean) of 85.6% ± 0.6%]. The average genotype concordance maintained across all the samples was 99.5% ± 0.4%, regardless of sample type or pooling strategy. We did not detect any errors in the Mendelian patterns of inheritance of genotypes between the parents and offspring within each trio. We also demonstrated the ability to detect minor allele frequencies within the pooled samples that conform to predicted models. Conclusion Our described PCR-based sample multiplex approach and the ability to use WGA material for NGS may enable researchers to perform deep resequencing studies and explore variants at very low frequencies and cost. PMID:22994565

  4. 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

  5. Ultra-deep Illumina sequencing accurately identifies MHC class IIb alleles and provides evidence for copy number variation in the guppy (Poecilia reticulata).

    PubMed

    Lighten, Jackie; van Oosterhout, Cock; Paterson, Ian G; McMullan, Mark; Bentzen, Paul

    2014-07-01

    We address the bioinformatic issue of accurately separating amplified genes of the major histocompatibility complex (MHC) from artefacts generated during high-throughput sequencing workflows. We fit observed ultra-deep sequencing depths (hundreds to thousands of sequences per amplicon) of allelic variants to expectations from genetic models of copy number variation (CNV). We provide a simple, accurate and repeatable method for genotyping multigene families, evaluating our method via analyses of 209 b of MHC class IIb exon 2 in guppies (Poecilia reticulata). Genotype repeatability for resequenced individuals (N = 49) was high (100%) within the same sequencing run. However, repeatability dropped to 83.7% between independent runs, either because of lower mean amplicon sequencing depth in the initial run or random PCR effects. This highlights the importance of fully independent replicates. Significant improvements in genotyping accuracy were made by greatly reducing type I genotyping error (i.e. accepting an artefact as a true allele), which may occur when using low-depth allele validation thresholds used by previous methods. Only a small amount (4.9%) of type II error (i.e. rejecting a genuine allele as an artefact) was detected through fully independent sequencing runs. We observed 1-6 alleles per individual, and evidence of sharing of alleles across loci. Variation in the total number of MHC class II loci among individuals, both among and within populations was also observed, and some genotypes appeared to be partially hemizygous; total allelic dosage added up to an odd number of allelic copies. Collectively, observations provide evidence of MHC CNV and its complex basis in natural populations.

  6. 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

  7. 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

  8. PredPPCrys: Accurate Prediction of Sequence Cloning, Protein Production, Purification and Crystallization Propensity from Protein Sequences Using Multi-Step Heterogeneous Feature Fusion and Selection

    PubMed Central

    Wang, Huilin; Wang, Mingjun; Tan, Hao; Li, Yuan; Zhang, Ziding; Song, Jiangning

    2014-01-01

    X-ray crystallography is the primary approach to solve the three-dimensional structure of a protein. However, a major bottleneck of this method is the failure of multi-step experimental procedures to yield diffraction-quality crystals, including sequence cloning, protein material production, purification, crystallization and ultimately, structural determination. Accordingly, prediction of the propensity of a protein to successfully undergo these experimental procedures based on the protein sequence may help narrow down laborious experimental efforts and facilitate target selection. A number of bioinformatics methods based on protein sequence information have been developed for this purpose. However, our knowledge on the important determinants of propensity for a protein sequence to produce high diffraction-quality crystals remains largely incomplete. In practice, most of the existing methods display poorer performance when evaluated on larger and updated datasets. To address this problem, we constructed an up-to-date dataset as the benchmark, and subsequently developed a new approach termed ‘PredPPCrys’ using the support vector machine (SVM). Using a comprehensive set of multifaceted sequence-derived features in combination with a novel multi-step feature selection strategy, we identified and characterized the relative importance and contribution of each feature type to the prediction performance of five individual experimental steps required for successful crystallization. The resulting optimal candidate features were used as inputs to build the first-level SVM predictor (PredPPCrys I). Next, prediction outputs of PredPPCrys I were used as the input to build second-level SVM classifiers (PredPPCrys II), which led to significantly enhanced prediction performance. Benchmarking experiments indicated that our PredPPCrys method outperforms most existing procedures on both up-to-date and previous datasets. In addition, the predicted crystallization targets of

  9. 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

  10. Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies

    PubMed Central

    2013-01-01

    The formalin-fixed, paraffin-embedded (FFPE) biopsy is a challenging sample for molecular assays such as targeted next-generation sequencing (NGS). We compared three methods for FFPE DNA quantification, including a novel PCR assay (‘QFI-PCR’) that measures the absolute copy number of amplifiable DNA, across 165 residual clinical specimens. The results reveal the limitations of commonly used approaches, and demonstrate the value of an integrated workflow using QFI-PCR to improve the accuracy of NGS mutation detection and guide changes in input that can rescue low quality FFPE DNA. These findings address a growing need for improved quality measures in NGS-based patient testing. PMID:24001039

  11. Sequencing the Unrearranged Human Immunoglobin

    SciTech Connect

    Warren, Rene

    2010-06-03

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

  12. 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.

  13. 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.

  14. Non-contiguous finished genome sequence and description of Kallipyga massiliensis gen. nov., sp. nov., a new member of the family Clostridiales Incertae Sedis XI

    PubMed Central

    Hugon, Perrine; Ramasamy, Dhamodharan; Robert, Catherine; Couderc, Carine; Raoult, Didier; Fournier, Pierre-Edouard

    2013-01-01

    Kallipyga massiliensis strain ph2T is the type strain of Kallipyga massiliensis gen. nov., sp. nov., the type species of the new genus Kallipyga within the family Clostridiales Incertae Sedis XI. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. K. massiliensis is an obligate anaerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,770,679 bp long genome (1 chromosome but no plasmid) contains 1,575 protein-coding and 50 RNA genes, including 4 rRNA genes. PMID:24501634

  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 Enorma massiliensis gen. nov., sp. nov., a new member of the Family Coriobacteriaceae

    PubMed Central

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

    2013-01-01

    Enorma massiliensis strain phIT is the type strain of E. massiliensis gen. nov., sp. nov., the type species of a new genus within the family Coriobacteriaceae, Enorma gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. E. massiliensis strain phIT is a Gram-positive, obligately anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,280,571 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 62.0% and contains 1,901 protein-coding and 51 RNA genes, including 3 rRNA genes. PMID:23991260

  17. Use of Optical Mapping in Bacterial Genome Finishing

    SciTech Connect

    Kumar, Dibyendu

    2010-06-03

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

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

    PubMed Central

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

    2016-01-01

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

  19. 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.

  20. Urolithiasis in finishing pigs.

    PubMed

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

    2004-11-01

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

  1. 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.

  2. 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.

  3. Panel-based Genetic Diagnostic Testing for Inherited Eye Diseases is Highly Accurate and Reproducible and More Sensitive for Variant Detection Than Exome Sequencing

    PubMed Central

    Bujakowska, Kinga M.; Sousa, Maria E.; Fonseca-Kelly, Zoë D.; Taub, Daniel G.; Janessian, Maria; Wang, Dan Yi; Au, Elizabeth D.; Sims, Katherine B.; Sweetser, David A.; Fulton, Anne B.; Liu, Qin; Wiggs, Janey L.; Gai, Xiaowu; Pierce, Eric A.

    2015-01-01

    Purpose Next-generation sequencing (NGS) based methods are being adopted broadly for genetic diagnostic testing, but the performance characteristics of these techniques have not been fully defined with regard to test accuracy and reproducibility. Methods We developed a targeted enrichment and NGS approach for genetic diagnostic testing of patients with inherited eye disorders, including inherited retinal degenerations, optic atrophy and glaucoma. In preparation for providing this Genetic Eye Disease (GEDi) test on a CLIA-certified basis, we performed experiments to measure the sensitivity, specificity, reproducibility as well as the clinical sensitivity of the test. Results The GEDi test is highly reproducible and accurate, with sensitivity and specificity for single nucleotide variant detection of 97.9% and 100%, respectively. The sensitivity for variant detection was notably better than the 88.3% achieved by whole exome sequencing (WES) using the same metrics, due to better coverage of targeted genes in the GEDi test compared to commercially available exome capture sets. Prospective testing of 192 patients with IRDs indicated that the clinical sensitivity of the GEDi test is high, with a diagnostic rate of 51%. Conclusion The data suggest that based on quantified performance metrics, selective targeted enrichment is preferable to WES for genetic diagnostic testing. PMID:25412400

  4. Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models.

    PubMed

    Andrews, T D; Whittle, B; Field, M A; Balakishnan, B; Zhang, Y; Shao, Y; Cho, V; Kirk, M; Singh, M; Xia, Y; Hager, J; Winslade, S; Sjollema, G; Beutler, B; Enders, A; Goodnow, C C

    2012-05-01

    Accurate identification of sparse heterozygous single-nucleotide variants (SNVs) is a critical challenge for identifying the causative mutations in mouse genetic screens, human genetic diseases and cancer. When seeking to identify causal DNA variants that occur at such low rates, they are overwhelmed by false-positive calls that arise from a range of technical and biological sources. We describe a strategy using whole-exome capture, massively parallel DNA sequencing and computational analysis, which identifies with a low false-positive rate the majority of heterozygous and homozygous SNVs arising de novo with a frequency of one nucleotide substitution per megabase in progeny of N-ethyl-N-nitrosourea (ENU)-mutated C57BL/6j mice. We found that by applying a strategy of filtering raw SNV calls against known and platform-specific variants we could call true SNVs with a false-positive rate of 19.4 per cent and an estimated false-negative rate of 21.3 per cent. These error rates are small enough to enable calling a causative mutation from both homozygous and heterozygous candidate mutation lists with little or no further experimental validation. The efficacy of this approach is demonstrated by identifying the causative mutation in the Ptprc gene in a lymphocyte-deficient strain and in 11 other strains with immune disorders or obesity, without the need for meiotic mapping. Exome sequencing of first-generation mutant mice revealed hundreds of unphenotyped protein-changing mutations, 52 per cent of which are predicted to be deleterious, which now become available for breeding and experimental analysis. We show that exome sequencing data alone are sufficient to identify induced mutations. This approach transforms genetic screens in mice, establishes a general strategy for analysing rare DNA variants and opens up a large new source for experimental models of human disease.

  5. Advanced cleaning by mass finishing

    SciTech Connect

    McCoy, M.W.

    1983-10-01

    This paper describes a testing program that examined the effectiveness of vibratory finishing for removing a variety of radioactively contaminated soils. The vibratory finishing process was studied by measuring the radiation levels of the test material, the lining of the vibratory finishing tub, and the media. Many soils including corrosion products, scale, oil, grease and paint were removed by the vibratory finishing process. The results of this program indicate that vibratory finishing should be an effective cleaning process for a variety of manufacturing operations.

  6. 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.

  7. Advanced cleaning by mass finishing

    NASA Astrophysics Data System (ADS)

    McCoy, M. W.

    1983-10-01

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

  8. 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...

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. Dimensioning, Tolerancing, and Machine Finishes.

    ERIC Educational Resources Information Center

    Adams, George C.

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

  18. 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…

  19. 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.

