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Sample records for carbon isonuclear sequence

  1. K-Shell Photoabsorption Cross Sections for the Magnesium Isonuclear Sequence

    Science.gov (United States)

    Abdel-Naby, Shahin; Hasoglu, Fatih; Gorczyca, Thomas

    2011-05-01

    With the improved spectral resolution of launched X-ray telescopes, there is a demand for highly-accurate K-shell photoabsorption cross sections. Such data are needed for modeling astrophysical plasmas, interpreting the observed spectra from distant cosmic emitters, and determining the elemental abundances of the interstellar medium (ISM). Here we present new calculations for photoabsorption of the entire Mg isonuclear sequence using state-of-the-art R-matrix methods, including important spectator Auger broadening and inner-shell relaxation effects. Unlike our earlier work on carbon, oxygen, and neon ions, and the present work on multiply-ionized magnesium, the calculations for neutral Mg and singly-ionized Mg+ are complicated by additional M-shell occupancy, which leads to a larger R-matrix box and difficulties in implementing the quantum defect theoretical spectator Auger decay method for low-lying resonances. With the improved spectral resolution of launched X-ray telescopes, there is a demand for highly-accurate K-shell photoabsorption cross sections. Such data are needed for modeling astrophysical plasmas, interpreting the observed spectra from distant cosmic emitters, and determining the elemental abundances of the interstellar medium (ISM). Here we present new calculations for photoabsorption of the entire Mg isonuclear sequence using state-of-the-art R-matrix methods, including important spectator Auger broadening and inner-shell relaxation effects. Unlike our earlier work on carbon, oxygen, and neon ions, and the present work on multiply-ionized magnesium, the calculations for neutral Mg and singly-ionized Mg+ are complicated by additional M-shell occupancy, which leads to a larger R-matrix box and difficulties in implementing the quantum defect theoretical spectator Auger decay method for low-lying resonances. This work was funded in part by NASA's Astronomy Physics Research and Analysis (APRA) program.

  2. Photoionization of the 4d subshell of the La isonuclear sequence

    Science.gov (United States)

    Kalyadan, Sindhu; Varma, Hari R.; Deshmukh, P. C.; Costello, J. T.; Hayden, P.; Manson, S. T.

    2015-05-01

    Photoionization studies along isonuclear sequences provide the required systematic data which are useful in many practical applications and also for testing the accuracy of various theoretical models. In the present work, we report on 4d subshell photoionization studies of some of the members of La (Z = 57) isonuclear sequence (La3+, La9+ and La11+) using relativistic random phase approximation (RRPA). Photoionization cross sections, σ, angular distribution asymmetry parameters, β, and the individual dipole matrix elements for 4d3/2 and 4d5/2 subshells are presented along with the 4d branching ratios of these ions. It is found that in La3+, the branching ratios show significant departure from the statistical value 1.5 due to the presence of Cooper minimum in the 4d --> f ionization channels. This departure is minor for the case of La9+ and La11+ since the Cooper minimum in these cases occur in the discrete part of the 4d spectrum.

  3. Term structure of 4d-electron configurations and calculated spectrum in Sn-isonuclear sequence

    International Nuclear Information System (INIS)

    Al-Rabban, Moza M.

    2006-01-01

    Theoretical calculations of term structure are carried out for the ground configurations 4d w , of atomic ions in the Sn isonuclear sequence. Atomic computations are performed to give a detailed account of the transitions in Sn +6 to Sn +13 ions. The spectrum is calculated for the most important excited configurations 4p 5 4d n+1 , 4d n-1 4f 1 , and 4d n-1 5p 1 with respect to the ground configuration 4d n , with n=8-1, respectively. The importance of 4p-4d, 4d-4f, and 4d-5p transitions is stressed, as well as the need for the configuration-interaction CI treatment of the Δn=0 transitions. In the region of importance for extreme ultraviolet (EUV) lithography around 13.4nm, the strongest lines were expected to be 4d n -4p 5 4d n+1 and 4d n -4d n-1 4f 1

  4. Interaction of 4p54dN+1 and 4p64dN-14f configurations and its influence on the photoexcitation and emission spectra in the isoelectronic and isonuclear sequences

    International Nuclear Information System (INIS)

    Kucas, S; Karazija, R; Jonauskas, V; Momkauskaite, A

    2009-01-01

    The strong interaction of 4p 5 4d N+1 + 4p 6 4d N-1 4f configurations and its influence on the photoexcitation and emission spectra corresponding to the excitations from the ground level of 4p 6 4d N have been considered. The results are presented for the isoelectronic sequences from the ionization degree q = 5 up to q = 29-37 as well as for the isonuclear sequences of Sn q+ and W q+ . It is shown that depending on the number of 4d electrons, the variation of spectra in the isoelectronic sequences corresponds to three different types. At N = 4 and N = 6-9, the strong concentration of lines takes place in the whole isoelectronic sequence, except for small ionization degrees. At N ≤ 3, the width of photoexcitation and emission spectra also obtains a relatively larger value at small ionization degrees, decreases with ionization degree rising, but tends to increase again at large ionization degrees. In the whole isoelectronic sequence, a very narrow group of a few intense lines is obtained for N = 5. The transitions from the excited levels mainly proceed to the lowest level of the ground configuration; it is the reason for the similarity of photoexcitation and emission spectra. The quenching of many lines and the concentration of line strengths in a few transitions indicate the existence of some wavefunction basis with strict selection rules for dipole transitions.

  5. K lines in the sulphur isonuclear sequence

    International Nuclear Information System (INIS)

    Palmeri, P.; Mendoza, C.; Bautista, M.A.; Garcia, J.; Kallman, T.R.

    2006-01-01

    Accurate and complete sets of atomic data are being computed for the radiative and Auger processes giving rise to K lines in ions of sulphur. AUTOSTRUCTURE, HFR and BPRM codes are used, taking into account configuration interaction, core relaxation and relativistic effects so as to generate data following an approach used in our previous studies on iron and oxygen. Level energies, wavelengths, A-values and Auger rates are compared with available measurements and previous calculations

  6. Analysis of isoelectron isonuclear series of holovalent tetraelectron compounds as a system of bicomponent chemical compounds

    Energy Technology Data Exchange (ETDEWEB)

    Vigdorovich, V.N.; Dzhuraev, T.D.

    1985-03-01

    Analogs and prototypes of the compounds supplementing the system of isoelectron isonuclear series of holovalent tetraelectron compounds by Gorunova are revealed. The investigation of all series of tetraelectron ovalenthol compounds allows one to supplement the variety of known series used for regular tracing and forecasting of compound properties (series of cation and anion substitutions by isonuclear series of the A/sup 4/B/sup 4/, A/sup 3/B/sup 5/, A/sup 1/B/sup 7/ type and others compounds. The above series for medium ordinal numbers anti Z equal 10, 14, 18, 23 and 36 permit to illustrate the possibility of existence of such analogs or series, for example for the compounds of the type A/sup 3/-- B/sup 5/:AlN-BP or Z=1(f AlP-ScN-BV (for Z=14), ScP-AlV (for Z=18), GaP-AlAs-YN-BNb (for Z=23) and YAs-GaNb-InV-ScSb-LaP-AlPr (for Z=36).

  7. Analysis of isoelectron isonuclear series of holovalent tetraelectron compounds as a system of bicomponent chemical compounds

    International Nuclear Information System (INIS)

    Vigdorovich, V.N.; Dzhuraev, T.D.

    1985-01-01

    Analogs and prototypes of the compounds supplementing the system of isoelectron isonuclear series of holovalent tetraelectron compounds by Gorunova are revealed. The investigation of all series of tetraelectron ovalenthol compounds allows one to supplement the variety of known series used for regular tracing and forecasting of compound properties (series of cation and anion substitutions by isonuclear series of the A 4 B 4 , A 3 B 5 , A 1 B 7 type and others compounds. The above series for medium ordinal numbers anti Z equal 10, 14, 18, 23 and 36 permit to illustrate the possibility of existence of such analogs or series, for example for the compounds of the type A 3 -- B 5 :AlN-BP or Z=1(f AlP-ScN-BV (for Z=14), ScP-AlV (for Z=18), GaP-AlAs-YN-BNb ( for Z=23) and YAs-GaNb-InV-ScSb-LaP-AlPr (for Z=36)

  8. Comparisons on Genetic Diversity among the Isonuclear-Alloplasmic Male Sterile Lines and Their Maintainer Lines in Rice

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    Jin-quan LI

    2007-06-01

    Full Text Available Four sets of rice isonuclear-alloplasmic lines including 16 male sterile lines and their maintainer lines were analyzed by using 91 pairs of SSR primers to study the genetic diversity of nuclear genome and their relative relationships. A total of 169 alleles were detected in the 16 lines, with a frequency of polymorphic loci of 53.85% and an average number of alleles per locus of 1.8, and the average gene diversity was 0.228. Four sets of the isonuclear-alloplasmic male sterile lines shared 146 identical alleles, corresponding to 86.39% of the total alleles; meanwhile, there are 23 different alleles among the tested materials, being 13.61% of the total alleles. On average, 78.70% identical alleles and 21.30% different alleles of the total alleles were detected between the isonuclear-alloplasmic male sterile lines and their maintainer lines. There were 53.85% identical alleles and 46.15% different alleles of the total alleles among the homozygous allonucleus male sterile lines. The fingerprints were established for some male sterile lines and maintainer lines. All the materials tested were divided into three groups at the 0.2 genetic distance based on the cluster analysis. Eight lines of Huanong A and Huayu A (including Huanong B and Huayu B were in the first group, four lines of Kezhen A (including Kezhen B in the second group, and four lines of Zhenshan 97A (including Zhenshan 97B in the third group. For the isonuclear-alloplasmic male sterile lines, the similarity coefficient between Y (Yegong type and WA (wild abortive type or between CW (Raoping wild rice and WA type reached 87–98%.

  9. Distorted-wave calculations of electron impact ionisation in the Ni isonuclear sequence

    Energy Technology Data Exchange (ETDEWEB)

    Griffin, D C; Pindzola, M S

    1988-10-14

    Electron impact ionisation cross sections for Ni/sup +/, Ni/sup 3+/, Ni/sup 5+/, Ni/sup 6+/, Ni/sup 7+/, Ni/sup 8+/, Ni/sup 12+/, Ni/sup 14+/, and Ni/sup 16+/ are calculated in the distorted-wave approximation. These calculations include contributions from direct ionisation and inner-shell excitation followed by autoionisation. For Ni/sup 12+/, Ni/sup 14+/, and Ni/sup 16+/ we report not only on ionisation cross sections from the ground states but also from the metastable states of these ions. Experimental cross section measurements exist for all ions reported here, except Ni/sup 16+/. The agreement between experiment and theory is reasonably good and improves with ionisation stage.

  10. Oxidative Stress and Aberrant Programmed Cell Death Are Associated With Pollen Abortion in Isonuclear Alloplasmic Male-Sterile Wheat

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    Zihan Liu

    2018-05-01

    Full Text Available Cytoplasmic male sterility is crucial for the utilization of hybrid heterosis and it possibly occurs in parallel with tapetal programmed cell death (PCD and oxidative metabolism responses. However, little is known about the mechanisms that underlie pollen abortion in wheat. Therefore, we obtained two isonuclear alloplasmic male sterile lines (IAMSLs with Aegilops kotschyi and Ae. juvenalis cytoplasm. Compared with the maintainer line, cytochemical analyses of the anthers demonstrated that the IAMSLs exhibited anomalous tapetal PCD and organelles, with premature PCD in K87B1-706A and delayed PCD in Ju87B1-706A. We also found that the dynamic trends in reactive oxygen species (ROS were consistent in these two IAMSLs during anther development and they were potentially associated with the initiation of tapetal PCD. In addition, the activities of ROS-scavenging enzymes increased rapidly, whereas non-enzymatic antioxidants were downregulated together with excess ROS production in IAMSLs. Real-time PCR analysis showed that the expression levels of superoxide dismutase, catalase, and ascorbate peroxidase genes, which encode important antioxidant enzymes, were significantly upregulated during early pollen development. Thus, we inferred that excessive ROS and the abnormal transcript levels of antioxidant enzyme genes disrupted the balance of the antioxidant system and the presence of excess ROS may have been related to aberrant tapetal PCD progression, thereby affecting the development of microspores and ultimately causing male sterility. These relationships between the mechanism of PCD and ROS metabolism provide new insights into the mechanisms responsible for abortive pollen in wheat.

  11. An improved method for quantitatively measuring the sequences of total organic carbon and black carbon in marine sediment cores

    Science.gov (United States)

    Xu, Xiaoming; Zhu, Qing; Zhou, Qianzhi; Liu, Jinzhong; Yuan, Jianping; Wang, Jianghai

    2018-01-01

    Understanding global carbon cycle is critical to uncover the mechanisms of global warming and remediate its adverse effects on human activities. Organic carbon in marine sediments is an indispensable part of the global carbon reservoir in global carbon cycling. Evaluating such a reservoir calls for quantitative studies of marine carbon burial, which closely depend on quantifying total organic carbon and black carbon in marine sediment cores and subsequently on obtaining their high-resolution temporal sequences. However, the conventional methods for detecting the contents of total organic carbon or black carbon cannot resolve the following specific difficulties, i.e., (1) a very limited amount of each subsample versus the diverse analytical items, (2) a low and fluctuating recovery rate of total organic carbon or black carbon versus the reproducibility of carbon data, and (3) a large number of subsamples versus the rapid batch measurements. In this work, (i) adopting the customized disposable ceramic crucibles with the microporecontrolled ability, (ii) developing self-made or customized facilities for the procedures of acidification and chemothermal oxidization, and (iii) optimizing procedures and carbon-sulfur analyzer, we have built a novel Wang-Xu-Yuan method (the WXY method) for measuring the contents of total organic carbon or black carbon in marine sediment cores, which includes the procedures of pretreatment, weighing, acidification, chemothermal oxidation and quantification; and can fully meet the requirements of establishing their highresolution temporal sequences, whatever in the recovery, experimental efficiency, accuracy and reliability of the measurements, and homogeneity of samples. In particular, the usage of disposable ceramic crucibles leads to evidently simplify the experimental scenario, which further results in the very high recovery rates for total organic carbon and black carbon. This new technique may provide a significant support for

  12. Frictional properties and slip stability of active faults within carbonate-evaporite sequences: The role of dolomite and anhydrite

    NARCIS (Netherlands)

    Scuderi, M.M.; Niemeijer, A.R.; Collettini, C.; Marone, C.

    2013-01-01

    Seismological observations show that many destructive earthquakes nucleate within, or propagate through, thick sequences of carbonates and evaporites. For example, along the Apennines range (Italy) carbonate and evaporite sequences are present at hypocentral depths for recent major earthquakes

  13. Comparative analysis of mitochondrial genomes between the hau cytoplasmic male sterility (CMS) line and its iso-nuclear maintainer line in Brassica juncea to reveal the origin of the CMS-associated gene orf288.

    Science.gov (United States)

    Heng, Shuangping; Wei, Chao; Jing, Bing; Wan, Zhengjie; Wen, Jing; Yi, Bin; Ma, Chaozhi; Tu, Jinxing; Fu, Tingdong; Shen, Jinxiong

    2014-04-30

    Cytoplasmic male sterility (CMS) is not only important for exploiting heterosis in crop plants, but also as a model for investigating nuclear-cytoplasmic interaction. CMS may be caused by mutations, rearrangement or recombination in the mitochondrial genome. Understanding the mitochondrial genome is often the first and key step in unraveling the molecular and genetic basis of CMS in plants. Comparative analysis of the mitochondrial genome of the hau CMS line and its maintainer line in B. juneca (Brassica juncea) may help show the origin of the CMS-associated gene orf288. Through next-generation sequencing, the B. juncea hau CMS mitochondrial genome was assembled into a single, circular-mapping molecule that is 247,903 bp in size and 45.08% in GC content. In addition to the CMS associated gene orf288, the genome contains 35 protein-encoding genes, 3 rRNAs, 25 tRNA genes and 29 ORFs of unknown function. The mitochondrial genome sizes of the maintainer line and another normal type line "J163-4" are both 219,863 bp and with GC content at 45.23%. The maintainer line has 36 genes with protein products, 3 rRNAs, 22 tRNA genes and 31 unidentified ORFs. Comparative analysis the mitochondrial genomes of the hau CMS line and its maintainer line allowed us to develop specific markers to separate the two lines at the seedling stage. We also confirmed that different mitotypes coexist substoichiometrically in hau CMS lines and its maintainer lines in B. juncea. The number of repeats larger than 100 bp in the hau CMS line (16 repeats) are nearly twice of those found in the maintainer line (9 repeats). Phylogenetic analysis of the CMS-associated gene orf288 and four other homologous sequences in Brassicaceae show that orf288 was clearly different from orf263 in Brassica tournefortii despite of strong similarity. The hau CMS mitochondrial genome was highly rearranged when compared with its iso-nuclear maintainer line mitochondrial genome. This study may be useful for studying the

  14. Carbon dynamics in corn-soybean sequences as estimated from natural carbon-13 abundance

    International Nuclear Information System (INIS)

    Huggins, D.R.; Clapp, C.E.; Allmaras, R.R.; Lamb, J.A.; Layese, M.F.

    1998-01-01

    Carbon flow in terrestrial ecosystems regulates partitioning between soil organic C (SOC) and atmospheric CO2. Our objectives were to assess SOC dynamics using natural 13C abundance in corn (Zea mays L., a C4 species)-soybean [Glycine max (L.) Merr., a C3 species] sequences. Fifteen treatments of continuous corn, continuous soybean, various sequences of corn and soybean, and fallow were initiated in 1981 at Lamberton, MN, on a Webster clay loam (fine-loamy, mixed, mesic Typic Haplaquoll). In 1991, soil and aboveground shoot samples from all treatments were analyzed for total organic C and delta 13C. Carbon inputs, delta 13C, and SOC were integrated into a two-pool model to evaluate C dynamics of corn and soybean. Total SOC was similar across all treatments after 10 yr; however, differences in soil delta 13C occurred between continuous corn (delta 13C = -17.2 per thous and) and continuous soybean (delta 13C = -18.2 per thousand). Modeled C dynamics showed SOC decay rates of 0.011 yr-1 for C4-derived C and 0.007 yr-1 for C3-derived C, and humification rates of 0.16 yr-1 for corn and 0.11 yr-1 for soybean. Decay and humification rates were slightly lower than those found in other Corn Belt studies. Levels of SOC were predicted to decline an additional 7 to 18% with current C inputs from either corn or soybean, respectively. Annual C additions required for SOC maintenance averaged 5.6 Mg C ha-1, 1.4 to 2.1 times greater than previously reported estimates. Controlled variation in natural 13C abundance in corn-soybean rotations during a 10-yr period adequately traced C dynamics

  15. Application of sequence stratigraphy to carbonate reservoir prediction, Early Palaeozoic eastern Warburton basin, South Australia

    Energy Technology Data Exchange (ETDEWEB)

    Xiaowen S.; Stuart, W.J.

    1996-12-31

    The Early Palaeozoic Warburton Basin underlies the gas and oil producing Cooper and Eromanga Basins. Postdepositional tectonism created high potential fracture porosities, complicating the stratigraphy and making reservoir prediction difficult. Sequence stratigraphy integrating core, cuttings, well-log, seismic and biostratigraphic data has recognized a carbonate-dominated to mixed carbonate/siliciclastic supersequence comprising several depositional sequences. Biostratigraphy based on trilobites and conodonts ensures reliable well and seismic correlations across structurally complex areas. Lithofacies interpretation indicates sedimentary environments ranging from carbonate inner shelf, peritidal, shelf edge, deep outer shelf and slope to basin. Log facies show gradually upward shallowing trends or abrupt changes indicating possible sequence boundaries. With essential depositional models and sequence analysis from well data, seismic facies suggest general reflection configurations including parallel-continuous layered patterns indicating uniform neuritic shelf, and mounded structures suggesting carbonate build-ups and pre-existing volcanic relief. Seismic stratigraphy also reveals inclined slope and onlapping margins of a possibly isolated platform geometry. The potential reservoirs are dolomitized carbonates containing oomoldic, vuggy, intercrystalline and fracture porosities in lowstand systems tracts either on carbonate mounds and shelf crests or below shelf edge. The source rock is a deep basinal argillaceous mudstone, and the seal is fine-grained siltstone/shale of the transgressive system tract.

  16. Application of sequence stratigraphy to carbonate reservoir prediction, Early Palaeozoic eastern Warburton basin, South Australia

    Energy Technology Data Exchange (ETDEWEB)

    Xiaowen S.; Stuart, W.J.

    1996-01-01

    The Early Palaeozoic Warburton Basin underlies the gas and oil producing Cooper and Eromanga Basins. Postdepositional tectonism created high potential fracture porosities, complicating the stratigraphy and making reservoir prediction difficult. Sequence stratigraphy integrating core, cuttings, well-log, seismic and biostratigraphic data has recognized a carbonate-dominated to mixed carbonate/siliciclastic supersequence comprising several depositional sequences. Biostratigraphy based on trilobites and conodonts ensures reliable well and seismic correlations across structurally complex areas. Lithofacies interpretation indicates sedimentary environments ranging from carbonate inner shelf, peritidal, shelf edge, deep outer shelf and slope to basin. Log facies show gradually upward shallowing trends or abrupt changes indicating possible sequence boundaries. With essential depositional models and sequence analysis from well data, seismic facies suggest general reflection configurations including parallel-continuous layered patterns indicating uniform neuritic shelf, and mounded structures suggesting carbonate build-ups and pre-existing volcanic relief. Seismic stratigraphy also reveals inclined slope and onlapping margins of a possibly isolated platform geometry. The potential reservoirs are dolomitized carbonates containing oomoldic, vuggy, intercrystalline and fracture porosities in lowstand systems tracts either on carbonate mounds and shelf crests or below shelf edge. The source rock is a deep basinal argillaceous mudstone, and the seal is fine-grained siltstone/shale of the transgressive system tract.

  17. Stratigraphy and stable isotope geochemistry of the carbonate sequence from the Paraguay belt

    International Nuclear Information System (INIS)

    Santos, Roberto Ventura.; Alvarenga, Carlos Jose Souza de; Dantas, Elton Luiz

    2001-01-01

    Two main Neoproterozoic carbonate sequences occur central Brazil both of which are stratiphicaly above glacial derived sediments. An older carbonate sequence occurs over the Sao Francisco Craton and in the surrounding folded belts (Rio Preto, Aracuai Ribeira and Brasilia). These carbonates overlie glacial diamictites that were related to the 'Sturtian' event dated between 0.7 and 0.9 Ga (Toulkeridis et al. 1999, Santos et al., 2000). A second carbonate sequence is described in the Paraguay Belt and postdated Vendian/Varegian glaciation sediments from the end of the Neoproterozoic. This glacial event has been reported in many studies concerning the Gondwana and the Laurentia supercontinent (Trompette, 1996; Condon and Prave, 2000; Myrow and Kaufman, 1999). In the Paraguay Belt the Vendian- Varangian glaciation rocks are characterized by a glaciomarine sequence, that occur at the border of the basin, and by glacial derived turbidites deposits, that occur in the deeper parts of the basin (Alvarenga and Trompette, 1992). Near the city of Corumba this glaciomarine sequence is overlaid by carbonate rocks containing Ediacaran-like fauna in which has been described Corumbella werneri and Cloudina Lucianoi (Hahn et al., 1982; Walde et al., 1982; Zaine and Fairchild, 1985; 1987). These carbonates have been interpreted as cap carbonates and the age of their fossils have been attributed to the Vendian Superior (590-545 MA) (Alvarenga and Trompette, 1992, Trompette 1996). Isotope stratigraphy studies have been widely used to study cap carbonate rocks that overlie Sturtian and Vendian- Varagian glaciogenic rocks. Stratigraphic correlation of these units is usually difficult because their lack fossils and there is no precise dating method that could be applied to these rocks. Hence, most studies concerning Neoproterozoic carbonates have concentrated on their stromatilites and microfossils content as well as on carbon isotope variations. In the present study, we present new carbon

  18. Recognition of depositional sequences and stacking patterns, Late Devonian (Frasnian) carbonate platforms, Alberta basin

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, J.H.; Reeckmann, S.A.; Sarg, J.F.; Greenlee, S.M.

    1987-05-01

    Six depositional sequences bounded by regional unconformities or their correlative equivalents (sequence boundaries) have been recognized in Late Devonian (Frasnian) carbonate platforms in the Alberta basin. These sequences consist of a predictable vertical succession of smaller scale shoaling-upward cycles (parasequences). Parasequences are arranged in retrogradational, aggradational, and progradational stacking patterns that can be modeled as a sediment response to relative changes in sea level. Sequence boundaries are recognized by onlap onto underlying shelf or shelf margin strata. This onlap includes shelf margin wedges and deep marine onlap. In outcrop sections shelf margin wedges exhibit an abrupt juxtaposition of shallow water facies over deeper water deposits with no gradational facies changes at the boundaries. High on the platform, subaerial exposure fabrics may be present. The shelf margin wedges are interpreted to have formed during lowstands in sea level and typically exhibit an aggradational stacking pattern. On the platform, two types of sequences are recognized. A type 1 cycle occurs where the sequence boundary is overlain by a flooding surface and subsequent parasequences exhibit retrogradational stacking. In a type 2 cycle the sequence boundary is overlain by an aggradational package of shallow water parasequences, followed by a retrogradational package. These two types of sequences can be modeled using a sinusoidal eustatic sea level curve superimposed on thermo-tectonic subsidence.

  19. C, Sr and Sr isotopic composition on probable vendian- tommotian carbonate sequences in Nw Argentina

    International Nuclear Information System (INIS)

    Sial, A. N.; Ferreira, V.P; Toselli, A.J.; Acenolaza, F.G; Pimentel, M.M; Parada, M.A; Alonso, R.N

    2001-01-01

    C-isotope stratigraphy is one of the most powerfool tools in Precambrian chronostratigraphy, especially when sediments lack recognizable animal fossils. The δ 13 C secular variation curves for marine carbonates in the Neoproterozoic-Cambrian interval show strong positive-negative excursions, several of them interpreted as the stratigraphic position of ancient ice ages (Hoffman et al. 1998). The Sr isotope composition of the seawater for this age interval is characterized by a continuous increase of 87 Sr/ 86 Sr that is interrupted, several times, by sharp rises, which represent important changes in the Earth history (Montanez et al. 2000). Only limited data on the behavior of C and Sr isotopes in carbonates are available in South America. We examine here carbonate sequences from the Argentine Precordillera, San Juan province, and from other carbonate sequences in NW Argentina that could be, potentially, proxies for the Precambrian-Cambrian transition. We have studied their δ 13 C and 87 Sr/ 86 Sr chemostratigraphy and compare it to global C and Sr isotope secular variation curves for this time span. This study aims to improve the relatively coarse stratigraphic resolution provided only by the study of the fossil record in some of the carbonate successions under consideration (au)

  20. Comparative transcriptome analysis of isonuclear-alloplasmic lines unmask key transcription factor genes and metabolic pathways involved in sterility of maize CMS-C.

    Science.gov (United States)

    Li, Chuan; Zhao, Zhuofan; Liu, Yongming; Liang, Bing; Guan, Shuxian; Lan, Hai; Wang, Jing; Lu, Yanli; Cao, Moju

    2017-01-01

    Although C-type cytoplasmic male sterility (CMS-C) is one of the most attractive tools for maize hybrid seed production, the detailed regulation network of the male sterility remains unclear. In order to identify the CMS-C sterility associated genes and/or pathways, the comparison of the transcriptomes between the CMS-C line C48-2 and its isonuclear-alloplasmic maintainer line N48-2 at pollen mother cell stage (PS), an early development stage of microspore, and mononuclear stage (MS), an abortive stage of microspore, were analyzed. 2,069 differentially expressed genes (DEGs) between the two stages were detected and thought to be essential for the spikelet development of N48-2. 453 of the 2,069 DEGs were differentially expressed at MS stage between the two lines and thought to be participated in the process or the causes of microspore abortion. Among the 453 DEGs, 385 (84.99%) genes were down-regulated and only 68 (15.01%) genes were up-regulated in C48-2 at MS stage. The dramatic decreased expression of the four DEGs encoding MYB transcription factors and the DEGs involved in "polyamine metabolic process", "Cutin, suberine and wax biosynthesis", "Fatty acid elongation", "Biosynthesis of unsaturated fatty acids" and "Proline metabolism" might play an important role in the sterility of C48-2. This study will point out some directions for detailed molecular analysis and better understanding of sterility of CMS-C in maize.

  1. Comparative transcriptome analysis of isonuclear-alloplasmic lines unmask key transcription factor genes and metabolic pathways involved in sterility of maize CMS-C

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    Chuan Li

    2017-05-01

    Full Text Available Although C-type cytoplasmic male sterility (CMS-C is one of the most attractive tools for maize hybrid seed production, the detailed regulation network of the male sterility remains unclear. In order to identify the CMS-C sterility associated genes and/or pathways, the comparison of the transcriptomes between the CMS-C line C48-2 and its isonuclear-alloplasmic maintainer line N48-2 at pollen mother cell stage (PS, an early development stage of microspore, and mononuclear stage (MS, an abortive stage of microspore, were analyzed. 2,069 differentially expressed genes (DEGs between the two stages were detected and thought to be essential for the spikelet development of N48-2. 453 of the 2,069 DEGs were differentially expressed at MS stage between the two lines and thought to be participated in the process or the causes of microspore abortion. Among the 453 DEGs, 385 (84.99% genes were down-regulated and only 68 (15.01% genes were up-regulated in C48-2 at MS stage. The dramatic decreased expression of the four DEGs encoding MYB transcription factors and the DEGs involved in “polyamine metabolic process”, “Cutin, suberine and wax biosynthesis”, “Fatty acid elongation”, “Biosynthesis of unsaturated fatty acids” and “Proline metabolism” might play an important role in the sterility of C48-2. This study will point out some directions for detailed molecular analysis and better understanding of sterility of CMS-C in maize.

  2. Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901.

    Directory of Open Access Journals (Sweden)

    2005-11-01

    Full Text Available We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a "minimal" model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously.

  3. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901.

    Directory of Open Access Journals (Sweden)

    Martin Wu

    2005-11-01

    Full Text Available We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a "minimal" model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously.

  4. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901.

    Science.gov (United States)

    Wu, Martin; Ren, Qinghu; Durkin, A Scott; Daugherty, Sean C; Brinkac, Lauren M; Dodson, Robert J; Madupu, Ramana; Sullivan, Steven A; Kolonay, James F; Haft, Daniel H; Nelson, William C; Tallon, Luke J; Jones, Kristine M; Ulrich, Luke E; Gonzalez, Juan M; Zhulin, Igor B; Robb, Frank T; Eisen, Jonathan A

    2005-11-01

    We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a "minimal" model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously.

  5. Sequence stratigraphy in a mixed carbonate-silicilastic depositional system (Middle Miocene; Styrian Basin, Austria)

    Science.gov (United States)

    Friebe, J. Georg

    1993-07-01

    The mixed carbonate-siliciclastic Weißenegg (Allo-) Formation records three depositional sequences corresponding approximately to the TB 2.3, TB 2.4 and TB 2.5 global cycles. Sea-level fluctuations were of the order of at least 30 m. Siliciclastic lowstand systems tracts comprise lignite deposits, reworked basement and tidal siltstones (above a tectonically enhanced sequence boundary) as well as coastal sand bars. Coastal sands of the transgressive systems tract contain distinct layers of well cemented nodules. They are interpreted as the first stage in hardground formation and record superimposed minor sea-level fluctuations. Coral patch reefs and rhodolith platforms developed during transgressive phases and were subsequently drowned and/or suffocated by siliciclastics during early highstand. Shallowing upwards siliciclastic parasequences, each terminated by a bank of rhodolith limestone, form the (late) highstand systems tract. The limestone beds record superimposed fourth-order transgressive pulses. Occasionally a carbonate highstand wedge developed. Lowstand carbonate shedding occurred where the top of a platform which suffered incipient drowning during highstand was near sealevel again during the following lowstand. Late highstand delta progradation is common.

  6. Cyclic architecture of a carbonate sequence, early Aptian Shuaiba formation, Al Huwaisah field, Oman

    Energy Technology Data Exchange (ETDEWEB)

    Groetsch, J. (Shell Research, Rijswijk (Netherlands))

    1993-09-01

    Sequence stratigraphy of carbonates is a topic of ongoing controversy. In particular, small-scale shallowing-upward cycles can provide some key information needed for interpretation of carbonate sequences and/or third-order sea level changes. The early Aptian Shuaiba Formation in the Al Huwaisah field consists of about 90 m of shallow-water limestones. Throughout the formation, an overall decreasing influx of fine detritus is notable toward the top. The sequence can be subdivided into a basal unit and an overlying unit. Both units are composed of meter-scale shallowing-upward cycles of different composition, which can be recognized in core and well logs. Fourier analysis of the first principle component of a set of well logs (GR, FDC, CNL, Sonic) revealed an abrupt change in spectral behavior between the two units. Toward the top, the spectra are [open quotes]cleaning upward[close quotes] with an increasing pronunciation of a peak grouping of 1: 2: 5, suggesting a better preservation of orbital variations in the upper unit. Preservation of orbital forcing in shallowing-upward cycles requires rapid rates of sedimentation. In addition, increased shallow-water carbonate production on the platform is indicated by the appearance of reefal organisms. Hence, a higher rate of sedimentation and therefore a faster aggradation of the platform is inferred for the upper unit, which could have resulted from an increased rate of relative sea level rise. The sudden facies differentiation on the broad Arabian shelf in the upper part of the early Aptian reflects the development of an intrashelf basin. Changes in rate of relative sea level rise on the Arabian shelf might explain the repeated alternation from an easily correlatable ramp-type sedimentation, with slightly higher input of fine terrigenous sediment (e.g., lower unit of Shuaiba Formation) and a differentiation into platform and intrashelf basin facies due to faster aggradation (e.g., upper unit of Shuaiba Formation).