  20. Figure and finish of grazing incidence mirrors

    SciTech Connect

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

    1989-08-01

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

  1. 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

  2. A Tooth Surface Finishing Method with a New Tool of a Vitrified Cubic Boron Nitride Wheel for Involute Internal Spline

    NASA Astrophysics Data System (ADS)

    Mizuno, Sadao; Morita, Tetuya; Ariura, Yasutsune

    For highly accurate and highly efficient tooth surface finishing, a vitrified cubic boron nitride (CBN) wheel or an electro-deposited CBN wheel exhibits superior performance. Honing by an involute spline tooth meshing is effective due to the generating motion. However, a lack of wheel rigidity and an inadequate feed motion of the wheel tend to reduce the finishing performance. As a result, it is difficult to keep the tooth surface smooth. In this study, the finishing with a vitrified CBN wheel is carried out using a new honing tool. The finishing performance is compared with that obtained using an electro-deposited wheel, and the finishing is carried out by braking an internal spline axis. The influence of different feed methods is investigated on the roughness of the finished tooth surface. The finishing using a vitrified CBN wheel and braking an internal spline axis shows superior performance.

  3. Accurate and practical identification of 20 Fusarium species by seven-locus sequence analysis and reverse line blot hybridization, and an in vitro antifungal susceptibility study.

    PubMed

    Wang, He; Xiao, Meng; Kong, Fanrong; Chen, Sharon; Dou, Hong-Tao; Sorrell, Tania; Li, Ruo-Yu; Xu, Ying-Chun

    2011-05-01

    Eleven reference and 25 clinical isolates of Fusarium were subject to multilocus DNA sequence analysis to determine the species and haplotypes of the fusarial isolates from Beijing and Shandong, China. Seven loci were analyzed: the translation elongation factor 1 alpha gene (EF-1α); the nuclear rRNA internal transcribed spacer (ITS), large subunit (LSU), and intergenic spacer (IGS) regions; the second largest subunit of the RNA polymerase gene (RPB2); the calmodulin gene (CAM); and the mitochondrial small subunit (mtSSU) rRNA gene. We also evaluated an IGS-targeted PCR/reverse line blot (RLB) assay for species/haplotype identification of Fusarium. Twenty Fusarium species and seven species complexes were identified. Of 25 clinical isolates (10 species), the Gibberella (Fusarium) fujikuroi species complex was the commonest (40%) and was followed by the Fusarium solani species complex (FSSC) (36%) and the F. incarnatum-F. equiseti species complex (12%). Six FSSC isolates were identified to the species level as FSSC-3+4, and three as FSSC-5. Twenty-nine IGS, 27 EF-1α, 26 RPB2, 24 CAM, 18 ITS, 19 LSU, and 18 mtSSU haplotypes were identified; 29 were unique, and haplotypes for 24 clinical strains were novel. By parsimony informative character analysis, the IGS locus was the most phylogenetically informative, and the rRNA gene regions were the least. Results by RLB were concordant with multilocus sequence analysis for all isolates. Amphotericin B was the most active drug against all species. Voriconazole MICs were high (>8 μg/ml) for 15 (42%) isolates, including FSSC. Analysis of larger numbers of isolates is required to determine the clinical utility of the seven-locus sequence analysis and RLB assay in species classification of fusaria. PMID:21389150

  4. 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

  5. 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...

  6. 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

  7. 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

  8. 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.

  9. 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...

  10. 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...

  11. 27 CFR 25.231 - Finished beer.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

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

  12. 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...

  13. 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...

  14. 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.

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

    PubMed Central

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

    2012-01-01

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

  16. Finishing genomes with limited resources: lessons from an ensemble of microbial genomes

    PubMed Central

    2010-01-01

    While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores. PMID:20398345

  17. 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...

  18. 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

  19. 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.

  20. 25 CFR 301.8 - Finish.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 25 Indians 2 2014-04-01 2014-04-01 false Finish. 301.8 Section 301.8 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER AND TURQUOISE PRODUCTS; STANDARDS § 301.8 Finish. All silver is to be hand polished....

  1. 25 CFR 301.8 - Finish.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 25 Indians 2 2012-04-01 2012-04-01 false Finish. 301.8 Section 301.8 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER AND TURQUOISE PRODUCTS; STANDARDS § 301.8 Finish. All silver is to be hand polished....

  2. 25 CFR 301.8 - Finish.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

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

  3. 25 CFR 301.8 - Finish.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 2 2011-04-01 2011-04-01 false Finish. 301.8 Section 301.8 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER AND TURQUOISE PRODUCTS; STANDARDS § 301.8 Finish. All silver is to be hand polished....

  4. 25 CFR 301.8 - Finish.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 25 Indians 2 2013-04-01 2013-04-01 false Finish. 301.8 Section 301.8 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER AND TURQUOISE PRODUCTS; STANDARDS § 301.8 Finish. All silver is to be hand polished....

  5. 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 ...

  6. 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.

  7. The Genome Sequencing Center at NCGR

    SciTech Connect

    Schilkey, Faye

    2010-06-02

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

  8. 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

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

    ScienceCinema

    Jenkins, David [EdgeBio

    2016-07-12

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

  10. 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.

  11. 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.``

  12. Plutonium finishing plant dangerous waste training plan

    SciTech Connect

    ENTROP, G.E.

    1999-05-24

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

  13. The Adolescent Who Does Not Finish Anything.

    ERIC Educational Resources Information Center

    Breiner, Sander J.

    1985-01-01

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

  14. 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

  15. 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.

  16. Deterministic magnetorheological finishing of optical aspheric mirrors

    NASA Astrophysics Data System (ADS)

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

    2009-05-01

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

  17. Accurate Inference of Local Phased Ancestry of Modern Admixed Populations

    PubMed Central

    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

  18. 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

  19. Validation of rice genome sequence by optical mapping

    PubMed Central

    Zhou, Shiguo; Bechner, Michael C; Place, Michael; Churas, Chris P; Pape, Louise; Leong, Sally A; Runnheim, Rod; Forrest, Dan K; Goldstein, Steve; Livny, Miron; Schwartz, David C

    2007-01-01

    Background Rice feeds much of the world, and possesses the simplest genome analyzed to date within the grass family, making it an economically relevant model system for other cereal crops. Although the rice genome is sequenced, validation and gap closing efforts require purely independent means for accurate finishing of sequence build data. Results To facilitate ongoing sequencing finishing and validation efforts, we have constructed a whole-genome SwaI optical restriction map of the rice genome. The physical map consists of 14 contigs, covering 12 chromosomes, with a total genome size of 382.17 Mb; this value is about 11% smaller than original estimates. 9 of the 14 optical map contigs are without gaps, covering chromosomes 1, 2, 3, 4, 5, 7, 8 10, and 12 in their entirety – including centromeres and telomeres. Alignments between optical and in silico restriction maps constructed from IRGSP (International Rice Genome Sequencing Project) and TIGR (The Institute for Genomic Research) genome sequence sources are comprehensive and informative, evidenced by map coverage across virtually all published gaps, discovery of new ones, and characterization of sequence misassemblies; all totalling ~14 Mb. Furthermore, since optical maps are ordered restriction maps, identified discordances are pinpointed on a reliable physical scaffold providing an independent resource for closure of gaps and rectification of misassemblies. Conclusion Analysis of sequence and optical mapping data effectively validates genome sequence assemblies constructed from large, repeat-rich genomes. Given this conclusion we envision new applications of such single molecule analysis that will merge advantages offered by high-resolution optical maps with inexpensive, but short sequence reads generated by emerging sequencing platforms. Lastly, map construction techniques presented here points the way to new types of comparative genome analysis that would focus on discernment of structural differences

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

    DOE PAGES

    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.

  1. 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.

  2. Toward Magnetorheological Finishing of Magnetic Materials

    SciTech Connect

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

    2007-10-24

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

  3. 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

  4. 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…

  5. 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.

  6. 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...

  7. 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...

  8. 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).

  9. Sequencing, Assembly and Analysis of Human Microbial Communities

    SciTech Connect

    Petrosino, Joe

    2010-06-04

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

  10. Towards Experimental Annotation of Genes by High Throughput Sequencing

    SciTech Connect

    Bradbury, Andrew

    2010-06-03

    Andrew Bradbury of Los Alamos National Laboratory discusses turning annotation into a sequencing pipeline on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  11. 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).

  12. 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.

  13. Characterization of M40J Desized and Finished Fibers

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

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

  14. 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... Requirements § 18.33 Finish of surface joints. Flat surfaces between bolt holes that form any part of a flame... § 18.31(a)(6). All metal surfaces forming a flame-arresting path shall be finished during...

  15. Why do photo finish images look weird?

    NASA Astrophysics Data System (ADS)

    Gregorcic, Bor; Planinsic, Gorazd

    2012-09-01

    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 is also suitable for a student project activity.

  16. Acidic magnetorheological finishing of infrared polycrystalline materials

    DOE PAGES

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

    2016-10-12

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

  17. 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.

  18. 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.

  19. The surface finish of light-cured composite resin materials.

    PubMed

    Sidhu, S K; Henderson, L J

    1993-01-01

    A necessity for any dental restorative material is its ability to take and maintain a smooth surface finish. Composite resin restorative materials with fillers and matrix of differing hardness are difficult to finish and polish. The use of aluminum trioxide discs is a popular and acceptable method of finishing composite restorative materials where the material is accessible. Burs and stones are used for finishing and polishing inaccessible areas. This study was undertaken to compare the surface finish of composite resin restorative material when finished with white stones, superfine diamond burs and aluminum trioxide discs. The finished surface was measured with a profilometer and the roughness average value used to compare the surfaces. The aluminum trioxide discs gave the best and most consistent results. It was possible to attain similar results with the superfine diamond bur. However, the results were highly variable. None of the methods used achieved the smoothness of composite resin cured against a transparent matrix.

  20. Accurate monotone cubic interpolation

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1991-01-01

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

  1. 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.

  2. Forage systems for beef production from conception to slaughter: III. Finishing systems.

    PubMed

    Allen, V G; Fontenot, J P; Kelly, R F; Notter, D R

    1996-03-01

    Fall-weaned Angus calves grazed or were fed different forages during winter followed by 1) N-fertilized tall fescue (Festuca arundinacea Schreb.) grazed alone, 2) bluegrass (Poa pratensis L.)-white clover (Trifolium repens L.) sequence grazed with tall fescue-red clover (Trifolium pratense L.), or 3) bluegrass-white clover sequence grazed with alfalfa (Medicago sativa L.)-orchardgrass (Dactylis glomerata L.). Heifers were supplemented with grain at 1% of BW from April until slaughter in July. One-half of steers were supplemented with grain at 1% of BW from July until slaughter in October. Remaining steers were fed no grain but were finished on corn silage supplemented with .9 kg of soybean meal per steer daily, from October until slaughter in late January. Including alfalfa-orchardgrass in systems during the finishing phase resulted in higher daily and total gains during the grazing period, and carcasses had more marbling and higher USDA quality grades at slaughter compared with carcasses of cattle on systems using fescue-red clover. Correlation of final weight with carcass characteristics was low (r < .5). Performance and carcass characteristics were influenced as much or more by forage consumed during the previous wintering phase as by forage fed during the finishing phase. Wintering cattle on stockpiled fescue-alfalfa or alfalfa-orchardgrass hay generally resulted in higher BW at slaughter and more desirable carcass characteristics than systems using tall fescue alone or in combination with red clover. This was particularly notable in steers that grazed without grain until October and were finished on corn silage plus supplement. Final BW and carcass characteristics in all cattle were improved by full season grazing followed by feeding corn silage, compared with cattle finished with grain on pasture.