  7. Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks

    OpenAIRE

    Kumar, Manish; Gazara, Rajesh Kumar; Verma, Sandhya; Kumar, Madan; Verma, Praveen Kumar; Thakur, Indu Shekhar

    2016-01-01

    The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO2)-sequestering bacterium isolated from marble mining rocks in the Umra area, Rajasthan, India. This strain grows chemolithotrophically on media that contain sodium bicarbonate (NaHCO3) as the sole carbon source. Here, we report the genome sequence of 5.07?Mb Serratia sp. ISTD04.

  8. Effects of heavy metals and phenol on the operation of sequencing batch reactor added activated carbon

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Sang Hoon; Lim, Ji Hun; Park, Chul Hwan; Lee, Jin Won [Dept. of Chemical Engineering, Kwangwoon University, Seoul (Korea); Kim, Sang Yong [Korea Institute of Industrial Technology (Korea); Park, Jin Yong [Dept. of Environmental Engineering, Hallym University (Korea); Lee, Yong Myun [Osung Envi-Tech Company (Korea)

    2000-04-01

    The process of sequencing batch reactor(SBR) added the activated carbon were studied. To investigate the influence of the activated carbon on the treatment of organic materials and the effects of heavy metals on the process, three different kinds of granular activated carbons(GAC) were tested. Teh decrease of SCOD(soluble chemical oxygen demand) was measured at the different concentrations of the activated carbon. Synergistic effects of GAC on the biological activity in the SBR were confirmed from the data comparing adsorbed loadings with apparent loadings. When SBR was operated with GAC, the efficiency of wastewater treatment increased 16%. By comparing the adsorbed amount of SCOD estimated from Freundlich isotherm and the decrease of apparent loading, biological synergistic effect was confirmed. The inhibition of SBR performance from heavy metals or toxic chemicals could be reduced when GAC was added into the SBR process. Pb, Cd, Cr, and phenol were tested as typical inhibitors. When 10mg/L inhibitor was introduced into the SBR process which includes 500 mg/L GAC, the efficiency was increased as 32.6%, 27.2%, 22.3%, and 9.4%, respectively. 22 refs., 13 figs., 3 tabs.

  9. The sequence stratigraphy, sedimentology, and economic importance of evaporite carbonate transitions: a review

    Science.gov (United States)

    Sarg, J. F.

    2001-04-01

    World-class hydrocarbon accumulations occur in many ancient evaporite-related basins. Seals and traps of such accumulations are, in many cases, controlled by the stratigraphic distribution of carbonate-evaporite facies transitions. Evaporites may occur in each of the systems tracts within depositional sequences. Thick evaporite successions are best developed during sea level lowstands due to evaporative drawdown. Type 1 lowstand evaporite systems are characterized by thick wedges that fill basin centers, and onlap basin margins. Very thick successions (i.e. saline giants) represent 2nd-order supersequence set (20-50 m.y.) lowstand systems that cap basin fills, and provide the ultimate top seals for the hydrocarbons contained within such basins. Where slope carbonate buildups occur, lowstand evaporites that onlap and overlap these buildups show a lateral facies mosaic directly related to the paleo-relief of the buildups. This facies mosaic, as exemplified in the Silurian of the Michigan basin, ranges from nodular mosaic anhydrite of supratidal sabkha origin deposited over the crests of the buildups, to downslope subaqueous facies of bedded massive/mosaic anhydrite and allochthonous dolomite-anhydrite breccias. Facies transitions near the updip onlap edges of evaporite wedges can provide lateral seals to hydrocarbons. Porous dolomites at the updip edges of lowstand evaporites will trap hydrocarbons where they onlap nonporous platform slope deposits. The Desert Creek Member of the Paradox Formation illustrates this transition. On the margins of the giant Aneth oil field in southeastern Utah, separate downdip oil pools have accumulated where dolomudstones and dolowackestones with microcrystalline porosity onlap the underlying highstand platform slope. Where lowstand carbonate units exist in arid basins, the updip facies change from carbonates to evaporite-rich facies can also provide traps for hydrocarbons. The change from porous dolomites composed of high

  10. Sequence Dependent Interactions Between DNA and Single-Walled Carbon Nanotubes

    Science.gov (United States)

    Roxbury, Daniel

    It is known that single-stranded DNA adopts a helical wrap around a single-walled carbon nanotube (SWCNT), forming a water-dispersible hybrid molecule. The ability to sort mixtures of SWCNTs based on chirality (electronic species) has recently been demonstrated using special short DNA sequences that recognize certain matching SWCNTs of specific chirality. This thesis investigates the intricacies of DNA-SWCNT sequence-specific interactions through both experimental and molecular simulation studies. The DNA-SWCNT binding strengths were experimentally quantified by studying the kinetics of DNA replacement by a surfactant on the surface of particular SWCNTs. Recognition ability was found to correlate strongly with measured binding strength, e.g. DNA sequence (TAT)4 was found to bind 20 times stronger to the (6,5)-SWCNT than sequence (TAT)4T. Next, using replica exchange molecular dynamics (REMD) simulations, equilibrium structures formed by (a) single-strands and (b) multiple-strands of 12-mer oligonucleotides adsorbed on various SWCNTs were explored. A number of structural motifs were discovered in which the DNA strand wraps around the SWCNT and 'stitches' to itself via hydrogen bonding. Great variability among equilibrium structures was observed and shown to be directly influenced by DNA sequence and SWCNT type. For example, the (6,5)-SWCNT DNA recognition sequence, (TAT)4, was found to wrap in a tight single-stranded right-handed helical conformation. In contrast, DNA sequence T12 forms a beta-barrel left-handed structure on the same SWCNT. These are the first theoretical indications that DNA-based SWCNT selectivity can arise on a molecular level. In a biomedical collaboration with the Mayo Clinic, pathways for DNA-SWCNT internalization into healthy human endothelial cells were explored. Through absorbance spectroscopy, TEM imaging, and confocal fluorescence microscopy, we showed that intracellular concentrations of SWCNTs far exceeded those of the incubation

  11. Metre-scale cyclicity in Middle Eocene platform carbonates in northern Egypt: Implications for facies development and sequence stratigraphy

    Science.gov (United States)

    Tawfik, Mohamed; El-Sorogy, Abdelbaset; Moussa, Mahmoud

    2016-07-01

    The shallow-water carbonates of the Middle Eocene in northern Egypt represent a Tethyan reef-rimmed carbonate platform with bedded inner-platform facies. Based on extensive micro- and biofacies documentation, five lithofacies associations were defined and their respective depositional environments were interpreted. Investigated sections were subdivided into three third-order sequences, named S1, S2 and S3. Sequence S1 is interpreted to correspond to the Lutetian, S2 corresponds to the Late Lutetian and Early Bartonian, and S3 represents the Late Bartonian. Each of the three sequences was further subdivided into fourth-order cycle sets and fifth-order cycles. The complete hierarchy of cycles can be correlated along 190 km across the study area, and highlighting a general "layer-cake" stratigraphic architecture. The documentation of the studied outcrops may contribute to the better regional understanding of the Middle Eocene formations in northern Egypt and to Tethyan pericratonic carbonate models in general.

  12. Carbonate deposition, Pyramid Lake subbasin, Nevada: 1. Sequence of formation and elevational distribution of carbonate deposits (Tufas)

    Science.gov (United States)

    Benson, L.

    1994-01-01

    During the late Quarternary, the elevation of terrace cutting and carbonate deposition in the Pyramid Lake subbasin were controlled by constancy of lake level imposed by spill to adjoining subbasins. Sill elevations are 1177-1183 m (Mud Lake Slough Sill), 1207 m (Emerson Pass Sill), and 1265 m (Darwin Pass Sill). Carbonate deposition was favored by: (1) hydrologic closure, (2) proximity to a source of calcium, (3) elevated water temperature, and (4) a solid substrate. The thickness and aspect of tufa are a function oflake-level dynamics. Relatively thin sheets and pendant sheets were deposited during a rising or falling lake. The upper parts of thick reef-form tufas have a horizontal aspect and were deposited in a lake which was stabilized by spill to the Carson Desert subbasin. The lower parts of the reef-form tufas are thinner and their outer surface has a vertical aspect, indicating that the lower part formed in a receding lake. The thickest and most complete sequences of tufa are mounds that border the Pyramid Lake shore. The tops of the tallest mounds reach the elevation of the Darwin Pass Sill and many mounds have been eroded to the elevations of the Mud Lake Slough Sill of the Emerson Pass Sill. The sequence of tufa formation (from oldest to youngest) displayed in these mounds is: (1) a beachrock containing carbonate-cemented volcanic cobbles, (2) broken and eroded old spheroids that contain thinolitic tufa and an outer rind of dense laminated tufa, (3) large cylindrical (tubular) tufas capped by (4) coatings of old dense tufas, and (5) several generations of old branching tufa commonly associated with thin, platy tufas and coatings of thinolitic tufa, (6) young spheroids that contain poorly oriented young thinolitic tufa in the center and several generations of radially oriented young thinolitic tufas near the outer edge, (7) a transitional thinolite-to-branching tufa, (8) two or more layers of young branching tufa, (9) a 0.5-cm-thick layer of fine

  13. Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks.

    Science.gov (United States)

    Kumar, Manish; Gazara, Rajesh Kumar; Verma, Sandhya; Kumar, Madan; Verma, Praveen Kumar; Thakur, Indu Shekhar

    2016-10-20

    The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO 2 )-sequestering bacterium isolated from marble mining rocks in the Umra area, Rajasthan, India. This strain grows chemolithotrophically on media that contain sodium bicarbonate (NaHCO 3 ) as the sole carbon source. Here, we report the genome sequence of 5.07 Mb Serratia sp. ISTD04. Copyright © 2016 Kumar et al.

  14. Enhanced biological phosphorus removal in a sequencing batch reactor using propionate as the sole carbon source.

    Science.gov (United States)

    Pijuan, M; Saunders, A M; Guisasola, A; Baeza, J A; Casas, C; Blackall, L L

    2004-01-05

    An enhanced biological phosphorus removal (EBPR) system was developed in a sequencing batch reactor (SBR) using propionate as the sole carbon source. The microbial community was followed using fluorescence in situ hybridization (FISH) techniques and Candidatus 'Accumulibacter phosphatis' were quantified from the start up of the reactor until steady state. A series of SBR cycle studies was performed when 55% of the SBR biomass was Accumulibacter, a confirmed polyphosphate accumulating organism (PAO) and when Candidatus 'Competibacter phosphatis', a confirmed glycogen-accumulating organism (GAO), was essentially undetectable. These experiments evaluated two different carbon sources (propionate and acetate), and in every case, two different P-release rates were detected. The highest rate took place while there was volatile fatty acid (VFA) in the mixed liquor, and after the VFA was depleted a second P-release rate was observed. This second rate was very similar to the one detected in experiments performed without added VFA.A kinetic and stoichiometric model developed as a modification of Activated Sludge Model 2 (ASM2) including glycogen economy, was fitted to the experimental profiles. The validation and calibration of this model was carried out with the cycle study experiments performed using both VFAs. The effect of pH from 6.5 to 8.0 on anaerobic P-release and VFA-uptake and aerobic P-uptake was also studied using propionate. The optimal overall working pH was around 7.5. This is the first study of the microbial community involved in EBPR developed with propionate as a sole carbon source along with detailed process performance investigations of the propionate-utilizing PAOs. Copyright 2003 Wiley Periodicals, Inc.

  15. First-principles study of high-conductance DNA sequencing with carbon nanotube electrodes

    KAUST Repository

    Chen, X.

    2012-03-26

    Rapid and cost-effective DNA sequencing at the single nucleotide level might be achieved by measuring a transverse electronic current as single-stranded DNA is pulled through a nanometer-sized pore. In order to enhance the electronic coupling between the nucleotides and the electrodes and hence the current signals, we employ a pair of single-walled close-ended (6,6) carbon nanotubes (CNTs) as electrodes. We then investigate the electron transport properties of nucleotides sandwiched between such electrodes by using first-principles quantum transport theory. In particular, we consider the extreme case where the separation between the electrodes is the smallest possible that still allows the DNA translocation. The benzene-like ring at the end cap of the CNT can strongly couple with the nucleobases and therefore it can both reduce conformational fluctuations and significantly improve the conductance. As such, when the electrodes are closely spaced, the nucleobases can pass through only with their base plane parallel to the plane of CNT end caps. The optimal molecular configurations, at which the nucleotides strongly couple to the CNTs, and which yield the largest transmission, are first identified. These correspond approximately to the lowest energy configurations. Then the electronic structures and the electron transport of these optimal configurations are analyzed. The typical tunneling currents are of the order of 50 nA for voltages up to 1 V. At higher bias, where resonant transport through the molecular states is possible, the current is of the order of several μA. Below 1 V, the currents associated to the different nucleotides are consistently distinguishable, with adenine having the largest current, guanine the second largest, cytosine the third and, finally, thymine the smallest. We further calculate the transmission coefficient profiles as the nucleotides are dragged along the DNA translocation path and investigate the effects of configurational variations

  16. Spectral Sequences of Type Ia Supernovae. I. Connecting Normal and Subluminous SNe Ia and the Presence of Unburned Carbon

    Energy Technology Data Exchange (ETDEWEB)

    Heringer, E.; Kerkwijk, M. H. van [Department of Astronomy and Astrophysics, University of Toronto, 50 Saint George Street, Toronto, ON M5S 3H4 (Canada); Sim, S. A. [Astrophysics Research Centre, School of Mathematics and Physics, Queens University Belfast, Belfast BT7 1NN (United Kingdom); Kerzendorf, W. E. [European Southern Observatory (ESO), Karl-Schwarzschild-Straße 2, D-85748 Garching (Germany)

    2017-09-01

    Type Ia supernovae (SNe Ia) are generally agreed to arise from thermonuclear explosions of carbon–oxygen white dwarfs. The actual path to explosion, however, remains elusive, with numerous plausible parent systems and explosion mechanisms suggested. Observationally, SNe Ia have multiple subclasses, distinguished by their light curves and spectra. This raises the question of whether these indicate that multiple mechanisms occur in nature or that explosions have a large but continuous range of physical properties. We revisit the idea that normal and 91bg-like SNe can be understood as part of a spectral sequence in which changes in temperature dominate. Specifically, we find that a single ejecta structure is sufficient to provide reasonable fits of both the normal SN Ia SN 2011fe and the 91bg-like SN 2005bl, provided that the luminosity and thus temperature of the ejecta are adjusted appropriately. This suggests that the outer layers of the ejecta are similar, thus providing some support for a common explosion mechanism. Our spectral sequence also helps to shed light on the conditions under which carbon can be detected in premaximum SN Ia spectra—we find that emission from iron can “fill in” the carbon trough in cool SNe Ia. This may indicate that the outer layers of the ejecta of events in which carbon is detected are relatively metal-poor compared to events in which carbon is not detected.

  17. Influence of Layup Sequence on the Surface Accuracy of Carbon Fiber Composite Space Mirrors

    Science.gov (United States)

    Yang, Zhiyong; Liu, Qingnian; Zhang, Boming; Xu, Liang; Tang, Zhanwen; Xie, Yongjie

    2018-04-01

    Layup sequence is directly related to stiffness and deformation resistance of the composite space mirror, and error caused by layup sequence can affect the surface precision of composite mirrors evidently. Variation of layup sequence with the same total thickness of composite space mirror changes surface form of the composite mirror, which is the focus of our study. In our research, the influence of varied quasi-isotropic stacking sequences and random angular deviation on the surface accuracy of composite space mirrors was investigated through finite element analyses (FEA). We established a simulation model for the studied concave mirror with 500 mm diameter, essential factors of layup sequences and random angular deviations on different plies were discussed. Five guiding findings were described in this study. Increasing total plies, optimizing stacking sequence and keeping consistency of ply alignment in ply placement are effective to improve surface accuracy of composite mirror.

  18. Sedimentology and High Resolution Sequence Stratigraphy of the Middle Jurassic Dhruma Formation Carbonates Outcrops in the Central Saudi Arabia

    Science.gov (United States)

    Yousif, Ibrahim; Abdullatif, Osman; Makkawi, Mohammed; Abdulghani, Waleed

    2017-04-01

    This study investigates the microfacies and sequence stratigraphic frame work of the Middle Jurassic Dhruma Formation in outcrops in central Saudi Arabia. The study contributes to the efforts to understand and enhance local and regional stratigraphic relationship and correlation of the Jurassic carbonate sequences and their significance to reservoir description and prediction in the subsurcae. The study describes and characterizes the sedimentology, microfacies and the stratigraphy of Dhruma Formation from outcrop sections having a total thickness of 70 m. Detailed microfacies and high-resolution stratigraphical analysis were carried out to determine microfacies, cyclicity, sequences and staking pattern. The study revealed ten lithofacies namely: oolitic grainstone,bioclastic oolitic grainstone, oolitic grapestone, bioclastic grainstone,foraminiferal packstone, echinoderm packstone, peloidal packstone to grainstone,skeletal wackestone to packstone, mudstone, and marlstone.These lithofacies were grouped into five lithofacies associations that deposited on a carbonate ramp setting. The depositional environment ranging from low energy lagoonal setting to high-energy shoals and banks to low energy outer ramp setting. Five high-resolution composite sequences have been defined and each sequence is composed at the bottom of intercalated mudstone/wackestone that passing up into grainstone lithofacies.The composite sequences range in thickness from 7 to 15 m, while the parasequences range from 0.5 to 1.5 m. The composite sequences extend laterally for a distance of more than 350 m. The overall composite section shows a shallowing upward succession of the 4th to the 5th order high-resolution sequences.The dominant lithofacies are the grainy ones, which constitute 30%, 50% and 80% of the studied sections. Furthermore, the parasequences thickness and their bio-components are increasing towards the top. The muddy lithofacies intensively affected the vertical continuity of the

  19. Effects of stacking sequence on fracture mechanisms in quasi-isotropic Carbon/epoxy laminates under tensile loading

    International Nuclear Information System (INIS)

    Hessabi, Z. R.; Majidi, B.; Aghazadeh, J.

    2006-01-01

    The progress of damage in quasi-isotropic carbon/epoxy laminates under tensile loading has been Investigated microscopically. One significant mode of failure in laminated composites is delamination initiating at free edges. The interlaminar stress in the boundary ply along the free edges of a laminated composite is the main factor to cause delamination. The laminate stacking sequence affects the interlaminar stress distribution and consequently may change the mode of failure. It is of design importance to determine a suitable criterion based on stress analysis to obtain the best stacking sequence. In the present work, tensile properties of six samples with different stacking sequences have been examined. Results showed that stress analysis at distance very close to the free edges is a suitable criterion to predict the initiation of delamination and the stacking sequence of [90/45/0/-45] s , has the highest strength among the others. Furthermore finite element analysis showed that the adjacent ±45 plies cause premature delamination during tensile loading

  20. Impact ejecta and carbonate sequence in the eastern sector of the Chicxulub crater

    Science.gov (United States)

    Urrutia-Fucugauchi, Jaime; Chavez-Aguirre, Jose Maria; Pérez-Cruz, Ligia; De la Rosa, Jose Luis

    2008-12-01

    The Chicxulub 200 km diameter crater located in the Yucatan platform of the Gulf of Mexico formed 65 Myr ago and has since been covered by Tertiary post-impact carbonates. The sediment cover and absence of significant volcanic and tectonic activity in the carbonate platform have protected the crater from erosion and deformation, making Chicxulub the only large multi-ring crater in which ejecta is well preserved. Ejecta deposits have been studied by drilling/coring in the southern crater sector and at outcrops in Belize, Quintana Roo and Campeche; little information is available from other sectors. Here, we report on the drilling/coring of a section of ˜34 m of carbonate breccias at 250 m depth in the Valladolid area (120 km away from crater center), which are interpreted as Chicxulub proximal ejecta deposits. The Valladolid breccias correlate with the carbonate breccias cored in the Peto and Tekax boreholes to the south and at similar radial distance. This constitutes the first report of breccias in the eastern sector close to the crater rim. Thickness of the Valladolid breccias is less than that at the other sites, which may indicate erosion of the ejecta deposits before reestablishment of carbonate deposition. The region east of the crater rim appears different from regions to the south and west, characterized by high density and scattered distribution of sinkholes.

  1. Minimizing N2O emissions and carbon footprint on a full-scale activated sludge sequencing batch reactor.

    Science.gov (United States)

    Rodriguez-Caballero, A; Aymerich, I; Marques, Ricardo; Poch, M; Pijuan, M

    2015-03-15

    A continuous, on-line quantification of the nitrous oxide (N2O) emissions from a full-scale sequencing batch reactor (SBR) placed in a municipal wastewater treatment plant (WWTP) was performed in this study. In general, N2O emissions from the biological wastewater treatment system were 97.1 ± 6.9 g N2O-N/Kg [Formula: see text] consumed or 6.8% of the influent [Formula: see text] load. In the WWTP of this study, N2O emissions accounted for over 60% of the total carbon footprint of the facility, on average. Different cycle configurations were implemented in the SBR aiming at reaching acceptable effluent values. Each cycle configuration consisted of sequences of aerated and non-aerated phases of different time length being controlled by the ammonium set-point fixed. Cycles with long aerated phases showed the largest N2O emissions, with the consequent increase in carbon footprint. Cycle configurations with intermittent aeration (aerated phases up to 20-30 min followed by short anoxic phases) were proven to effectively reduce N2O emissions, without compromising nitrification performance or increasing electricity consumption. This is the first study in which a successful operational strategy for N2O mitigation is identified at full-scale. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Carbon, nitrogen, and oxygen abundances in main-sequence stars. II. 20 F and G stars

    International Nuclear Information System (INIS)

    Clegg, R.E.S.; Lambert, D.L.; Tomkin, J.

    1981-01-01

    High-resolution Reticon spectra of red and near-infrared C I, N I, and O I lines have been analyzed to determine C, N, and O abundances in a sample of 20 F and G main-sequence stars. Their iron abundances, which have been determined from analysis of additional Reticon spectra of red Fe I lines, cover the range -0.9< or =[Fe/H]< or =+0.4. Sulfur abundances have also been obtained

  3. DNA sequencing, anatomy, and calcification patterns support a monophyletic, subarctic, carbonate reef-forming Clathromorphum (Hapalidiaceae, Corallinales, Rhodophyta).

    Science.gov (United States)

    Adey, Walter H; Hernandez-Kantun, Jazmin J; Johnson, Gabriel; Gabrielson, Paul W

    2015-02-01

    For the first time, morpho-anatomical characters that were congruent with DNA sequence data were used to characterize several genera in Hapalidiaceae-the major eco-engineers of Subarctic carbonate ecosystems. DNA sequencing of three genes (SSU, rbcL, ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit gene and psbA, photosystem II D1 protein gene), along with patterns of cell division, cell elongation, and calcification supported a monophyletic Clathromorphum. Two characters were diagnostic for this genus: (i) cell division, elongation, and primary calcification occurred only in intercalary meristematic cells and in a narrow vertical band (1-2 μm wide) resulting in a "meristem split" and (ii) a secondary calcification of interfilament crystals was also produced. Neopolyporolithon was resurrected for N. reclinatum, the generitype, and Clathromorphum loculosum was transferred to this genus. Like Clathromorphum, cell division, elongation, and calcification occurred only in intercalary meristematic cells, but in a wider vertical band (over 10-20 μm), and a "meristem split" was absent. Callilithophytum gen. nov. was proposed to accommodate Clathromorphum parcum, the obligate epiphyte of the northeast Pacific endemic geniculate coralline, Calliarthron. Diagnostic for this genus were epithallial cells terminating all cell filaments (no dorsi-ventrality was present), and a distinct "foot" was embedded in the host. Leptophytum, based on its generitype, L. laeve, was shown to be a distinct genus more closely related to Clathromorphum than to Phymatolithon. All names of treated species were applied unequivocally by linking partial rbcL sequences from holotype, isotype, or epitype specimens with field-collected material. Variation in rbcL and psbA sequences suggested that multiple species may be passing under each currently recognized species of Clathromorphum and Neopolyporolithon. © 2014 Phycological Society of America.

  4. Controls on facies and sequence stratigraphy of an upper Miocene carbonate ramp and platform, Melilla basin, NE Morocco

    Science.gov (United States)

    Cunningham, K.J.; Collins, Luke S.

    2002-01-01

    Upwelling of cool seawater, paleoceanographic circulation, paleoclimate, local tectonics and relative sea-level change controlled the lithofacies and sequence stratigraphy of a carbonate ramp and overlying platform that are part of a temporally well constrained carbonate complex in the Melilla basin, northeastern Morocco. At Melilla, from oldest to youngest, a third-order depositional sequence within the carbonate complex contains (1) a retrogradational, transgressive, warm temperate-type rhodalgal ramp; (2) an early highstand, progradational, bioclastic platform composed mainly of a temperate-type, bivalve-rich molechfor facies; and (3) late highstand, progradational to downstepping, subtropical/tropical-type chlorozoan fringing Porites reefs. The change from rhodalgal ramp to molechfor platform occurred at 7.0??0.14 Ma near the Tortonian/Messinian boundary. During a late stage in the development of the bioclastic platform a transition from temperate-type molechfor facies to subtropical/tropical-type chlorozoan facies occurred and is bracketed by chron 3An.2n (??? 6.3-6.6 Ma). Comparison to a well-dated carbonate complex in southeastern Spain at Cabo de Gata suggests that upwelling of cool seawater influenced production of temperate-type limestone within the ramp and platform at Melilla during postulated late Tortonian-early Messinian subtropical/tropical paleoclimatic conditions in the western Paleo-Mediterranean region. The upwelling of cool seawater across the bioclastic platform at Melilla could be related to the beginning of 'siphoning' of deep, cold Atlantic waters into the Paleo-Mediterranean Sea at 7.17 Ma. The facies change within the bioclastic platform from molechfor to chlorozoan facies may be coincident with a reduction of the siphoning of Atlantic waters and the end of upwelling at Melilla during chron 3An.2n. The ramp contains one retrogradational parasequence and the bioclastic platform three progradational parasequences. Minor erosional surfaces

  5. Quantitative controls on location and architecture of carbonate depositional sequences: upper miocene, cabo de gata region, se Spain

    Science.gov (United States)

    Franseen, E.K.; Goldstein, R.H.; Farr, M.R.

    1998-01-01

    Sequence stratigraphy, pinning-point relative sea-level curves, and magnetostratigraphy provide the quantitative data necessary to understand how rates of sea-level change and different substrate paleoslopes are dominant controls on accumulation rate, carbonate depositional sequence location, and internal architecture. Five third-order (1-10 my) and fourth-order (0.1-1.0 my) upper Miocene carbonate depositional sequences (DS1A, DS1B, DS2, DS3, TCC) formed with superimposed higher-frequency sea-level cycles in an archipelago setting in SE Spain. Overall, our study indicates when areas of high substrate slope (> 15??) are in shallow water, independent of climate, the location and internal architecture of carbonate deposits are not directly linked to sea-level position but, instead, are controlled by location of gently sloping substrates and processes of bypass. In contrast, if carbonate sediments are generated where substrates of low slope ( 15.6 cm/ky to ??? 2 cm/ky and overall relative sea level rose at rates of 17-21.4 cm/ky. Higher frequency sea-level rates were about 111 to more than 260 cm/ky, producing onlapping, fining- (deepening-) upward cycles. Decreasing accumulation rates resulted from decreasing surface area for shallow-water sediment production, drowning of shallow-water substrates, and complex sediment dispersal related to the archipelago setting. Typical systems tract and parasequence development should not be expected in "bypass ramp" settings; facies of onlapping strata do not track base level and are likely to be significantly different compared to onlapping strata associated with coastal onlap. Basal and upper DS2 reef megabreccias (indicating the transition from cool to warmer climatic conditions) were eroded from steep upslope positions and redeposited downslope onto areas of gentle substrate during rapid sea-level falls (> 22.7 cm/ky) of short duration. Such rapid sea-level falls and presence of steep slopes are not conducive to formation of

  6. The effect of the multi-pass non-circular drawing sequence on mechanical properties and microstructure evolution of low-carbon steel

    International Nuclear Information System (INIS)

    Lee, Jung Wan; Baek, Hyun Moo; Hwang, Sun Kwang; Son, Il-Heon; Bae, Chul Min; Im, Yong-Taek

    2014-01-01

    Highlights: • A multi-pass non-circular drawing sequence is proposed to make high-strength wires. • The sequence was designed and applied for a low-carbon steel wire up to the 10th pass. • Many LAGBs and small grain size of the wire produced by the sequence were obtained. • High plastic deformation was imposed on the wire, resulting in grain refinement. • The sequence made fine-grained wires with improved UTS, ductility and fatigue life. - Abstract: In this study, the multi-pass non-circular drawing sequence was investigated for manufacturing high-strength wires with better ductility in a simple continuous way without adding additional alloys and heat treatment considering the effect of microstructure evolution and die geometry of the sequence on the mechanical properties of low-carbon steel during the process. For this purpose, the non-circular drawing sequence was designed and applied up to the 10th pass at room temperature. Mechanical properties and microstructure evolution of the specimen processed by the sequence were investigated by tension, Vickers micro-hardness, electron backscattering diffraction (EBSD), and fatigue tests compared with those for the conventional wire-drawing process. From the EBSD results, the higher low angle grain boundaries length per unit area and smaller average grain size of the specimen processed by the non-circular drawing sequence were obtained than those of the specimen processed by the wire-drawing process for the 8th pass. These results indicated that more plastic deformation was imposed in the material by the non-circular drawing sequence, resulting in grain refinement of the deformed specimen compared to the wire-drawing process. It is demonstrated that the multi-pass non-circular drawing sequence could be beneficial in producing fine-grained wires with improved ultimate tensile strength, ductility, and fatigue property by simply changing drawing dies geometry of the conventional wire-drawing process

  7. Constraining controls on carbonate sequences with high-resolution chronostratigraphy: Upper Miocene, Cabo de Gata region, SE Spain

    Science.gov (United States)

    Montgomery, P.; Farr, M.R.; Franseen, E.K.; Goldstein, R.H.

    2001-01-01

    A high-resolution chronostratigraphy has been developed for Miocene shallow-water carbonate strata in the Cabo de Gata region of SE Spain for evaluation of local, regional and global factors that controlled platform architecture prior to and during the Messinian salinity crisis. Paleomagnetic data were collected from strata at three localities. Mean natural remanent magnetization (NRM) ranges between 1.53 ?? 10-8 and 5.2 ?? 10-3 Am2/kg. Incremental thermal and alternating field demagnetization isolated the characteristic remanent magnetization (ChRM). Rock magnetic studies show that the dominant magnetic mineral is magnetite, but mixtures of magnetite and hematite occur. A composite chronostratigraphy was derived from five stratigraphic sections. Regional stratigraphic data, biostratigraphic data, and an 40Ar/39Ar date of 8.5 ?? 0.1 Ma, for an interbedded volcanic flow, place the strata in geomagnetic polarity Chrons C4r to C3r. Sequence-stratigraphic and diagenetic evidence indicate a major unconformity at the base of depositional sequence (DS)3 that contains a prograding reef complex, suggesting that approximately 250 000 yr of record (Subchrons C3Br.2r to 3Br.1r) are missing near the Messinian-Tortonian boundary. Correlation to the GPTS shows that the studied strata represent five third- to fourth-order DSs. Basal units are temperate to subtropical ramps (DS1A, DS1B, DS2); these are overlain by subtropical to tropical reefal platforms (DS3), which are capped by subtropical to tropical cyclic carbonates (Terminal Carbonate Complex, TCC). Correlation of the Cabo de Gata record to the Melilla area of Morocco, and the Sorbas basin of Spain indicate that early - Late Tortonian ramp strata from these areas are partially time-equivalent. Similar strata are extensively developed in the Western Mediterranean and likely were influenced by a cool climate or influx of nutrients during an overall rise in global sea-level. After ramp deposition, a sequence boundary (SB3) in

  8. Sequence stratigraphy from ``spot'' outcrops—example from a carbonate-dominated setting: Devonian-Carboniferous transition, Dinant synclinorium (Belgium)

    Science.gov (United States)

    Van Steenwinkel, M.

    1990-12-01

    The application of sequence stratigraphy appears to be perfectly valid in isolated "spot" outcrops, which usually are badly exposed and located in areas of strong tectonic overprint. The case study presented here is in a carbonate-dominated setting at the northern edge of the Cornwall-Rhenish basin, during latest Devonian and earliest Carboniferous times. The approach taken involved the analysis of facies and vertical facies evolutions, in combination with detailed biostratigraphy. The subsequent deduction of deepening and shallowing events, and the understanding of the sedimentary response to these events in different palaeogeographical positions, are the basis for lateral correlation of facies sequences. A similar trend in the changes of deepenings and shallowings throughout the area, regardless of lateral facies differentiation, indicates a relationship between bathymetric changes and relative sea-level changes, that is independent of local differences in the sedimentation or subsidence rates. The studied stratigraphic interval, with its apparently "abrupt" changes in facies or lithology, is the sedimentary response to six, gradually changing trends in the rate of relative sea-level fall and rise. End-Devonian, offshore highstand deposits (1) are capped by an unconformity surface or by a surface of submarine erosion and nondeposition, representing a sequence boundary (2). The overlying lowstand unit consists of a basal (3) and an upper (4) part. The basal part contains an oolitic and crinoidal sand shoals, associated with a transgressive lag deposit in offshore position; the upper, main part is a prograding wedge of shallow-marine crinoidal sands, intercalated with increasingly deeper-water shaly facies (higher-order fluctuation). This lowstand unit was deposited during the initial, slow phase of relative sea-level rise. It levelled the topographic relief before the final drowning during the subsequent rapid (near the rise inflection point) relative sea

  9. Integrated analysis of 454 and Illumina transcriptomic sequencing characterizes carbon flux and energy source for fatty acid synthesis in developing Lindera glauca fruits for woody biodiesel.