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

    PubMed Central

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

    2009-01-01

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

  4. Lysine requirement for growing-finishing immunocastrated male pigs.

    PubMed

    Alebrante, Leandro; Donzele, Juarez Lopes; Donzele, Rita Flavia Miranda de Oliveira; da Silva, Francisco Carlos de Oliveira; Kiefer, Charles; Rocha, Gabriel Cipriano

    2015-12-01

    Eighty boars (19.3 ± 2.49 kg) were vaccinated twice (100 and 128 days of age) against gonadotropin releasing hormone (Vivax™ vaccine), for a randomised block design study aiming to evaluate five digestible lysine (DLys) level treatments, with three phase-feeding per treatments (9-8-7; 10-9-8; 11-10-9; 12-11-10 and 13-12-11 g/kg) during the growing-finishing phases (54-100, 100-128 and 128-155 days of age, respectively). Pigs were fed their respective diets ad libitum from 54 to 155 days and weighed at 100, 128 and 155 days. Pig loin (Longissimus dorsi) area, loin depth and backfat thickness were measured by ultrasound at 100 and 155 days. Hot carcass weight, meat quantity and meat yield were measured at slaughter. From 54 to 100 days (pre-immunocastration), DLys levels linearly improved pig feed conversion and loin area, the level of DLys for minimum feed conversion and maximum loin area was 13 g/kg. However, DLys levels had no effect on the performance of boars from 54 to 128 days (pre-immunocastration), nor on the performance and carcass parameters of immunocastrated male pigs between 54 and 155 days. A sequence of diets containing 9, 8 and 7 g/kg of DLys fed from 54 to 100, 100 to 128 and 128 to 155 days, respectively, meet the requirement of growing-finishing immunocastrated male pigs. PMID:26245916

  5. 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.

  6. Analysis of finishing reactive distillation columns

    SciTech Connect

    Espinosa, J.; Aguirre, P.; Frey, T.; Stichlmair, J.

    1999-01-01

    In this paper, a novel method to deal with the design and the synthesis of finishing reactive distillation columns with one reactive core, two rectifying sections, and one stripping section is presented. The attention of the work is concentrated on three subjects: (1) the feasibility of a given separation at both finite and total reflux operation; (2) the minimum energy demand operation; (3) the distribution of the reaction between the reactor and the finishing reactive column. The design problem presents the same grade of difficulty as that found in the design of conventional extractive columns. A geometric based method is used to explain key features of reactive distillation. Here, the relation between the reaction yield and the distillate flow rate plays a role similar to that of the entrainer flow in extractive distillation. Hence, special attention is given to the behavior of the profiles inside the rectifying section below the reactive core. The methodology is illustrated using the well-known MTBE case study.

  7. 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.

  8. Preference for starting and finishing behavior patterns.

    PubMed Central

    Shimp, C P; Sabulsky, S L; Childers, L J

    1989-01-01

    Pigeon's key pecking was reinforced with food in two experiments in which the correspondence between preference for starting one of two reinforced behavior patterns and the likelihood of finishing it subsequently was examined. Reinforcers were scheduled according to concurrent schedules for two classes of interresponse times, modified such that reinforcers followed a center-key peck terminating either a shorter interresponse time started by a left-key peck or a longer interresponse time started by a right-key peck. In Experiment 1, the times when reinforcers potentially were available were not discriminated, whereas in Experiment 2 they were. Absolute reinforced pattern durations were varied. The relative frequency of starting a particular pattern was highly correlated with relative frequency of that completed pattern in both experiments. Other relations between starting and finishing a pattern depended on whether reinforced interresponse times were discriminated. For instance, preference for starting a pattern sometimes correlated negatively with the likelihood of subsequently completing it. The present experiments are described as capturing part of the ordinary language meaning of "intention," according to which an organism's behavior at one moment sets the occasion for an observer to say that the organism "intends" in the future to engage in one behavior rather than another. PMID:2584918

  9. Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing

    PubMed Central

    Beitzel, Brett; Chain, Patrick S. G.; Davenport, Matthew G.; Donaldson, Eric; Frieman, Matthew; Kugelman, Jeffrey; Kuhn, Jens H.; O’Rear, Jules; Sabeti, Pardis C.; Wentworth, David E.; Wiley, Michael R.; Yu, Guo-Yun; Sozhamannan, Shanmuga; Bradburne, Christopher

    2014-01-01

    ABSTRACT Thanks to high-throughput sequencing technologies, genome sequencing has become a common component in nearly all aspects of viral research; thus, we are experiencing an explosion in both the number of available genome sequences and the number of institutions producing such data. However, there are currently no common standards used to convey the quality, and therefore utility, of these various genome sequences. Here, we propose five “standard” categories that encompass all stages of viral genome finishing, and we define them using simple criteria that are agnostic to the technology used for sequencing. We also provide genome finishing recommendations for various downstream applications, keeping in mind the cost-benefit trade-offs associated with different levels of finishing. Our goal is to define a common vocabulary that will allow comparison of genome quality across different research groups, sequencing platforms, and assembly techniques. PMID:24939889

  10. Standards for sequencing viral genomes in the era of high-throughput sequencing.

    PubMed

    Ladner, Jason T; Beitzel, Brett; Chain, Patrick S G; Davenport, Matthew G; Donaldson, Eric F; Frieman, Matthew; Kugelman, Jeffrey R; Kuhn, Jens H; O'Rear, Jules; Sabeti, Pardis C; Wentworth, David E; Wiley, Michael R; Yu, Guo-Yun; Sozhamannan, Shanmuga; Bradburne, Christopher; Palacios, Gustavo

    2014-01-01

    Thanks to high-throughput sequencing technologies, genome sequencing has become a common component in nearly all aspects of viral research; thus, we are experiencing an explosion in both the number of available genome sequences and the number of institutions producing such data. However, there are currently no common standards used to convey the quality, and therefore utility, of these various genome sequences. Here, we propose five "standard" categories that encompass all stages of viral genome finishing, and we define them using simple criteria that are agnostic to the technology used for sequencing. We also provide genome finishing recommendations for various downstream applications, keeping in mind the cost-benefit trade-offs associated with different levels of finishing. Our goal is to define a common vocabulary that will allow comparison of genome quality across different research groups, sequencing platforms, and assembly techniques.

  11. 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.

  12. [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

  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.

  14. Case Report: Whole exome sequencing helps in accurate molecular diagnosis in siblings with a rare co-occurrence of paternally inherited 22q12 duplication and autosomal recessive non-syndromic ichthyosis.

    PubMed Central

    Gupta, Aayush; Sharma, Yugal; Deo, Kirti; Vellarikkal, Shamsudheen; Jayarajan, Rijith; Dixit, Vishal; Verma, Ankit; Scaria, Vinod; Sivasubbu, Sridhar

    2015-01-01

    Lamellar ichthyosis (LI), considered an autosomal recessive monogenic genodermatosis, has an incidence of approximately 1 in 250,000. Usually associated with mutations in the transglutaminase gene ( TGM1), mutations in six other genes have, less frequently, been shown to be causative. Two siblings, born in a collodion membrane, presented with fish like scales all over the body. Karyotyping revealed duplication of the chromosome arm on 22q12+ in the father and two siblings. Whole exome sequencing revealed a homozygous p.Gly218Ser variation in TGM1; a variation reported earlier in an isolated Finnish population in association with autosomal recessive non-syndromic ichthyosis. This concurrence of a potentially benign 22q12+ duplication and LI, both rare individually, is reported here likely for the first time. PMID:26594337

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

    PubMed

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

    2012-02-01

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

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

    PubMed

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

    2012-02-01

    Legionellosis (Legionnaires' disease; LD) is a form of severe pneumonia caused by species of Legionella bacteria. Because inhalation of Legionella-contaminated aerosol is considered the major infection route, routine assessments of potential infection sources such as hot water systems, air-conditioner cooling water, and municipal fountains are of great importance. In this study, we utilized in vitro culture and multilocus sequence analysis (MLSA) targeting 16S rRNA, mip, rpoB, and mip-rpoB concatenation to isolate and identify Legionella spp. from 5 municipal fountains in Chengdu City, Sichuan Province, China. Our results demonstrated that 16S rRNA was useful for initial identification, as it could recognize isolates robustly at the genus level, while the genes mip, rpoB, and mip-rpoB concatenation could confidently discriminate Legionella species. Notably, the three subspecies of L. pneumophila could be distinguished by the analysis based on rpoB. The serotyping result of strain CD-1 was consistent with genetic analysis based on the concatenation of mip and rpoB. Despite regular maintenance and sanitizing methods, 4 of the 5 municipal fountains investigated in this study were positive for Legionella contamination. Thus, regularly scheduled monitoring of municipal fountains is urgently needed as well as vigilant disinfection. Although the application of MLSA for inspection of potential sites of infection in public areas is not standard procedure, further investigations may prove its usefulness. PMID:22367947

  18. Accurate Optical Reference Catalogs

    NASA Astrophysics Data System (ADS)

    Zacharias, N.

    2006-08-01

    Current and near future all-sky astrometric catalogs on the ICRF are reviewed with the emphasis on reference star data at optical wavelengths for user applications. The standard error of a Hipparcos Catalogue star position is now about 15 mas per coordinate. For the Tycho-2 data it is typically 20 to 100 mas, depending on magnitude. The USNO CCD Astrograph Catalog (UCAC) observing program was completed in 2004 and reductions toward the final UCAC3 release are in progress. This all-sky reference catalogue will have positional errors of 15 to 70 mas for stars in the 10 to 16 mag range, with a high degree of completeness. Proper motions for the about 60 million UCAC stars will be derived by combining UCAC astrometry with available early epoch data, including yet unpublished scans of the complete set of AGK2, Hamburg Zone astrograph and USNO Black Birch programs. Accurate positional and proper motion data are combined in the Naval Observatory Merged Astrometric Dataset (NOMAD) which includes Hipparcos, Tycho-2, UCAC2, USNO-B1, NPM+SPM plate scan data for astrometry, and is supplemented by multi-band optical photometry as well as 2MASS near infrared photometry. The Milli-Arcsecond Pathfinder Survey (MAPS) mission is currently being planned at USNO. This is a micro-satellite to obtain 1 mas positions, parallaxes, and 1 mas/yr proper motions for all bright stars down to about 15th magnitude. This program will be supplemented by a ground-based program to reach 18th magnitude on the 5 mas level.

  19. MicroFinish Topographer: surface finish metrology for large and small optics

    NASA Astrophysics Data System (ADS)

    Parks, Robert E.