    Science.gov (United States)

    Lin, Zixin; An, Jiyong; Wang, Jia; Niu, Jun; Ma, Chao; Wang, Libing; Yuan, Guanshen; Shi, Lingling; Liu, Lili; Zhang, Jinsong; Zhang, Zhixiang; Qi, Ji; Lin, Shanzhi

    2017-01-01

    Lindera glauca fruit with high quality and quantity of oil has emerged as a novel potential source of biodiesel in China, but the molecular regulatory mechanism of carbon flux and energy source for oil biosynthesis in developing fruits is still unknown. To better develop fruit oils of L. glauca as woody biodiesel, a combination of two different sequencing platforms (454 and Illumina) and qRT-PCR analysis was used to define a minimal reference transcriptome of developing L. glauca fruits, and to construct carbon and energy metabolic model for regulation of carbon partitioning and energy supply for FA biosynthesis and oil accumulation. We first analyzed the dynamic patterns of growth tendency, oil content, FA compositions, biodiesel properties, and the contents of ATP and pyridine nucleotide of L. glauca fruits from seven different developing stages. Comprehensive characterization of transcriptome of the developing L. glauca fruit was performed using a combination of two different next-generation sequencing platforms, of which three representative fruit samples (50, 125, and 150 DAF) and one mixed sample from seven developing stages were selected for Illumina and 454 sequencing, respectively. The unigenes separately obtained from long and short reads (201, and 259, respectively, in total) were reconciled using TGICL software, resulting in a total of 60,031 unigenes (mean length = 1061.95 bp) to describe a transcriptome for developing L. glauca fruits. Notably, 198 genes were annotated for photosynthesis, sucrose cleavage, carbon allocation, metabolite transport, acetyl-CoA formation, oil synthesis, and energy metabolism, among which some specific transporters, transcription factors, and enzymes were identified to be implicated in carbon partitioning and energy source for oil synthesis by an integrated analysis of transcriptomic sequencing and qRT-PCR. Importantly, the carbon and energy metabolic model was well established for oil biosynthesis of developing L

  10. RNA sequencing analysis reveals new findings of hyperbaric oxygen treatment on rats with acute carbon monoxide poisoning.

    Science.gov (United States)

    Wang, Wenlan; Xue, Li; Li, Ya; Li, Rong; Xie, Xiaoping; Bao, Junxiang; Hai, Chunxu; Li, Jinsheng

    2016-01-01

    To elucidate the altered gene network in the brains of carbon monoxide (CO) poisoned rats after treatment with hyperbaric oxygen (HBO₂). RNA sequencing (RNA-seq) analysis was performed to examine differentially expressed genes (DEGs) in brain tissue samples from nine male rats: a normal control group; a CO poisoning group; and an HBO₂ treatment group (three rats/group). Reverse transcription polymerase chain reaction (RT-PCR) and real-time quantitative PCR were used for validation of the DEGs in another 18 male rats (six rats/group). RNA-seq revealed that two genes were upregulated (4.18 and 8.76 log to the base 2 fold change) (p⟨0.05) in the CO-poisoned rats relative to the control rats; two genes were upregulated (3.88 and 7.69 log to the base 2 fold change); and 23 genes were downregulated (3.49-15.12 log to the base 2 fold change) (p⟨0.05) in the brains of the HBO₂-treated rats relative to the CO-poisoned rats. Target prediction of DEGs by gene network analysis and analysis of pathways affected suggested that regulation of gene expressions of dopamine metabolism and nitric oxide (NO) synthesis were significantly affected by CO poisoning and HBO₂ treatment. Results of RT-PCR and real-time quantitative PCR indicated that four genes (Pomc, GH-1, Pr1 and Fshβ) associated with hormone secretion in the hypothalamic-pituitary system have potential as markers for prognosis of CO. This study is the first RNA-seq analysis profile of HBO₂ treatment on rats with acute CO poisoning. It concludes that changes of hormone secretion in the hypothalamic-pituitary system, dopamine metabolism and NO synthesis involved in brain damage and behavior abnormalities after CO poisoning and HBO₂ therapy may regulate these changes.

  11. Basin analysis in the Southern Tethyan margin: Facies sequences, stratal pattern and subsidence history highlight extension-to-inversion processes in the Cretaceous Panormide carbonate platform (NW Sicily)

    Science.gov (United States)

    Basilone, Luca; Sulli, Attilio

    2018-01-01

    In the Mediterranean, the South-Tethys paleomargin experienced polyphased tectonic episodes and paleoenvironmental perturbations during Mesozoic time. The Cretaceous shallow-water carbonate successions of the Panormide platform, outcropping in the northern edge of the Palermo Mountains (NW Sicily), were studied by integrating facies and stratal pattern with backstripping analysis to recognize the tectonics vs. carbonate sedimentation interaction. The features of the Requienid limestone, including geometric configuration, facies sequence, lithological changes and significance of the top-unconformity, highlight that at the end of the Lower Cretaceous the carbonate platform was tectonically dismembered in various rotating fault-blocks. The variable trends of the subsidence curves testify to different responses, both uplift and downthrow, of various platform-blocks impacted by extensional tectonics. Physical stratigraphic and facies analysis of the Rudistid limestone highlight that during the Upper Cretaceous the previously carbonate platform faulted-blocks were subjected to vertical movements in the direction opposite to the displacement produced by the extensional tectonics, indicating a positive tectonic inversion. Comparisons with other sectors of the Southern Tethyan and Adria paleomargins indicate that during the Cretaceous these areas underwent the same extensional and compressional stages occurring in the Panormide carbonate platform, suggesting a regional scale significance, in time and kinematics, for these tectonic events.

  12. Stable isotope composition of bulk and secondary carbonates from the Quaternary loess-paleosol sequence in Sutto, Hungary

    DEFF Research Database (Denmark)

    Koeniger, Paul; Barta, Gabriella; Thiel, Christine

    2014-01-01

    reveal pedogenetic information during the different climatic phases. Carbon and oxygen isotope analyses are valuable to classify secondary carbonates and to serve as proxies for the interpretation of paleoenvironmental conditions, e.g. moisture conditions, leaching, the role of organic matter...

  13. Experimental and Numerical Studies on Fiber Deformation and Formability in Thermoforming Process Using a Fast-Cure Carbon Prepreg: Effect of Stacking Sequence and Mold Geometry

    Science.gov (United States)

    Bae, Daeryeong; Kim, Shino; Lee, Wonoh; Yi, Jin Woo; Um, Moon Kwang; Seong, Dong Gi

    2018-01-01

    A fast-cure carbon fiber/epoxy prepreg was thermoformed against a replicated automotive roof panel mold (square-cup) to investigate the effect of the stacking sequence of prepreg layers with unidirectional and plane woven fabrics and mold geometry with different drawing angles and depths on the fiber deformation and formability of the prepreg. The optimum forming condition was determined via analysis of the material properties of epoxy resin. The non-linear mechanical properties of prepreg at the deformation modes of inter- and intra-ply shear, tensile and bending were measured to be used as input data for the commercial virtual forming simulation software. The prepreg with a stacking sequence containing the plain-woven carbon prepreg on the outer layer of the laminate was successfully thermoformed against a mold with a depth of 20 mm and a tilting angle of 110°. Experimental results for the shear deformations at each corner of the thermoformed square-cup product were compared with the simulation and a similarity in the overall tendency of the shear angle in the path at each corner was observed. The results are expected to contribute to the optimization of parameters on materials, mold design and processing in the thermoforming mass-production process for manufacturing high quality automotive parts with a square-cup geometry. PMID:29883413

  14. Experimental and Numerical Studies on Fiber Deformation and Formability in Thermoforming Process Using a Fast-Cure Carbon Prepreg: Effect of Stacking Sequence and Mold Geometry

    Directory of Open Access Journals (Sweden)

    Daeryeong Bae

    2018-05-01

    Full Text Available A fast-cure carbon fiber/epoxy prepreg was thermoformed against a replicated automotive roof panel mold (square-cup to investigate the effect of the stacking sequence of prepreg layers with unidirectional and plane woven fabrics and mold geometry with different drawing angles and depths on the fiber deformation and formability of the prepreg. The optimum forming condition was determined via analysis of the material properties of epoxy resin. The non-linear mechanical properties of prepreg at the deformation modes of inter- and intra-ply shear, tensile and bending were measured to be used as input data for the commercial virtual forming simulation software. The prepreg with a stacking sequence containing the plain-woven carbon prepreg on the outer layer of the laminate was successfully thermoformed against a mold with a depth of 20 mm and a tilting angle of 110°. Experimental results for the shear deformations at each corner of the thermoformed square-cup product were compared with the simulation and a similarity in the overall tendency of the shear angle in the path at each corner was observed. The results are expected to contribute to the optimization of parameters on materials, mold design and processing in the thermoforming mass-production process for manufacturing high quality automotive parts with a square-cup geometry.

  15. Soil carbon and nitrogen sequestration over an age sequence of Pinus patula plantations in Zimbabwean Eastern Highlands

    NARCIS (Netherlands)

    Mujuru, L.; Gotora, T.; Velthorst, E.J.; Nyamangara, J.; Hoosbeek, M.R.

    2014-01-01

    Forests play a major role in regulating the rate of increase of global atmospheric carbon dioxide (CO2) concentrations creating a need to investigate the ability of exotic plantations to sequester atmospheric CO2. This study examined pine plantations located in the Eastern Highlands of Zimbabwe

  16. Molecular and elemental analyses of the carbonaceous matter in the gold and uranium bearing Vaal Reef carbon seams, Witwatersrand sequence

    International Nuclear Information System (INIS)

    Zumberge, J.E.; Sigleo, A.C.; Nagy, B.

    1978-01-01

    The thin Vaal Reef carbon seams consist of a complex, solid, and solvent insoluble, polymer-like substance, containing mainly hydrocarbons and some organic sulphur and oxygen compounds. These carbon seams are not pure carbon, e.g. graphite, and do not contain only hydrocarbons. According to modern terminology the Vaal Reef carbonaceous matter is most appropriately referred to as kerogen rather than carbon or thucholite. This kerogen is not the result of the polymerization of gaseous or liquid hydrocarbons, but rather of the polymerization of biochemicals from decayed, primitive Precambrian micro-organisms. These microbiota formed mats in which uranium minerals and gold became incorporated before burial under younger sediments. Organic geochemistry was first developed as a means to elucidate the nature and composition of petroleum and coal. Later it was successfully used in lunar sample, planetary surface, and meteorite studies as well as in investigations of kerogens in terrestrial sediments of various ages. Considering economic geology, organic geochemistry holds promise for elucidating the origin and helping in the exploration of carbonaceous ore deposits. The purpose of this report is to review some of the major current organic geochemical methods and to illustrate these by the analysis of the Vaal Reef kerogen. The samples were analysed by a directly connected high vacuum pyrolysis system-gas chromatograph-organic mass spectrometer. Additional analyses were performed by a combined scanning electron microscope-electron microprobe, by the techniques of electron paramagnetic resonance spectroscopy, and by neutron activation analysis

  17. Carbon isotope composition of intermediates of the starch-malate sequence and level of the crassulacean acid metabolism in leaves of Kalanchoe blossfeldiana Tom Thumb.

    Science.gov (United States)

    Deleens, E; Garnier-Dardart, J; Queiroz, O

    1979-09-01

    Isotype analyses were performed on biochemical fractions isolated from leaves of Kalanchoe blossfeldiana Tom Thumb. during aging under long days or short days. Irrespective of the age or photoperiodic conditions, the intermediates of the starch-malate sequence (starch, phosphorylated compounds and organic acids) have a level of (13)C higher than that of soluble sugars, cellulose and hemicellulose. In short days, the activity of the crassulacean acid metabolism pathway is predominant as compared to that of C3 pathway: leaves accumulate organic acids, rich in (13)C. In long days, the activity of the crassulacean acid metabolism pathway increases as the leaves age, remaining, however, relatively low as compared to that of C3 pathway: leaves accumulate soluble sugars, poor in (13)C. After photoperiodic change (long days→short days), isotopic modifications of starch and organic acids suggest evidence for a lag phase in the establishment of the crassulacean acid metabolism pathway specific to short days. The relative proportions of carbon from a C3-origin (RuBPC acitivity as strong discriminating step, isotope discrimination in vivo=20‰) or C4-origin (PEPC activity as weak discriminating step, isotope discrimination in vivo=4‰) present in the biochemical fractions were calculated from their δ(13)C values. Under long days, 30 to 70% versus 80 to 100% under short days, of the carbon of the intermediates linked to the starch-malate sequence, or CAM pathway (starch, phosphorylated compounds and organic acids), have a C4-origin. Products connected to the C3 pathway (free sugars, cellulose, hemicellulose) have 0 to 50% of their carbon, arising from reuptake of the C4 from malate, under long days versus 30 to 70% under short days.

  18. Apoptosis-inducing signal sequence mutation in carbonic anhydrase IV identified in patients with the RP17 form of retinitis pigmentosa

    Science.gov (United States)

    Rebello, George; Ramesar, Rajkumar; Vorster, Alvera; Roberts, Lisa; Ehrenreich, Liezle; Oppon, Ekow; Gama, Dumisani; Bardien, Soraya; Greenberg, Jacquie; Bonapace, Giuseppe; Waheed, Abdul; Shah, Gul N.; Sly, William S.

    2004-01-01

    Genetic and physical mapping of the RP17 locus on 17q identified a 3.6-megabase candidate region that includes the gene encoding carbonic anhydrase IV (CA4), a glycosylphosphatidylinositol-anchored protein that is highly expressed in the choriocapillaris of the human eye. By sequencing candidate genes in this region, we identified a mutation that causes replacement of an arginine with a tryptophan (R14W) in the signal sequence of the CA4 gene at position -5 relative to the signal sequence cleavage site. This mutation was found to cosegregate with the disease phenotype in two large families and was not found in 36 unaffected family members or 100 controls. Expression of the mutant cDNA in COS-7 cells produced several findings, suggesting a mechanism by which the mutation can explain the autosomal dominant disease. In transfected COS-7 cells, the R14W mutation (i) reduced the steady-state level of carbonic anhydrase IV activity expressed by 28% due to a combination of decreased synthesis and accelerated turnover; (ii) led to up-regulation of immunoglobulin-binding protein, double-stranded RNA-regulated protein kinase-like ER kinase, and CCAAT/enhancer-binding protein homologous protein, markers of the unfolded protein response and endoplasmic reticulum stress; and (iii) induced apoptosis, as evidenced by annexin V binding and terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling staining, in most cells expressing the mutant, but not the WT, protein. We suggest that a high level of expression of the mutant allele in the endothelial cells of the choriocapillaris leads to apoptosis, leading in turn to ischemia in the overlying retina and producing autosomal dominant retinitis pigmentosa. PMID:15090652

  19. Removal of absorbable organic halides (aox) from recycled paper mill effluent using granular activated carbon-sequencing batch biofilm reactor (GAC-SBBR)

    International Nuclear Information System (INIS)

    Mohamad, A.B.; Rahman, R.A.; Kadhum, A.A.H.; Abdullah, S.R.S.; Shaari, S.

    2006-01-01

    Paper mills generate varieties of pollutants depending upon the type of the pulping process. Paper mill wastewaters have high chemical oxygen demand (COD) and colour, indicating high concentrations of recalcitrant organics. The study was conducted employing a Granular Activated Carbon - Sequencing Batch Biofilm Reactor (GAC-SBBR), containing 3.0 L working volume, operated in aerobic condition and packed with 200 g/L of 2-3 mm granular activated carbon (coconut shells) as a medium for biofilm growth. For the first couple of month, the HRT was 36 hours and the HRT of this reactor was adjusted to 24 hours in order to evaluate the performance of the system. The treated wastewater sample for these studies came from a recycle paper factory from MNI Sdn Bhd with 4 different samples characteristics. The adsorbable organic halides (AOX) to be determined and treated were Pentachlorophenol (PCP), 2,3,4,5-Tetrachlorophenol (2,3,4,5-TeCP), 2,4,6-Trichlorophenol (2,4,6-TCP), 2,4-Dichlorophenol ( 2,4-DCP), 2-Chlorophenol (CP) and phenol. Results showed that, the biofilm attached onto granular activated carbon (GAC) could substantially remove these recalcitrant in the wastewater. More over, results from the studies showed that high removal was achieved by the biofilm SBR with 10-100% removal of AOX and depending on HRT. (Author)

  20. Impacts of extreme weather events and climate variability on carbon exchanges in an age-sequence of managed temperate pine forests from 2003 to 201

    Science.gov (United States)

    Arain, M. A.

    2017-12-01

    North American temperate forests are a critical component of the global carbon cycle and regional water resources. A large portion of these forests has traditionally been managed for timber production and other uses. The response of these forests, which are in different stages of development, to extreme weather events such as drought and heat stresses, climate variability and management regimes is not fully understood. In this study, eddy covariance flux measurements in an age sequence (77-, 42-, and 14-years old as of 2016) of white pine (Pinus strobus L.) plantation forests in southern Ontario, Canada are examined to determine the impact of heat and drought stresses and climate variability over a 14 year period (2003 to 2016). The mean annual net ecosystem productivity (NEP) values were 195 ± 87, 512 ±161 and 103 ± 103 g C m-2 year-1 in 77-, 42- and 14-year-old forests respectively, over the study period. The youngest forest became a net carbon sink in the fifth year of its growth. Air temperature was a dominant control on carbon fluxes and heat stress reduced photosynthesis much more as compared to ecosystem respiration in the growing season. A large decrease in annual NEP was observed during years experiencing heat waves. Drought stress had the strongest impact on the middle age forest which had the largest carbon sink and water demand. In contrast, young forest was more sensitive to heat stress, than drought. Severity of heat and drought stress impacts was highly dependent on the timing of these events. Simultaneous occurrence of heat and drought stress in the early growing season such as in 2012 and 2016 had a drastic negative impact on carbon balance in these forests due to plant-soil-atmosphere feedbacks. Future research should consider the timing of the extreme events, the stage of forest development and effects of extreme events on component fluxes. This research helps to assess the vulnerability of managed forests and their ecological and hydrological

  1. Cyclic Sequences, Events and Evolution of the Sino-Korean Plate,with a Discussion on the Evolution of Molar-tooth Carbonates,Phosphorites and Source Rocks

    Institute of Scientific and Technical Information of China (English)

    MENG Xianghua; GE Ming

    2003-01-01

    This paper gives an account of the research that the authors conducted on the cyclic sequences, events and evolutionary history from Proterozoic to Meso-Cenozoic in the Sino-Korean plate based on the principle of the Cosmos-Earth System. The authors divided this plate into 20 super-cyclic or super-mega-cyclic periods and more than 100 Oort periods. The research focused on important sea flooding events, uplift interruption events, tilting movement events, molar-tooth carbonate events, thermal events, polarity reversal events, karst events, volcanic explosion events and storm events, as well as types of resource areas and paleotectonic evolution. By means of the isochronous theory of the Cosmos-Earth System periodicity and based on long-excentricity and periodicity, the authors elaborately studied the paleogeographic evolution of the aulacogen of the Sino-Korean plate, the oolitic beach platform formation, the development of foreland basin and continental rift valley basin, and reconstructed the evolution of tectonic paleogeography and stratigraphic framework in the Sino-Korean plate in terms of evolutionary maps. Finally, the authors gave a profound discussion on the formation and development of molar-tooth carbonates, phosphorites and source rocks.

  2. Characterization of dissolved organic matter during landfill leachate treatment by sequencing batch reactor, aeration corrosive cell-Fenton, and granular activated carbon in series

    International Nuclear Information System (INIS)

    Bu Lin; Wang Kun; Zhao Qingliang; Wei Liangliang; Zhang Jing; Yang Junchen

    2010-01-01

    Landfill leachate is generally characterized as a complex recalcitrant wastewater containing high concentration of dissolved organic matter (DOM). A combination of sequencing batch reactor (SBR) + aeration corrosive cell-Fenton (ACF) + granular activated carbon (GAC) adsorption in series was proposed for the purpose of removing pollutants in the leachate. Fractionation was also performed to investigate the composition changes and characteristics of the leachate DOM in each treatment process. Experimental results showed that organic matter, in terms of chemical oxygen demand (COD), 5-day biological oxygen demand (BOD 5 ), and dissolved organic carbon (DOC), was reduced by 97.2%, 99.1%, and 98.7%, respectively. To differentiate the DOM portions, leachates were separated into five fractions by XAD-8 and XAD-4 resins: hydrophobic acid (HPO-A), hydrophobic neutral (HPO-N), transphilic acid (TPI-A), transphilic neutral (TPI-N), and hydrophilic fraction (HPI). The predominant fraction in the raw leachate was HPO-A (36% of DOC), while the dominant fraction in the final effluent was HPI (53% of DOC). Accordingly, macromolecules were degraded to simpler ones in a relatively narrow range below 1000 Da. Spectral and chromatographic analyses also showed that most humic-like substances in all fractions were effectively removed during the treatments and led to a simultaneous decrease in aromaticity.

  3. Characterization of dissolved organic matter during landfill leachate treatment by sequencing batch reactor, aeration corrosive cell-Fenton, and granular activated carbon in series

    Energy Technology Data Exchange (ETDEWEB)

    Bu Lin [School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); Wang Kun [State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), Harbin Institute of Technology, Harbin 150090 (China); School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); Zhao Qingliang, E-mail: zhql1962@yahoo.com.cn [State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), Harbin Institute of Technology, Harbin 150090 (China); School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); Wei Liangliang; Zhang Jing; Yang Junchen [School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China)

    2010-07-15

    Landfill leachate is generally characterized as a complex recalcitrant wastewater containing high concentration of dissolved organic matter (DOM). A combination of sequencing batch reactor (SBR) + aeration corrosive cell-Fenton (ACF) + granular activated carbon (GAC) adsorption in series was proposed for the purpose of removing pollutants in the leachate. Fractionation was also performed to investigate the composition changes and characteristics of the leachate DOM in each treatment process. Experimental results showed that organic matter, in terms of chemical oxygen demand (COD), 5-day biological oxygen demand (BOD{sub 5}), and dissolved organic carbon (DOC), was reduced by 97.2%, 99.1%, and 98.7%, respectively. To differentiate the DOM portions, leachates were separated into five fractions by XAD-8 and XAD-4 resins: hydrophobic acid (HPO-A), hydrophobic neutral (HPO-N), transphilic acid (TPI-A), transphilic neutral (TPI-N), and hydrophilic fraction (HPI). The predominant fraction in the raw leachate was HPO-A (36% of DOC), while the dominant fraction in the final effluent was HPI (53% of DOC). Accordingly, macromolecules were degraded to simpler ones in a relatively narrow range below 1000 Da. Spectral and chromatographic analyses also showed that most humic-like substances in all fractions were effectively removed during the treatments and led to a simultaneous decrease in aromaticity.

  4. Carbonization

    Energy Technology Data Exchange (ETDEWEB)

    Hennebutte, H G; Goutal, E

    1921-07-04

    Materials such as coal, peat, or schist are subjected to a rising temperature in successive stages in apparatus in which the distillation products are withdrawn at each stage. For example in a three-stage process, the acid products of the first or low-temperature stage are fixed in a suitable reagent, the basic products from a second or higher-temperature stage are absorbed in an acid reagent, hydrocarbons being retained by solvents, while the third are subjected to a pyrogenation process carried out in a closed vessel. Wherein the material is subjected in stages to a rising temperature, the gasified products being withdrawn at each stage, and are prevented as far as possible from mixing with the carbonized products.

  5. Treatability studies with granular activated carbon (GAC) and sequencing batch reactor (SBR) system for textile wastewater containing direct dyes

    International Nuclear Information System (INIS)

    Sirianuntapiboon, Suntud; Sansak, Jutarat

    2008-01-01

    The GAC-SBR efficiency was decreased with the increase of dyestuff concentration or the decrease of bio-sludge concentration. The system showed the highest removal efficiency with synthetic textile wastewater (STWW) containing 40 mg/L direct red 23 or direct blue 201 under MLSS of 3000 mg/L and hydraulic retention time (HRT) of 7.5 days. But, the effluent NO 3 - was higher than that of the influent. Direct red 23 was more effective than direct blue 201 to repress the GAC-SBR system efficiency. The dyes removal efficiency of the system with STWW containing direct red 23 was reduced by 30% with the increase of direct red 23 from 40 mg/L to 160 mg/L. The system with raw textile wastewater (TWW) showed quite low BOD 5 TKN and dye removal efficiencies of only 64.7 ± 4.9% and 50.2 ± 6.9%, respectively. But its' efficiencies could be increased by adding carbon sources (BOD 5 ). The dye removal efficiency with TWW was increased by 30% and 20% by adding glucose (TWW + glucose) or Thai rice noodle wastewater (TWW + TRNWW), respectively. SRT of the systems were 28 ± 1 days and 31 ± 2 days with TWW + glucose and TWW + TRNWW, respectively

  6. Treatability studies with granular activated carbon (GAC) and sequencing batch reactor (SBR) system for textile wastewater containing direct dyes

    Energy Technology Data Exchange (ETDEWEB)

    Sirianuntapiboon, Suntud [Department of Environmental Technology, School of Energy Environment and Materials, King Mongkut' s University of Technology, Thonburi, Bangmod, Thung-kru, Bangkok 10140 (Thailand)], E-mail: suntud.sir@kmutt.ac.th; Sansak, Jutarat [Department of Environmental Technology, School of Energy Environment and Materials, King Mongkut' s University of Technology, Thonburi, Bangmod, Thung-kru, Bangkok 10140 (Thailand)

    2008-11-30

    The GAC-SBR efficiency was decreased with the increase of dyestuff concentration or the decrease of bio-sludge concentration. The system showed the highest removal efficiency with synthetic textile wastewater (STWW) containing 40 mg/L direct red 23 or direct blue 201 under MLSS of 3000 mg/L and hydraulic retention time (HRT) of 7.5 days. But, the effluent NO{sub 3}{sup -} was higher than that of the influent. Direct red 23 was more effective than direct blue 201 to repress the GAC-SBR system efficiency. The dyes removal efficiency of the system with STWW containing direct red 23 was reduced by 30% with the increase of direct red 23 from 40 mg/L to 160 mg/L. The system with raw textile wastewater (TWW) showed quite low BOD{sub 5} TKN and dye removal efficiencies of only 64.7 {+-} 4.9% and 50.2 {+-} 6.9%, respectively. But its' efficiencies could be increased by adding carbon sources (BOD{sub 5}). The dye removal efficiency with TWW was increased by 30% and 20% by adding glucose (TWW + glucose) or Thai rice noodle wastewater (TWW + TRNWW), respectively. SRT of the systems were 28 {+-} 1 days and 31 {+-} 2 days with TWW + glucose and TWW + TRNWW, respectively.

  7. Treatability studies with granular activated carbon (GAC) and sequencing batch reactor (SBR) system for textile wastewater containing direct dyes.

    Science.gov (United States)

    Sirianuntapiboon, Suntud; Sansak, Jutarat

    2008-11-30

    The GAC-SBR efficiency was decreased with the increase of dyestuff concentration or the decrease of bio-sludge concentration. The system showed the highest removal efficiency with synthetic textile wastewater (STWW) containing 40 mg/L direct red 23 or direct blue 201 under MLSS of 3,000 mg/L and hydraulic retention time (HRT) of 7.5 days. But, the effluent NO(3)(-) was higher than that of the influent. Direct red 23 was more effective than direct blue 201 to repress the GAC-SBR system efficiency. The dyes removal efficiency of the system with STWW containing direct red 23 was reduced by 30% with the increase of direct red 23 from 40 mg/L to 160 mg/L. The system with raw textile wastewater (TWW) showed quite low BOD(5) TKN and dye removal efficiencies of only 64.7+/-4.9% and 50.2+/-6.9%, respectively. But its' efficiencies could be increased by adding carbon sources (BOD(5)). The dye removal efficiency with TWW was increased by 30% and 20% by adding glucose (TWW+glucose) or Thai rice noodle wastewater (TWW+TRNWW), respectively. SRT of the systems were 28+/-1 days and 31+/-2 days with TWW+glucose and TWW+TRNWW, respectively.

  8. Characteristics, stratigraphic architecture, and time framework of multi-order mixed siliciclastic and carbonate depositional sequences, outcropping Cisco Group (Late Pennsylvanian and Early Permian), Eastern Shelf, north-central Texas, USA

    Science.gov (United States)

    Yang, Wan; Kominz, Michelle A.

    2003-01-01

    The Cisco Group on the Eastern Shelf of the Midland Basin is composed of fluvial, deltaic, shelf, shelf-margin, and slope-to-basin carbonate and siliciclastic rocks. Sedimentologic and stratigraphic analyses of 181 meter-to-decimeter-scale depositional sequences exposed in the up-dip shelf indicated that the siliciclastic and carbonate parasequences in the transgressive systems tracts (TST) are thin and upward deepening, whereas those in highstand systems tracts (HST) are thick and upward shallowing. The sequences can be subdivided into five types on the basis of principal lithofacies, and exhibit variable magnitude of facies shift corresponding to variable extents of marine transgression and regression on the shelf. The sequence stacking patterns and their regional persistence suggest a three-level sequence hierarchy controlled by eustasy, whereas local and regional changes in lithology, thickness, and sequence type, magnitude, and absence were controlled by interplay of eustasy, differential shelf subsidence, depositional topography, and pattern of siliciclastic supply. The outcropping Cisco Group is highly incomplete with an estimated 6-11% stratigraphic completeness. The average duration of deposition of the major (third-order) sequences is estimated as 67-102 ka on the up-dip shelf and increases down dip, while the average duration of the major sequence boundaries (SB) is estimated as 831-1066 ka and decreases down dip. The nondepositional and erosional hiatus on the up-dip shelf was represented by lowstand deltaic systems in the basin and slope.

  9. Water-table and discharge changes associated with the 2016-2017 seismic sequence in central Italy: hydrogeological data and a conceptual model for fractured carbonate aquifers

    Science.gov (United States)

    Petitta, Marco; Mastrorillo, Lucia; Preziosi, Elisabetta; Banzato, Francesca; Barberio, Marino Domenico; Billi, Andrea; Cambi, Costanza; De Luca, Gaetano; Di Carlo, Giuseppe; Di Curzio, Diego; Di Salvo, Cristina; Nanni, Torquato; Palpacelli, Stefano; Rusi, Sergio; Saroli, Michele; Tallini, Marco; Tazioli, Alberto; Valigi, Daniela; Vivalda, Paola; Doglioni, Carlo

    2018-01-01

    A seismic sequence in central Italy from August 2016 to January 2017 affected groundwater dynamics in fractured carbonate aquifers. Changes in spring discharge, water-table position, and streamflow were recorded for several months following nine Mw 5.0-6.5 seismic events. Data from 22 measurement sites, located within 100 km of the epicentral zones, were analyzed. The intensity of the induced changes were correlated with seismic magnitude and distance to epicenters. The additional post-seismic discharge from rivers and springs was found to be higher than 9 m3/s, totaling more than 0.1 km3 of groundwater release over 6 months. This huge and unexpected contribution increased streamflow in narrow mountainous valleys to previously unmeasured peak values. Analogously to the L'Aquila 2009 post-earthquake phenomenon, these hydrogeological changes might reflect an increase of bulk hydraulic conductivity at the aquifer scale, which would increase hydraulic heads in the discharge zones and lower them in some recharge areas. The observed changes may also be partly due to other mechanisms, such as shaking and/or squeezing effects related to intense subsidence in the core of the affected area, where effects had maximum extent, or breaching of hydraulic barriers.

  10. FACIES PARTITIONING AND SEQUENCE STRATIGRAPHY OF A MIXED SILICICLASTIC-CARBONATE RAMP STACK IN THE GELASIAN OF SICILY (S ITALY: A POTENTIAL MODEL FOR ICEHOUSE, DISTALLY-STEEPENED HETEROZOAN RAMPS

    Directory of Open Access Journals (Sweden)

    FRANCESCO MASSARI

    2012-11-01

    Full Text Available The Gelasian succession of the Capodarso area (Enna-Caltanissetta basin, Sicily, Italy consists of an offlapping stack of cycles composed of siliciclastic units passing to carbonate heterozoan, clino-stratified wedges, developed from a growing positive tectonic structure. Identification of a number of facies tracts, based on sedimentary facies, biofacies and taphofacies, provided important information about the differentiation and characterisation of systems tracts and key stratal surfaces of sequence stratigraphy. The bulk of carbonate wedges are interpreted as representing the rapid falling-stage progradation of distally steepened ramps. The inferred highest rate of carbonate production during forced regressions was concomitant with active downramp resedimentation by storm-driven downwelling flows, leading to storing of most carbonate sediment on the ramp slope as clino-beds of the prograding bodies. Comparison of the Capodarso ramps with other icehouse carbonate ramps, with particular regard to the Mediterranean Plio-Pleistocene, provides clues for defining some common features. These are inferred to include: (1 brief, rapid episodes of progradation concomitant with orbitally-forced sea-level changes, resulting in limited ramp width; (2 preferential fostering of growth and downramp resedimentation of heterozoan carbonates during glacial hemicycles marked by enhanced atmospheric and marine circulation; (3 building out from positive features of entirely submerged distally-steepened ramps with storm-wave-graded profile and distinctive clinoforms; (4 ramp stacks generally consisting of mixed clastic-carbonate sequences showing an ordered spectrum of distinct frequencies; (5 rapid, continuous changes in environmental parameters, leading to the short-lived persistence of faunal communities, climax communities generally having insufficient time to form. 