    2011-09-01

    The MicroFinish Topographer (MFT) is the result of an interest in directly measuring the surface roughness of large optics without the need for using replicas that may degrade the measurement data and that contaminate the surface. Once the MFT proved itself on large optics it was immediately suggested that a similar device should be designed for small optics. All this really took was turning the original MFT upside down and placing small specimens on a holder. This one device tests samples from 10 mm diameter to 10 m with phase measuring interferometry that does not need vibration isolation. Further, the MFT form factor makes it ideal for use in doing on-machine surface finish metrology.

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

    NASA Astrophysics Data System (ADS)

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

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

  1. 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

  2. 7 CFR 58.525 - Storage of finished product.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

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

  3. 7 CFR 58.525 - Storage of finished product.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

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

  4. 7 CFR 58.525 - Storage of finished product.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

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

  5. 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...

  6. 16 CFR 1508.7 - Construction and finishing.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

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

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

    EPA Science Inventory

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

  8. 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.

  9. 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

  10. 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

  11. 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

  12. Increasing the Scale of Deep Sequencing Data Analysis with BioHDF

    SciTech Connect

    Smith, Todd

    2010-06-03

    Todd Smith of Geospiza discusses how BioHDF systems can be used with next generation DNA sequencing technologies on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  13. 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

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

    ScienceCinema

    Appel, Maryke [Kappa Biosystems

    2016-07-12

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

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

    SciTech Connect

    Appel, Maryke

    2012-06-01

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

  16. 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.

  17. 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

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

    SciTech Connect

    Chain, Patrick

    2009-05-27

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

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

    PubMed

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

    2012-09-12

    Acrylamide is formed from reducing sugars and asparagine during the preparation of French fries. The commercial preparation of French fries is a multistage process involving the preparation of frozen, par-fried potato strips for distribution to catering outlets, where they are finish-fried. The initial blanching, treatment in glucose solution, and par-frying steps are crucial because they determine the levels of precursors present at the beginning of the finish-frying process. To minimize the quantities of acrylamide in cooked fries, it is important to understand the impact of each stage on the formation of acrylamide. Acrylamide, amino acids, sugars, moisture, fat, and color were monitored at time intervals during the frying of potato strips that had been dipped in various concentrations of glucose and fructose during a typical pretreatment. A mathematical model based on the fundamental chemical reaction pathways of the finish-frying was developed, incorporating moisture and temperature gradients in the fries. This showed the contribution of both glucose and fructose to the generation of acrylamide and accurately predicted the acrylamide content of the final fries. PMID:22924541

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

    PubMed

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

    2012-09-12

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

  1. Phosphorus requirement of finishing feedlot calves.

    PubMed

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

    2002-06-01

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

  2. 40 CFR 425.10 - Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS LEATHER TANNING AND FINISHING... finished leather by chemically dissolving the hide hair, chrome tanning, and retan-wet finishing....

  3. Ultrasound for wool dyeing and finishing.

    PubMed

    McNeil, S J; McCall, R A

    2011-01-01

    The effects of ultrasound at 35-39 kHz on several wool dyeing and finishing processes have been investigated as a way of reducing environmental impact. Ultrasound improved the effectiveness of cleaning scoured wool in water and to a lesser extent in water-nonionic surfactant. Scanning electron microscopy did not indicate any surface damage. Fluorescence microscopy revealed increased levels of sulphydryl groups on the wool surface suggesting ultrasound caused the removal of thioester-bound lipids. Ultrasound pre-treatment increased the effectiveness of subsequent oxidative-reductive bleaching, but had no effect on the uptake of acid levelling and acid milling dyes. The pre-treatment retarded the uptake of reactive dye, possibly by increasing the crystallinity of the fibre or removing surface bound lipids. Ultrasound did not improve dyeing under conditions that are currently used in industry, but did show potential to reduce the chemical and energy requirements of dyeing wool with reactive and acid milling dyes, but not acid levelling dyes. PMID:20675174

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  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. Effect of silicone finishes on the burning behavior of polyester

    NASA Astrophysics Data System (ADS)

    Boyon, Julien Xavier Eric

    Polyester fibers are widely used as filling in home applications such as pillows or comforters. Silicone finishes can be used to reduce friction between fibers during processing or as softeners to impart a pleasant down like hand on the fibers. However, it has been reported that these added silicone-based finishes may have a negative effect on the burning behavior of polyester. This research examined the possible mechanisms that can modify the response of polyester fibers when subjected to a flame source. In this study, a spunbond needled polyester nonwoven substrate was treated with different commercial silicone-based finishes. A vertical flame test was used to compare the effect of silicone finishes on the burning behavior of polyester to the inherent burning behavior of untreated polyester. Thermogravimetric analyses (TGA) were performed on spunbond polyester fabric samples to investigate the influence of silicone finishes on the thermal degradation of polyester in air. Residues from TGA were examined using Scanning Electron Microscopy coupled with elemental analysis. Vertical flammability testing showed that even at a low level, the application of silicone-based finishes on a polyester substrate resulted in a dramatic increase of the flame propagation by preventing its inherent response to heat. Thermograms suggested that the silicone finishes had little or no effect on the thermal degradation of polyester substrates.

  10. 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.

  11. 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...

  12. 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...

  13. 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...

  14. Electrocoagulation treatment of metal finishing wastewater.

    PubMed

    Odongo, Isabel E; McFarland, Michael J

    2014-07-01

    Electrocoagulation has been found to be a consistent and reliable industrial wastewater treatment process capable of removing heavy metals to levels well below pretreatment discharge standards. Results from the testing of a 113 L/min pilot scale electrocoagulation unit indicated that electrocoagulation was capable of decreasing the cadmium, chromium, and nickel concentrations from 0.14, 18.1, and 0.06 parts per million (ppm) to 0.029, 0.039, and 0.020 ppm respectively, at a 1-min hydraulic retention time. In the presence of a strong chelating substance, electrocoagulation performance was found to be effective in reducing both chromium and nickel concentrations to levels well below discharge limits. At a pH of 8.0, chromium and nickel influent concentrations of 0.328 and 0.062 ppm, respectively, were reduced to 0.005 and 0.04 ppm. The electrocoagulation removal efficiency for chromium remained high at over 98% and appeared to be unaffected by the presence of chelating substances. Utilizing aluminum as the sacrificial anode improved the removal efficiency of targeted heavy metals when the industrial wastewater was treated under acidic conditions. At a pH of 5.6, the influent concentrations of the regulated heavy metals cadmium, chromium, and nickel were reduced from 0.55, 49.7, and 13.7 ppm, respectively, to 0.013, 2.7, and 0.8 ppm at a 1-min hydraulic retention time. The results of these tests suggest that the formation of ferric hydroxide and aluminum hydroxide through the electrocoagulation process may be an effective approach for treating metal finishing wastewaters.

  15. An Inside Look at the JGI’s Sequencing Operation

    SciTech Connect

    Daum, Chris

    2010-06-02

    Chris Daum of the DOE Joint Genome Institute discusses how the DOE JGI's Production Sequencing group optimizes the sequencer pipelines and assesses quality on the Production line on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  16. 30 CFR 18.33 - Finish of surface joints.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...-arresting path shall be plane to within a maximum deviation of one-half the maximum clearance specified in § 18.31(a)(6). All metal surfaces forming a flame-arresting path shall be finished during...

  17. 30 CFR 18.33 - Finish of surface joints.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...-arresting path shall be plane to within a maximum deviation of one-half the maximum clearance specified in § 18.31(a)(6). All metal surfaces forming a flame-arresting path shall be finished during...

  18. 30 CFR 18.33 - Finish of surface joints.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...-arresting path shall be plane to within a maximum deviation of one-half the maximum clearance specified in § 18.31(a)(6). All metal surfaces forming a flame-arresting path shall be finished during...

  19. 30 CFR 18.33 - Finish of surface joints.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...-arresting path shall be plane to within a maximum deviation of one-half the maximum clearance specified in § 18.31(a)(6). All metal surfaces forming a flame-arresting path shall be finished during...

  20. Portable flooring protects finished surfaces, is easily moved

    NASA Technical Reports Server (NTRS)

    Carmody, R. J.

    1964-01-01

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

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

    SciTech Connect

    ENTROP, G.E.

    1999-12-03

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

  2. 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...

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

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

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

  5. 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

  6. 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

  7. 55. VIEW OF FINISHED CONCRETE COUNTERWEIGHT CAR SUPPORTED BY BLOCK ...

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

    55. VIEW OF FINISHED CONCRETE COUNTERWEIGHT CAR SUPPORTED BY BLOCK AND TACKLE ASSEMBLY LOOKING WEST, Date unknown, circa January 1948. - Variable Angle Launcher Complex, Variable Angle Launcher, CA State Highway 39 at Morris Reservior, Azusa, Los Angeles County, CA

  8. Synteny-based mapping-by-sequencing enabled by targeted enrichment.

    PubMed

    Galvão, Vinicius C; Nordström, Karl J V; Lanz, Christa; Sulz, Patric; Mathieu, Johannes; Posé, David; Schmid, Markus; Weigel, Detlef; Schneeberger, Korbinian

    2012-08-01

    Mapping-by-sequencing, as implemented in SHOREmap ('SHOREmapping'), is greatly accelerating the identification of causal mutations. The original SHOREmap approach based on resequencing of bulked segregants required a highly accurate and complete reference sequence. However, current whole-genome or transcriptome assemblies from next-generation sequencing data of non-model organisms do not produce chromosome-length scaffolds. We have therefore developed a method that exploits synteny with a related genome for genetic mapping. We first demonstrate how mapping-by-sequencing can be performed using a reduced number of markers, and how the associated decrease in the number of markers can be compensated for by enrichment of marker sequences. As proof of concept, we apply this method to Arabidopsis thaliana gene models ordered by synteny with the genome sequence of the distant relative Brassica rapa, whose genome has several large-scale rearrangements relative to A. thaliana. Our approach provides an alternative method for high-resolution genetic mapping in species that lack finished genome reference sequences or for which only RNA-seq assemblies are available. Finally, for improved identification of causal mutations by fine-mapping, we introduce a new likelihood ratio test statistic, transforming local allele frequency estimations into a confidence interval similar to conventional mapping intervals.

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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.

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

    ScienceCinema

    Muzny, Donna [Baylor College of Medicine

    2016-07-12

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

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

    ScienceCinema

    Lane, Todd [SNL

    2016-07-12

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

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

    ScienceCinema

    FitzGerald, Michael [Broad Institute

    2016-07-12

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

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

    SciTech Connect

    Lane, Todd

    2012-06-01

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

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

    SciTech Connect

    Muzny, Donna

    2012-06-01

    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.

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

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... woven fabric finishing subcategory. 410.40 Section 410.40 Protection of Environment ENVIRONMENTAL... Fabric Finishing Subcategory § 410.40 Applicability; description of the woven fabric finishing... following types of textile mills: woven fabric finishers, which may include any or all of the following...

  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. 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

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

    PubMed

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

    2011-05-01

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

  3. 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

  4. 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.

  5. Influence of surface finish on the cleanability of stainless steel.

    PubMed

    Frank, J F; Chmielewski, R

    2001-08-01

    Stainless steel for fabricating food processing equipment is available with various surface finishes. The objective of this research was to determine the effect of surface finish on cleanability. Nine samples of stainless steel, type 304, from various manufacturers including no finish (hot rolled and pickled), #4 finish, 2B mechanical polished, and electropolished were tested. Cleanability was assessed by using coupon samples soiled with either cultured milk inoculated with spores of Bacillus stearothermophilus or by growth of a Pseudomonas sp. biofilm. Samples were cleaned by immersion in a turbulent bath of 1.28% sodium hydroxide at 66 degrees C for 3 min followed by a sterile water rinse, neutralizing in 0.1% phosphoric acid for 30 s, rinsing in phosphate buffer, sanitizing in 100 ppm hypochlorite, neutralizing in sodium thiosulfate, and drying. To determine residual milk soil, coupon samples were covered with PM indicator agar and incubated for 25 h at 58 degrees C. Other coupons were subjected to an additional 10 soiling or cleaning cycles, and the residual protein was measured by using epifluorescent microscopy and image analysis. Results indicate that the spore count was more precise for measuring initial cleanability of the finished samples, and the protein residue determination was useful for determining the effect of repeated cleaning. Data on the removal of milk soil suggest that stainless steel should be purchased based on measures of surface defects rather than finish type. Surface defects, as determined using a surface roughness gauge, produced a correlation of 0.82 with spore counts. Data also indicated that biofilm was more difficult to remove than milk-based soil. PMID:11510656

  6. 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.

  7. 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…

  8. 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

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

    SciTech Connect

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

    1991-10-01

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

  10. 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...

  11. 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...

  12. 16 CFR 1509.8 - Construction and finishing.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... REGULATIONS REQUIREMENTS FOR NON-FULL-SIZE BABY CRIBS § 1509.8 Construction and finishing. (a) All wood surfaces of non-full-size baby cribs shall be smooth and free from splinters. (b) All wood parts of non-full-size baby cribs shall be free from splits, cracks, or other defects that might lead to...

  13. 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...

  14. Cement Finishing. Pre-Apprenticeship Phase 2 Training. Instructor's Guide.

    ERIC Educational Resources Information Center

    Nama, Joe

    This instructor's guide accompanies the self-paced student training modules on cement finishing, available separately as CE 031 576. Introductory materials include a description of the components of the pre-apprenticeship project, discussion of teacher's role in students' completion of the modules, and scope and contents of Phase 2 training. Each…

  15. Carpentry and Finishing Procedures. Building Maintenance. Module II. Instructor's Guide.

    ERIC Educational Resources Information Center

    Hawk, Sam; Brunk, Art

    This curriculum guide, keyed to the building maintenance competency profile developed by industry and education professionals, provides three units on carpentry and finishing procedures. The first unit, Exterior Carpentry, contains the following lessons: carpentry safety procedures, ladder and scaffolding safety, door installation/repair,…

  16. 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…

  17. Plutonium Finishing Plant assessment of confinement system bypass leakage

    SciTech Connect

    Dick, J.D.

    1996-09-30

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

  18. 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...

  19. 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…

  20. 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…

  1. 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...

  2. 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.

  3. Profitable capitation requires accurate costing.

    PubMed

    West, D A; Hicks, L L; Balas, E A; West, T D

    1996-01-01

    In the name of costing accuracy, nurses are asked to track inventory use on per treatment basis when more significant costs, such as general overhead and nursing salaries, are usually allocated to patients or treatments on an average cost basis. Accurate treatment costing and financial viability require analysis of all resources actually consumed in treatment delivery, including nursing services and inventory. More precise costing information enables more profitable decisions as is demonstrated by comparing the ratio-of-cost-to-treatment method (aggregate costing) with alternative activity-based costing methods (ABC). Nurses must participate in this costing process to assure that capitation bids are based upon accurate costs rather than simple averages. PMID:8788799

  4. 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

  5. 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

  6. 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

  7. 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...

  8. 40 CFR 63.5395 - How do I measure the density of a finish?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... density of a finish, the reference method is EPA Method 24 of appendix A of 40 CFR part 60. You may use... National Emission Standards for Hazardous Air Pollutants for Leather Finishing Operations Testing...

  9. 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.

  10. 40 CFR 425.20 - Applicability; description of the hair save, chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS LEATHER TANNING AND FINISHING... cattle-like hides into finished leather by hair save unhairing, chrome tanning, and retan-wet finishing....

  11. Accurate SHAPE-directed RNA structure determination

    PubMed Central

    Deigan, Katherine E.; Li, Tian W.; Mathews, David H.; Weeks, Kevin M.

    2009-01-01

    Almost all RNAs can fold to form extensive base-paired secondary structures. Many of these structures then modulate numerous fundamental elements of gene expression. Deducing these structure–function relationships requires that it be possible to predict RNA secondary structures accurately. However, RNA secondary structure prediction for large RNAs, such that a single predicted structure for a single sequence reliably represents the correct structure, has remained an unsolved problem. Here, we demonstrate that quantitative, nucleotide-resolution information from a SHAPE experiment can be interpreted as a pseudo-free energy change term and used to determine RNA secondary structure with high accuracy. Free energy minimization, by using SHAPE pseudo-free energies, in conjunction with nearest neighbor parameters, predicts the secondary structure of deproteinized Escherichia coli 16S rRNA (>1,300 nt) and a set of smaller RNAs (75–155 nt) with accuracies of up to 96–100%, which are comparable to the best accuracies achievable by comparative sequence analysis. PMID:19109441

  12. Accurate documentation and wound measurement.

    PubMed

    Hampton, Sylvie

    This article, part 4 in a series on wound management, addresses the sometimes routine yet crucial task of documentation. Clear and accurate records of a wound enable its progress to be determined so the appropriate treatment can be applied. Thorough records mean any practitioner picking up a patient's notes will know when the wound was last checked, how it looked and what dressing and/or treatment was applied, ensuring continuity of care. Documenting every assessment also has legal implications, demonstrating due consideration and care of the patient and the rationale for any treatment carried out. Part 5 in the series discusses wound dressing characteristics and selection.

  13. 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... POINT 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...

  14. 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... POINT 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...

  15. 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... POINT 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...

  16. 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...

  17. 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... 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...

  18. 40 CFR 410.40 - Applicability; description of the woven fabric finishing subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 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....

  19. 40 CFR 410.60 - Applicability; description of the carpet finishing subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... carpet finishing subcategory. 410.60 Section 410.60 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Carpet Finishing Subcategory § 410.60 Applicability; description of the carpet finishing subcategory. The provisions of...

  20. 40 CFR 410.60 - Applicability; description of the carpet finishing subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... carpet finishing subcategory. 410.60 Section 410.60 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Carpet Finishing Subcategory § 410.60 Applicability; description of the carpet finishing subcategory. The provisions of...

  1. 40 CFR 410.60 - Applicability; description of the carpet finishing subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... carpet finishing subcategory. 410.60 Section 410.60 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Carpet Finishing Subcategory § 410.60 Applicability; description of the carpet finishing subcategory. The provisions of...

  2. 40 CFR 410.60 - Applicability; description of the carpet finishing subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... carpet finishing subcategory. 410.60 Section 410.60 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Carpet Finishing Subcategory § 410.60 Applicability; description of the carpet finishing subcategory. The provisions of...

  3. 40 CFR 410.60 - Applicability; description of the carpet finishing subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... carpet finishing subcategory. 410.60 Section 410.60 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Carpet Finishing Subcategory § 410.60 Applicability; description of the carpet finishing subcategory. The provisions of...

  4. 21 CFR 181.26 - Drying oils as components of finished resins.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Drying oils as components of finished resins. 181... Prior-Sanctioned Food Ingredients § 181.26 Drying oils as components of finished resins. Substances classified as drying oils, when migrating from food-packaging material (as components of finished...

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

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 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....

  6. 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....

  7. 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....

  8. 40 CFR 410.40 - Applicability; description of the woven fabric finishing subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 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....

  9. 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...

  10. 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...

  11. 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...

  12. 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... 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. 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...

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

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... finished water reservoir requirements? 141.510 Section 141.510 Protection of Environment ENVIRONMENTAL... 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...

  15. 40 CFR 141.511 - What is required of new finished water reservoirs?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 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...

  16. 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...

  17. 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...

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

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 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...

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

    PubMed

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

    2006-08-01

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

  1. Methods for accurate homology modeling by global optimization.

    PubMed

    Joo, Keehyoung; Lee, Jinwoo; Lee, Jooyoung

    2012-01-01

    High accuracy protein modeling from its sequence information is an important step toward revealing the sequence-structure-function relationship of proteins and nowadays it becomes increasingly more useful for practical purposes such as in drug discovery and in protein design. We have developed a protocol for protein structure prediction that can generate highly accurate protein models in terms of backbone structure, side-chain orientation, hydrogen bonding, and binding sites of ligands. To obtain accurate protein models, we have combined a powerful global optimization method with traditional homology modeling procedures such as multiple sequence alignment, chain building, and side-chain remodeling. We have built a series of specific score functions for these steps, and optimized them by utilizing conformational space annealing, which is one of the most successful combinatorial optimization algorithms currently available.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. Dust control technology usage patterns in the drywall finishing industry.

    PubMed

    Young-Corbett, Deborah E; Nussbaum, Maury A

    2009-06-01

    A telephone survey was conducted to quantify drywall finishing industry usage rates of dust control technology, identify barriers to technology adoption, and explore firm owner perception of risk. Industry use of the following technologies was described: wet methods, respiratory protection, pole sanders, ventilated sanders, and low-dust joint compound. A survey instrument composed of both Likert-type scaled items and open-ended items was developed and administered by telephone to the census population of the owners of member firms of trade associations: Finishing Contractors Association and Association of the Wall and Ceiling Industries. Of 857 firms, 264 interviews were completed. Along with descriptive statistics, results were analyzed to examine effects of firm size and union affiliation on responses. Responses to open-ended items were analyzed using content analysis procedures. Firm owners rated the risk of dust to productivity and customer satisfaction as low-moderate. Half rated the dust as having some impact on worker health, with higher impacts indicated by owners of small firms. Among the available control technologies, respiratory protection was used most frequently. Several barriers to implementation of the more effective control technologies were identified. Barriers associated with technology usability, productivity, and cost, as well as misperceptions of risk, should be addressed to improve dust control in the drywall finishing industry.

  7. 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.

  8. 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

  9. 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

  10. SPLASH: Accurate OH maser positions

    NASA Astrophysics Data System (ADS)

    Walsh, Andrew; Gomez, Jose F.; Jones, Paul; Cunningham, Maria; Green, James; Dawson, Joanne; Ellingsen, Simon; Breen, Shari; Imai, Hiroshi; Lowe, Vicki; Jones, Courtney

    2013-10-01

    The hydroxyl (OH) 18 cm lines are powerful and versatile probes of diffuse molecular gas, that may trace a largely unstudied component of the Galactic ISM. SPLASH (the Southern Parkes Large Area Survey in Hydroxyl) is a large, unbiased and fully-sampled survey of OH emission, absorption and masers in the Galactic Plane that will achieve sensitivities an order of magnitude better than previous work. In this proposal, we request ATCA time to follow up OH maser candidates. This will give us accurate (~10") positions of the masers, which can be compared to other maser positions from HOPS, MMB and MALT-45 and will provide full polarisation measurements towards a sample of OH masers that have not been observed in MAGMO.