  11. Sedimentary facies analysis of a high-frequency, small-scale, peritidal carbonate sequence in the Lower Jurassic of the Tripolis carbonate unit (central western Crete, Greece: Long-lasting emergence and fossil laminar dolocretes horizons

    Directory of Open Access Journals (Sweden)

    Fotini A. Pomoni

    2016-07-01

    Full Text Available The study examines a Lower Jurassic (late Liassic cyclic lagoonal–peritidal stratigraphic unit outcropping in central western Crete (Tripolis unit, which corresponds to the eastern (internal part of the mainland Gavrovo-Tripolis platform, the most significant external platform of the Hellenides. The studied Tripolis carbonate sequence consists of meter-scale, shallowing-upward successions of restricted inner-carbonate platform facies, including cyclically repeated subtidal, intertidal and supratidal facies, that are separated by erosion surfaces (elementary cycles. Each cycle starts with relatively open-marine facies, which are overlain by shallower, more restricted facies (tidal flat progradation. The lithofacies association includes dolomitic intraclastic–peloidal–bioclastic wackestones–packstones/floatstones and grainstones/rudstones dominated by a restricted shallow-marine fauna (bivalves, gastropods, ostracods and seldom benthic foraminifers, representing a shallow subtidal to intertidal, moderately high-energy environment within an inner-platform setting (peritidal environment to restricted lagoon. This lithofacies association has been intermittently subaerially exposed and has undergone diagenetic processes in an inter- or supratidal environment, exhibiting features of vadose diagenesis and pedogenesis due to long-lasting exposure along certain horizons. The peritidal facies are capped by dolocretes controlled by root-activities (laminar dolocretes, peloidal–pisoid dolocretes and massive dolocretes, marking the end of each depositional cycle, and, thus, distinguishing the successive episodes of a prolonged subaerial exposure period and birth of paleosol horizons. Dolocretes consist a diagenetic facies, characterized by several vadose and pedogenic fabrics, including fenestral cavities with geopetal structures, “flower spar” to blocky sparry cement in primary pores, micritic coatings, crudely pelleted walls, alveolar

  12. Performance evaluation of a granular activated carbon-sequencing batch biofilm reactor pilot plant system used in treating real wastewater from recycled paper industry.

    Science.gov (United States)

    Muhamad, Mohd Hafizuddin; Sheikh Abdullah, Siti Rozaimah; Mohamad, Abu Bakar; Rahman, Rakmi Abdul; Kadhum, Abdul Amir Hasan

    2012-01-01

    A pilot scale granular activated carbon-sequencing batch biofilm reactor with a capacity of 2.2 m3 was operated for over three months to evaluate its performance treating real recycled paper industry wastewater under different operational conditions. In this study, dissolved air floatation (DAF) and clarifier effluents were used as influent sources of the pilot plant. During the course of the study, the reactor was able to biodegrade the contaminants in the incoming recycled paper mill wastewater in terms of chemical oxygen demand (COD), adsorbable organic halides (AOX; specifically 2,4-dichlorophenol (2,4-DCP)) and ammoniacal nitrogen (NH3-N) removal efficiencies at varying hydraulic retention times (HRTs) of 1-3 days, aeration rates (ARs) of 2.1-3.4 m3/min and influent feed concentration of 40-950 mg COD/l. Percentages of COD, 2,4-DCP and NH3-N removals increased with increasing HRT, resulting in more than 90% COD, 2,4-DCP and NH3-N removals at HRT values above two days. Degradation of COD, 2,4-DCP and NH3-N were seriously affected by variation of ARs, which resulted in significant decrease of COD, 2,4-DCP and NH3-N removals by decreasing ARs from 3.4 m3/min to 2.1 m3/min, varying in the ranges of 24-80%, 6-96% and 5-42%, respectively. In comparison to the clarifier effluent, the treatment performance of DAF effluent, containing high COD concentration, resulted in a higher COD removal of 82%. The use of diluted DAF effluent did not improve significantly the COD removal. Higher NH3-N removal efficiency of almost 100% was observed during operation after maintenance shutdown compared to normal operation, even at the same HRT of one day due to the higher dissolved oxygen concentrations (1-7 mg/l), while no significant difference in COD removal efficiency was observed.

  13. Photoionization of multiply charged ions at the advanced light source

    International Nuclear Information System (INIS)

    Schlachter, A.S.; Kilcoyne, A.L.D.; Aguilar, A.; Gharaibeh, M.F.; Emmons, E.D.; Scully, S.W.J.; Phaneuf, R.A.; Muller, A.; Schippers, S.; Alvarez, I.; Cisneros, C.; Hinojosa, G.; McLaughlin, B.M.

    2004-01-01

    Photoionization of multiply charged ions is studied using the merged-beams technique at the Advanced Light Source. Absolute photoionization cross sections have been measured for a variety of ions along both isoelectronic and isonuclear sequences

  14. Evaluation of Cross-Hole Seismic Tomography for Imaging Low Resistance Intervals and Associated Carbonate Sediments in Coastal Plain Sequences on the Savannah River Site, South Carolina

    Energy Technology Data Exchange (ETDEWEB)

    Cumbest, R. J.

    1999-01-05

    The objectives of the pilot study were to investigate the limitations of the technique for imaging the presence, extent, and boundaries of the low-resistance intervals and associated carbonate sediments.

  15. Sequence-Stratigraphic Analysis of the Regional Observation Monitoring Program (ROMP) 29A Test Corehole and Its Relation to Carbonate Porosity and Regional Transmissivity in the Floridan Aquifer System, Highlands County, Florida

    Science.gov (United States)

    Ward, W. C.; Cunningham, K.J.; Renken, R.A.; Wacker, M.A.; Carlson, J.I.

    2003-01-01

    An analysis was made to describe and interpret the lithology of a part of the Upper Floridan aquifer penetrated by the Regional Observation Monitoring Program (ROMP) 29A test corehole in Highlands County, Florida. This information was integrated into a one-dimensional hydrostratigraphic model that delineates candidate flow zones and confining units in the context of sequence stratigraphy. Results from this test corehole will serve as a starting point to build a robust three-dimensional sequence-stratigraphic framework of the Floridan aquifer system. The ROMP 29A test corehole penetrated the Avon Park Formation, Ocala Limestone, Suwannee Limestone, and Hawthorn Group of middle Eocene to Pliocene age. The part of the Avon Park Formation penetrated in the ROMP 29A test corehole contains two composite depositional sequences. A transgressive systems tract and a highstand systems tract were interpreted for the upper composite sequence; however, only a highstand systems tract was interpreted for the lower composite sequence of the deeper Avon Park stratigraphic section. The composite depositional sequences are composed of at least five high-frequency depositional sequences. These sequences contain high-frequency cycle sets that are an amalgamation of vertically stacked high-frequency cycles. Three types of high-frequency cycles have been identified in the Avon Park Formation: peritidal, shallow subtidal, and deeper subtidal high-frequency cycles. The vertical distribution of carbonate-rock diffuse flow zones within the Avon Park Formation is heterogeneous. Porous vuggy intervals are less than 10 feet, and most are much thinner. The volumetric arrangement of the diffuse flow zones shows that most occur in the highstand systems tract of the lower composite sequence of the Avon Park Formation as compared to the upper composite sequence, which contains both a backstepping transgressive systems tract and a prograding highstand systems tract. Although the porous and permeable

  16. Profile of microbial communities on carbonate stones of the medieval church of San Leonardo di Siponto (Italy) by Illumina-based deep sequencing.

    Science.gov (United States)

    Chimienti, Guglielmina; Piredda, Roberta; Pepe, Gabriella; van der Werf, Inez Dorothé; Sabbatini, Luigia; Crecchio, Carmine; Ricciuti, Patrizia; D'Erchia, Anna Maria; Manzari, Caterina; Pesole, Graziano

    2016-10-01

    Comprehensive studies of the biodiversity of the microbial epilithic community on monuments may provide critical insights for clarifying factors involved in the colonization processes. We carried out a high-throughput investigation of the communities colonizing the medieval church of San Leonardo di Siponto (Italy) by Illumina-based deep sequencing. The metagenomic analysis of sequences revealed the presence of Archaea, Bacteria, and Eukarya. Bacteria were Actinobacteria, Proteobacteria, Bacteroidetes, Cyanobacteria, Chloroflexi, Firmicutes and Candidatus Saccharibacteria. The predominant phylum was Actinobacteria, with the orders Actynomycetales and Rubrobacteriales, represented by the genera Pseudokineococcus, Sporichthya, Blastococcus, Arthrobacter, Geodermatophilus, Friedmanniella, Modestobacter, and Rubrobacter, respectively. Cyanobacteria sequences showing strong similarity with an uncultured bacterium sequence were identified. The presence of the green algae Oocystaceae and Trebuxiaceae was revealed. The microbial diversity was explored at qualitative and quantitative levels, evaluating the richness (the number of operational taxonomic units (OTUs)) and the abundance of reads associated with each OTU. The rarefaction curves approached saturation, suggesting that the majority of OTUs were recovered. The results highlighted a structured community, showing low diversity, made up of extremophile organisms adapted to desiccation and UV radiation. Notably, the microbiome appeared to be composed not only of microorganisms possibly involved in biodeterioration but also of carbonatogenic bacteria, such as those belonging to the genus Arthrobacter, which could be useful in bioconservation. Our investigation demonstrated that molecular tools, and in particular the easy-to-run next-generation sequencing, are powerful to perform a microbiological diagnosis in order to plan restoration and protection strategies.

  17. Effect of fiber angle orientation and stacking sequence on mixed mode fracture toughness of carbon fiber reinforced plastics: Numerical and experimental investigations

    International Nuclear Information System (INIS)

    Naghipour, P.; Bartsch, M.; Chernova, L.; Hausmann, J.; Voggenreiter, H.

    2010-01-01

    This paper focuses on the effect of fiber orientation and stacking sequence on the progressive mixed mode delamination failure in composite laminates using fracture experiments and finite element (FE) simulations. Every laminate is modelled numerically combining damageable layers with defined fiber orientations and cohesive zone interface elements, subjected to mixed mode bending. The numerical simulations are then calibrated and validated through experiments, conducted following standardized mixed mode delamination tests. The numerical model is able to successfully capture the experimentally observed effects of fiber angle orientations and variable stacking sequences on the global load-displacement response and mixed mode inter-laminar fracture toughness of the various laminates. For better understanding of the failure mechanism, fracture surfaces of laminates with different stacking sequences are also studied using scanning electron microscopy (SEM).

  18. Some aspects of the development of the Vaal Reef uranium-gold carbon seams, Witwatersrand sequence: organic geochemical and microbiological considerations

    International Nuclear Information System (INIS)

    Zumberge, J.E.; Nagy, B.; Nagy, L.A.

    1981-01-01

    The solvent-insoluble organic matter (kerogen) that is the predominant syngenetic component of the Vaal Reef carbon seams was analyzed by combined high-vacuum pyrolysis gas-chromatography mass spectrometry, combined electron microprobe-scanning electron microscopy and electron paramagnetic resonance spectroscopy. The pyrolysis results indicate that the Vaal Reef carbon is a random polymer-type matter consisting mainly of aromatic and short-chain aliphatic hydrocarbons, as well as aromatic and other organic-sulfur constituents. Scanning electron microscopy revealed coccoid and filamentous microstructures in the carbonaceous seams. These structures are conceivably of biological affinity and may be fossil blue-green algae and (or) bacteria. Gold is often concentrated at the interfaces of admixed clay-carbon microenvironments. This implies physical and chemical interactions between clays and organic matter conducive to the entrapment of detrital gold during deposition and the crystallization of colloidal/dissolved gold in the carbon seams. High concentrations of organic free radicals (molecules with unpaired electrons) in the carbonaceous matter, deduced from electron paramagnetic resonance spectroscopy, suggest that radiation emitted from uranium played a unique role in the reconstitution and polymerization of the progenitor biochemicals

  19. C, Sr and Pb isotopic chemostratigraphy in precambrian carbonate sequences in the eastern transversal domain of the Borborema Province, northastern Brazil

    International Nuclear Information System (INIS)

    Santos, V. H.; Ferreira, V.P.; Sial, A.N; Babinski, M; Pimentel, M.M

    2001-01-01

    The Transversal Domain, in the Borborema Structural Province, northeastern Brazil, is characterized by a system of NE-trending, left-lateral, transcurrent mega-structure and dextral E-W trending fault zones (Jardim de Sa, 1994). This domain is formed by supracrustal metasedimentary and metavolcansedimentary sequences overlying a gneissic-migmatitic basement. Geological sequences of this domain exhibit distinct lithotectono-stratigraphy that characterize different terranes, separated by shear zones developed during the Cariris Velhos cycle (1.1-0.95 Ga), and that have been reworked during the Brasiliano orogen at the end of the Neoproterozoic (Brito Neves et al., 1995). The objective of this work is to show the results of C, Sr and Pb isotope studies performed in marble lens located near (and in both sides) the proposed boundary between two tectono-stratigraphic terranes (Alto Moxoto and Rio Capibaribe) in the Transversal Domain (au)

  20. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  1. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  2. Carbon transformations in deep granitic groundwater by attached bacterial populations characterized with 16S-rRNA gene sequencing technique and scanning electron microscopy

    International Nuclear Information System (INIS)

    Ekendahl, S.; Arlinger, J.; Staahl, F.; Pedersen, K.

    1993-10-01

    This report presents molecular characterization of attached bacterial populations growing in slowly flowing (1-3 mm s -1 ) artesian groundwater from deep crystalline bed-rock of the Stripa research mine, south central Sweden. The assimilation rate of CO 2 and lactate, and the lactate respiration rates were also determined. The bacteria studied grew in anoxic, high pH, 9-10, and low redox artesian groundwater flowing up through tubings from two levels of a borehole designated V2, 812-820 m and 970-1240 m below ground. The major groups of bacteria were found. Signature bases placed them in the appropriate systematic groups. All belonged to the Proteobacterial groups beta and gamma. One group was found only at the 812-820 m level, where it constituted 63% of the sequenced clones, whereas the second group existed almost exclusively and constituted 85% of the sequenced clones at the 970-1240 m level. The third group was equally distributed between the levels. A few other bacteria were also found. None of the 16S-rRNA genes from the dominating bacteria resembled any of the other by more than 90% similarity, and none of them resembled anything in the database by more than 96%. Temperature did not seem to have any effect on species composition at the deeper level. SEM images showed rods appearing in microcolonies. The difference in population diversity between the two levels studied presumably reflect the different environments. The earlier proposed presence of sulphate reducing bacteria could no be confirmed

  3. Successful treatment of high azo dye concentration wastewater using combined anaerobic/aerobic granular activated carbon-sequencing batch biofilm reactor (GAC-SBBR): simultaneous adsorption and biodegradation processes.

    Science.gov (United States)

    Hosseini Koupaie, E; Alavi Moghaddam, M R; Hashemi, S H

    2013-01-01

    The application of a granular activated carbon-sequencing batch biofilm reactor (GAC-SBBR) for treatment of wastewater containing 1,000 mg/L Acid Red 18 (AR18) was investigated in this research. The treatment system consisted of a sequencing batch reactor equipped with moving GAC as biofilm support. Each treatment cycle consisted of two successive anaerobic (14 h) and aerobic (8 h) reaction phases. Removal of more than 91% chemical oxygen demand (COD) and 97% AR18 was achieved in this study. Investigation of dye decolorization kinetics showed that the dye removal was stimulated by the adsorption capacity of the GAC at the beginning of the anaerobic phase and then progressed following a first-order reaction. Based on COD analysis results, at least 77.8% of the dye total metabolites were mineralized during the applied treatment system. High-performance liquid chromatography analysis revealed that more than 97% of 1-naphthyalamine-4-sulfonate as one of the main sulfonated aromatic constituents of AR18 was removed during the aerobic reaction phase. According to the scanning electron microscopic analysis, the microbial biofilms grew in most cavities and pores of the GAC, but not on the external surfaces of the GAC.

  4. Proteochemometric Modeling of the Interaction Space of Carbonic Anhydrase and its Inhibitors: An Assessment of Structure-based and Sequence-based Descriptors.

    Science.gov (United States)

    Rasti, Behnam; Namazi, Mohsen; Karimi-Jafari, M H; Ghasemi, Jahan B

    2017-04-01

    Due to its physiological and clinical roles, carbonic anhydrase (CA) is one of the most interesting case studies. There are different classes of CAinhibitors including sulfonamides, polyamines, coumarins and dithiocarbamates (DTCs). However, many of them hardly act as a selective inhibitor against a specific isoform. Therefore, finding highly selective inhibitors for different isoforms of CA is still an ongoing project. Proteochemometrics modeling (PCM) is able to model the bioactivity of multiple compounds against different isoforms of a protein. Therefore, it would be extremely applicable when investigating the selectivity of different ligands towards different receptors. Given the facts, we applied PCM to investigate the interaction space and structural properties that lead to the selective inhibition of CA isoforms by some dithiocarbamates. Our models have provided interesting structural information that can be considered to design compounds capable of inhibiting different isoforms of CA in an improved selective manner. Validity and predictivity of the models were confirmed by both internal and external validation methods; while Y-scrambling approach was applied to assess the robustness of the models. To prove the reliability and the applicability of our findings, we showed how ligands-receptors selectivity can be affected by removing any of these critical findings from the modeling process. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Water circulation control on carbonate-δ18O records in a low permeability clay formation and surrounding limestones: The Upper Dogger-Oxfordian sequence from the eastern Paris basin, France

    International Nuclear Information System (INIS)

    Lavastre, Veronique; Ader, Magali; Buschaert, Stephane; Petit, Eddy; Javoy, Marc

    2011-01-01

    Research highlights: → Up. Dog./Oxf. sequence is investigated for radioactive waste disposal feasibilities. → Marine carbonates suffered isotopic exchanges with meteoric water. → Modelling shows that very low W/R ratio can explain isotopic changes in clay layer. → Higher W/R ratio are needed to reach isotopic changes in carbonated layers. → Confirmed barrier property of clay layer was probably reached during early burial. - Abstract: Upper Dogger to Oxfordian Formations in the eastern part of the Paris basin (France) are currently being investigated by the French nuclear waste management agency (Andra), testing the feasibility of long-term deep nuclear waste disposal in the Callovo-Oxfordian claystones. Characterising the hydrogeological behaviour of the Callovo-Oxfordian claystones is, therefore, essential in evaluating its potential as a geological barrier. In order to evaluate and quantify water/rock interactions experienced over geological time by these Formations, bulk carbonate δ 13 C and δ 18 O were measured and calculations of water-rock ratios were used to explain carbonate-δ 18 O changes. Meteoric porewater and a maximum temperature reached of about 40 deg. C were considered. The Jurassic marine carbonate δ 13 C was preserved in the Callovo-Oxfordian claystones and in the overlying limestones (-0.28 per mille to 3.39 per mille/PDB), while the δ 18 O values are lower by 0-5 per mille (-6.25 per mille to -1.32 per mille/PDB). Calculations show that Upper Dogger and Oxfordian Limestone δ 18 O data: (i)have random-like distribution through theoretical δ 18 O-W/R curves and (ii)suggest that water/rock ratios (0.08-0.4) needed to explain δ 18 O changes are higher by a factor of about 2-20 compared to the present-day water/rock ratio. These features indicate advection in both aquifers. According to the history of the Paris basin, this hydrogeological behaviour could have been effective since Jurassic/Cretaceous transition times. Inversely, the

  6. Water circulation control on carbonate-{delta}{sup 18}O records in a low permeability clay formation and surrounding limestones: The Upper Dogger-Oxfordian sequence from the eastern Paris basin, France

    Energy Technology Data Exchange (ETDEWEB)

    Lavastre, Veronique, E-mail: veronique.lavastre@univ-st-etienne.fr [Universite de Lyon, Universite Jean Monnet, F-42023 Saint Etienne (France)] [CNRS, UMR 6524, LMV, F-42023 Saint Etienne (France)] [Laboratoire de Geochimie des Isotopes Stables, Institut de Physique du Globe de Paris and Universite Paris 7 - UMR CNRS 7154, 4, place Jussieu, 75252 Paris cedex 05 (France); Ader, Magali [Laboratoire de Geochimie des Isotopes Stables, Institut de Physique du Globe de Paris and Universite Paris 7 - UMR CNRS 7154, 4, place Jussieu, 75252 Paris cedex 05 (France); Buschaert, Stephane [Andra, Parc de la Croix Blanche, 7-8 rue Jean Monnet, 92 298 Chatenay-Malabry Cedex (France); Petit, Eddy; Javoy, Marc [Laboratoire de Geochimie des Isotopes Stables, Institut de Physique du Globe de Paris and Universite Paris 7 - UMR CNRS 7154, 4, place Jussieu, 75252 Paris cedex 05 (France)

    2011-05-15

    Research Highlights: > Up. Dog./Oxf. sequence is investigated for radioactive waste disposal feasibilities. > Marine carbonates suffered isotopic exchanges with meteoric water. > Modelling shows that very low W/R ratio can explain isotopic changes in clay layer. > Higher W/R ratio are needed to reach isotopic changes in carbonated layers. > Confirmed barrier property of clay layer was probably reached during early burial. - Abstract: Upper Dogger to Oxfordian Formations in the eastern part of the Paris basin (France) are currently being investigated by the French nuclear waste management agency (Andra), testing the feasibility of long-term deep nuclear waste disposal in the Callovo-Oxfordian claystones. Characterising the hydrogeological behaviour of the Callovo-Oxfordian claystones is, therefore, essential in evaluating its potential as a geological barrier. In order to evaluate and quantify water/rock interactions experienced over geological time by these Formations, bulk carbonate {delta}{sup 13}C and {delta}{sup 18}O were measured and calculations of water-rock ratios were used to explain carbonate-{delta}{sup 18}O changes. Meteoric porewater and a maximum temperature reached of about 40 deg. C were considered. The Jurassic marine carbonate {delta}{sup 13}C was preserved in the Callovo-Oxfordian claystones and in the overlying limestones (-0.28 per mille to 3.39 per mille/PDB), while the {delta}{sup 18}O values are lower by 0-5 per mille (-6.25 per mille to -1.32 per mille/PDB). Calculations show that Upper Dogger and Oxfordian Limestone {delta}{sup 18}O data: (i)have random-like distribution through theoretical {delta}{sup 18}O-W/R curves and (ii)suggest that water/rock ratios (0.08-0.4) needed to explain {delta}{sup 18}O changes are higher by a factor of about 2-20 compared to the present-day water/rock ratio. These features indicate advection in both aquifers. According to the history of the Paris basin, this hydrogeological behaviour could have been

  7. Some properties of a granular activated carbon-sequencing batch reactor (GAC-SBR) system for treatment of textile wastewater containing direct dyes.

    Science.gov (United States)

    Sirianuntapiboon, Suntud; Sadahiro, Ohmomo; Salee, Paneeta

    2007-10-01

    Resting (living) bio-sludge from a domestic wastewater treatment plant was used as an adsorbent of both direct dyes and organic matter in a sequencing batch reactor (SBR) system. The dye adsorption capacity of the bio-sludge was not increased by acclimatization with direct dyes. The adsorption of Direct Red 23 and Direct Blue 201 onto the bio-sludge was almost the same. The resting bio-sludge showed higher adsorption capacity than the autoclaved bio-sludge. The resting bio-sludge that was acclimatized with synthetic textile wastewater (STWW) without direct dyes showed the highest Direct Blue 201, COD, and BOD(5) removal capacities of 16.1+/-0.4, 453+/-7, and 293+/-9 mg/g of bio-sludge, respectively. After reuse, the dye adsorption ability of deteriorated bio-sludge was recovered by washing with 0.1% sodium dodecyl sulfate (SDS) solution. The direct dyes in the STWW were also easily removed by a GAC-SBR system. The dye removal efficiencies were higher than 80%, even when the system was operated under a high organic loading of 0.36kgBOD(5)/m(3)-d. The GAC-SBR system, however, showed a low direct dye removal efficiency of only 57+/-2.1% with raw textile wastewater (TWW) even though the system was operated with an organic loading of only 0.083kgBOD(5)/m(3)-d. The dyes, COD, BOD(5), and total kjeldalh nitrogen removal efficiencies increased up to 76.0+/-2.8%, 86.2+/-0.5%, 84.2+/-0.7%, and 68.2+/-2.1%, respectively, when 0.89 g/L glucose (organic loading of 0.17kgBOD(5)/m(3)-d) was supplemented into the TWW.

  8. Application of response surface methodology (RSM) for optimisation of COD, NH3-N and 2,4-DCP removal from recycled paper wastewater in a pilot-scale granular activated carbon sequencing batch biofilm reactor (GAC-SBBR).

    Science.gov (United States)

    Muhamad, Mohd Hafizuddin; Sheikh Abdullah, Siti Rozaimah; Mohamad, Abu Bakar; Abdul Rahman, Rakmi; Hasan Kadhum, Abdul Amir

    2013-05-30

    In this study, the potential of a pilot-scale granular activated carbon sequencing batch biofilm reactor (GAC-SBBR) for removing chemical oxygen demand (COD), ammoniacal nitrogen (NH3-N) and 2,4-dichlorophenol (2,4-DCP) from recycled paper wastewater was assessed. For this purpose, the response surface methodology (RSM) was employed, using a central composite face-centred design (CCFD), to optimise three of the most important operating variables, i.e., hydraulic retention time (HRT), aeration rate (AR) and influent feed concentration (IFC), in the pilot-scale GAC-SBBR process for recycled paper wastewater treatment. Quadratic models were developed for the response variables, i.e., COD, NH3-N and 2,4-DCP removal, based on the high value (>0.9) of the coefficient of determination (R(2)) obtained from the analysis of variance (ANOVA). The optimal conditions were established at 750 mg COD/L IFC, 3.2 m(3)/min AR and 1 day HRT, corresponding to predicted COD, NH3-N and 2,4-DCP removal percentages of 94.8, 100 and 80.9%, respectively. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. Latest Permian carbonate carbon isotope variability traces heterogeneous organic carbon accumulation and authigenic carbonate formation

    Science.gov (United States)

    Schobben, Martin; van de Velde, Sebastiaan; Gliwa, Jana; Leda, Lucyna; Korn, Dieter; Struck, Ulrich; Vinzenz Ullmann, Clemens; Hairapetian, Vachik; Ghaderi, Abbas; Korte, Christoph; Newton, Robert J.; Poulton, Simon W.; Wignall, Paul B.

    2017-11-01

    Bulk-carbonate carbon isotope ratios are a widely applied proxy for investigating the ancient biogeochemical carbon cycle. Temporal carbon isotope trends serve as a prime stratigraphic tool, with the inherent assumption that bulk micritic carbonate rock is a faithful geochemical recorder of the isotopic composition of seawater dissolved inorganic carbon. However, bulk-carbonate rock is also prone to incorporate diagenetic signals. The aim of the present study is to disentangle primary trends from diagenetic signals in carbon isotope records which traverse the Permian-Triassic boundary in the marine carbonate-bearing sequences of Iran and South China. By pooling newly produced and published carbon isotope data, we confirm that a global first-order trend towards depleted values exists. However, a large amount of scatter is superimposed on this geochemical record. In addition, we observe a temporal trend in the amplitude of this residual δ13C variability, which is reproducible for the two studied regions. We suggest that (sub-)sea-floor microbial communities and their control on calcite nucleation and ambient porewater dissolved inorganic carbon δ13C pose a viable mechanism to induce bulk-rock δ13C variability. Numerical model calculations highlight that early diagenetic carbonate rock stabilization and linked carbon isotope alteration can be controlled by organic matter supply and subsequent microbial remineralization. A major biotic decline among Late Permian bottom-dwelling organisms facilitated a spatial increase in heterogeneous organic carbon accumulation. Combined with low marine sulfate, this resulted in varying degrees of carbon isotope overprinting. A simulated time series suggests that a 50 % increase in the spatial scatter of organic carbon relative to the average, in addition to an imposed increase in the likelihood of sampling cements formed by microbial calcite nucleation to 1 out of 10 samples, is sufficient to induce the observed signal of carbon

  10. Latest Permian carbonate carbon isotope variability traces heterogeneous organic carbon accumulation and authigenic carbonate formation

    Directory of Open Access Journals (Sweden)

    M. Schobben

    2017-11-01

    Full Text Available Bulk-carbonate carbon isotope ratios are a widely applied proxy for investigating the ancient biogeochemical carbon cycle. Temporal carbon isotope trends serve as a prime stratigraphic tool, with the inherent assumption that bulk micritic carbonate rock is a faithful geochemical recorder of the isotopic composition of seawater dissolved inorganic carbon. However, bulk-carbonate rock is also prone to incorporate diagenetic signals. The aim of the present study is to disentangle primary trends from diagenetic signals in carbon isotope records which traverse the Permian–Triassic boundary in the marine carbonate-bearing sequences of Iran and South China. By pooling newly produced and published carbon isotope data, we confirm that a global first-order trend towards depleted values exists. However, a large amount of scatter is superimposed on this geochemical record. In addition, we observe a temporal trend in the amplitude of this residual δ13C variability, which is reproducible for the two studied regions. We suggest that (sub-sea-floor microbial communities and their control on calcite nucleation and ambient porewater dissolved inorganic carbon δ13C pose a viable mechanism to induce bulk-rock δ13C variability. Numerical model calculations highlight that early diagenetic carbonate rock stabilization and linked carbon isotope alteration can be controlled by organic matter supply and subsequent microbial remineralization. A major biotic decline among Late Permian bottom-dwelling organisms facilitated a spatial increase in heterogeneous organic carbon accumulation. Combined with low marine sulfate, this resulted in varying degrees of carbon isotope overprinting. A simulated time series suggests that a 50 % increase in the spatial scatter of organic carbon relative to the average, in addition to an imposed increase in the likelihood of sampling cements formed by microbial calcite nucleation to 1 out of 10 samples, is sufficient to induce the

  11. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  12. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  14. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  16. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  17. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  18. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  19. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  20. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  1. Molecular indicators for palaeoenvironmental change in a Messinian evaporitic sequence (Vena del Gesso, Italy). II: High-resolution variations in abundances and 13C contents of free and sulphur-bound carbon skeletons in a single marl bed

    Science.gov (United States)

    Kenig, F.; Damste, J. S.; Frewin, N. L.; Hayes, J. M.; De Leeuw, J. W.

    1995-01-01

    The extractable organic matter of 10 immature samples from a marl bed of one evaporitic cycle of the Vena del Gesso sediments (Gessoso-solfifera Fm., Messinian, Italy) was analyzed quantitatively for free hydrocarbons and organic sulphur compounds. Nickel boride was used as a desulphurizing agent to recover sulphur-bound lipids from the polar and asphaltene fractions. Carbon isotopic compositions (delta vs PDB) of free hydrocarbons and of S-bound hydrocarbons were also measured. Relationships between these carbon skeletons, precursor biolipids, and the organisms producing them could then be examined. Concentrations of S-bound lipids and free hydrocarbons and their delta values were plotted vs depth in the marl bed and the profiles were interpreted in terms of variations in source organisms, 13 C contents of the carbon source, and environmentally induced changes in isotopic fractionation. The overall range of delta values measured was 24.7%, from -11.6% for a component derived from green sulphur bacteria (Chlorobiaceae) to -36.3% for a lipid derived from purple sulphur bacteria (Chromatiaceae). Deconvolution of mixtures of components deriving from multiple sources (green and purple sulphur bacteria, coccolithophorids, microalgae and higher plants) was sometimes possible because both quantitative and isotopic data were available and because either the free or S-bound pool sometimes appeared to contain material from a single source. Several free n-alkanes and S-bound lipids appeared to be specific products of upper-water-column primary producers (i.e. algae and cyanobacteria). Others derived from anaerobic photoautotrophs and from heterotrophic protozoa (ciliates), which apparently fed partly on Chlorobiaceae. Four groups of n-alkanes produced by algae or cyanobacteria were also recognized based on systematic variations of abundance and isotopic composition with depth. For hydrocarbons probably derived from microalgae, isotopic variations are well correlated with

  2. SAXS study on activated carbons

    International Nuclear Information System (INIS)

    Bota, A.; Heringer, D.; Mihalffy, T.

    1999-01-01

    SAXS fractal analysis of activated carbons is presented. It gives very useful information about the structural changes of the carbon skeleton. From the fact, that the sequence of the activation and the heat treatment affect the fractal behaviours more drastically than the particle size distribution of the structural units, it follows that all changes in the pore and matrix structure may reduce principally to the bonding of the crystallite units. (K.A.)

  3. Carbon Isotope Chemostratigraphy, the Baby and the Bathwater

    Science.gov (United States)

    Arthur, M. A.