  11. 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.

  12. Accurate thickness measurement of graphene.

    PubMed

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

    2016-03-29

    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.

  13. 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.

  14. 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

  15. Noncontiguous finished genome sequence and description of Murdochiella massiliensis strain SIT12 sp. nov.

    PubMed

    Vicino, E; Traore, S I; Cimmino, T; Dubourg, G; Labas, N; Andrieu, C; Di Pinto, F; Sokhna, C; Diallo, A; Raoult, D; Rolain, J M

    2016-11-01

    Murdochiella massiliensis strain SIT12 (= CSUR P1987 = DSM 29078) is the type strain of M. massiliensis sp. nov. This bacterium was isolated from the stool of a healthy 2-year-old Senegalese boy. M. massiliensis is an anaerobic, Gram-positive coccus. The genome size of M. massiliensis strain SIT12 is 1 642 295 bp with 48.9% G+C content and assembled into two scaffolds. PMID:27660714

  16. Noncontiguous finished genome sequence and description of Murdochiella massiliensis strain SIT12 sp. nov.

    PubMed

    Vicino, E; Traore, S I; Cimmino, T; Dubourg, G; Labas, N; Andrieu, C; Di Pinto, F; Sokhna, C; Diallo, A; Raoult, D; Rolain, J M

    2016-11-01

    Murdochiella massiliensis strain SIT12 (= CSUR P1987 = DSM 29078) is the type strain of M. massiliensis sp. nov. This bacterium was isolated from the stool of a healthy 2-year-old Senegalese boy. M. massiliensis is an anaerobic, Gram-positive coccus. The genome size of M. massiliensis strain SIT12 is 1 642 295 bp with 48.9% G+C content and assembled into two scaffolds.

  17. 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

  18. 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, ...

  19. 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...

  20. 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

  1. 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.

  2. 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

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

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 12 2010-07-01 2010-07-01 true Example Logs for Recording Leather... Finishing Operations Part 63, Subpt. TTTT, Fig. 1 Figure 1 to Subpart TTTT of Part 63—Example Logs for Recording Leather Finish Use and HAP Content Month:______Year:______ Finish Inventory Log Finish type...

  4. 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...

  5. 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 §...

  6. Determination of heavy metal toxicity of finished leather solid waste.

    PubMed

    Aslan, Ahmet

    2009-05-01

    This paper investigates the toxicity in leather products of heavy metals known to be detrimental to the ecosystem. Heavy metal concentrations in leather samples were identified with ICP-OES, and toxicity was determined using a MetPLATE bioassay. Chromium and aluminium were found to constitute 98% of the total concentration of heavy metals in finished leather tanned with chromium and aluminium salts, while in some vegetable-tanned leather, zirconium was the only heavy metal identified. The average inhibition values for chromium, aluminium and vegetable tanned leather were 98.08%, 97.04% and 62.36%, respectively. PMID:19165404

  7. Determination of heavy metal toxicity of finished leather solid waste.

    PubMed

    Aslan, Ahmet

    2009-05-01

    This paper investigates the toxicity in leather products of heavy metals known to be detrimental to the ecosystem. Heavy metal concentrations in leather samples were identified with ICP-OES, and toxicity was determined using a MetPLATE bioassay. Chromium and aluminium were found to constitute 98% of the total concentration of heavy metals in finished leather tanned with chromium and aluminium salts, while in some vegetable-tanned leather, zirconium was the only heavy metal identified. The average inhibition values for chromium, aluminium and vegetable tanned leather were 98.08%, 97.04% and 62.36%, respectively.

  8. 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

  9. 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.

  10. Accident Analysis for the Plutonium Finishing Plant Polycube Stabilization Process

    SciTech Connect

    NELSON-MAKI, B.B.

    2001-05-14

    The Polycube Stabilization Project involves low temperature oxidation, without combustion, of polystyrene cubes using the production muffle furnaces in Glovebox HC-21C located in the Remote Mechanical ''C'' (RMC) Line in Room 230A in the 234-52 Facility. Polycubes are polystyrene cubes containing various concentrations of plutonium and uranium oxides. Hundreds of these cubes were manufactured for criticality experiments, and currently exist as unstabilized storage forms at the Plutonium Finishing Plant (PFP). This project is designed to stabilize and prepare the polycube material for stable storage using a process very similar to the earlier processing of sludges in these furnaces. The significant difference is the quantity of hydrogenous material present, and the need to place additional controls on the heating rate of the material. This calculation note documents the analyses of the Representative Accidents identified in Section 2.4.4 of Hazards Analysis for the Plutonium Finishing Plant Polycube Stabilization Process, HNF-7278 (HNF 2000). These two accidents, ''Deflagration in Glovebox HC-21C due to Loss of Power'' and ''Seismic Failure of Glovebox HC-21C'', will be further assessed in this accident analysis.

  11. 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

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  7. Finishing and proof testing of windows for manned space craft

    NASA Astrophysics Data System (ADS)

    Miska, Herbert A.

    1993-12-01

    The development of the Space Shuttle Orbiter in the early 1970s marked the first time that a fracture mechanics approach was taken to the design of the window systems of a manned space craft. Earlier vehicles were never subjected to repeated launch and re-entry and therefore fatigue or slow crack growth were not major concerns. The design and proof test methodology evolved at that time continues to be applied in the development of the window systems for the Space Station Freedom. A combination of fixed abrasive grinding, lapping, and chemical machining is employed on the fused silica window panes to insure that sub- surface damage is carefully controlled and minimized. All panes are proof tested under controlled atmospheric conditions which preclude crack growth during the test. This paper also covers some of the history of space craft window design, the rationale for the material choices as well as a review of the finishing and test methods employed.

  8. Plutonium Finishing Plant Transition Project mission analysis report

    SciTech Connect

    Courson, D.B.

    1994-09-21

    This report defines the mission for the Plutonium Finishing Plant Transition Project (PFPTP) using a systems engineering approach. This mission analysis will be the basis for the functional analysis which will further define and break down the mission statement into all of the detailed functions required to accomplish the mission. The functional analysis is then used to develop requirements, allocate those requirements to functions, and eventually be used to design the system. This report: presents the problem which will be addressed, defines PFP Transition Project, defines the overall mission statement, describes the existing, initial conditions, defines the desired, final conditions, identifies the mission boundaries and external interfaces, identifies the resources required to carry out the mission, describes the uncertainties and risks, and discusses the measures which will be used to determine success.

  9. 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

  10. 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

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

    SciTech Connect

    DICK, J.D.

    2000-02-28

    The Plutonium Finishing Plant (PFP) WAC System includes sub-systems 25A through 25K. Specific system boundaries and justifications are contained in HNF-SD-CP-SDD-005, ''Definition and Means of Maintaining the Ventilation System Confinement Portion of the PFP Safety Envelope.'' The procurement requirements associated with the system necessitates procurement of some system equipment as Commercial Grade Items in accordance with HNF-PRO-268, ''Control of Purchased Items and Services.'' This document lists safety class and safety significant components for the Heating Ventilation Air Conditioning and specifies the critical characteristics for Commercial Grade Items, as required by HNF-PRO-268 and HNF-PRO-1819. These are the minimum specifications that the equipment must meet in order to properly perform its safety function. There may be several manufacturers or models that meet the critical characteristics for any one item.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

    Barman, Anwesa; Das, Manas

    2016-05-01

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

  14. 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.

  15. Subaperture approaches to finishing and testing astronomical optics

    NASA Astrophysics Data System (ADS)

    Forbes, Gregory W.; Tricard, Marc

    2004-07-01

    We describe the application of both stitching interferometry and magneto-rheological finishing (MRF) to the surface metrology and final figure correction of large optics. These particular subaperture technologies help to address the need for flexible systems that improve both overall manufacturing time and cost effectiveness. MRF can achieve high volumetric removal rates with a small-footprint tool that is perfectly conformable and highly stable. This tool is therefore well suited to finishing large optics (including aspheres) and correcting mid-spatial frequency errors. The system does not need vacuum, reduces microroughness to below one nm rms on most materials, and is able to meet the figure tolerance specs for astronomical optics. Such a technology is ideally complemented by a system for the stitching of interferometric subaperture data. Stitching inherently enables the testing of larger apertures with higher resolution and, thanks to the inbuilt calibration, even to higher accuracy in many situations. Moreover, given the low-order character of the dominant residual uncertainties in the stitched full-aperture data, such an approach is well suited to adaptive mirrors because the actuators correct precisely these deformations. While this approach enables the non-null testing of parts with greater aspheric departure and can lead to a significantly reduced non-common air path in the testing of long-radius concave parts, it is especially effective for convex optics. That is, stitching is particularly well suited to the testing of secondary mirrors and, alongside the testing of the off-axis primary segments, these are clearly critical challenges for extremely large telescope (ELT) projects.

  16. 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

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

    PubMed

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

    2016-09-01

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

  18. 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.

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

    ScienceCinema

    Weinstock, George [Washington University

    2016-07-12

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

  20. 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.

  1. 46 CFR 116.422 - Ceilings, linings, trim, interior finish and decorations.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Ceilings, linings, trim, interior finish and decorations... PASSENGERS CONSTRUCTION AND ARRANGEMENT Fire Protection § 116.422 Ceilings, linings, trim, interior finish and decorations. (a) Ceilings, linings, and any furring incidental to their installation in...

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

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 4 2014-10-01 2014-10-01 false Ceilings, linings, trim, interior finish and decorations... PASSENGERS CONSTRUCTION AND ARRANGEMENT Fire Protection § 116.422 Ceilings, linings, trim, interior finish and decorations. (a) Ceilings, linings, and any furring incidental to their installation in...

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

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 4 2013-10-01 2013-10-01 false Ceilings, linings, trim, interior finish and decorations... PASSENGERS CONSTRUCTION AND ARRANGEMENT Fire Protection § 116.422 Ceilings, linings, trim, interior finish and decorations. (a) Ceilings, linings, and any furring incidental to their installation in...

  4. 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...

  5. 40 CFR 410.20 - Applicability; description of the wool finishing subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...: wool finishers, including carbonizing, fulling, dyeing, bleaching, rinsing, fireproofing, and other... 40 Protection of Environment 29 2011-07-01 2009-07-01 true Applicability; description of the wool... (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Wool Finishing...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Roughage is mechanically processed to increase digestibility, and handling and mixing characteristics in finishing diets. Roughage is fed to promote rumen health and decrease digestive upset, but inclusion in finishing diets is limited due to the cost per unit of energy. Rumination behavior may be a...

  7. 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...

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

    Code of Federal Regulations, 2011 CFR

    2011-04-01

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

  9. "Miss! I'm Done!" Finishing Craft Assignments as a Situated Activity System in Preschool

    ERIC Educational Resources Information Center

    Deunk, Marjolein; Berenst, Jan; de Glopper, Kees

    2010-01-01

    We describe the Situated Activity System of finishing craft assignments in preschool: the specific, routinized way that child and teacher jointly close the child's craft assignment, employing a specific discourse pattern. We analyzed the interactions of 14 Dutch children between 2.1 and 3.10 years old while they were finishing their craft…

  10. 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

    ... contaminants in uncovered finished water reservoirs; and potential assessment approaches to determine the... 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...