    2008-12-01

    Secular variations in the carbon isotopic values of carbonate sediments and rocks and their individual components have been applied successfully to problems of stratigraphic correlation and for interpretation of past changes in the global carbon cycle. However, this methodology is not without problems. A major tenet of stable isotope chemostratigraphy involves sampling and analyzing multiple, widely separated sequences, and, if possible, multiple carbon-bearing components (e.g., carbonate and organic carbon) in order to demonstrate a global signal. In some cases, this methodology has been short-circuited in the zeal to reveal a new event or excursion, particularly for time intervals for which adequate sequences are somewhat rare. Likewise, although most carbonate researchers are quite aware of the possible importance of diagenesis, particularly in organic-carbon rich sequences or in shoal-water carbonate sequences with longer-term subaerial exposure events, such overprints commonly go unrecognized or are considered of minor impact. Studies of stable isotope variations in carbonate sequences should always employ textural and geochemical methodologies for detecting and even quantifying diagenesis, if possible. Although some diagenetically overprinted or misinterpreted geochemical data have undoubtedly appeared in the literature, there are many excellent examples of global carbon isotope variations in records expressed in pelagic biogenic carbonate, marine organic carbon, platform carbonates, and terrestrial organic matter. Arguably, one of the best-documented examples is the Cenomanian-Turonian (ca. 93 Ma) positive carbon isotope excursion. The amplitude of the Cenomanian-Turonian carbon isotope excursion is similar among all types of records, but there are subtle pattern differences that arise from differences in sedimentation rate among and within sequences. Organic carbon and carbonate carbon isotope signals also may differ in phasing and amplitude for certain

  4. Sequences for Student Investigation

    Science.gov (United States)

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  5. Sequence History Update Tool

    Science.gov (United States)

    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.

  6. Carbon/carbon composite materials

    International Nuclear Information System (INIS)

    Thebault, J.; Orly, P.

    2006-01-01

    Carbon/carbon composites are singular materials from their components, their manufacturing process as well as their characteristics. This paper gives a global overview of these particularities and applications which make them now daily used composites. (authors)

  7. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  8. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  9. The Colliding Beams Sequencer

    International Nuclear Information System (INIS)

    Johnson, D.E.; Johnson, R.P.

    1989-01-01

    The Colliding Beam Sequencer (CBS) is a computer program used to operate the pbar-p Collider by synchronizing the applications programs and simulating the activities of the accelerator operators during filling and storage. The Sequencer acts as a meta-program, running otherwise stand alone applications programs, to do the set-up, beam transfers, acceleration, low beta turn on, and diagnostics for the transfers and storage. The Sequencer and its operational performance will be described along with its special features which include a periodic scheduler and command logger. 14 refs., 3 figs

  10. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  11. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  12. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  13. Dynamic Sequence Assignment.

    Science.gov (United States)

    1983-12-01

    D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

  14. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  15. General LTE Sequence

    OpenAIRE

    Billal, Masum

    2015-01-01

    In this paper,we have characterized sequences which maintain the same property described in Lifting the Exponent Lemma. Lifting the Exponent Lemma is a very powerful tool in olympiad number theory and recently it has become very popular. We generalize it to all sequences that maintain a property like it i.e. if p^{\\alpha}||a_k and p^\\b{eta}||n, then p^{{\\alpha}+\\b{eta}}||a_{nk}.

  16. Carbonate aquifers

    Science.gov (United States)

    Cunningham, Kevin J.; Sukop, Michael; Curran, H. Allen

    2012-01-01

    Only limited hydrogeological research has been conducted using ichnology in carbonate aquifer characterization. Regardless, important applications of ichnology to carbonate aquifer characterization include its use to distinguish and delineate depositional cycles, correlate mappable biogenically altered surfaces, identify zones of preferential groundwater flow and paleogroundwater flow, and better understand the origin of ichnofabric-related karst features. Three case studies, which include Pleistocene carbonate rocks of the Biscayne aquifer in southern Florida and Cretaceous carbonate strata of the Edwards–Trinity aquifer system in central Texas, demonstrate that (1) there can be a strong relation between ichnofabrics and groundwater flow in carbonate aquifers and (2) ichnology can offer a useful methodology for carbonate aquifer characterization. In these examples, zones of extremely permeable, ichnofabric-related macroporosity are mappable stratiform geobodies and as such can be represented in groundwater flow and transport simulations.

  17. Iso-nuclear tungsten dielectronic recombination rates for use in magnetically-confined fusion plasmas

    Science.gov (United States)

    Kwon, D.-H.; Lee, W.; Preval, S.; Ballance, C. P.; Behar, E.; Colgan, J.; Fontes, C. J.; Nakano, T.; Li, B.; Ding, X.; Dong, C. Z.; Fu, Y. B.; Badnell, N. R.; O'Mullane, M.; Chung, H.-K.; Braams, B. J.

    2018-01-01

    Under the auspices of the IAEA Atomic and Molecular Data Center and the Korean Atomic Energy Research Institute, our assembled group of authors has reviewed the current state of dielectronic recombination (DR) rate coefficients for various ion stages of tungsten (W). Subsequent recommendations were based upon available experimental data, first-principle calculations carried out in support of this paper and from available recombination data within existing atomic databases. If a recommendation was possible, data were compiled, evaluated and fitted to a functional form with associated uncertainty information retained, where available. This paper also considers the variation of the W fractional abundance due to the underlying atomic data when employing different data sets.

  18. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  19. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  20. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  1. Carbon-On-Carbon Manufacturing

    Science.gov (United States)

    Mungas, Gregory S. (Inventor); Buchanan, Larry (Inventor); Banzon, Jr., Jose T. (Inventor)

    2017-01-01

    The presently disclosed technology relates to carbon-on-carbon (C/C) manufacturing techniques and the resulting C/C products. One aspect of the manufacturing techniques disclosed herein utilizes two distinct curing operations that occur at different times and/or using different temperatures. The resulting C/C products are substantially non-porous, even though the curing operation(s) substantially gasify a liquid carbon-entrained filler material that saturates a carbon fabric that makes up the C/C products.

  2. Porous carbons

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Abstract. Carbon in dense as well as porous solid form is used in a variety of applications. Activated porous carbons are made through pyrolysis and activation of carbonaceous natural as well as synthetic precursors. Pyrolysed woods replicate the structure of original wood but as such possess very low surface areas and ...

  3. Carbon photonics

    Energy Technology Data Exchange (ETDEWEB)

    Konov, V I [A M Prokhorov General Physics Institute, Russian Academy of Sciences, Moscow (Russian Federation)

    2015-11-30

    The properties of new carbon materials (single-crystal and polycrystalline CVD diamond films and wafers, single-wall carbon nanotubes and graphene) and the prospects of their use as optical elements and devices are discussed. (optical elements of laser devices)

  4. Agaricus bisporus genome sequence: a commentary.

    Science.gov (United States)

    Kerrigan, Richard W; Challen, Michael P; Burton, Kerry S

    2013-06-01

    The genomes of two isolates of Agaricus bisporus have been sequenced recently. This soil-inhabiting fungus has a wide geographical distribution in nature and it is also cultivated in an industrialized indoor process ($4.7bn annual worldwide value) to produce edible mushrooms. Previously this lignocellulosic fungus has resisted precise econutritional classification, i.e. into white- or brown-rot decomposers. The generation of the genome sequence and transcriptomic analyses has revealed a new classification, 'humicolous', for species adapted to grow in humic-rich, partially decomposed leaf material. The Agaricus biporus genomes contain a collection of polysaccharide and lignin-degrading genes and more interestingly an expanded number of genes (relative to other lignocellulosic fungi) that enhance degradation of lignin derivatives, i.e. heme-thiolate peroxidases and β-etherases. A motif that is hypothesized to be a promoter element in the humicolous adaptation suite is present in a large number of genes specifically up-regulated when the mycelium is grown on humic-rich substrate. The genome sequence of A. bisporus offers a platform to explore fungal biology in carbon-rich soil environments and terrestrial cycling of carbon, nitrogen, phosphorus and potassium. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. Main sequence mass loss

    International Nuclear Information System (INIS)

    Brunish, W.M.; Guzik, J.A.; Willson, L.A.; Bowen, G.

    1987-01-01

    It has been hypothesized that variable stars may experience mass loss, driven, at least in part, by oscillations. The class of stars we are discussing here are the δ Scuti variables. These are variable stars with masses between about 1.2 and 2.25 M/sub θ/, lying on or very near the main sequence. According to this theory, high rotation rates enhance the rate of mass loss, so main sequence stars born in this mass range would have a range of mass loss rates, depending on their initial rotation velocity and the amplitude of the oscillations. The stars would evolve rapidly down the main sequence until (at about 1.25 M/sub θ/) a surface convection zone began to form. The presence of this convective region would slow the rotation, perhaps allowing magnetic braking to occur, and thus sharply reduce the mass loss rate. 7 refs

  6. Electricity sequence control

    International Nuclear Information System (INIS)

    Shin, Heung Ryeol

    2010-03-01

    The contents of the book are introduction of control system, like classification and control signal, introduction of electricity power switch, such as push-button and detection switch sensor for induction type and capacitance type machinery for control, solenoid valve, expression of sequence and type of electricity circuit about using diagram, time chart, marking and term, logic circuit like Yes, No, and, or and equivalence logic, basic electricity circuit, electricity sequence control, added condition, special program control about choice and jump of program, motor control, extra circuit on repeat circuit, pause circuit in a conveyer, safety regulations and rule about classification of electricity disaster and protective device for insulation.

  7. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    , Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...... information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity...

  8. INTERACTION OF CARBON DIOXIDE WITH CARBON ADSORBENTS BELOW 400 C

    Energy Technology Data Exchange (ETDEWEB)

    Deitz, V R; Carpenter, F G; Arnold, R G

    1963-06-15

    The adsorption of carbon dioxide on carbon adsorbents (FT carbon, coconut charcoal, acid-washed bone char) and adsorbents containing basic calcium phosphate (hydroxylapatite, bone char, ash of bone char) was studied. Special consideration was given to the pretreatment of the materials. The carbons equilibrated as rapidly as the temperature; the basic calcium phosphates showed a rapid initial adsorption followed by a very slow rate which continued for days. Linear adsorption isotherms were found on FT carbon and the isosteric heats varied slightiy with coverage. The isotherms for the remaining materials had varying curvature and were for the most part in the same sequence as the estimated surface areas. The isosteric heats of carbon dioxide correlated very well with the magnitude of surface hydroxyl groups, an estimate of which was made from the chemical composition. There appeared to be three increasing levels of interaction: (1) pure physical adsorption; (2) an adsorption complex having 'bicarbonate structure'; and (3) an adsorption complex having 'carbonate structure'. (auth)

  9. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

  10. THE RHIC SEQUENCER

    International Nuclear Information System (INIS)

    VAN ZEIJTS, J.; DOTTAVIO, T.; FRAK, B.; MICHNOFF, R.

    2001-01-01

    The Relativistic Heavy Ion Collider (RHIC) has a high level asynchronous time-line driven by a controlling program called the ''Sequencer''. Most high-level magnet and beam related issues are orchestrated by this system. The system also plays an important task in coordinated data acquisition and saving. We present the program, operator interface, operational impact and experience

  11. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  12. simple sequence repeat (SSR)

    African Journals Online (AJOL)

    In the present study, 78 mapped simple sequence repeat (SSR) markers representing 11 linkage groups of adzuki bean were evaluated for transferability to mungbean and related Vigna spp. 41 markers amplified characteristic bands in at least one Vigna species. The transferability percentage across the genotypes ranged ...

  13. Carbon monoxide

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-12-31

    The document identifies the main sources of carbon monoxide (CO) in the general outdoor atmosphere, describes methods of measuring and monitoring its concentration levels in the United Kingdom, and discusses the effects of carbon monoxide on human health. Following its review, the Panel has put forward a recommendation for an air quality standard for carbon monoxide in the United Kingdom of 10 ppm, measured as a running 8-hour average. The document includes tables and graphs of emissions of CO, in total and by emission source, and on the increase in blood levels of carboxyhaemoglobin with continuing exposure to CO. 11 refs., 4 figs., 4 tabs.

  14. Targeted sequencing of plant genomes

    Science.gov (United States)

    Mark D. Huynh

    2014-01-01

    Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

  15. Almost convergence of triple sequences

    OpenAIRE

    Ayhan Esi; M.Necdet Catalbas

    2013-01-01

    In this paper we introduce and study the concepts of almost convergence and almost Cauchy for triple sequences. Weshow that the set of almost convergent triple sequences of 0's and 1's is of the first category and also almost everytriple sequence of 0's and 1's is not almost convergent.Keywords: almost convergence, P-convergent, triple sequence.

  16. A few Smarandache Integer Sequences

    OpenAIRE

    Ibstedt, Henry

    2010-01-01

    This paper deals with the analysis of a few Smarandache Integer Sequences which first appeared in Properties or the Numbers, F. Smarandache, University or Craiova Archives, 1975. The first four sequences are recurrence generated sequences while the last three are concatenation sequences.

  17. Calcium Carbonate

    Science.gov (United States)

    ... Calcium is needed by the body for healthy bones, muscles, nervous system, and heart. Calcium carbonate also ... to your pharmacist or contact your local garbage/recycling department to learn about take-back programs in ...

  18. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  19. Stratigraphical analysis of the neoproterozoic sedimentary sequences of the Sao Francisco Basin

    International Nuclear Information System (INIS)

    Martins, Mariela; Lemos, Valesca Brasil

    2007-01-01

    A stratigraphic analysis was performed under the principles of Sequence Stratigraphy on the neoproterozoic sedimentary sequences of the Sao Francisco Basin (Central Brazil). Three periods of deposition separated by unconformities were recognized in the Sao Francisco Megasequence: (1) Sequences 1 and 2, a cryogenian glaciogenic sequence, followed by a distal scarp carbonate ramp, developed during stable conditions, (2) Sequence 3, a Upper Cryogenian stack homoclinal ramps with mixed carbonate-siliciclastic sedimentation, deposited under a progressive influence of compressional stresses of the Brasiliano Cycle, (3) Sequence 4, a Lower Ediacaran shallow platform dominated by siliciclastic sedimentation of molassic nature, the erosion product of the nearby uplifted thrust sheets. Each of the carbonate-bearing sequences presents a distinct δ 13 C isotopic signature. The superposition to the global curve for carbon isotopic variation allowed the recognition of a major depositional hiatus between the Paranoa and Sao Francisco Megasequences, and suggested that the glacial diamictite deposition (Jequitai Formation) took place most probably around 800 Ma. This constrains the Sao Francisco Megasequence deposition to the interval between 800 and 600 Ma (the known ages of the Brasiliano Orogeny defines the upper limit). A minor depositional hiatus (700.680 Ma) was also identified separating sequences 2 and 3. Isotopic analyses suggest that from then on, more restricted environmental conditions were established in the basin, probably associated with a first order global event, which prevailed throughout deposition of the Sequence 3. (author)

  20. Infiltrated carbon foam composites

    Science.gov (United States)

    Lucas, Rick D. (Inventor); Danford, Harry E. (Inventor); Plucinski, Janusz W. (Inventor); Merriman, Douglas J. (Inventor); Blacker, Jesse M. (Inventor)

    2012-01-01

    An infiltrated carbon foam composite and method for making the composite is described. The infiltrated carbon foam composite may include a carbonized carbon aerogel in cells of a carbon foam body and a resin is infiltrated into the carbon foam body filling the cells of the carbon foam body and spaces around the carbonized carbon aerogel. The infiltrated carbon foam composites may be useful for mid-density ablative thermal protection systems.

  1. Multilocus Sequence Typing

    OpenAIRE

    Belén, Ana; Pavón, Ibarz; Maiden, Martin C.J.

    2009-01-01

    Multilocus sequence typing (MLST) was first proposed in 1998 as a typing approach that enables the unambiguous characterization of bacterial isolates in a standardized, reproducible, and portable manner using the human pathogen Neisseria meningitidis as the exemplar organism. Since then, the approach has been applied to a large and growing number of organisms by public health laboratories and research institutions. MLST data, shared by investigators over the world via the Internet, have been ...

  2. Achalasia Carcinoma Sequence

    OpenAIRE

    Makmun, Dadang

    2001-01-01

    We report a case of carcinoma of the esophagus in a 58 years old woman with achalasia, who has been diagnosed since 30 years ago, which initiated by surgical treatment (myotomy) and the symptoms recurred since 3 years ago. According to the progress of the disease, Malignancy was strongly suspected due to prolonged stasis and mucosal irritation caused by achalasia (achalasia carcinoma sequence). Because of these contributing factors for the development of serious complications such as Malignan...

  3. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  4. Sequencing BPS spectra

    International Nuclear Information System (INIS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-01-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  5. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  6. Carbon sequestration.

    Science.gov (United States)

    Lal, Rattan

    2008-02-27

    Developing technologies to reduce the rate of increase of atmospheric concentration of carbon dioxide (CO2) from annual emissions of 8.6PgCyr-1 from energy, process industry, land-use conversion and soil cultivation is an important issue of the twenty-first century. Of the three options of reducing the global energy use, developing low or no-carbon fuel and sequestering emissions, this manuscript describes processes for carbon (CO2) sequestration and discusses abiotic and biotic technologies. Carbon sequestration implies transfer of atmospheric CO2 into other long-lived global pools including oceanic, pedologic, biotic and geological strata to reduce the net rate of increase in atmospheric CO2. Engineering techniques of CO2 injection in deep ocean, geological strata, old coal mines and oil wells, and saline aquifers along with mineral carbonation of CO2 constitute abiotic techniques. These techniques have a large potential of thousands of Pg, are expensive, have leakage risks and may be available for routine use by 2025 and beyond. In comparison, biotic techniques are natural and cost-effective processes, have numerous ancillary benefits, are immediately applicable but have finite sink capacity. Biotic and abiotic C sequestration options have specific nitches, are complementary, and have potential to mitigate the climate change risks.

  7. Foundations of Sequence-to-Sequence Modeling for Time Series

    OpenAIRE

    Kuznetsov, Vitaly; Mariet, Zelda

    2018-01-01

    The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...

  8. Novel expressed sequence tag- simple sequence repeats (EST ...

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  9. Draft Genome Sequences of Three β-Lactam-Catabolizing Soil Proteobacteria

    DEFF Research Database (Denmark)

    Crofts, Terence S.; Wang, Bin; Spivak, Aaron

    2017-01-01

    Most antibiotics are derived from the soil, but their catabolism there, which is necessary to close the antibiotic carbon cycle, remains uncharacterized. We report the first draft genome sequences of soil Proteobacteria identified for subsisting solely on β-lactams as their carbon sources...

  10. Infinite sequences and series

    CERN Document Server

    Knopp, Konrad

    1956-01-01

    One of the finest expositors in the field of modern mathematics, Dr. Konrad Knopp here concentrates on a topic that is of particular interest to 20th-century mathematicians and students. He develops the theory of infinite sequences and series from its beginnings to a point where the reader will be in a position to investigate more advanced stages on his own. The foundations of the theory are therefore presented with special care, while the developmental aspects are limited by the scope and purpose of the book. All definitions are clearly stated; all theorems are proved with enough detail to ma

  11. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    fast alignment algorithm, called 'Alignment By Scanning' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman

  12. Next-Generation Sequencing Platforms

    Science.gov (United States)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  13. Complete genome sequence of the aerobic facultative methanotroph Methylocella silvestris BL2.

    Science.gov (United States)

    Chen, Yin; Crombie, Andrew; Rahman, M Tanvir; Dedysh, Svetlana N; Liesack, Werner; Stott, Matthew B; Alam, Maqsudul; Theisen, Andreas R; Murrell, J Colin; Dunfield, Peter F

    2010-07-01

    Methylocella silvestris BL2 is an aerobic methanotroph originally isolated from an acidic forest soil in Germany. It is the first fully authenticated facultative methanotroph. It grows not only on methane and other one-carbon (C(1)) substrates, but also on some compounds containing carbon-carbon bonds, such as acetate, pyruvate, propane, and succinate. Here we report the full genome sequence of this bacterium.

  14. Complete Genome Sequence of the Aerobic Facultative Methanotroph Methylocella silvestris BL2▿

    Science.gov (United States)

    Chen, Yin; Crombie, Andrew; Rahman, M. Tanvir; Dedysh, Svetlana N.; Liesack, Werner; Stott, Matthew B.; Alam, Maqsudul; Theisen, Andreas R.; Murrell, J. Colin; Dunfield, Peter F.

    2010-01-01

    Methylocella silvestris BL2 is an aerobic methanotroph originally isolated from an acidic forest soil in Germany. It is the first fully authenticated facultative methanotroph. It grows not only on methane and other one-carbon (C1) substrates, but also on some compounds containing carbon-carbon bonds, such as acetate, pyruvate, propane, and succinate. Here we report the full genome sequence of this bacterium. PMID:20472789

  15. Complete Genome Sequence of the Aerobic Facultative Methanotroph Methylocella silvestris BL2▿

    OpenAIRE

    Chen, Yin; Crombie, Andrew; Rahman, M. Tanvir; Dedysh, Svetlana N.; Liesack, Werner; Stott, Matthew B.; Alam, Maqsudul; Theisen, Andreas R.; Murrell, J. Colin; Dunfield, Peter F.

    2010-01-01

    Methylocella silvestris BL2 is an aerobic methanotroph originally isolated from an acidic forest soil in Germany. It is the first fully authenticated facultative methanotroph. It grows not only on methane and other one-carbon (C1) substrates, but also on some compounds containing carbon-carbon bonds, such as acetate, pyruvate, propane, and succinate. Here we report the full genome sequence of this bacterium.

  16. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

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

  17. The advantages of SMRT sequencing

    OpenAIRE

    Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

    2013-01-01

    Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

  18. Putting instruction sequences into effect

    NARCIS (Netherlands)

    Bergstra, J.A.

    2011-01-01

    An attempt is made to define the concept of execution of an instruction sequence. It is found to be a special case of directly putting into effect of an instruction sequence. Directly putting into effect of an instruction sequences comprises interpretation as well as execution. Directly putting into

  19. Region segmentation along image sequence

    International Nuclear Information System (INIS)

    Monchal, L.; Aubry, P.

    1995-01-01

    A method to extract regions in sequence of images is proposed. Regions are not matched from one image to the following one. The result of a region segmentation is used as an initialization to segment the following and image to track the region along the sequence. The image sequence is exploited as a spatio-temporal event. (authors). 12 refs., 8 figs

  20. Bilan CarboneR - Implementation

    International Nuclear Information System (INIS)

    Wolff, Aurelie

    2015-01-01

    Bilan Carbone TM , a method for calculating greenhouse gas emissions, was developed to help companies and territorial authorities estimate emissions from their activities or on their territories. After validating the audit perimeter and determining the emission categories to be taken into account, activity data is collected and greenhouse gas emissions are calculated using the tool. Besides accounting greenhouse gas emissions at any given time, the inventory evaluates impact on climate and energy dependence. This helps organizations deal with their emissions by classifying them, implementing action plans to reduce emissions and starting a dynamic process taking into account carbon in their strategic decisions

  1. Log-balanced combinatorial sequences

    Directory of Open Access Journals (Sweden)

    Tomislav Došlic

    2005-01-01

    Full Text Available We consider log-convex sequences that satisfy an additional constraint imposed on their rate of growth. We call such sequences log-balanced. It is shown that all such sequences satisfy a pair of double inequalities. Sufficient conditions for log-balancedness are given for the case when the sequence satisfies a two- (or more- term linear recurrence. It is shown that many combinatorially interesting sequences belong to this class, and, as a consequence, that the above-mentioned double inequalities are valid for all of them.

  2. New MR pulse sequence

    International Nuclear Information System (INIS)

    Harms, S.E.; Flamig, D.P.; Griffey, R.H.

    1990-01-01

    This paper describes a method for fat suppression for three-dimensional MR imaging. The FATS (fat-suppressed acquisition with echo time shortened) sequence employs a pair of opposing adiabatic half-passage RF pulses tuned on fat resonance. The imaging parameters are as follows: TR, 20 msec; TE, 21.7-3.2 msec; 1,024 x 128 x 128 acquired matrix; imaging time, approximately 11 minutes. A series of 54 examinations were performed. Excellent fat suppression with water excitation is achieved in all cases. The orbital images demonstrate superior resolution of small orbital lesions. The high signal-to-noise ratio (SNR) in cranial studies demonstrates excellent petrous bone and internal auditory canal anatomy

  3. Chromium isotopes in carbonates — A tracer for climate change and for reconstructing the redox state of ancient seawater

    DEFF Research Database (Denmark)

    Frei, Robert; Gaucher, Claudio; Døssing, Lasse Nørbye

    2011-01-01

    Strontium and carbon isotopes of marine carbonates are routinely applied for chemostratigraphic cross correlations of time-equivalent sedimentary sequences and for calibration of the compositional evolution of seawater throughout Earth's history, mainly for the purpose of reconstructing ancient c...

  4. Quantum-Sequencing: Fast electronic single DNA molecule sequencing

    Science.gov (United States)

    Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

    2014-03-01

    A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

  5. Carbonizing process

    Energy Technology Data Exchange (ETDEWEB)

    1923-11-22

    In the downward distillation of coal, shale, lignite, or the like, the heat is generated by the combustion of liquid or gaseous fuel above the charge the zone of carbonization thus initiated travelling downwards through the charge. The combustible gases employed are preferably those resulting from the process but gases such as natural gas may be employed. The charge is in a moistened and pervious state the lower parts being maintained at a temperature not above 212/sup 0/F until influenced by contact with the carbonization zone and steam may be admitted to increase the yield of ammonia. The combustible gases may be supplied with insufficient air so as to impart to them a reducing effect.

  6. Carbon aerogels

    International Nuclear Information System (INIS)

    Berthon-Fabry, S.; Achard, P.

    2003-06-01

    The carbon aerogel is a nano-porous material at open porosity, electrical conductor. The aerogels morphology is variable in function of the different synthesis parameters. This characteristic offers to the aerogels a better adaptability to many applications: electrodes (super condensers, fuel cells). The author presents the materials elaboration and their applications. It provides also the research programs: fundamental research, realization of super-condenser electrodes, fuel cells electrodes, gas storage materials and opaque materials for thermal insulation. (A.L.B.)

  7. Universal sequence map (USM of arbitrary discrete sequences

    Directory of Open Access Journals (Sweden)

    Almeida Jonas S

    2002-02-01

    Full Text Available Abstract Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. Results We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM, is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR. The latter enables the representation of 4 unit type sequences (like DNA as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. Conclusions USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules.

  8. Cyclic Cratonic Carbonates and Phanerozoic Calcite Seas.

    Science.gov (United States)

    Wilkinson, Bruce H.

    1982-01-01

    Discusses causes of cyclicity in cratonic carbonate sequences and evidence for and potential significance of postulated primary calcite sediment components in past Paleozoic seas, outlining problems, focusing on models explaining existing data, and identifying background. Future sedimentary geologists will need to address these and related areas…

  9. Carbon cycle

    Energy Technology Data Exchange (ETDEWEB)

    Jaeger, J; Halbritter, G; Neumann-Hauf, G

    1982-05-01

    This report contains a review of literature on the subjects of the carbon cycle, the increase of the atmospheric CO/sub 2/ concentration and the possible impacts of an increased CO/sub 2/ concentration on the climate. In addition to this survey, the report discusses the questions that are still open and the resulting research needs. During the last twenty years a continual increase of the atmospheric carbon dioxide concentration by about 1-2 ppm per years has been observed. In 1958 the concentration was 315 ppm and this increased to 336 ppm in 1978. A rough estimate shows that the increase of the atmospheric carbon dioxide concentration is about half of the amount of carbon dioxide added to the atmosphere by the combustion of fossil fuels. Two possible sinks for the CO/sub 2/ released into the atmosphere are known: the ocean and the biota. The role of the biota is, however, unclear, since it can act both as a sink and as a source. Most models of the carbon cycle are one-dimensional and cannot be used for accurate predictions. Calculations with climate models have shown that an increased atmospheric CO/sub 2/ concentration leads to a warming of the earth's surface and lower atmosphere. Calculations show that a doubling of the atmospheric CO/sub 2/-concentration would lead to a net heating of the lower atmosphere and earth's surface by a global average of about 4 W m/sup -2/. Greater uncertainties arise in estimating the change in surface temperature resulting from this change in heating rate. It is estimated that the global average annual surface temperature would change between 1.5 and 4.5 K. There are, however, latitudinal and seasonal variations of the impact of increased CO/sub 2/ concentration. Other meteorological variables (e.g. precipitation, wind speed etc.) would also be changed. It appears that the impacts of the other products of fossil fuel combustion are unlikely to counteract the impacts of CO/sub 2/ on the climate.

  10. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  11. Genomic sequencing in clinical trials

    OpenAIRE

    Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

    2011-01-01

    Abstract Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to fin...

  12. Biosensors for DNA sequence detection

    Science.gov (United States)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  13. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  14. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  15. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  16. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

    2012-01-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS...

  17. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    Directory of Open Access Journals (Sweden)

    Kirkness Ewen

    2006-10-01

    Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

  18. Carbons and carbon supported catalysts in hydroprocessing

    Energy Technology Data Exchange (ETDEWEB)

    Furimsky, Edward

    2009-07-01

    This book is a comprehensive summary of recent research in the field and covers all areas of carbons and carbon materials. The potential application of carbon supports, particularly those of carbon black (CB) and activated carbon (AC) in hydroprocessing catalysis are covered. Novel carbon materials such as carbon fibers and carbon nano tubes (CNT) are also covered, including the more recent developments in the use of fullerenes in hydroprocessing applications. Although the primary focus of this book is on carbons and carbon supported catalysts, it also identifies the difference in the effect of carbon supports compared with the oxidic supports, particularly that of the Al{sub 2}O{sub 3}. The difference in catalyst activity and stability was estimated using both model compounds and real feeds under variable conditions. The conditions applied during the preparation of carbon supported catalysts are also comprehensively covered and include various methods of pretreatment of carbon supports to enhance catalyst performance. The model compounds results consistently show higher hydrodesulfurization and hydrodeoxygenation activities of carbon supported catalysts than that of the Al{sub 2}O{sub 3} supported catalysts. Also, the deactivation of the former catalysts by coke deposition was much less evident. Chapter 6.3.1.3 is on carbon-supported catalysts: coal-derived liquids.

  19. SVX Sequencer Board

    International Nuclear Information System (INIS)

    Utes, M.

    1997-01-01

    The SVX Sequencer boards are 9U by 280mm circuit boards that reside in slots 2 through 21 of each of eight Eurocard crates in the D0 Detector Platform. The basic purpose is to control the SVX chips for data acquisition and when a trigger occurs, to gather the SVX data and relay the data to the VRB boards in the Movable Counting House. Functions and features are as follows: (1) Initialization of eight SVX chip strings using the MIL-STD-1553 data bus; (2) Real time manipulation of the SVX control lines to effect data acquisition, digitization, and readout based on the NRZ/Clock signals from the Controller; (3) Conversion of 8-bit electrical SVX readout data to an optical signal operating at 1.062 Gbit/sec, sent to the VRB. Eight HDIs will be serviced per board; (4) Built-in logic analyzer which can record the most important control and data lines during a data acquisition cycle and put this recorded information onto the 1553 bus; (5) Identification header and end of data trailer tacked onto data stream; (6) 1553 register which can read the current values of the control and data lines; (7) 1553 register which can test the optical link; (8) 1553 registers for crossing pulse width, calibration pulse voltage, and calibration pipeline select; (9) 1553 register for reading the optical drivers status link; (10) 1553 register for power control of SVX chips and ignoring bad SVX strings; (11) Front panel displays and LEDs show the board status at a glance; (12) In-system programmable EPLDs are programmed via 1553 or Altera's 'Bitblaster'; (13) Automatic readout abort after 45us; (14) Supplies BUSY signal back to Trigger Framework; (15) Supports a heartbeat system to prevent excessive SVX current draw; and (16) Supports a SVX power trip feature if heartbeat failure occurs.

  20. Sequence Algebra, Sequence Decision Diagrams and Dynamic Fault Trees

    International Nuclear Information System (INIS)

    Rauzy, Antoine B.

    2011-01-01

    A large attention has been focused on the Dynamic Fault Trees in the past few years. By adding new gates to static (regular) Fault Trees, Dynamic Fault Trees aim to take into account dependencies among events. Merle et al. proposed recently an algebraic framework to give a formal interpretation to these gates. In this article, we extend Merle et al.'s work by adopting a slightly different perspective. We introduce Sequence Algebras that can be seen as Algebras of Basic Events, representing failures of non-repairable components. We show how to interpret Dynamic Fault Trees within this framework. Finally, we propose a new data structure to encode sets of sequences of Basic Events: Sequence Decision Diagrams. Sequence Decision Diagrams are very much inspired from Minato's Zero-Suppressed Binary Decision Diagrams. We show that all operations of Sequence Algebras can be performed on this data structure.

  1. Carbon classified?

    DEFF Research Database (Denmark)

    Lippert, Ingmar

    2012-01-01

    . Using an actor- network theory (ANT) framework, the aim is to investigate the actors who bring together the elements needed to classify their carbon emission sources and unpack the heterogeneous relations drawn on. Based on an ethnographic study of corporate agents of ecological modernisation over...... a period of 13 months, this paper provides an exploration of three cases of enacting classification. Drawing on ANT, we problematise the silencing of a range of possible modalities of consumption facts and point to the ontological ethics involved in such performances. In a context of global warming...

  2. Carbon Footprints

    OpenAIRE

    Rahel Aichele; Gabriel Felbermayr

    2011-01-01

    Lässt sich der Beitrag eines Landes zum weltweiten Klimaschutz an der Veränderung seines CO2-Ausstoßes messen, wie es im Kyoto-Abkommen implizit unterstellt wird? Oder ist aufgrund der Bedeutung des internationalen Güterhandels der Carbon Footprint – der alle CO2-Emissionen erfasst, die durch die Absorption (d.h. Konsum und Investitionen) eines Landes entstehen – das bessere Maß? Die Autoren erstellen eine Datenbank mit den Footprints von 40 Ländern für den Zeitraum 1995–2007. Die deskriptive...