  11. 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...

  12. 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...

  13. Development of USTES Aptitude Test Battery for Photograph Finisher (Any Industry) I 976.886.

    ERIC Educational Resources Information Center

    Wisconsin State Employment Service, Madison.

    To develop General Aptitude Test Battery (GATB) norms for the occupation of photograph finisher, 59 female workers employed as photograph finishers in Wisconsin were administered all 12 tests of the GATB and the Research Questionnaire-Background during July 1969. Supervisory ratings of job proficiency were made at approximately the same time as…

  14. 21 CFR 181.26 - Drying oils as components of finished resins.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) PRIOR-SANCTIONED FOOD INGREDIENTS Specific Prior-Sanctioned Food Ingredients § 181.26 Drying oils as components of finished resins. Substances... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Drying oils as components of finished resins....

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

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) PRIOR-SANCTIONED FOOD INGREDIENTS Specific Prior-Sanctioned Food Ingredients § 181.26 Drying oils as components of finished resins. Substances... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Drying oils as components of finished resins....

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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

  1. 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.

  2. 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...

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

    PubMed

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

    2017-01-01

    Biopart Assembly Standard for Idempotent Cloning (BASIC) is a simple, accurate, and robust DNA assembly method. The method is based on linker-mediated DNA assembly and provides highly accurate DNA assembly with 99 % correct assemblies for four parts and 90 % correct assemblies for seven parts [1]. The BASIC standard defines a single entry vector for all parts flanked by the same prefix and suffix sequences and its idempotent nature means that the assembled construct is returned in the same format. Once a part has been adapted into the BASIC format it can be placed at any position within a BASIC assembly without the need for reformatting. This allows laboratories to grow comprehensive and universal part libraries and to share them efficiently. The modularity within the BASIC framework is further extended by the possibility of encoding ribosomal binding sites (RBS) and peptide linker sequences directly on the linkers used for assembly. This makes BASIC a highly versatile library construction method for combinatorial part assembly including the construction of promoter, RBS, gene variant, and protein-tag libraries. In comparison with other DNA assembly standards and methods, BASIC offers a simple robust protocol; it relies on a single entry vector, provides for easy hierarchical assembly, and is highly accurate for up to seven parts per assembly round [2]. PMID:27671933

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

    PubMed

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

    2017-01-01

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

  5. 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

  6. Temperature Control of Hot Strip Finishing Mill with Inter Stand Cooling

    NASA Astrophysics Data System (ADS)

    Sekiguchi, Kunio; Anbe, Yoshiharu; Imanari, Hiroyuki

    It is important for hot strip mill to keep finishing mill delivery temperature to it’s target value because of yield strength and tensile strength of rolled strip. We propose a new method for finishing mill delivery temperature control (FDTC) of a hot strip mill using inter stand strip coolant (ISC). FDTC consists of initial setting (before threading) values calculation of ISC flow rate and finishing mill speed, feed forward FDTC (FF-FDTC) and feedback FDTC (FB-FDTC). The mathematical strip temperature model of finishing mill was identified using normal operating data and some tests. Actual mill application with 7 stands finishing mill showed good FDTC results and also it made possible to increase rolling speed which increase production rate.

  7. 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

  8. Toward a Catalog of Human Genes and Proteins: Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs

    PubMed Central

    Wiemann, Stefan; Weil, Bernd; Wellenreuther, Ruth; Gassenhuber, Johannes; Glassl, Sabine; Ansorge, Wilhelm; Böcher, Michael; Blöcker, Helmut; Bauersachs, Stefan; Blum, Helmut; Lauber, Jürgen; Düsterhöft, Andreas; Beyer, Andreas; Köhrer, Karl; Strack, Normann; Mewes, Hans-Werner; Ottenwälder, Birgit; Obermaier, Brigitte; Tampe, Jens; Heubner, Dagmar; Wambutt, Rolf; Korn, Bernhard; Klein, Michaela; Poustka, Annemarie

    2001-01-01

    With the complete human genomic sequence being unraveled, the focus will shift to gene identification and to the functional analysis of gene products. The generation of a set of cDNAs, both sequences and physical clones, which contains the complete and noninterrupted protein coding regions of all human genes will provide the indispensable tools for the systematic and comprehensive analysis of protein function to eventually understand the molecular basis of man. Here we report the sequencing and analysis of 500 novel human cDNAs containing the complete protein coding frame. Assignment to functional categories was possible for 52% (259) of the encoded proteins, the remaining fraction having no similarities with known proteins. By aligning the cDNA sequences with the sequences of the finished chromosomes 21 and 22 we identified a number of genes that either had been completely missed in the analysis of the genomic sequences or had been wrongly predicted. Three of these genes appear to be present in several copies. We conclude that full-length cDNA sequencing continues to be crucial also for the accurate identification of genes. The set of 500 novel cDNAs, and another 1000 full-coding cDNAs of known transcripts we have identified, adds up to cDNA representations covering 2%–5 % of all human genes. We thus substantially contribute to the generation of a gene catalog, consisting of both full-coding cDNA sequences and clones, which should be made freely available and will become an invaluable tool for detailed functional studies. [The sequence data described in this paper have been submitted to the EMBL database under the accession nos. given in Table 2.] PMID:11230166

  9. 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

  10. A fast and accurate method for echocardiography strain rate imaging

    NASA Astrophysics Data System (ADS)

    Tavakoli, Vahid; Sahba, Nima; Hajebi, Nima; Nambakhsh, Mohammad Saleh

    2009-02-01

    Recently Strain and strain rate imaging have proved their superiority with respect to classical motion estimation methods in myocardial evaluation as a novel technique for quantitative analysis of myocardial function. Here in this paper, we propose a novel strain rate imaging algorithm using a new optical flow technique which is more rapid and accurate than the previous correlation-based methods. The new method presumes a spatiotemporal constancy of intensity and Magnitude of the image. Moreover the method makes use of the spline moment in a multiresolution approach. Moreover cardiac central point is obtained using a combination of center of mass and endocardial tracking. It is proved that the proposed method helps overcome the intensity variations of ultrasound texture while preserving the ability of motion estimation technique for different motions and orientations. Evaluation is performed on simulated, phantom (a contractile rubber balloon) and real sequences and proves that this technique is more accurate and faster than the previous methods.

  11. Establishing Trailer Ventilation (Boarding) Requirements for Finishing Pigs during Transport

    PubMed Central

    McGlone, John; Sapkota, Avi; Johnson, Anna; Kephart, Rebecca

    2014-01-01

    Simple Summary Transport is an inevitable process in the modern swine industry due to the multiple-site approach to raising pigs and transport can be a significant source of stress to the animals, which raises a welfare concern. Maintaining the environment inside the transport trailer is crucial for pig comfort. This study aims to determine the amount of ventilation, or varied side-wall boarding, required to keep pigs within their thermal comfort zone. Examination of 302 trailers transporting 48,143 pigs found that pig losses were highest when low boarding levels (open sides) were used in cold air temperatures (<5 °C). In mild air temperatures (5 to 26 °C), boarding levels had little impact on pig losses. Abstract Specifically, this study aimed to establish the effects on mortality and morbidity of boarding levels (amount of side-wall trailer ventilation) for finishing pigs in mild weather (8.80 ± 0.30 °C, 71.70% ± 1.12% humidity). Pigs from commercial finishing sites were transported in 302 pot-bellied trailers to commercial processing plants. Measures collected at the processing plant were rates of dead on arrival (DOA), non-ambulatory, non-injured (NANI), non-ambulatory, injured (NAI), and total dead and down (D&D). Boarding levels (% that side walls were closed off with inserted boards) were divided into 3 bins: low, medium, and high, and outside temperature was divided into 4 bins <5 °C, 5.10–10 °C, and 10.10–15 °C and >15 °C. Average rates of DOA, NANI, NAI, and D&D were approximately 0.30%, 0.12%, 0.04%, and 0.46%, respectively. The D&D was highest when boarding level was low with temperatures <5 °C (p < 0.05). However, variations in boarding level (medium and high boarding) in the temperature range of 5.10 °C to 23.30 °C did not affect pig losses. PMID:26480321

  12. 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 ...

  13. 40 CFR Figure 1 to Subpart Tttt of... - Example Logs for Recording Leather Finish Use and HAP Content

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... operation Monthly Summary of Finish Usage Upholstery leather(≥4 grams) Upholstery leather(Water-resistant/specialty leather Nonwater-resistant leather Number of Entries Total Finish Usage (pounds)...

  14. A highly accurate heuristic algorithm for the haplotype assembly problem

    PubMed Central

    2013-01-01

    Background Single nucleotide polymorphisms (SNPs) are the most common form of genetic variation in human DNA. The sequence of SNPs in each of the two copies of a given chromosome in a diploid organism is referred to as a haplotype. Haplotype information has many applications such as gene disease diagnoses, drug design, etc. The haplotype assembly problem is defined as follows: Given a set of fragments sequenced from the two copies of a chromosome of a single individual, and their locations in the chromosome, which can be pre-determined by aligning the fragments to a reference DNA sequence, the goal here is to reconstruct two haplotypes (h1, h2) from the input fragments. Existing algorithms do not work well when the error rate of fragments is high. Here we design an algorithm that can give accurate solutions, even if the error rate of fragments is high. Results We first give a dynamic programming algorithm that can give exact solutions to the haplotype assembly problem. The time complexity of the algorithm is O(n × 2t × t), where n is the number of SNPs, and t is the maximum coverage of a SNP site. The algorithm is slow when t is large. To solve the problem when t is large, we further propose a heuristic algorithm on the basis of the dynamic programming algorithm. Experiments show that our heuristic algorithm can give very accurate solutions. Conclusions We have tested our algorithm on a set of benchmark datasets. Experiments show that our algorithm can give very accurate solutions. It outperforms most of the existing programs when the error rate of the input fragments is high. PMID:23445458

  15. Maintenance implementation plan for the Plutonium Finishing Plant. Revision 3

    SciTech Connect

    Meldrom, C.A.

    1996-03-01

    This document outlines the Maintenance Implementation Plan (MIP) for the Plutonium Finishing Plant (PFP) located at the Hanford site at Richland, Washington. This MIP describes the PFP maintenance program relative to DOE order 4330.4B. The MIP defines the key actions needed to meet the guidelines of the Order to produce a cost-effective and efficient maintenance program. A previous report identified the presence of significant quantities of Pu-bearing materials within PFP that pose risks to workers. PFP`s current mission is to develop, install and operate processes which will mitigate these risks. The PFP Maintenance strategy is to equip the facility with systems and equipment able to sustain scheduled PFP operations. The current operating run is scheduled to last seven years. Activities following the stabilization operation will involve an Environmental Impact Statement (EIS) to determine future plant activities. This strategy includes long-term maintenance of the facility for safe occupancy and material storage. The PFP maintenance staff used the graded approach to dictate the priorities of the improvement and upgrade actions identified in Chapter 2 of this document. The MIP documents PFP compliance to the DOE 4330.4B Order. Chapter 2 of the MIP follows the format of the Order in addressing the eighteen elements. As this revision is a total rewrite, no sidebars are included to highlight changes.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  17. Titanium-niobium, a new finishing wire alloy.