  3. Chameleon sequences in neurodegenerative diseases

    International Nuclear Information System (INIS)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-01-01

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  4. Direct, rapid RNA sequence analysis

    International Nuclear Information System (INIS)

    Peattie, D.A.

    1987-01-01

    The original methods of RNA sequence analysis were based on enzymatic production and chromatographic separation of overlapping oligonucleotide fragments from within an RNA molecule followed by identification of the mononucleotides comprising the oligomer. Over the past decade the field of nucleic acid sequencing has changed dramatically, however, and RNA molecules now can be sequenced in a variety of more streamlined fashions. Most of the more recent advances in RNA sequencing have involved one-dimensional electrophoretic separation of 32 P-end-labeled oligoribonucleotides on polyacrylamide gels. In this chapter the author discusses two of these methods for determining the nucleotide sequences of RNA molecules rapidly: the chemical method and the enzymatic method. Both methods are direct and degradative, i.e., they rely on fragmatic and chemical approaches should be utilized. The single-strand-specific ribonucleases (A, T 1 , T 2 , and S 1 ) provide an efficient means to locate double-helical regions rapidly, and the chemical reactions provide a means to determine the RNA sequence within these regions. In addition, the chemical reactions allow one to assign interactions to specific atoms and to distinguish secondary interactions from tertiary ones. If the RNA molecule is small enough to be sequenced directly by the enzymatic or chemical method, the probing reactions can be done easily at the same time as sequencing reactions

  5. Chameleon sequences in neurodegenerative diseases.

    Science.gov (United States)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to "helix to strand (HE)", "helix to coil (HC)" and "strand to coil (CE)" alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Farey sequences and resistor networks

    Indian Academy of Sciences (India)

    Green's function, while the perturbation of a network is investigated in [3]. ... In Theorem 1 below, we employ the Farey sequence to establish a strict .... We next show that the Farey sequence method is applicable for circuits with n or fewer.

  7. DNA Sequencing by Capillary Electrophoresis

    Science.gov (United States)

    Karger, Barry L.; Guttman, Andras

    2009-01-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

  8. Graphene nanodevices for DNA sequencing

    NARCIS (Netherlands)

    Heerema, S.J.; Dekker, C.

    2016-01-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with

  9. Chameleon sequences in neurodegenerative diseases

    Energy Technology Data Exchange (ETDEWEB)

    Bahramali, Golnaz [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Goliaei, Bahram, E-mail: goliaei@ut.ac.ir [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of); Salari, Ali [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of)

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  10. Commercial Art: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a commercial art vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  11. Syntheses of protoporphyrin-IX regioselectivity carbon-13 labelled at the alpha-vinyl carbons

    International Nuclear Information System (INIS)

    Smith, K.M.; Fujinari, E.M.

    1986-01-01

    A method for transformation of readily available beta-vinyl 99% carbon-13 enriched derivatives of protoporphyrin-IX dimethyl ester into the less accessible alpha-vinyl labelled isomers is described. The procedure involves thallium(III) promoted vinyl carbon rearrangement, and proceeds through 2,2-dimethoxyethyl, formylmethyl, 2-hydroxyethyl and 2-chloroethyl porphyrins; the rearranged vinyl groups are regenerated from 2-chloroethyl in the last step by treatment with base. No evidence of vinyl carbon scrambling in the sequence is observed, and spectroscopic data of the products are given. (author)

  12. Rapid Diagnostics of Onboard Sequences

    Science.gov (United States)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  13. Accident sequence quantification with KIRAP

    International Nuclear Information System (INIS)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong.

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP's cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs

  14. Accident sequence quantification with KIRAP

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP`s cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs.

  15. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S K

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  16. Trading forest carbon

    Science.gov (United States)

    The nature of carbon in forests is discussed from the perspective of carbon trading. Carbon inventories, specifically in the area of land use and forestry are reviewed for the Pacific Northwest. Carbon turnover in forests is discussed as it relates to carbon sequestration. Scient...

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

    Science.gov (United States)

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

    2012-10-04

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

  18. NEW COOLING SEQUENCES FOR OLD WHITE DWARFS

    International Nuclear Information System (INIS)

    Renedo, I.; Althaus, L. G.; GarcIa-Berro, E.; Miller Bertolami, M. M.; Romero, A. D.; Corsico, A. H.; Rohrmann, R. D.

    2010-01-01

    We present full evolutionary calculations appropriate for the study of hydrogen-rich DA white dwarfs. This is done by evolving white dwarf progenitors from the zero-age main sequence, through the core hydrogen-burning phase, the helium-burning phase, and the thermally pulsing asymptotic giant branch phase to the white dwarf stage. Complete evolutionary sequences are computed for a wide range of stellar masses and for two different metallicities, Z = 0.01, which is representative of the solar neighborhood, and Z = 0.001, which is appropriate for the study of old stellar systems, like globular clusters. During the white dwarf cooling stage, we self-consistently compute the phase in which nuclear reactions are still important, the diffusive evolution of the elements in the outer layers and, finally, we also take into account all the relevant energy sources in the deep interior of the white dwarf, such as the release of latent heat and the release of gravitational energy due to carbon-oxygen phase separation upon crystallization. We also provide colors and magnitudes for these sequences, based on a new set of improved non-gray white dwarf model atmospheres, which include the most up-to-date physical inputs like the Lyα quasi-molecular opacity. The calculations are extended down to an effective temperature of 2500 K. Our calculations provide a homogeneous set of evolutionary cooling tracks appropriate for mass and age determinations of old DA white dwarfs and for white dwarf cosmochronology of the different Galactic populations.

  19. GENOME-ENABLED DISCOVERY OF CARBON SEQUESTRATION GENES IN POPLAR

    Energy Technology Data Exchange (ETDEWEB)

    DAVIS J M

    2007-10-11

    Plants utilize carbon by partitioning the reduced carbon obtained through photosynthesis into different compartments and into different chemistries within a cell and subsequently allocating such carbon to sink tissues throughout the plant. Since the phytohormones auxin and cytokinin are known to influence sink strength in tissues such as roots (Skoog & Miller 1957, Nordstrom et al. 2004), we hypothesized that altering the expression of genes that regulate auxin-mediated (e.g., AUX/IAA or ARF transcription factors) or cytokinin-mediated (e.g., RR transcription factors) control of root growth and development would impact carbon allocation and partitioning belowground (Fig. 1 - Renewal Proposal). Specifically, the ARF, AUX/IAA and RR transcription factor gene families mediate the effects of the growth regulators auxin and cytokinin on cell expansion, cell division and differentiation into root primordia. Invertases (IVR), whose transcript abundance is enhanced by both auxin and cytokinin, are critical components of carbon movement and therefore of carbon allocation. Thus, we initiated comparative genomic studies to identify the AUX/IAA, ARF, RR and IVR gene families in the Populus genome that could impact carbon allocation and partitioning. Bioinformatics searches using Arabidopsis gene sequences as queries identified regions with high degrees of sequence similarities in the Populus genome. These Populus sequences formed the basis of our transgenic experiments. Transgenic modification of gene expression involving members of these gene families was hypothesized to have profound effects on carbon allocation and partitioning.

  20. Carbon Monoxide Information Center

    Medline Plus

    Full Text Available ... Education Centers Carbon Monoxide Information Center Carbon Monoxide Information Center En Español The Invisible Killer Carbon monoxide, ... Install one and check its batteries regularly. View Information About CO Alarms Other CO Topics Safety Tips ...

  1. Global Carbon Budget 2017

    NARCIS (Netherlands)

    Le Quere, Corinne; Andrew, Robbie M.; Friedlingstein, Pierre; Sitch, Stephen; Pongratz, Julia; Manning, Andrew C.; Korsbakken, Jan Ivar; Peters, Glen P.; Canadell, Josep G.; Jackson, Robert B.; Boden, Thomas A.; Tans, Pieter P.; Andrews, Oliver D.; Arora, Vivek K.; Bakker, Dorothee C. E.; Barbero, Leticia; Becker, Meike; Betts, Richard A.; Bopp, Laurent; Chevallier, Frederic; Chini, Louise P.; Ciais, Philippe; Cosca, Catherine E.; Cross, Jessica; Currie, Kim; Gasser, Thomas; Harris, Ian; Hauck, Judith; Haverd, Vanessa; Houghton, Richard A.; Hunt, Christopher W.; Hurtt, George; Ilyina, Tatiana; Jain, Atul K.; Kato, Etsushi; Kautz, Markus; Keeling, Ralph F.; Goldewijk, Kees Klein; Koertzinger, Arne; Landschuetzer, Peter; Lefevre, Nathalie; Lenton, Andrew; Lienert, Sebastian; Lima, Ivan; Lombardozzi, Danica; Metzl, Nicolas; Millero, Frank; Monteiro, Pedro M. S.; Munro, David R.; Nabel, Julia E. M. S.; Nakaoka, Shin-ichiro; Nojiri, Yukihiro; Padin, X. Antonio; Peregon, Anna; Pfeil, Benjamin; Pierrot, Denis; Poulter, Benjamin; Rehder, Gregor; Reimer, Janet; Roedenbeck, Christian; Schwinger, Jorg; Seferian, Roland; Skjelvan, Ingunn; Stocker, Benjamin D.; Tian, Hanqin; Tilbrook, Bronte; Tubiello, Francesco N.; van der Laan-Luijkx, Ingrid T.; van der Werf, Guido R.; van Heuven, Steven; Viovy, Nicolas; Vuichard, Nicolas; Walker, Anthony P.; Watson, Andrew J.; Wiltshire, Andrew J.; Zaehle, Soenke; Zhu, Dan

    2018-01-01

    Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere - the "global carbon budget" - is important to better understand the global carbon cycle, support the development of climate policies, and project

  2. Carbon Monoxide Information Center

    Medline Plus

    Full Text Available ... Education Safety Education Centers Carbon Monoxide Information Center Carbon Monoxide Information Center En Español The Invisible Killer Carbon monoxide, also known as CO, is called the " ...

  3. GROUPING WEB ACCESS SEQUENCES uSING SEQUENCE ALIGNMENT METHOD

    OpenAIRE

    BHUPENDRA S CHORDIA; KRISHNAKANT P ADHIYA

    2011-01-01

    In web usage mining grouping of web access sequences can be used to determine the behavior or intent of a set of users. Grouping websessions is how to measure the similarity between web sessions. There are many shortcomings in traditional measurement methods. The taskof grouping web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-groupsimilarity is done using sequence alignment method. This paper introduces a new method to group we...

  4. LPTAU, Quasi Random Sequence Generator

    International Nuclear Information System (INIS)

    Sobol, Ilya M.

    1993-01-01

    1 - Description of program or function: LPTAU generates quasi random sequences. These are uniformly distributed sets of L=M N points in the N-dimensional unit cube: I N =[0,1]x...x[0,1]. These sequences are used as nodes for multidimensional integration; as searching points in global optimization; as trial points in multi-criteria decision making; as quasi-random points for quasi Monte Carlo algorithms. 2 - Method of solution: Uses LP-TAU sequence generation (see references). 3 - Restrictions on the complexity of the problem: The number of points that can be generated is L 30 . The dimension of the space cannot exceed 51

  5. Weak disorder in Fibonacci sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Naim, E [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Krapivsky, P L [Department of Physics and Center for Molecular Cybernetics, Boston University, Boston, MA 02215 (United States)

    2006-05-19

    We study how weak disorder affects the growth of the Fibonacci series. We introduce a family of stochastic sequences that grow by the normal Fibonacci recursion with probability 1 - {epsilon}, but follow a different recursion rule with a small probability {epsilon}. We focus on the weak disorder limit and obtain the Lyapunov exponent that characterizes the typical growth of the sequence elements, using perturbation theory. The limiting distribution for the ratio of consecutive sequence elements is obtained as well. A number of variations to the basic Fibonacci recursion including shift, doubling and copying are considered. (letter to the editor)

  6. Path of Carbon in Photosynthesis III.

    Science.gov (United States)

    Benson, A. A.; Calvin, M.

    1948-06-01

    Although the overall reaction of photosynthesis can be specified with some degree of certainty (CO{sub 2} + H{sub 2}O + light {yields} sugars + possibly other reduced substances), the intermediates through which the carbon passes during the course of this reduction have, until now, been largely a matter of conjecture. The availability of isotopic carbon, that is, a method of labeling the carbon dioxide, provides the possibility of some very direct experiments designed to recognize these intermediates and, perhaps, help to understand the complex sequence and interplay of reactions which must constitute the photochemical process itself. The general design of such experiments is an obvious one, namely the exposure of the green plant to radioactive carbon dioxide and light under a variety of conditions and for continually decreasing lengths of time, followed by the identification of the compounds into which the radioactive carbon is incorporated under each condition and time period. From such data it is clear that in principle, at least, it should be possible to establish the sequence of compounds in time through which the carbon passes on its path from carbon dioxide to the final products. In the course of shortening the photosynthetic times, one times, one ultimately arrives at the condition of exposing the plants to the radioactive carbon dioxide with a zero illumination time, that is, in the dark. Actually, in the work the systematic order of events was reversed, and they have begun by studying first the dark fixation and then the shorter photosynthetic times. The results of the beginnings of this sort of a systematic investigation are given in Table I which includes three sets of experiments, namely a dark fixation experiment and two photosynthetic experiments, one of 30 seconds duration and the other of 60 seconds duration.

  7. Integral Ring Carbon-Carbon Piston

    Science.gov (United States)

    Northam, G. Burton (Inventor)

    1999-01-01

    An improved structure for a reciprocating internal combustion engine or compressor piston fabricate from carbon-carbon composite materials is disclosed. An integral ring carbon-carbon composite piston, disclosed herein, reduces the need for piston rings and for small clearances by providing a small flexible, integral component around the piston that allows for variation in clearance due to manufacturing tolerances, distortion due to pressure and thermal loads, and variations in thermal expansion differences between the piston and cylinder liner.

  8. Carbon dioxide sequestration by mineral carbonation

    NARCIS (Netherlands)

    Huijgen, W.J.J.

    2007-01-01

    The increasing atmospheric carbon dioxide (CO2) concentration, mainly caused by fossil fuel combustion, has lead to concerns about global warming. A possible technology that can contribute to the reduction of carbon dioxide emissions is CO2 sequestration by mineral carbonation. The basic concept

  9. Sequence analysis of Leukemia DNA

    Science.gov (United States)

    Nacong, Nasria; Lusiyanti, Desy; Irawan, Muhammad. Isa

    2018-03-01

    Cancer is a very deadly disease, one of which is leukemia disease or better known as blood cancer. The cancer cell can be detected by taking DNA in laboratory test. This study focused on local alignment of leukemia and non leukemia data resulting from NCBI in the form of DNA sequences by using Smith-Waterman algorithm. SmithWaterman algorithm was invented by TF Smith and MS Waterman in 1981. These algorithms try to find as much as possible similarity of a pair of sequences, by giving a negative value to the unequal base pair (mismatch), and positive values on the same base pair (match). So that will obtain the maximum positive value as the end of the alignment, and the minimum value as the initial alignment. This study will use sequences of leukemia and 3 sequences of non leukemia.

  10. Integrated sequence analysis. Final report

    International Nuclear Information System (INIS)

    Andersson, K.; Pyy, P.

    1998-02-01

    The NKS/RAK subprojet 3 'integrated sequence analysis' (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term 'methodology' denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  11. Optimization of sequence alignment for simple sequence repeat regions

    Directory of Open Access Journals (Sweden)

    Ogbonnaya Francis C

    2011-07-01

    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

  12. Composite carbon foam electrode

    Science.gov (United States)

    Mayer, Steven T.; Pekala, Richard W.; Kaschmitter, James L.

    1997-01-01

    Carbon aerogels used as a binder for granularized materials, including other forms of carbon and metal additives, are cast onto carbon or metal fiber substrates to form composite carbon thin film sheets. The thin film sheets are utilized in electrochemical energy storage applications, such as electrochemical double layer capacitors (aerocapacitors), lithium based battery insertion electrodes, fuel cell electrodes, and electrocapacitive deionization electrodes. The composite carbon foam may be formed by prior known processes, but with the solid particles being added during the liquid phase of the process, i.e. prior to gelation. The other forms of carbon may include carbon microspheres, carbon powder, carbon aerogel powder or particles, graphite carbons. Metal and/or carbon fibers may be added for increased conductivity. The choice of materials and fibers will depend on the electrolyte used and the relative trade off of system resistivty and power to system energy.

  13. ADDRESS SEQUENCES FOR MULTI RUN RAM TESTING

    Directory of Open Access Journals (Sweden)

    V. N. Yarmolik

    2014-01-01

    Full Text Available A universal approach for generation of address sequences with specified properties is proposed and analyzed. A modified version of the Antonov and Saleev algorithm for Sobol sequences genera-tion is chosen as a mathematical description of the proposed method. Within the framework of the proposed universal approach, the Sobol sequences form a subset of the address sequences. Other sub-sets are also formed, which are Gray sequences, anti-Gray sequences, counter sequences and sequenc-es with specified properties.

  14. Carbon Nanomembranes

    Science.gov (United States)

    Angelova, Polina; Gölzhäuser, Armin

    2017-03-01

    This chapter describes the formation and properties of one nanometer thick carbon nanomembranes (CNMs), made by electron induced cross-linking of aromatic self-assembled monolayers (SAMs). The cross-linked SAMs are robust enough to be released from the surface and placed on solid support or over holes as free-standing membranes. Annealing at 1000K transforms CNMs into graphene accompanied by a change of mechanical stiffness and electrical resistance. The developed fabrication approach is scalable and provides molecular level control over thickness and homogeneity of the produced CNMs. The mechanisms of electron-induced cross-linking process are discussed in details. A variety of polyaromatic thiols: oligophenyls as well as small and extended condensed polycyclic hydrocarbons have been successfully employed, demonstrating that the structural and functional properties of the resulting nanomembranes are strongly determined by the structure of molecular monolayers. The mechanical properties of CNMs (Young's modulus, tensile strength and prestress) are characterized by bulge testing. The interpretation of the bulge test data relates the Young's modulus to the properties of single molecules and to the structure of the pristine SAMs. The gas transport through the CNM is measured onto polydimethylsiloxane (PDMS) - thin film composite membrane. The established relationship of permeance and molecular size determines the molecular sieving mechanism of permeation through this ultrathin sheet.

  15. Carbon 14

    International Nuclear Information System (INIS)

    2002-03-01

    Carbon 14 is one of the most abundant radionuclides of natural and artificial origin in the environment. The aim of this conference day organized by the French society of radioprotection (SFRP) was to take stock of our knowledge about this radionuclide (origins, production, measurement, management, effects on health..): state-of-the-art of 14 C metrology; dating use of 14 C; 14 C management and monitoring of the Hague site environment; Electricite de France (EdF) and 14 C; radiological and sanitary impact of 14 C contamination at the Ganagobie site (Haute-Provence, France); metabolism and biological effects of 14 C; 14 C behaviour in the marine environment near Cogema-La Hague plant; distribution of 14 C activities in waters, mud and sediments of the Loire river estuary; dynamical modeling of transfers in the aquatic and terrestrial environment of 14 C released by nuclear power plants in normal operation: human dose calculation using the Calvados model and application to the Loire river; 14 C distribution in continents; modeling of 14 C transfers in the terrestrial environment from atmospheric sources. (J.S.)

  16. Fast and secure retrieval of DNA sequences

    NARCIS (Netherlands)

    2014-01-01

    Sequence models are retrieved from a sequences index. The sequence models model DNA or RNA sequences stored in a database, and each comprises a finite memory tree source model and parameters for the finite memory tree source model. One or more DNA or RNA sequences stored in the database are

  17. Decidability of uniform recurrence of morphic sequences

    OpenAIRE

    Durand , Fabien

    2012-01-01

    We prove that the uniform recurrence of morphic sequences is decidable. For this we show that the number of derived sequences of uniformly recurrent morphic sequences is bounded. As a corollary we obtain that uniformly recurrent morphic sequences are primitive substitutive sequences.

  18. Radiation damage in carbon-carbon composites

    International Nuclear Information System (INIS)

    Burchell, T.D.; Eartherly, W.P.; Nelson, G.E.

    1992-01-01

    Graphite and carbon-carbon composite materials are widely used in plasma facing applications in current Tokamak devices such as TFTR and DIIID in the USA, JET, Tore Supra and TEXTOR in Europe, and JT-60U in Japan. Carbon-carbon composites are attractive choices for Tokamak limiters and diverters because of their low atomic number, high thermal shock resistance, high melting point, and high thermal conductivity. Next generation machines such as the International Thermonuclear Experimental Reactor (ITER) will utilize carbon-carbon composites in their first wall and diverter. ITER will be an ignition machine and thus will produce substantial neutron fluences from the D-T fusion reaction. The resultant high energy neutrons will cause carbon atom displacements in the plasma facing materials which will markedly affect their structure and physical properties. The effect of neutron damage on graphite has been studied for over forty years. Recently the effects of neutron irradiation on the fusion relevant graphite GraphNOL N3M was reviewed. In contrast to graphite, relatively little work has been performed to elucidate the effects of neutron irradiation on carbon-carbon composites. The results of our previous irradiation experiments have been published elsewhere. Here the irradiation induced dimensional changes in 1D, 2D, and 3D carbon-carbon composites are reported for fluences up to 4.7 dpa at an irradiation temperature of 600 degree C

  19. Sequence Factorization with Multiple References.

    Directory of Open Access Journals (Sweden)

    Sebastian Wandelt

    Full Text Available The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1 the size of the factorization, 2 the time for factorization, and 3 the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%, factorization speed (0.01 MB/s to more than 600 MB/s, and main memory usage (few dozen MB to dozens of GB. Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

  20. Carbon nanotube composite materials

    Science.gov (United States)

    O'Bryan, Gregory; Skinner, Jack L; Vance, Andrew; Yang, Elaine Lai; Zifer, Thomas

    2015-03-24

    A material consisting essentially of a vinyl thermoplastic polymer, un-functionalized carbon nanotubes and hydroxylated carbon nanotubes dissolved in a solvent. Un-functionalized carbon nanotube concentrations up to 30 wt % and hydroxylated carbon nanotube concentrations up to 40 wt % can be used with even small concentrations of each (less than 2 wt %) useful in producing enhanced conductivity properties of formed thin films.

  1. Mutagenicity of carbon nanomaterials

    DEFF Research Database (Denmark)

    Wallin, Håkan; Jacobsen, Nicklas Raun; White, Paul A

    2011-01-01

    Carbon nanomaterials such carbon nanotubes, graphene and fullerenes are some the most promising nanomaterials. Although carbon nanomaterials have been reported to possess genotoxic potential, it is imperitive to analyse the data on the genotoxicity of carbon nanomaterials in vivo and in vitro...

  2. Mesoporous carbon materials

    Science.gov (United States)

    Dai, Sheng; Fulvio, Pasquale Fernando; Mayes, Richard T.; Wang, Xiqing; Sun, Xiao-Guang; Guo, Bingkun

    2014-09-09

    A conductive mesoporous carbon composite comprising conductive carbon nanoparticles contained within a mesoporous carbon matrix, wherein the conductive mesoporous carbon composite possesses at least a portion of mesopores having a pore size of at least 10 nm and up to 50 nm, and wherein the mesopores are either within the mesoporous carbon matrix, or are spacings delineated by surfaces of said conductive carbon nanoparticles when said conductive carbon nanoparticles are fused with each other, or both. Methods for producing the above-described composite, devices incorporating them (e.g., lithium batteries), and methods of using them, are also described.

  3. Pyrolyzed thin film carbon

    Science.gov (United States)

    Tai, Yu-Chong (Inventor); Liger, Matthieu (Inventor); Harder, Theodore (Inventor); Konishi, Satoshi (Inventor); Miserendino, Scott (Inventor)

    2010-01-01

    A method of making carbon thin films comprises depositing a catalyst on a substrate, depositing a hydrocarbon in contact with the catalyst and pyrolyzing the hydrocarbon. A method of controlling a carbon thin film density comprises etching a cavity into a substrate, depositing a hydrocarbon into the cavity, and pyrolyzing the hydrocarbon while in the cavity to form a carbon thin film. Controlling a carbon thin film density is achieved by changing the volume of the cavity. Methods of making carbon containing patterned structures are also provided. Carbon thin films and carbon containing patterned structures can be used in NEMS, MEMS, liquid chromatography, and sensor devices.

  4. Analysis of Pteridium ribosomal RNA sequences by rapid direct sequencing.

    Science.gov (United States)

    Tan, M K

    1991-08-01

    A total of 864 bases from 5 regions interspersed in the 18S and 26S rRNA molecules from various clones of Pteridium covering the general geographical distribution of the genus was analysed using a rapid rRNA sequencing technique. No base difference has been detected amongst the three major lineages, two of which apparently separated before the breakup of the ancient supercontinent, Pangaea. These regions of the rRNA sequences have thus been conserved for at least 160 million years and are here compared with other eukaryotic, especially plant rRNAs.

  5. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  6. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  7. Transformed composite sequences for improved qubit addressing

    Science.gov (United States)

    Merrill, J. True; Doret, S. Charles; Vittorini, Grahame; Addison, J. P.; Brown, Kenneth R.

    2014-10-01

    Selective laser addressing of a single atom or atomic ion qubit can be improved using narrow-band composite pulse sequences. We describe a Lie-algebraic technique to generalize known narrow-band sequences and introduce sequences related by dilation and rotation of sequence generators. Our method improves known narrow-band sequences by decreasing both the pulse time and the residual error. Finally, we experimentally demonstrate these composite sequences using 40Ca+ ions trapped in a surface-electrode ion trap.

  8. Sequences, groups, and number theory

    CERN Document Server

    Rigo, Michel

    2018-01-01

    This collaborative book presents recent trends on the study of sequences, including combinatorics on words and symbolic dynamics, and new interdisciplinary links to group theory and number theory. Other chapters branch out from those areas into subfields of theoretical computer science, such as complexity theory and theory of automata. The book is built around four general themes: number theory and sequences, word combinatorics, normal numbers, and group theory. Those topics are rounded out by investigations into automatic and regular sequences, tilings and theory of computation, discrete dynamical systems, ergodic theory, numeration systems, automaton semigroups, and amenable groups.  This volume is intended for use by graduate students or research mathematicians, as well as computer scientists who are working in automata theory and formal language theory. With its organization around unified themes, it would also be appropriate as a supplemental text for graduate level courses.

  9. Explaining the harmonic sequence paradox.

    Science.gov (United States)

    Schmidt, Ulrich; Zimper, Alexander

    2012-05-01

    According to the harmonic sequence paradox, an expected utility decision maker's willingness to pay for a gamble whose expected payoffs evolve according to the harmonic series is finite if and only if his marginal utility of additional income becomes zero for rather low payoff levels. Since the assumption of zero marginal utility is implausible for finite payoff levels, expected utility theory - as well as its standard generalizations such as cumulative prospect theory - are apparently unable to explain a finite willingness to pay. This paper presents first an experimental study of the harmonic sequence paradox. Additionally, it demonstrates that the theoretical argument of the harmonic sequence paradox only applies to time-patient decision makers, whereas the paradox is easily avoided if time-impatience is introduced. ©2011 The British Psychological Society.

  10. Carbon tetrachloride desorption from activated carbon

    International Nuclear Information System (INIS)

    Jonas, L.A.; Sansone, E.B.

    1981-01-01

    Carbon tetrachloride was desorbed from a granular activated carbon subsequent to its adsorption under various vapor exposure periods. The varied conditions of exposure resulted in a range of partially saturated carbon beds which, when followed by a constant flow rate for desorption, generated different forms of the desorbing concentration versus time curve. A method of analyzing the desorption curves is presented which permits extraction of the various desorbing rates from the different desorption and to relate this to the time required for such regeneration. The Wheeler desorption kinetic equation was used to calculate the pseudo first order desorption rate constant for the carbon. The desorption rate constant was found to increase monotonically with increasing saturation of the bed, permitting the calculation of the maximum desorption rate constant for the carbon at 100% saturation. The Retentivity Index of the carbon, defined as the dimensionless ratio of the adsorption to the desorption rate constant, was found to be 681

  11. Integrated sequence analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; Pyy, P

    1998-02-01

    The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  12. Matrix transformations and sequence spaces

    International Nuclear Information System (INIS)

    Nanda, S.

    1983-06-01

    In most cases the most general linear operator from one sequence space into another is actually given by an infinite matrix and therefore the theory of matrix transformations has always been of great interest in the study of sequence spaces. The study of general theory of matrix transformations was motivated by the special results in summability theory. This paper is a review article which gives almost all known results on matrix transformations. This also suggests a number of open problems for further study and will be very useful for research workers. (author)

  13. Green's theorem and Gorenstein sequences

    OpenAIRE

    Ahn, Jeaman; Migliore, Juan C.; Shin, Yong-Su

    2016-01-01

    We study consequences, for a standard graded algebra, of extremal behavior in Green's Hyperplane Restriction Theorem. First, we extend his Theorem 4 from the case of a plane curve to the case of a hypersurface in a linear space. Second, assuming a certain Lefschetz condition, we give a connection to extremal behavior in Macaulay's theorem. We apply these results to show that $(1,19,17,19,1)$ is not a Gorenstein sequence, and as a result we classify the sequences of the form $(1,a,a-2,a,1)$ th...

  14. Carbon fuel cells with carbon corrosion suppression

    Science.gov (United States)

    Cooper, John F [Oakland, CA

    2012-04-10

    An electrochemical cell apparatus that can operate as either a fuel cell or a battery includes a cathode compartment, an anode compartment operatively connected to the cathode compartment, and a carbon fuel cell section connected to the anode compartment and the cathode compartment. An effusion plate is operatively positioned adjacent the anode compartment or the cathode compartment. The effusion plate allows passage of carbon dioxide. Carbon dioxide exhaust channels are operatively positioned in the electrochemical cell to direct the carbon dioxide from the electrochemical cell.

  15. Determining Inorganic and Organic Carbon.

    Science.gov (United States)

    Koistinen, Jaana; Sjöblom, Mervi; Spilling, Kristian

    2017-11-21

    Carbon is the element which makes up the major fraction of lipids and carbohydrates, which could be used for making biofuel. It is therefore important to provide enough carbon and also follow the flow into particulate organic carbon and potential loss to dissolved organic forms of carbon. Here we present methods for determining dissolved inorganic carbon, dissolved organic carbon, and particulate organic carbon.

  16. Sequences in language and text

    CERN Document Server

    Mikros, George K

    2015-01-01

    The aim of this volume is to present the diverse but highly interesting area of the quantitative analysis of the sequence of various linguistic structures. The collected articles present a wide spectrum of quantitative analyses of linguistic syntagmatic structures and explore novel sequential linguistic entities. This volume will be interesting to all researchers studying linguistics using quantitative methods.

  17. Probabilistic studies of accident sequences

    International Nuclear Information System (INIS)

    Villemeur, A.; Berger, J.P.

    1986-01-01

    For several years, Electricite de France has carried out probabilistic assessment of accident sequences for nuclear power plants. In the framework of this program many methods were developed. As the interest in these studies was increasing and as adapted methods were developed, Electricite de France has undertaken a probabilistic safety assessment of a nuclear power plant [fr

  18. MRI sequences and their parameters

    International Nuclear Information System (INIS)

    Teissier, J.M.

    1993-01-01

    Listing basic sequences and their present variants makes a synthetic classification of the various acquisition modes possible. The knowledge of the advantages of each of them, as well as of their disadvantages and restraints, seems to be an essential prerequisite to an optimal utilization of each magnetic resonance imaging system. (author)

  19. Degree sequence in message transfer

    Science.gov (United States)

    Yamuna, M.

    2017-11-01

    Message encryption is always an issue in current communication scenario. Methods are being devised using various domains. Graphs satisfy numerous unique properties which can be used for message transfer. In this paper, I propose a message encryption method based on degree sequence of graphs.

  20. Fractals in DNA sequence analysis

    Institute of Scientific and Technical Information of China (English)

    Yu Zu-Guo(喻祖国); Vo Anh; Gong Zhi-Min(龚志民); Long Shun-Chao(龙顺潮)

    2002-01-01

    Fractal methods have been successfully used to study many problems in physics, mathematics, engineering, finance,and even in biology. There has been an increasing interest in unravelling the mysteries of DNA; for example, how can we distinguish coding and noncoding sequences, and the problems of classification and evolution relationship of organisms are key problems in bioinformatics. Although much research has been carried out by taking into consideration the long-range correlations in DNA sequences, and the global fractal dimension has been used in these works by other people, the models and methods are somewhat rough and the results are not satisfactory. In recent years, our group has introduced a time series model (statistical point of view) and a visual representation (geometrical point of view)to DNA sequence analysis. We have also used fractal dimension, correlation dimension, the Hurst exponent and the dimension spectrum (multifractal analysis) to discuss problems in this field. In this paper, we introduce these fractal models and methods and the results of DNA sequence analysis.

  1. On primes in Lucas sequences

    Czech Academy of Sciences Publication Activity Database

    Křížek, Michal; Somer, L.

    2015-01-01

    Roč. 53, č. 1 (2015), s. 2-23 ISSN 0015-0517 R&D Projects: GA ČR GA14-02067S Institutional support: RVO:67985840 Keywords : Lucas sequence * primes Subject RIV: BA - General Mathematics http://www.fq.math.ca/Abstracts/53-1/somer.pdf

  2. Is sequence awareness mandatory for perceptual sequence learning: An assessment using a pure perceptual sequence learning design.

    Science.gov (United States)

    Deroost, Natacha; Coomans, Daphné

    2018-02-01

    We examined the role of sequence awareness in a pure perceptual sequence learning design. Participants had to react to the target's colour that changed according to a perceptual sequence. By varying the mapping of the target's colour onto the response keys, motor responses changed randomly. The effect of sequence awareness on perceptual sequence learning was determined by manipulating the learning instructions (explicit versus implicit) and assessing the amount of sequence awareness after the experiment. In the explicit instruction condition (n = 15), participants were instructed to intentionally search for the colour sequence, whereas in the implicit instruction condition (n = 15), they were left uninformed about the sequenced nature of the task. Sequence awareness after the sequence learning task was tested by means of a questionnaire and the process-dissociation-procedure. The results showed that the instruction manipulation had no effect on the amount of perceptual sequence learning. Based on their report to have actively applied their sequence knowledge during the experiment, participants were subsequently regrouped in a sequence strategy group (n = 14, of which 4 participants from the implicit instruction condition and 10 participants from the explicit instruction condition) and a no-sequence strategy group (n = 16, of which 11 participants from the implicit instruction condition and 5 participants from the explicit instruction condition). Only participants of the sequence strategy group showed reliable perceptual sequence learning and sequence awareness. These results indicate that perceptual sequence learning depends upon the continuous employment of strategic cognitive control processes on sequence knowledge. Sequence awareness is suggested to be a necessary but not sufficient condition for perceptual learning to take place. Copyright © 2018 Elsevier B.V. All rights reserved.

  3. Teaching Task Sequencing via Verbal Mediation.

    Science.gov (United States)

    Rusch, Frank R.; And Others

    1987-01-01

    Verbal sequence training was used to teach a moderately mentally retarded woman to sequence job-related tasks. Learning to say the tasks in the proper sequence resulted in the employee performing her tasks in that sequence, and the employee was capable of mediating her own work behavior when scheduled changes occurred. (Author/JDD)

  4. Repdigits in k-Lucas sequences

    Indian Academy of Sciences (India)

    57(2) 2000 243-254) proved that 11 is the largest number with only one distinct digit (the so-called repdigit) in the sequence ( L n ( 2 ) ) n . In this paper, we address a similar problem in the family of -Lucas sequences. We also show that the -Lucas sequences have similar properties to those of -Fibonacci sequences ...

  5. Draft genome sequence of Acidithiobacillus ferrooxidans YQH-1

    Directory of Open Access Journals (Sweden)

    Lei Yan

    2015-12-01

    Full Text Available Acidithiobacillus ferrooxidans YQH-1 is a moderate acidophilic bacterium isolated from a river in a volcano of Northeast China. Here, we describe the draft genome of strain YQH-1, which was assembled into 123 contigs containing 3,111,222 bp with a G + C content of 58.63%. A large number of genes related to carbon dioxide fixation, dinitrogen fixation, pH tolerance, heavy metal detoxification, and oxidative stress defense were detected. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LJBT00000000.

  6. Draft Genome Sequence of Methylocella silvestris TVC, a Facultative Methanotroph Isolated from Permafrost

    OpenAIRE

    Wang, Jing; Geng, Kan; Farhan Ul Haque, Muhammad; Crombie, Andrew; Street, Lorna E.; Wookey, Philip A.; Ma, Ke; Murrell, J. Colin; Pratscher, Jennifer

    2018-01-01

    Permafrost environments play a crucial role in global carbon and methane cycling. We report here the draft genome sequence of Methylocella silvestris TVC, a new facultative methanotroph strain, isolated from the Siksik Creek catchment in the continuous permafrost zone of Inuvik (Northwest Territories, Canada).

  7. Draft Genome Sequence of Methylocella silvestris TVC, a Facultative Methanotroph Isolated from Permafrost.

    Science.gov (United States)

    Wang, Jing; Geng, Kan; Farhan Ul Haque, Muhammad; Crombie, Andrew; Street, Lorna E; Wookey, Philip A; Ma, Ke; Murrell, J Colin; Pratscher, Jennifer

    2018-02-22

    Permafrost environments play a crucial role in global carbon and methane cycling. We report here the draft genome sequence of Methylocella silvestris TVC, a new facultative methanotroph strain, isolated from the Siksik Creek catchment in the continuous permafrost zone of Inuvik (Northwest Territories, Canada). Copyright © 2018 Wang et al.

  8. Massive stars on the verge of exploding: the properties of oxygen sequence Wolf-Rayet stars

    NARCIS (Netherlands)

    Tramper, F.; Straal, S.M.; Sanyal, D.; Sana, H.; de Koter, A.; Gräfener, G.; Langer, N.; Vink, J.S.; de Mink, S.E.; Kaper, L.

    2015-01-01

    Context. Oxygen sequence Wolf-Rayet (WO) stars are a very rare stage in the evolution of massive stars. Their spectra show strong emission lines of helium-burning products, in particular highly ionized carbon and oxygen. The properties of WO stars can be used to provide unique constraints on the

  9. Synthesis of tetrahydrokhusitone. Annulation of the cyclohexane ring by free radical and carbanionic sequence of reactions

    Directory of Open Access Journals (Sweden)

    ZIVORAD CEKOVIC

    2003-05-01

    Full Text Available The synthesis of norcadinane sesquiterpene tetrahydrokhusitone 1 has been achieved by a new method for annulation of cyclohexane ring involving a sequence of free radical d-alkylation of the non-activated carbon atom and intramolecular carbanionic alkylation. (–-Menthol was used as the starting compound.

  10. Carbon Monoxide Safety

    Science.gov (United States)

    ... with the Media Fire Protection Technology Carbon monoxide safety outreach materials Keep your community informed about the ... KB | Spanish PDF 592 KB Handout: carbon monoxide safety Download this handout and add your organization's logo ...

  11. Trading forest carbon - OSU

    Science.gov (United States)

    Issues associate with trading carbon sequestered in forests are discussed. Scientific uncertainties associated with carbon measurement are discussed with respect to proposed accounting procedures. Major issues include: (1) Establishing baselines. (2) Determining additivity from f...

  12. Geochemistry of sedimentary carbonates

    National Research Council Canada - National Science Library

    Morse, John W; Mackenzie, Fred T

    1990-01-01

    .... The last major section is two chapters on the global cycle of carbon and human intervention, and the role of sedimentary carbonates as indicators of stability and changes in Earth's surface environment...

  13. Calcium carbonate overdose

    Science.gov (United States)

    Tums overdose; Calcium overdose ... Calcium carbonate can be dangerous in large amounts. ... Products that contain calcium carbonate are certain: Antacids (Tums, Chooz) Mineral supplements Hand lotions Vitamin and mineral supplements Other products may also contain ...

  14. Carbon Based Nanotechnology: Review

    Science.gov (United States)

    Srivastava, Deepak; Saini, Subhash (Technical Monitor)

    1999-01-01

    This presentation reviews publicly available information related to carbon based nanotechnology. Topics covered include nanomechanics, carbon based electronics, nanodevice/materials applications, nanotube motors, nano-lithography and H2O storage in nanotubes.

  15. Sodium carbonate poisoning

    Science.gov (United States)

    Sodium carbonate (known as washing soda or soda ash) is a chemical found in many household and industrial products. This article focuses on poisoning due to sodium carbonate. This article is for information only. Do NOT ...

  16. Carbon nanotube nanoelectrode arrays

    Science.gov (United States)

    Ren, Zhifeng; Lin, Yuehe; Yantasee, Wassana; Liu, Guodong; Lu, Fang; Tu, Yi

    2008-11-18

    The present invention relates to microelectode arrays (MEAs), and more particularly to carbon nanotube nanoelectrode arrays (CNT-NEAs) for chemical and biological sensing, and methods of use. A nanoelectrode array includes a carbon nanotube material comprising an array of substantially linear carbon nanotubes each having a proximal end and a distal end, the proximal end of the carbon nanotubes are attached to a catalyst substrate material so as to form the array with a pre-determined site density, wherein the carbon nanotubes are aligned with respect to one another within the array; an electrically insulating layer on the surface of the carbon nanotube material, whereby the distal end of the carbon nanotubes extend beyond the electrically insulating layer; a second adhesive electrically insulating layer on the surface of the electrically insulating layer, whereby the distal end of the carbon nanotubes extend beyond the second adhesive electrically insulating layer; and a metal wire attached to the catalyst substrate material.

  17. Graphitization in Carbon MEMS and Carbon NEMS

    Science.gov (United States)

    Sharma, Swati

    Carbon MEMS (CMEMS) and Carbon NEMS (CNEMS) are an emerging class of miniaturized devices. Due to the numerous advantages such as scalable manufacturing processes, inexpensive and readily available precursor polymer materials, tunable surface properties and biocompatibility, carbon has become a preferred material for a wide variety of future sensing applications. Single suspended carbon nanowires (CNWs) integrated on CMEMS structures fabricated by electrospinning of SU8 photoresist on photolithographially patterned SU8 followed by pyrolysis are utilized for understanding the graphitization process in micro and nano carbon materials. These monolithic CNW-CMEMS structures enable the fabrication of very high aspect ratio CNWs of predefined length. The CNWs thus fabricated display core---shell structures having a graphitic shell with a glassy carbon core. The electrical conductivity of these CNWs is increased by about 100% compared to glassy carbon as a result of enhanced graphitization. We explore various tunable fabrication and pyrolysis parameters to improve graphitization in the resulting CNWs. We also suggest gas-sensing application of the thus fabricated single suspended CNW-CMEMS devices by using the CNW as a nano-hotplate for local chemical vapor deposition. In this thesis we also report on results from an optimization study of SU8 photoresist derived carbon electrodes. These electrodes were applied to the simultaneous detection of traces of Cd(II) and Pb(II) through anodic stripping voltammetry and detection limits as low as 0.7 and 0.8 microgL-1 were achieved. To further improve upon the electrochemical behavior of the carbon electrodes we elucidate a modified pyrolysis technique featuring an ultra-fast temperature ramp for obtaining bubbled porous carbon from lithographically patterned SU8. We conclude this dissertation by suggesting the possible future works on enhancing graphitization as well as on electrochemical applications

  18. Carbon offsetting: sustaining consumption?

    OpenAIRE

    Heather Lovell; Harriet Bulkeley; Diana Liverman

    2009-01-01

    In this paper we examine how theories of sustainable and ethical consumption help us to understand a new, rapidly expanding type of consumer product designed to mitigate climate change: carbon offsets. The voluntary carbon offset market grew by 200% between 2005 and 2006, and there are now over 150 retailers of voluntary carbon offsets worldwide. Our analysis concentrates on the production and consumption of carbon offsets, drawing on ideas from governmentality and political ecology about how...

  19. Ions in carbon dioxide at an atmospheric pressure

    International Nuclear Information System (INIS)

    Ikezoe, Yasumasa; Onuki, Kaoru; Shimizu, Saburo; Nakajima, Hayato; Sato, Shoichi; Matsuoka, Shingo; Nakamura, Hirone; Tamura, Takaaki

    1985-01-01

    The formation and the subsequent reactions of positive and negative ions were observed by a time resolved atmospheric pressure ionization mass spectrometer (TRAPI) in an atmospheric pressure carbon dioxide added with small amounts of carbon monoxide and oxygen. A relatively stable ion of (44 x n) + (n >= 2) having a different reactivity from that of (CO 2 ) + sub(n) was found to be one of major ionic species in this gas system. This species was tentatively assigned as [O 2 (CO) 2 ] + (CO 2 )sub(n-2). A new reaction sequence of positive ions is proposed which can be operative in the radiolysis of carbon dioxide at 1 atm. (author)

  20. Nonparametric Inference for Periodic Sequences

    KAUST Repository

    Sun, Ying

    2012-02-01

    This article proposes a nonparametric method for estimating the period and values of a periodic sequence when the data are evenly spaced in time. The period is estimated by a "leave-out-one-cycle" version of cross-validation (CV) and complements the periodogram, a widely used tool for period estimation. The CV method is computationally simple and implicitly penalizes multiples of the smallest period, leading to a "virtually" consistent estimator of integer periods. This estimator is investigated both theoretically and by simulation.We also propose a nonparametric test of the null hypothesis that the data have constantmean against the alternative that the sequence of means is periodic. Finally, our methodology is demonstrated on three well-known time series: the sunspots and lynx trapping data, and the El Niño series of sea surface temperatures. © 2012 American Statistical Association and the American Society for Quality.

  1. Multi-qubit compensation sequences

    International Nuclear Information System (INIS)

    Tomita, Y; Merrill, J T; Brown, K R

    2010-01-01

    The Hamiltonian control of n qubits requires precision control of both the strength and timing of interactions. Compensation pulses relax the precision requirements by reducing unknown but systematic errors. Using composite pulse techniques designed for single qubits, we show that systematic errors for n-qubit systems can be corrected to arbitrary accuracy given either two non-commuting control Hamiltonians with identical systematic errors or one error-free control Hamiltonian. We also examine composite pulses in the context of quantum computers controlled by two-qubit interactions. For quantum computers based on the XY interaction, single-qubit composite pulse sequences naturally correct systematic errors. For quantum computers based on the Heisenberg or exchange interaction, the composite pulse sequences reduce the logical single-qubit gate errors but increase the errors for logical two-qubit gates.

  2. Cassini Mission Sequence Subsystem (MSS)

    Science.gov (United States)

    Alland, Robert

    2011-01-01

    This paper describes my work with the Cassini Mission Sequence Subsystem (MSS) team during the summer of 2011. It gives some background on the motivation for this project and describes the expected benefit to the Cassini program. It then introduces the two tasks that I worked on - an automatic system auditing tool and a series of corrections to the Cassini Sequence Generator (SEQ_GEN) - and the specific objectives these tasks were to accomplish. Next, it details the approach I took to meet these objectives and the results of this approach, followed by a discussion of how the outcome of the project compares with my initial expectations. The paper concludes with a summary of my experience working on this project, lists what the next steps are, and acknowledges the help of my Cassini colleagues.

  3. Carbon activity meter

    International Nuclear Information System (INIS)

    Roy, P.; Krankota, J.L.

    1975-01-01

    A carbon activity meter utilizing an electrochemical carbon cell with gaseous reference electrodes having particular application for measuring carbon activity in liquid sodium for the LMFBR project is described. The electrolyte container is electroplated with a thin gold film on the inside surface thereof, and a reference electrode consisting of CO/CO 2 gas is used. (U.S.)

  4. Protolytic carbon film technology

    Energy Technology Data Exchange (ETDEWEB)

    Renschler, C.L.; White, C.A.

    1996-04-01

    This paper presents a technique for the deposition of polyacrylonitrile (PAN) on virtually any surface allowing carbon film formation with only the caveat that the substrate must withstand carbonization temperatures of at least 600 degrees centigrade. The influence of processing conditions upon the structure and properties of the carbonized film is discussed. Electrical conductivity, microstructure, and morphology control are also described.

  5. Carbon Goes To…

    Science.gov (United States)

    Savasci, Funda

    2014-01-01

    The purposes of this activity are to help middle school students understand the carbon cycle and realize how human activities affect the carbon cycle. This activity consists of two parts. The first part of the activity focuses on the carbon cycle, especially before the Industrial Revolution, while the second part of the activity focuses on how…

  6. Global Carbon Budget 2016

    NARCIS (Netherlands)

    Le Quéré, Corinne; Andrew, Robbie M.; Canadell, Josep G.; Sitch, Stephen; Ivar Korsbakken, Jan; Peters, Glen P.; Manning, Andrew C.; Boden, Thomas A.; Tans, Pieter P.; Houghton, Richard A.; Keeling, Ralph F.; Alin, Simone; Andrews, Oliver D.; Anthoni, Peter; Barbero, Leticia; Bopp, Laurent; Chevallier, Frédéric; Chini, Louise P.; Ciais, Philippe; Currie, Kim; Delire, Christine; Doney, Scott C.; Friedlingstein, Pierre; Gkritzalis, Thanos; Harris, Ian A; Hauck, Judith; Haverd, Vanessa; Hoppema, Mario; Klein Goldewijk, Kees; Jain, Atul K.; Kato, Etsushi; Körtzinger, Arne; Landschützer, Peter; Lefèvre, Nathalie; Lenton, Andrew; Lienert, Sebastian; Lombardozzi, Danica; Melton, Joe R.; Metzl, Nicolas; Millero, Frank; Monteiro, Pedro M S; Munro, David R.; Nabel, Julia E M S; Nakaoka, Shin Ichiro; O'Brien, Kevin; Olsen, Are; Omar, Abdirahman M.; Ono, Tsuneo; Pierrot, Denis; Poulter, Benjamin; Rödenbeck, Christian; Salisbury, Joe; Schuster, Ute; Schwinger, Jörg; Séférian, Roland; Skjelvan, Ingunn; Stocker, Benjamin D.; Sutton, Adrienne J.; Takahashi, Taro; Tian, Hanqin; Tilbrook, Bronte; Van Der Laan-Luijkx, Ingrid T.; Van Der Werf, Guido R.; Viovy, Nicolas; Walker, Anthony P.; Wiltshire, Andrew J.; Zaehle, Sönke

    2016-01-01

    Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere-the "global carbon budget"-is important to better understand the global carbon cycle, support the development of climate policies, and project future

  7. Global Carbon Budget 2016

    NARCIS (Netherlands)

    Quéré, Le Corinne; Andrew, Robbie M.; Canadell, Josep G.; Sitch, Stephen; Korsbakken, Jan Ivar; Peters, Glen P.; Manning, Andrew C.; Boden, Thomas A.; Tans, Pieter P.; Houghton, Richard A.; Keeling, Ralph F.; Alin, Simone; Andrews, Oliver D.; Anthoni, Peter; Barbero, Leticia; Bopp, Laurent; Chevallier, Frédéric; Chini, Louise P.; Ciais, Philippe; Currie, Kim; Delire, Christine; Doney, Scott C.; Friedlingstein, Pierre; Gkritzalis, Thanos; Harris, Ian; Hauck, Judith; Haverd, Vanessa; Hoppema, Mario; Klein Goldewijk, Kees; Jain, Atul K.; Kato, Etsushi; Körtzinger, Arne; Landschützer, Peter; Lefèvre, Nathalie; Lenton, Andrew; Lienert, Sebastian; Lombardozzi, Danica; Melton, Joe R.; Metzl, Nicolas; Millero, Frank; Monteiro, Pedro M.S.; Munro, David R.; Nabel, Julia E.M.S.; Nakaoka, S.; O'Brien, Kevin; Olsen, Are; Omar, Abdirahman M.; Ono, Tsuneo; Pierrot, Denis; Poulter, Benjamin; Rödenbeck, Christian; Salisbury, Joe; Schuster, Ute; Schwinger, Jörg; Séférian, Roland; Skjelvan, Ingunn; Stocker, Benjamin D.; Sutton, Adrienne J.; Takahashi, Taro; Tian, Hanqin; Tilbrook, Bronte; Laan-Luijkx, van der Ingrid T.; Werf, van der Guido R.; Viovy, Nicolas; Walker, Anthony P.; Wiltshire, Andrew J.; Zaehle, Sönke

    2016-01-01

    Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere – the “global carbon budget” – is important to better understand the global carbon cycle, support the development of climate policies, and project

  8. Carbon pellet cloud striations

    International Nuclear Information System (INIS)

    Parks, P.B.

    1989-01-01

    Fine scale striations, with alternating rows of bright and dark zones, have been observed in the ablation clouds of carbon pellets injected into the TEXT tokamak. The striations extend along the magnetic field for about 1 cm with quite regular cross-field variations characterized by a wavelength of a few mm. Their potential as a diagnostic tool for measuring q-profiles in tokamaks provides motivation for investigating the origin of the striations. The authors propose that the striations are not due to a sequence of high and low ablation rates because of the finite thermal magnetic islands localized at rational surfaces, q = m/n, would be responsible for reducing the electron flux to the pellet region; the length of the closed field line which forms the local magnetic axis of the island is too long to prevent a depletion of plasma electrons in a flux tube intercepting the pellet for the duration 2 rp / vp . Instead, they propose that striations are the manifestation of the saturated state of growing fluctuations inside the cloud. The instability is generated by E x B rotation of the ablation cloud. The outward centrifugal force points down the ablation density gradient inducing the Rayleigh-Taylor instability. The instability is not present for wave numbers along the field lines, which may explain why the striations are long and uniform in that direction. The E field develops inside the ablation cloud as a result of cold electron return currents which are induced to cancel the incoming hot plasma electron current streaming along the field lines

  9. Carbon/Carbon Pistons for Internal Combustion Engines

    Science.gov (United States)

    Taylor, A. H.

    1986-01-01

    Carbon/carbon piston performs same function as aluminum pistons in reciprocating internal combustion engines while reducing weight and increasing mechanical and thermal efficiencies of engine. Carbon/carbon piston concept features low piston-to-cylinder wall clearance - so low piston rings and skirts unnecessary. Advantages possible by negligible coefficient of thermal expansion of carbon/carbon.

  10. Sequence complexity and work extraction

    International Nuclear Information System (INIS)

    Merhav, Neri

    2015-01-01

    We consider a simplified version of a solvable model by Mandal and Jarzynski, which constructively demonstrates the interplay between work extraction and the increase of the Shannon entropy of an information reservoir which is in contact with a physical system. We extend Mandal and Jarzynski’s main findings in several directions: first, we allow sequences of correlated bits rather than just independent bits. Secondly, at least for the case of binary information, we show that, in fact, the Shannon entropy is only one measure of complexity of the information that must increase in order for work to be extracted. The extracted work can also be upper bounded in terms of the increase in other quantities that measure complexity, like the predictability of future bits from past ones. Third, we provide an extension to the case of non-binary information (i.e. a larger alphabet), and finally, we extend the scope to the case where the incoming bits (before the interaction) form an individual sequence, rather than a random one. In this case, the entropy before the interaction can be replaced by the Lempel–Ziv (LZ) complexity of the incoming sequence, a fact that gives rise to an entropic meaning of the LZ complexity, not only in information theory, but also in physics. (paper)

  11. Entropic fluctuations in DNA sequences

    Science.gov (United States)

    Thanos, Dimitrios; Li, Wentian; Provata, Astero

    2018-03-01

    The Local Shannon Entropy (LSE) in blocks is used as a complexity measure to study the information fluctuations along DNA sequences. The LSE of a DNA block maps the local base arrangement information to a single numerical value. It is shown that despite this reduction of information, LSE allows to extract meaningful information related to the detection of repetitive sequences in whole chromosomes and is useful in finding evolutionary differences between organisms. More specifically, large regions of tandem repeats, such as centromeres, can be detected based on their low LSE fluctuations along the chromosome. Furthermore, an empirical investigation of the appropriate block sizes is provided and the relationship of LSE properties with the structure of the underlying repetitive units is revealed by using both computational and mathematical methods. Sequence similarity between the genomic DNA of closely related species also leads to similar LSE values at the orthologous regions. As an application, the LSE covariance function is used to measure the evolutionary distance between several primate genomes.

  12. Method and apparatus for biological sequence comparison

    Science.gov (United States)

    Marr, T.G.; Chang, W.I.

    1997-12-23

    A method and apparatus are disclosed for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence. 5 figs.

  13. Memory and learning with rapid audiovisual sequences

    Science.gov (United States)

    Keller, Arielle S.; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed. PMID:26575193

  14. Memory and learning with rapid audiovisual sequences.

    Science.gov (United States)

    Keller, Arielle S; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed.

  15. Multineuronal Spike Sequences Repeat with Millisecond Precision

    Directory of Open Access Journals (Sweden)

    Koki eMatsumoto

    2013-06-01

    Full Text Available Cortical microcircuits are nonrandomly wired by neurons. As a natural consequence, spikes emitted by microcircuits are also nonrandomly patterned in time and space. One of the prominent spike organizations is a repetition of fixed patterns of spike series across multiple neurons. However, several questions remain unsolved, including how precisely spike sequences repeat, how the sequences are spatially organized, how many neurons participate in sequences, and how different sequences are functionally linked. To address these questions, we monitored spontaneous spikes of hippocampal CA3 neurons ex vivo using a high-speed functional multineuron calcium imaging technique that allowed us to monitor spikes with millisecond resolution and to record the location of spiking and nonspiking neurons. Multineuronal spike sequences were overrepresented in spontaneous activity compared to the statistical chance level. Approximately 75% of neurons participated in at least one sequence during our observation period. The participants were sparsely dispersed and did not show specific spatial organization. The number of sequences relative to the chance level decreased when larger time frames were used to detect sequences. Thus, sequences were precise at the millisecond level. Sequences often shared common spikes with other sequences; parts of sequences were subsequently relayed by following sequences, generating complex chains of multiple sequences.

  16. Carbon isotope variations in the upper Carboniferous - Permian Mallemuk Mountain Group, eastern North Greenland

    International Nuclear Information System (INIS)

    Stemmerik, L.; Magaritz, M.

    1989-01-01

    Isotope data from Late Palaeozoic limestones of the Wandel Sea Basin in eastern North Greenland show a variation of δ 13 C from 0.0 0/00 to 5.7 0/00 vs PDB. Carbonates depleted in 13 C occur in the basal part of lower Moscovian, upper Moscovian and middle Gzhelian transgressive sequences. 13 C enriched limestones occur later in the cycles. The most 13 C enriched limestones occur in the youngest (late Early Permian-early Late Permian) part of the sequence in Amdrup Land. The isotopic data is believed to represent changes in the global carbon cycle. Thus 13 C enriched carbonates correlate to periods of burial of organic carbon mostly as coal, while 13 C depleted carbonates formed as the result of erosion and oxidation of organic carbon during sea-level low stands. (author)

  17. [Characterization of Black and Dichothrix Cyanobacteria Based on the 16S Ribosomal RNA Gene Sequence

    Science.gov (United States)

    Ortega, Maya

    2010-01-01

    My project focuses on characterizing different cyanobacteria in thrombolitic mats found on the island of Highborn Cay, Bahamas. Thrombolites are interesting ecosystems because of the ability of bacteria in these mats to remove carbon dioxide from the atmosphere and mineralize it as calcium carbonate. In the future they may be used as models to develop carbon sequestration technologies, which could be used as part of regenerative life systems in space. These thrombolitic communities are also significant because of their similarities to early communities of life on Earth. I targeted two cyanobacteria in my research, Dichothrix spp. and whatever black is, since they are believed to be important to carbon sequestration in these thrombolitic mats. The goal of my summer research project was to molecularly identify these two cyanobacteria. DNA was isolated from each organism through mat dissections and DNA extractions. I ran Polymerase Chain Reactions (PCR) to amplify the 16S ribosomal RNA (rRNA) gene in each cyanobacteria. This specific gene is found in almost all bacteria and is highly conserved, meaning any changes in the sequence are most likely due to evolution. As a result, the 16S rRNA gene can be used for bacterial identification of different species based on the sequence of their 16S rRNA gene. Since the exact sequence of the Dichothrix gene was unknown, I designed different primers that flanked the gene based on the known sequences from other taxonomically similar cyanobacteria. Once the 16S rRNA gene was amplified, I cloned the gene into specialized Escherichia coli cells and sent the gene products for sequencing. Once the sequence is obtained, it will be added to a genetic database for future reference to and classification of other Dichothrix sp.

  18. Activated carbons and gold

    International Nuclear Information System (INIS)

    McDougall, G.J.; Hancock, R.D.

    1980-01-01

    The literature on activated carbon is reviewed so as to provide a general background with respect to the effect of source material and activation procedure on carbon properties, the structure and chemical nature of the surface of the activated carbon, and the nature of absorption processes on carbon. The various theories on the absorption of gold and silver from cyanide solutions are then reviewed, followed by a discussion of processes for the recovery of gold and silver from cyanide solutions using activated carbon, including a comparison with zinc precipitation

  19. Carbon-14 waste management

    International Nuclear Information System (INIS)

    Bush, R.P.; Smith, G.M.; White, I.F

    1984-01-01

    Carbon-14 occurs in nature, but is also formed in nuclear reactors. Because of its long half-life and the biological significance of carbon, releases from nuclear facilities could have a significant radiological impact. Waste management strategies for carbon-14 are therefore of current concern. Carbon-14 is present in a variety of waste streams both at reactors and at reprocessing plants. A reliable picture of the production and release of carbon-14 from various reactor systems has been built up for the purposes of this study. A possible management strategy for carbon-14 might be the reduction of nitrogen impurity levels in core materials, since the activation of 14 N is usually the dominant source of carbon-14. The key problem in carbon-14 management is its retention of off-gas streams, particularly in the dissolver off-gas stream at reprocessing plants. Three alternative trapping processes that convert carbon dioxide into insoluble carbonates have been suggested. The results show that none of the options considered need be rejected on the grounds of potential radiation doses to individuals. All exposures should be as low as reasonably achievable, economic and social factors being taken into account. If, on these grounds, retention and disposal of carbon-14 is found to be beneficial, then, subject to the limitations noted, appropriate retention, immobilization and disposal technologies have been identified

  20. Carbon isotopic record from Upper Devonian carbonates at Dongcun in Guilin, southern China, supporting the world-wide pattern of carbon isotope excursions during Frasnian-Famennian transition

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Two positive δ13C excursions are presented in records from the Frasnian-Famennian (F-F) marine carbonate sediments in Europe, America, Africa, and Australia, having been considered as a worldwide pattern, and attributed to enhanced organic carbon burial during the F-F biological mass extinction. However, this worldwide pattern has not been revealed from the well-deposited Late Devonian sequences in southern China. In this paper, a detailed investigation has been made on the Late Devonian section at Dongcun, Guilin, southern China to constrain perturbations in δ13C of carbonates in the F-F deposited sequence. The result from this section also indicates two positive δ13C excursions during the F-F transition. The first excursion with an amplitude of 1.5‰ occurred at the bottom of linguiformis Zone, later than the early excursion existing in the Late rhenana Zone of the Late Devonian profiles in other continents, especially, in central Europe. This difference has been expected to be a result as conodont Palmatolepis linguiformis occurred earlier in southern China than other sites. The second excursion with an amplitude of 2.1‰ is located at the F-F boundary, same as the records from other continents. This result strongly supports the view that two carbon isotope positive excursions during the F-F transition are common in carbonate sediments, resulting from worldwide increases of organic carbon burial intensity.

  1. Static multiplicities in heterogeneous azeotropic distillation sequences

    DEFF Research Database (Denmark)

    Esbjerg, Klavs; Andersen, Torben Ravn; Jørgensen, Sten Bay

    1998-01-01

    In this paper the results of a bifurcation analysis on heterogeneous azeotropic distillation sequences are given. Two sequences suitable for ethanol dehydration are compared: The 'direct' and the 'indirect' sequence. It is shown, that the two sequences, despite their similarities, exhibit very...... different static behavior. The method of Petlyuk and Avet'yan (1971), Bekiaris et al. (1993), which assumes infinite reflux and infinite number of stages, is extended to and applied on heterogeneous azeotropic distillation sequences. The predictions are substantiated through simulations. The static sequence...

  2. Highly stretchable carbon aerogels.

    Science.gov (United States)

    Guo, Fan; Jiang, Yanqiu; Xu, Zhen; Xiao, Youhua; Fang, Bo; Liu, Yingjun; Gao, Weiwei; Zhao, Pei; Wang, Hongtao; Gao, Chao

    2018-02-28

    Carbon aerogels demonstrate wide applications for their ultralow density, rich porosity, and multifunctionalities. Their compressive elasticity has been achieved by different carbons. However, reversibly high stretchability of neat carbon aerogels is still a great challenge owing to their extremely dilute brittle interconnections and poorly ductile cells. Here we report highly stretchable neat carbon aerogels with a retractable 200% elongation through hierarchical synergistic assembly. The hierarchical buckled structures and synergistic reinforcement between graphene and carbon nanotubes enable a temperature-invariable, recoverable stretching elasticity with small energy dissipation (~0.1, 100% strain) and high fatigue resistance more than 10 6 cycles. The ultralight carbon aerogels with both stretchability and compressibility were designed as strain sensors for logic identification of sophisticated shape conversions. Our methodology paves the way to highly stretchable carbon and neat inorganic materials with extensive applications in aerospace, smart robots, and wearable devices.

  3. Carbon dioxide sequestration by direct mineral carbonation with carbonic acid

    Energy Technology Data Exchange (ETDEWEB)

    O' Connor, William K.; Dahlin, David C.; Nilsen, David N.; Walters, Richard P.; Turner, Paul C.

    2000-01-01

    The Albany Research Center (ARC) of the U.S. Dept. of Energy (DOE) has been conducting a series of mineral carbonation tests at its Albany, Oregon, facility over the past 2 years as part of a Mineral Carbonation Study Program within the DOE. Other participants in this Program include the Los Alamos National Laboratory, Arizona State University, Science Applications International Corporation, and the DOE National Energy Technology Laboratory. The ARC tests have focused on ex-situ mineral carbonation in an aqueous system. The process developed at ARC utilizes a slurry of water mixed with a magnesium silicate mineral, olivine [forsterite end member (Mg2SiO4)], or serpentine [Mg3Si2O5(OH)4]. This slurry is reacted with supercritical carbon dioxide (CO2) to produce magnesite (MgCO3). The CO2 is dissolved in water to form carbonic acid (H2CO3), which dissociates to H+ and HCO3 -. The H+ reacts with the mineral, liberating Mg2+ cations which react with the bicarbonate to form the solid carbonate. The process is designed to simulate the natural serpentinization reaction of ultramafic minerals, and for this reason, these results may also be applicable to in-situ geological sequestration regimes. Results of the baseline tests, conducted on ground products of the natural minerals, have been encouraging. Tests conducted at ambient temperature (22 C) and subcritical CO2 pressures (below 73 atm) resulted in very slow conversion to the carbonate. However, when elevated temperatures and pressures are utilized, coupled with continuous stirring of the slurry and gas dispersion within the water column, significant reaction occurs within much shorter reaction times. Extent of reaction, as measured by the stoichiometric conversion of the silicate mineral (olivine) to the carbonate, is roughly 90% within 24 hours, using distilled water, and a reaction temperature of 185?C and a partial pressure of CO2 (PCO2) of 115 atm. Recent tests using a bicarbonate solution, under identical reaction

  4. Carbon dioxide sequestration by direct mineral carbonation with carbonic acid

    Energy Technology Data Exchange (ETDEWEB)

    O' Connor, W.K.; Dahlin, D.C.; Nilsen, D.N.; Walters, R.P.; Turner, P.C.