    PubMed

    Dalstra, M; Denes, G; Melsen, B

    2000-02-01

    The mechanical properties of the newly introduced titanium-niobium finishing wires were investigated. Both in bending and torsional loading mode, the stiffness, yield point, post-yield behavior, and springback of titanium-niobium wires were experimentally determined and compared to those of equally sized stainless steel wires. The experimentally obtained values were also validated with theoretical values from engineering formulas of cantilever deformations. The ratios for these parameters for the two materials proved to be different in bending and torsion. The stiffness of titanium-niobium in bending is roughly half of that of stainless steel, whereas in torsion it is roughly one-third. These characteristics enable the clinician to use titanium-niobium for creative bends without the excessive force levels of steel wires. The springback of titanium-niobium in bending is 14% lower than that of steel, whereas in torsion it is about the same or even slightly higher than that of steel, thus making it possible to utilize the wire for even major third-order corrections. Finally, the weldability of titanium-niobium wires was found to be good, so it is possible to weld wires of different dimensions together for the generation of differentiated force systems. PMID:11168279

  18. Crude oil and finished fuel storage stability: an annotated review

    SciTech Connect

    Brinkman, D.W.; Bowden, J.N.; Giles, H.N.

    1980-02-01

    The Bartlesville Energy Technology Center (BETC) of the Deopartment of Energy (DOE) and the US Army Fuels and Lubricants Research laboratory (AFLRL) at Southwest Research Institute (SwRI) have been working together on a support effort for the Strategic Petroleum Reserve Office (SPRO) of DOE. One task within this effort was a detailed literature survey of previous experiences in long-term storage of crude oil and finished fuels with an emphasis on underground storage. Based on the discussion presented in this review, in the limited number of cases reported, the refinability of crude oil was not significantly affected by prolonged storage. It was found that most crudes will deposit a sludge during storage which may interfere with withdrawal pumping. This sludge is probably composed of wax, sediment, water, and possibly asphaltenes. Emulsions of the water-oil interface have been reported after prolonged storage which have been attributed to action of centrifugal pumps used to remove accumulated seepage water. It is possible that these emulsions resulted from biological activity, such as the anaerobic activity reported, but no hydrogen sulfide production was observed.

  19. Normal Force and Drag Force in Magnetorheological Finishing

    SciTech Connect

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

    2010-01-13

    The material removal in magnetorheological finishing (MRF) is known to be controlled by shear stress, tau, which equals drag force, Fd, divided by spot area, As. However, it is unclear how the normal force, Fn, affects the material removal in MRF and how the measured ratio of drag force to normal force Fd/Fn, equivalent to coefficient of friction, is related to material removal. This work studies, for the first time for MRF, the normal force and the measured ratio Fd/Fn as a function of material mechanical properties. Experimental data were obtained by taking spots on a variety of materials including optical glasses and hard ceramics with a spot-taking machine (STM). Drag force and normal force were measured with a dual load cell. Drag force decreases linearly with increasing material hardness. In contrast, normal force increases with hardness for glasses, saturating at high hardness values for ceramics. Volumetric removal rate decreases with normal force across all materials. The measured ratio Fd/Fn shows a strong negative linear correlation with material hardness. Hard materials exhibit a low “coefficient of friction”. The volumetric removal rate increases with the measured ratio Fd/Fn which is also correlated with shear stress, indicating that the measured ratio Fd/Fn is a useful measure of material removal in MRF.

  20. Pollution prevention and water conservation in metals finishing operations

    SciTech Connect

    O`Shaughnessy, J.; Clark, W.; Lizotte, R.P. Jr.; Mikutel, D.

    1996-11-01

    Attleboro, Massachusetts is the headquarters of the Materials and Controls Group of Texas Instruments Incorporated (Texas Instruments). In support of their activities, Texas Instruments operates a number of metal finishing and electroplating processes. The water supply and the wastewater treatment requirements are supplied throughout the facility from a central location. Water supply quality requirements varies with each manufacturing operation. As a result, manufacturing operations are classified as either high level or a lower water quality. The facility has two methods of wastewater treatment and disposal. The first method involves hydroxide and sulfide metals precipitation prior to discharge to a surface water. The second method involves metals precipitation, filtration, and discharge via sewer to the Attleboro WTF. The facility is limited to a maximum wastewater discharge of 460,000 gallons per day to surface water under the existing National Pollution Discharge Elimination System (NPDES) permit. There is also a hydraulic flow restriction on pretreated wastewater that is discharged to the Attleboro WTF. Both of these restrictions combined with increased production could cause the facility to reach the treatment capacity. The net effect is that wastewater discharge problems are becoming restrictive to the company`s growth. This paper reviews Texas Instruments efforts to overcome these restrictions through pollution prevention and reuse practices rather than expansion of end of pipe treatment methods.

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

    SciTech Connect

    Hunt, C.E.

    1996-05-01

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

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

    PubMed

    Bingham, P A; Hand, R J

    2005-03-17

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

  3. Integration of magnetorheological finishing (MRF) technology for ultraprecision optical manufacturing

    NASA Astrophysics Data System (ADS)

    Pun, Ashley M. H.; Chan, Norman S. W.; Louie, Derek C. H.; Li, Li-Man

    2003-05-01

    Magneto-rheological-finishing (MRF) technology is capable of substantially improving the surface figure of spherical lens to about 1/20 wavelength. Nonetheless, since MRF technology is an ultra-fine polishing process, in which only less than a few microns of material will be removed per cycle, time for making an aspheric surface from a best-fit sphere can be very significant. The situation can be worse if the surface profile is considerably deviated from its best-fit spherical surface. This is not desirable for actual production, and thus a manufacturing cell is proposed to enhance the efficiency of the high precision lens manufacturing process. On the other hand, MRF was suggested to be an alternative for lapping of surface of ceramic lens mould insert. Rather than using the abrasive particles in typical lapping process, the magnetized slurry in MRF is moved past the rotating surface of mould insert locally under the computer-control process so as to achieve the desired surface form accuracy.

  4. Fire hazard analysis for Plutonium Finishing Plant complex

    SciTech Connect

    MCKINNIS, D.L.

    1999-02-23

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

  5. Prophylometric and SEM analyses of four different finishing methods

    PubMed Central

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

    2013-01-01

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

  6. Study on ultra-precision magnetic abrasive finishing process using low frequency alternating magnetic field

    NASA Astrophysics Data System (ADS)

    Wu, Jinzhong; Zou, Yanhua; Sugiyama, Hitoshi

    2015-07-01

    We proposed a new ultra-precision magnetic abrasive finishing (MAF) process using low frequency alternating magnetic field in this paper. Magnetic cluster themselves may produce the up and down movement change under alternating magnetic force. The movement may not only promote the dispersion of micro-magnetic particles, but also improve stirring effect and cross-cutting effects of the abrasives, achieving circulation and update to ensure the stability of grinding tools. This process is considered to be able to efficiently apply in ultra-precision finishing of plane and complicated micro-surfaces. In this study, we investigated the effects of alternating magnetic field on magnetic field distribution, finishing force and abrasive behavior. Furthermore, a set of experimental devices have been designed for finishing SUS304 stainless steel plate. The present work is aimed at understanding finishing particularity of this process and studying impacts of important process parameters namely grinding fluid, rotational speed of magnetic pole, current frequency on change in finish surface and material removal. Experimental results indicate that the process can realize ultra-precision finishing of plane by using oily grinding fluid. In the present research, the surface roughness of SUS304 stainless steel plate was improved from 240.24 nm to 4.38 nm by this process.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  11. Associations between feed and water antimicrobial use in farrow-to-finish swine herds and antimicrobial resistance of fecal Escherichia coli from grow-finish pigs.

    PubMed

    Rosengren, Leigh B; Waldner, Cheryl L; Reid-Smith, Richard J; Dowling, Patricia M; Harding, John C S

    2007-01-01

    Escherichia coli (n = 1439), isolated from the feces of apparently healthy grow-finish pigs in 20 herds, were tested for susceptibility to 16 antimicrobials. Logistic regression models were developed for each resistance that was observed in more than 5% of the isolates. Each production phase's (suckling, nursery, grow-finish pigs or sows) antimicrobial exposure rate, through feed or water, was considered as a risk factor. Management variables were evaluated as potential confounders. Six resistance outcomes were associated with an antimicrobial use risk factor and four included exposures of pigs outside the grow-finish phase. In the case of sulfamethoxazole, the odds of resistance increased 2.3 times for every 100,000 pig-days of nursery pig exposure to sulfonamides. Thus, swine producers and veterinarians must be aware that antimicrobial use in pigs distant from market could have food safety repercussions. Five resistance outcomes were associated with exposure to an unrelated antimicrobial class. Most notably, the odds of sulfamethoxazole and chloramphenicol resistance were each six times higher in herds reporting high (more than 500/1,000 pig-days) grow-finish pig, macrolide exposure compared to herds with no macrolide use in grow-finish pigs. Therefore, the potential for co-selection should be considered in antimicrobial use decisions. This study emphasizes the importance of judicious antimicrobial use in pork production.

  12. 40 CFR 425.10 - Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

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

  13. 40 CFR 425.10 - Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

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

  14. 40 CFR 425.20 - Applicability; description of the hair save, chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

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

  15. 40 CFR 425.20 - Applicability; description of the hair save, chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

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

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

    Code of Federal Regulations, 2014 CFR

    2014-07-01

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

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

    Code of Federal Regulations, 2014 CFR

    2014-07-01

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

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

    EPA Science Inventory

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

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

    PubMed

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

    2016-07-01

    The original truth campaign was a branded, national smoking prevention mass media effort focused on at-risk youth ages 12-17. Today the truth brand focuses on the goal of finishing tobacco (truth FinishIt). There have been significant changes in the tobacco control landscape, leading FinishIt to focus on 15- to 21-year-olds. The present article reports on formative research and media monitoring data collected to pilot test a new truth FinishIt brand equity scale. The goals of this study were to (a) content analyze truth FinishIt mass media ads, (b) assess truth's social media and followers' perceptions of truth's digital brand identity, and (c) develop and feasibility test a new version of the truth FinishIt brand equity scale using data from an existing Truth Initiative media monitoring study. Through factor analysis, we identified a brand equity scale, as in previous research, consisting of 4 main constructs: brand loyalty, leadership/satisfaction, personality, and awareness. Targeted truth attitudes and beliefs about social perceptions, acceptability, and industry-related beliefs were regressed on the higher order factor and each of the 4 individual brand equity factors. Ordinary least squares regression models generally showed associations in the expected directions (positive for anti-tobacco and negative for pro-tobacco) between targeted attitudes/beliefs and truth FinishIt brand equity. This study succeeded in developing and validating a new truth FinishIt brand equity scale. The scale may be a valuable metric for future campaign evaluation. Future studies should examine the effects of truth FinishIt brand equity on tobacco use behavioral outcomes over time. PMID:27315354

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

    PubMed

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

    2016-07-01

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