    2000-07-01

    The Albany Research Center (ARC) of the US Department of Energy (DOE) has been conducting a series of mineral carbonation tests at its Albany, Oregon, facility over the past 2 years as part of a Mineral Carbonation Study Program within the DOE. The ARC tests have focused on ex-situ mineral carbonation in an aqueous system. The process developed at ARC utilizes a slurry of water mixed with a magnesium silicate mineral, olivine [forsterite and member (mg{sub 2}SiO{sub 4})], or serpentine [Mg{sub 3}Si{sub 2}O{sub 5}(OH){sub 4}]. This slurry is reacted with supercritical carbon dioxide (CO{sub 2}) to produce magnesite (MgCO{sub 3}). The CO{sub 2} is dissolved in water to form carbonic acid (H{sub 2}CO{sub 3}), which dissociates to H{sup +} and HCO{sub 3}{sup {minus}}. The H{sup +} reacts with the mineral, liberating Mg{sup 2+} cations which react with the bicarbonate to form the solid carbonate. The process is designed to simulate the natural serpentinization reaction of ultramafic minerals, and for this reason, these results may also be applicable to in-situ geological sequestration regimes. Results of the baseline tests, conducted on ground products of the natural minerals, have been encouraging. Tests conducted at ambient temperature (22 C) and subcritical CO{sub 2} pressures (below 73 atm) resulted in very slow conversion to the carbonate. However, when elevated temperatures and pressures are utilized, coupled with continuous stirring of the slurry and gas dispersion within the water column, significant reaction occurs within much shorter reaction times. Extent of reaction, as measured by the stoichiometric conversion of the silicate mineral (olivine) to the carbonate, is roughly 90% within 24 hours, using distilled water, and a reaction temperature of 185 C and a partial pressure of CO{sub 2} (P{sub CO{sub 2}}) of 115 atm. Recent tests using a bicarbonate solution, under identical reaction conditions, have achieved roughly 83% conversion of heat treated serpentine

  5. CRL 2688: A post-carbon-star object and probable planetary nebula progenitor

    International Nuclear Information System (INIS)

    Zuckerman, B.; Gilra, D.P.; Turner, B.E.; Morris, M.; Palmer, P.

    1976-01-01

    Millimeter-wavelength emission is observed toward CRL 2688 from H 12 CN, H 13 CN, CS, and HC 3 N. The similarity of this emission and that from the molecular envelope of the carbon star IRC+10216 establishes, beyond a reasonable doubt, that CRL 2688 is a post--carbon-star object. It appears probable that both of these objects will evolve into planetary nebulae. An evolutionary sequence leading from carbon stars to planetary nebulae is outlined

  6. Blind sequence-length estimation of low-SNR cyclostationary sequences

    CSIR Research Space (South Africa)

    Vlok, JD

    2014-06-01

    Full Text Available Several existing direct-sequence spread spectrum (DSSS) detection and estimation algorithms assume prior knowledge of the symbol period or sequence length, although very few sequence-length estimation techniques are available in the literature...

  7. Characterization of carbon ion-induced mutations in Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Shikazono, N.; Suzuki, C.; Kitamura, S.; Watanabe, H.; Tano, S.; Tanaka, A.

    2003-01-01

    Full text: Irradiation of Arabidopsis thaliana by carbon ions was carried out to investigate the mutational effect of ion particles in higher plants. The averaged mutation rate of carbon ions was 2.0 X 10 -6 / Gy, which was 18-fold higher than that of electrons. PCR analysis of the carbon ion-induced mutants showed that, out of 28 mutant alleles, 14 had point-like mutations within the gene, while 14 contained large structural alterations. In the case of 12 electron-induced mutants, 9 had point-like mutations within the gene, while 3 contained large structural alterations. These results suggest that carbon ions are more likely to induce large structural alterations compared with electrons. Further sequence analysis revealed that most of the point-like mutations induced by carbon ions were short deletions. In the case of rearrangements, DNA strand breaks were found to be rejoined using, if present, short homologous sequences for both types of radiation. After carbon ion-irradiation, small deletions were frequently observed around the breakpoints, whereas duplications of terminal sequence were found after electron-irradiation. These results suggest that non-homologous end joining (NHEJ) pathway operates after plant cells are exposed to both ion particles and electrons but that different mode of rejoining deals with the broken ends produced by each radiation. From the present results, it seems reasonable to assume that carbon ions could predominantly induce null mutations in Arabidopsis. The fact that the molecular nature of carbon ion-induced mutation was different from that of electrons and that the molecular mechanisms of cells to induce mutations appeared to be also different implicates that ion particle is not only valuable as a new mutagen but also useful as a new tool to study repair mechanisms of certain types of DNA damage

  8. Substantial global carbon uptake by cement carbonation

    OpenAIRE

    Xi, Fengming; Davis, Steven J.; Ciais, Philippe; Crawford-Brown, Douglas; Guan, Dabo; Pade, Claus; Shi, Tiemao; Syddall, Mark; Lv, Jie; Ji, Lanzhu; Bing, Longfei; Wang, Jiaoyue; Wei, Wei; Yang, Keun-Hyeok; Lagerblad, Björn

    2016-01-01

    Calcination of carbonate rocks during the manufacture of cement produced 5% of global CO2 emissions from all industrial process and fossil-fuel combustion in 20131, 2. Considerable attention has been paid to quantifying these industrial process emissions from cement production2, 3, but the natural reversal of the process—carbonation—has received little attention in carbon cycle studies. Here, we use new and existing data on cement materials during cement service life, demolition, and secondar...

  9. Proteomic analysis of carbon concentrating chemolithotrophic bacteria Serratia sp. for sequestration of carbon dioxide.

    Science.gov (United States)

    Bharti, Randhir K; Srivastava, Shaili; Thakur, Indu Shekhar

    2014-01-01

    A chemolithotrophic bacterium enriched in the chemostat in presence of sodium bicarbonate as sole carbon source was identified as Serratia sp. by 16S rRNA sequencing. Carbon dioxide sequestering capacity of bacterium was detected by carbonic anhydrase enzyme and ribulose-1, 5- bisphosphate carboxylase/oxygenase (RuBisCO). The purified carbonic anhydrase showed molecular weight of 29 kDa. Molecular weight of RuBisCO was 550 kDa as determined by fast protein liquid chromatography (FPLC), however, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) showed presence of two subunits whose molecular weights were 56 and 14 kDa. The Western blot analysis of the crude protein and purified sample cross reacted with RuBisCO large-subunit polypeptides antibodies showed strong band pattern at molecular weight around 56 kDa regions. Whole cell soluble proteins of Serratia sp. grown under autotrophic and heterotrophic conditions were resolved by two-dimensional gel electrophoresis and MALDI-TOF/MS for differential expression of proteins. In proteomic analysis of 63 protein spots, 48 spots were significantly up-regulated in the autotrophically grown cells; seven enzymes showed its utilization in autotrophic carbon fixation pathways and other metabolic activities of bacterium including lipid metabolisms indicated sequestration potency of carbon dioxide and production of biomaterials.

  10. Proteomic analysis of carbon concentrating chemolithotrophic bacteria Serratia sp. for sequestration of carbon dioxide.

    Directory of Open Access Journals (Sweden)

    Randhir K Bharti

    Full Text Available A chemolithotrophic bacterium enriched in the chemostat in presence of sodium bicarbonate as sole carbon source was identified as Serratia sp. by 16S rRNA sequencing. Carbon dioxide sequestering capacity of bacterium was detected by carbonic anhydrase enzyme and ribulose-1, 5- bisphosphate carboxylase/oxygenase (RuBisCO. The purified carbonic anhydrase showed molecular weight of 29 kDa. Molecular weight of RuBisCO was 550 kDa as determined by fast protein liquid chromatography (FPLC, however, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE showed presence of two subunits whose molecular weights were 56 and 14 kDa. The Western blot analysis of the crude protein and purified sample cross reacted with RuBisCO large-subunit polypeptides antibodies showed strong band pattern at molecular weight around 56 kDa regions. Whole cell soluble proteins of Serratia sp. grown under autotrophic and heterotrophic conditions were resolved by two-dimensional gel electrophoresis and MALDI-TOF/MS for differential expression of proteins. In proteomic analysis of 63 protein spots, 48 spots were significantly up-regulated in the autotrophically grown cells; seven enzymes showed its utilization in autotrophic carbon fixation pathways and other metabolic activities of bacterium including lipid metabolisms indicated sequestration potency of carbon dioxide and production of biomaterials.

  11. Infinite matrices and sequence spaces

    CERN Document Server

    Cooke, Richard G

    2014-01-01

    This clear and correct summation of basic results from a specialized field focuses on the behavior of infinite matrices in general, rather than on properties of special matrices. Three introductory chapters guide students to the manipulation of infinite matrices, covering definitions and preliminary ideas, reciprocals of infinite matrices, and linear equations involving infinite matrices.From the fourth chapter onward, the author treats the application of infinite matrices to the summability of divergent sequences and series from various points of view. Topics include consistency, mutual consi

  12. Carbon isotopes in mollusk shell carbonates

    Science.gov (United States)

    McConnaughey, Ted A.; Gillikin, David Paul

    2008-10-01

    Mollusk shells contain many isotopic clues about calcification physiology and environmental conditions at the time of shell formation. In this review, we use both published and unpublished data to discuss carbon isotopes in both bivalve and gastropod shell carbonates. Land snails construct their shells mainly from respired CO2, and shell δ13C reflects the local mix of C3 and C4 plants consumed. Shell δ13C is typically >10‰ heavier than diet, probably because respiratory gas exchange discards CO2, and retains the isotopically heavier HCO3 -. Respired CO2 contributes less to the shells of aquatic mollusks, because CO2/O2 ratios are usually higher in water than in air, leading to more replacement of respired CO2 by environmental CO2. Fluid exchange with the environment also brings additional dissolved inorganic carbon (DIC) into the calcification site. Shell δ13C is typically a few ‰ lower than ambient DIC, and often decreases with age. Shell δ13C retains clues about processes such as ecosystem metabolism and estuarine mixing. Ca2+ ATPase-based models of calcification physiology developed for corals and algae likely apply to mollusks, too, but lower pH and carbonic anhydrase at the calcification site probably suppress kinetic isotope effects. Carbon isotopes in biogenic carbonates are clearly complex, but cautious interpretation can provide a wealth of information, especially after vital effects are better understood.

  13. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed; Mansour, Essam; Kalnis, Panos

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern

  14. Computational analysis of sequence selection mechanisms.

    Science.gov (United States)

    Meyerguz, Leonid; Grasso, Catherine; Kleinberg, Jon; Elber, Ron

    2004-04-01

    Mechanisms leading to gene variations are responsible for the diversity of species and are important components of the theory of evolution. One constraint on gene evolution is that of protein foldability; the three-dimensional shapes of proteins must be thermodynamically stable. We explore the impact of this constraint and calculate properties of foldable sequences using 3660 structures from the Protein Data Bank. We seek a selection function that receives sequences as input, and outputs survival probability based on sequence fitness to structure. We compute the number of sequences that match a particular protein structure with energy lower than the native sequence, the density of the number of sequences, the entropy, and the "selection" temperature. The mechanism of structure selection for sequences longer than 200 amino acids is approximately universal. For shorter sequences, it is not. We speculate on concrete evolutionary mechanisms that show this behavior.

  15. The recurrence sequences via Sylvester matrices

    Science.gov (United States)

    Karaduman, Erdal; Deveci, Ömür

    2017-07-01

    In this work, we define the Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by using the Slyvester matrices which are obtained from the characteristic polynomials of the Pell and Jacobsthal sequences and then, we study the sequences defined modulo m. Also, we obtain the cyclic groups and the semigroups from the generating matrices of these sequences when read modulo m and then, we derive the relationships among the orders of the cyclic groups and the periods of the sequences. Furthermore, we redefine Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by means of the elements of the groups and then, we examine them in the finite groups.

  16. ON SOME RECURRENCE TYPE SMARANDACHE SEQUENCES

    OpenAIRE

    MAJUMDAR, A.A.K.; GUNARTO, H.

    2000-01-01

    In this paper, we study some properties of ten recurrence type Smarandache sequences, namely, the Smarandache odd, even, prime product, square product, higher-power product, permutation, consecutive, reverse, symmetric, and pierced chain sequences.

  17. "First generation" automated DNA sequencing technology.

    Science.gov (United States)

    Slatko, Barton E; Kieleczawa, Jan; Ju, Jingyue; Gardner, Andrew F; Hendrickson, Cynthia L; Ausubel, Frederick M

    2011-10-01

    Beginning in the 1980s, automation of DNA sequencing has greatly increased throughput, reduced costs, and enabled large projects to be completed more easily. The development of automation technology paralleled the development of other aspects of DNA sequencing: better enzymes and chemistry, separation and imaging technology, sequencing protocols, robotics, and computational advancements (including base-calling algorithms with quality scores, database developments, and sequence analysis programs). Despite the emergence of high-throughput sequencing platforms, automated Sanger sequencing technology remains useful for many applications. This unit provides background and a description of the "First-Generation" automated DNA sequencing technology. It also includes protocols for using the current Applied Biosystems (ABI) automated DNA sequencing machines. © 2011 by John Wiley & Sons, Inc.

  18. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

    Sheatfish and not EHNV. Generally, mistakes occurred at the ends of the sequences. This can be due to several factors. One is that the sequence has not been trimmed of the sequence primer sites. Another is the lack of quality control of the chromatogram. Finally, sequencing in just one direction can result...... diseases in Europe. As part of the EURL proficiency test for fish diseases it is required to sequence any RANA virus isolates found in any of the samples. It is also highly recommended to sequence the ISA virus to determine whether it be HPRΔ or HPR0. Furthermore, it is recommended that any VHSV and IHNV...... isolates be genotyped. As part of the evaluation of the proficiency results it was decided this year to look into the quality and similarity of the sequence results for selected viruses. Ampoule III in the proficiency test 2013 contained an EHNV isolate. The EURL received 43 sequences from 41 laboratories...

  19. Activated carbon from biomass

    Science.gov (United States)

    Manocha, S.; Manocha, L. M.; Joshi, Parth; Patel, Bhavesh; Dangi, Gaurav; Verma, Narendra

    2013-06-01

    Activated carbon are unique and versatile adsorbents having extended surface area, micro porous structure, universal adsorption effect, high adsorption capacity and high degree of surface reactivity. Activated carbons are synthesized from variety of materials. Most commonly used on a commercial scale are cellulosic based precursors such as peat, coal, lignite wood and coconut shell. Variation occurs in precursors in terms of structure and carbon content. Coir having very low bulk density and porous structure is found to be one of the valuable raw materials for the production of highly porous activated carbon and other important factor is its high carbon content. Exploration of good low cost and non conventional adsorbent may contribute to the sustainability of the environment and offer promising benefits for the commercial purpose in future. Carbonization of biomass was carried out in a horizontal muffle furnace. Both carbonization and activation were performed in inert nitrogen atmosphere in one step to enhance the surface area and to develop interconnecting porosity. The types of biomass as well as the activation conditions determine the properties and the yield of activated carbon. Activated carbon produced from biomass is cost effective as it is easily available as a waste biomass. Activated carbon produced by combination of chemical and physical activation has higher surface area of 2442 m2/gm compared to that produced by physical activation (1365 m2/gm).

  20. Carbon dioxide sensor

    Science.gov (United States)

    Dutta, Prabir K [Worthington, OH; Lee, Inhee [Columbus, OH; Akbar, Sheikh A [Hilliard, OH

    2011-11-15

    The present invention generally relates to carbon dioxide (CO.sub.2) sensors. In one embodiment, the present invention relates to a carbon dioxide (CO.sub.2) sensor that incorporates lithium phosphate (Li.sub.3PO.sub.4) as an electrolyte and sensing electrode comprising a combination of lithium carbonate (Li.sub.2CO.sub.3) and barium carbonate (BaCO.sub.3). In another embodiment, the present invention relates to a carbon dioxide (CO.sub.2) sensor has a reduced sensitivity to humidity due to a sensing electrode with a layered structure of lithium carbonate and barium carbonate. In still another embodiment, the present invention relates to a method of producing carbon dioxide (CO.sub.2) sensors having lithium phosphate (Li.sub.3PO.sub.4) as an electrolyte and sensing electrode comprising a combination of lithium carbonate (Li.sub.2CO.sub.3) and barium carbonate (BaCO.sub.3).

  1. Perfect sequences over the real quaternions

    OpenAIRE

    Kuznetsov, Oleg

    2017-01-01

    In this Thesis, perfect sequences over the real quaternions are first considered. Definitions for the right and left periodic autocorrelation functions are given, and right and left perfect sequences introduced. It is shown that the right (left) perfection of any sequence implies the left (right) perfection, so concepts of right and left perfect sequences over the real quaternions are equivalent. Unitary transformations of the quaternion space ℍ are then considered. Using the equivalence of t...

  2. Information decomposition method to analyze symbolical sequences

    International Nuclear Information System (INIS)

    Korotkov, E.V.; Korotkova, M.A.; Kudryashov, N.A.

    2003-01-01

    The information decomposition (ID) method to analyze symbolical sequences is presented. This method allows us to reveal a latent periodicity of any symbolical sequence. The ID method is shown to have advantages in comparison with application of the Fourier transformation, the wavelet transform and the dynamic programming method to look for latent periodicity. Examples of the latent periods for poetic texts, DNA sequences and amino acids are presented. Possible origin of a latent periodicity for different symbolical sequences is discussed

  3. Parallel sequencing lives, or what makes large sequencing projects successful.

    Science.gov (United States)

    Quilez, Javier; Vidal, Enrique; Dily, François Le; Serra, François; Cuartero, Yasmina; Stadhouders, Ralph; Graf, Thomas; Marti-Renom, Marc A; Beato, Miguel; Filion, Guillaume

    2017-11-01

    T47D_rep2 and b1913e6c1_51720e9cf were 2 Hi-C samples. They were born and processed at the same time, yet their fates were very different. The life of b1913e6c1_51720e9cf was simple and fruitful, while that of T47D_rep2 was full of accidents and sorrow. At the heart of these differences lies the fact that b1913e6c1_51720e9cf was born under a lab culture of Documentation, Automation, Traceability, and Autonomy and compliance with the FAIR Principles. Their lives are a lesson for those who wish to embark on the journey of managing high-throughput sequencing data. © The Author 2017. Published by Oxford University Press.

  4. MatrixPlot: visualizing sequence constraints

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Stærfeldt, Hans Henrik; Lund, Ole

    1999-01-01

    MatrixPlot: visualizing sequence constraints. Sub-title Abstract Summary : MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information...

  5. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

    Þórarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.

    2008-01-01

    Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment me...

  6. DNA sequence modeling based on context trees

    NARCIS (Netherlands)

    Kusters, C.J.; Ignatenko, T.; Roland, J.; Horlin, F.

    2015-01-01

    Genomic sequences contain instructions for protein and cell production. Therefore understanding and identification of biologically and functionally meaningful patterns in DNA sequences is of paramount importance. Modeling of DNA sequences in its turn can help to better understand and identify such

  7. Compact flow diagrams for state sequences

    NARCIS (Netherlands)

    Buchin, K.A.; Buchin, M.E.; Gudmundsson, J.; Horton, M.J.; Sijben, S.

    2016-01-01

    We introduce the concept of compactly representing a large number of state sequences, e.g., sequences of activities, as a flow diagram. We argue that the flow diagram representation gives an intuitive summary that allows the user to detect patterns among large sets of state sequences. Simplified,

  8. Blazar Sequence in Fermi Era Liang Chen

    Indian Academy of Sciences (India)

    Abstract. In this paper, we review the latest research results on the topic of blazar sequence. It seems that the blazar sequence is phenomenally ruled out, while the theoretical blazar sequence still holds. We point out that black hole mass is a dominated parameter accounting for high-power- high-synchrotron-peaked and ...

  9. Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

    Science.gov (United States)

    Tedersoo, Leho; Abarenkov, Kessy; Nilsson, R Henrik; Schüssler, Arthur; Grelet, Gwen-Aëlle; Kohout, Petr; Oja, Jane; Bonito, Gregory M; Veldre, Vilmar; Jairus, Teele; Ryberg, Martin; Larsson, Karl-Henrik; Kõljalg, Urmas

    2011-01-01

    Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.

  10. Accommodation and supply—a dual control on stratigraphic sequences

    Science.gov (United States)

    Schlager, Wolfgang

    1993-07-01

    It is widely accepted that both eustatic and tectonically controlled regional changes of sea level have contributed to the record of stratigraphic sequences. I suggest that environmental change be added as a third, autonomous control. Sedimentologic principles clearly indicate that sequences and their systems tracts are controlled by the interplay of two rates —the rate of change in accommodation (space available for sedimentation) and the rate of sediment supply. Sea level has direct control on accommodation, but its influence on sediment supply is remote and easily overshadowed by environmental factors. For instance, the record of the most recent sea-level rise is a transgressive systems tract where supply is low; it is a prograding highstand systems tract in deltas where the supply is high. Examples of sequence boundaries generated by changes in sediment supply include tectonically driven shifts in sediment input into basins, changes in ocean currents, pulsating supply from failure of submarine slopes and drowning of carbonate platforms by environmental stress. Furthermore, the stratigraphic sequences in fluviatile continental basins are physically removed from sea-level induced changes in accommodation and must have formed by changes in the rate and pattern of supply. Subaerial exposure of marine sediments at the sequence boundary is a most important criterion for recognizing sea level cycles as opposed to supply cycles. Other criteria include downstepping of shelf breaks and characteristic patterns in the spacing of time lines within sequences. Some third-order cycles (ca. 0.5-3 Ma duration) meet these criteria, others do not. Cycle-stacking patterns and the shifting facies belts on cratons indicate that many second- and third-order cycles lack pronounced exposure unconformities and represent gradual changes superimposed on more rapid, shorter oscillations. Seismic data yield poor images of these gradational changes because they lack resolution. Seismic

  11. Creating With Carbon

    Science.gov (United States)

    2003-01-01

    A subsidiary of SI Diamond Technology, Inc., Applied Nanotech, of Austin, Texas, is creating a buzz among various technology firms and venture capital groups interested in the company s progressive research on carbon-related field emission devices, including carbon nanotubes, filaments of pure carbon less than one ten-thousandth the width of human hair. Since their discovery in 1991, carbon nanotubes have gained considerable attention due to their unique physical properties. For example, a single perfect carbon nanotube can range from 10 to 100 times stronger than steel, per unit weight. Recent studies also indicate that the nanotubes may be the best heat-conducting material in existence. These properties, combined with the ease of growing thin films or nanotubes by a variety of deposition techniques, make the carbon-based material one of the most desirable for cold field emission cathodes.

  12. Carbon plasma gun

    International Nuclear Information System (INIS)

    Mendel, C.W. Jr.; Zagar, D.M.; Mills, G.S.; Humphries, S. Jr.; Goldstein, S.A.

    1980-01-01

    A family of plasma guns supplying highly ionized carbon plasma is described. The guns are simple and inexpensive to construct and are pulsed by small capacitor banks of a few hundred joules. The output consists of 10 17 --10 18 multiply ionized carbon ions traveling at about 10 7 cm/s. Neutral output is very low and arrives well after the ionized carbon. The guns and pulsers are very reliable

  13. The global carbon cycle

    International Nuclear Information System (INIS)

    Maier-Reimer, E.

    1991-01-01

    Basic concepts of the global carbon cycle on earth are described; by careful analyses of isotopic ratios, emission history and oceanic ventilation rates are derived, which provide crucial tests for constraining and calibrating models. Effects of deforestation, fertilizing, fossil fuel burning, soil erosion, etc. are quantified and compared, and the oceanic carbon process is evaluated. Oceanic and terrestrial biosphere modifications are discussed and a carbon cycle model is proposed

  14. Forests and carbon storage

    Science.gov (United States)

    Michael G. Ryan

    2008-01-01

    Forests store much carbon and their growth can be a carbon sink if disturbance or harvesting has killed or removed trees or if trees that can now regrow are planted where they did not historically occur. Forests and long-lived wood products currently offset 310 million metric tons of U.S. fossil fuel emissions of carbon--20 percent of the total (Pacala et al. 2007)....

  15. THE INFRARED SPECTRAL PROPERTIES OF MAGELLANIC CARBON STARS

    Energy Technology Data Exchange (ETDEWEB)

    Sloan, G. C. [Cornell Center for Astrophysics and Planetary Science, Cornell Univ., Ithaca, NY 14853-6801 (United States); Kraemer, K. E. [Institute for Scientific Research, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467 (United States); McDonald, I.; Zijlstra, A. A. [Jodrell Bank Centre for Astrophysics, Univ. of Manchester, Manchester M13 9PL (United Kingdom); Groenewegen, M. A. T. [Koninklijke Sterrenwacht van België, Ringlaan 3, B-1180 Brussels (Belgium); Wood, P. R. [Research School of Astronomy and Astrophysics, Australian National University, Canberra, ACT 2611 (Australia); Lagadec, E. [Observatoire de la Côte d’Azur, F-06300, Nice (France); Boyer, M. L. [CRESST and Observational Cosmology Lab, Code 665, NASA Goddard Space Flight Center, Greenbelt, MD, 20771 (United States); Kemper, F.; Srinivasan, S. [Academia Sinica, Institute of Astronomy and Astrophysics, 11F Astronomy-Mathematics Building, NTU/AS, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan, R.O.C. (China); Matsuura, M. [School of Physics and Astronomy, Cardiff University, Queen’s Buildings, The Parade, Cardiff, CF24 3AA (United Kingdom); Sahai, R. [Jet Propulsion Laboratory, California Institute of Technology, MS 183-900, Pasadena, CA 91109 (United States); Sargent, B. A. [Center for Imaging Science and Laboratory for Multiwavelength Astrophysics, Rochester Institute of Technology, 54 Lomb Memorial Drive, Rochester, NY 14623 (United States); Van Loon, J. Th. [Lennard Jones Laboratories, Keele University, Staffordshire ST5 5BG (United Kingdom); Volk, K., E-mail: sloan@isc.astro.cornell.edu [Space Telescope Science Institute, 3700 San Martin Dr., Baltimore, MD 21218 (United States)

    2016-07-20

    The Infrared Spectrograph on the Spitzer Space Telescope observed 184 carbon stars in the Magellanic Clouds. This sample reveals that the dust-production rate (DPR) from carbon stars generally increases with the pulsation period of the star. The composition of the dust grains follows two condensation sequences, with more SiC condensing before amorphous carbon in metal-rich stars, and the order reversed in metal-poor stars. MgS dust condenses in optically thicker dust shells, and its condensation is delayed in more metal-poor stars. Metal-poor carbon stars also tend to have stronger absorption from C{sub 2}H{sub 2} at 7.5 μ m. The relation between DPR and pulsation period shows significant apparent scatter, which results from the initial mass of the star, with more massive stars occupying a sequence parallel to lower-mass stars, but shifted to longer periods. Accounting for differences in the mass distribution between the carbon stars observed in the Small and Large Magellanic Clouds reveals a hint of a subtle decrease in the DPR at lower metallicities, but it is not statistically significant. The most deeply embedded carbon stars have lower variability amplitudes and show SiC in absorption. In some cases they have bluer colors at shorter wavelengths, suggesting that the central star is becoming visible. These deeply embedded stars may be evolving off of the asymptotic giant branch and/or they may have non-spherical dust geometries.

  16. THE INFRARED SPECTRAL PROPERTIES OF MAGELLANIC CARBON STARS

    International Nuclear Information System (INIS)

    Sloan, G. C.; Kraemer, K. E.; McDonald, I.; Zijlstra, A. A.; Groenewegen, M. A. T.; Wood, P. R.; Lagadec, E.; Boyer, M. L.; Kemper, F.; Srinivasan, S.; Matsuura, M.; Sahai, R.; Sargent, B. A.; Van Loon, J. Th.; Volk, K.

    2016-01-01

    The Infrared Spectrograph on the Spitzer Space Telescope observed 184 carbon stars in the Magellanic Clouds. This sample reveals that the dust-production rate (DPR) from carbon stars generally increases with the pulsation period of the star. The composition of the dust grains follows two condensation sequences, with more SiC condensing before amorphous carbon in metal-rich stars, and the order reversed in metal-poor stars. MgS dust condenses in optically thicker dust shells, and its condensation is delayed in more metal-poor stars. Metal-poor carbon stars also tend to have stronger absorption from C 2 H 2 at 7.5 μ m. The relation between DPR and pulsation period shows significant apparent scatter, which results from the initial mass of the star, with more massive stars occupying a sequence parallel to lower-mass stars, but shifted to longer periods. Accounting for differences in the mass distribution between the carbon stars observed in the Small and Large Magellanic Clouds reveals a hint of a subtle decrease in the DPR at lower metallicities, but it is not statistically significant. The most deeply embedded carbon stars have lower variability amplitudes and show SiC in absorption. In some cases they have bluer colors at shorter wavelengths, suggesting that the central star is becoming visible. These deeply embedded stars may be evolving off of the asymptotic giant branch and/or they may have non-spherical dust geometries.

  17. Carbon emissions in China

    International Nuclear Information System (INIS)

    Liu, Zhu

    2016-01-01

    This study analyzes the spatial-temporal pattern and processes of China's energy-related carbon emissions. Based on extensive quantitative analysis, it outlines the character and trajectory of China's energy-related carbon emissions during the period 1995-2010, examining the distribution pattern of China's carbon emissions from regional and sectoral perspectives and revealing the driving factors of China's soaring emission increase. Further, the book investigates the supply chain carbon emissions (the carbon footprints) of China's industrial sectors. Anthropogenic climate change is one of the most serious challenges currently facing humankind. China is the world's largest developing country, top primary energy consumer and carbon emitter. Achieving both economic growth and environmental conservation is the country's twofold challenge. Understanding the status, features and driving forces of China's energy-related carbon emissions is a critical aspect of attaining global sustainability. This work, for the first time, presents both key findings on and a systematic evaluation of China's carbon emissions from energy consumption. The results have important implications for global carbon budgets and burden-sharing with regard to climate change mitigation. The book will be of great interest to readers around the world, as it addresses a topic of truly global significance.

  18. Activated carbon material

    International Nuclear Information System (INIS)

    Evans, A.G.

    1978-01-01

    Activated carbon particles for use as iodine trapping material are impregnated with a mixture of selected iodine and potassium compounds to improve the iodine retention properties of the carbon. The I/K ratio is maintained at less than about 1 and the pH is maintained at above about 8.0. The iodine retention of activated carbon previously treated with or coimpregnated with triethylenediamine can also be improved by this technique. Suitable flame retardants can be added to raise the ignition temperature of the carbon to acceptable standards

  19. Carbon emissions in China

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zhu [Harvard Univ., Cambridge, MA (United States). Sustainability Science Program

    2016-07-01

    This study analyzes the spatial-temporal pattern and processes of China's energy-related carbon emissions. Based on extensive quantitative analysis, it outlines the character and trajectory of China's energy-related carbon emissions during the period 1995-2010, examining the distribution pattern of China's carbon emissions from regional and sectoral perspectives and revealing the driving factors of China's soaring emission increase. Further, the book investigates the supply chain carbon emissions (the carbon footprints) of China's industrial sectors. Anthropogenic climate change is one of the most serious challenges currently facing humankind. China is the world's largest developing country, top primary energy consumer and carbon emitter. Achieving both economic growth and environmental conservation is the country's twofold challenge. Understanding the status, features and driving forces of China's energy-related carbon emissions is a critical aspect of attaining global sustainability. This work, for the first time, presents both key findings on and a systematic evaluation of China's carbon emissions from energy consumption. The results have important implications for global carbon budgets and burden-sharing with regard to climate change mitigation. The book will be of great interest to readers around the world, as it addresses a topic of truly global significance.

  20. Changing global carbon cycle

    International Nuclear Information System (INIS)

    Canadell, Pep

    2007-01-01

    Full text: The increase in atmospheric carbon dioxide (C02) is the single largest human perturbation on the earth's radiative balance contributing to climate change. Its rate of change reflects the balance between anthropogenic carbon emissions and the dynamics of a number of terrestrial and ocean processes that remove or emit C02. It is the long term evolution of this balance that will determine to large extent the speed and magnitude of the human induced climate change and the mitigation requirements to stabilise atmospheric C02 concentrations at any given level. In this talk, we show new trends in global carbon sources and sinks, with particularly focus on major shifts occurring since 2000 when the growth rate of atmospheric C02 has reached its highest level on record. The acceleration in the C02 growth results from the combination of several changes in properties of the carbon cycle, including: acceleration of anthropogenic carbon emissions; increased carbon intensity of the global economy, and decreased efficiency of natural carbon sinks. We discuss in more detail some of the possible causes of the reduced efficiency of natural carbon sinks on land and oceans, such as the decreased net sink in the Southern Ocean and on terrestrial mid-latitudes due to world-wide occurrence of drought. All these changes reported here characterise a carbon cycle that is generating stronger than expected climate forcing, and sooner than expected

  1. Carbon Trading. Literature Overview

    International Nuclear Information System (INIS)

    Kerste, M.; Weda, J.; Rosenboom, N.

    2010-12-01

    From Pigou and Coase to the Kyoto Protocol, carbon trading has resulted in pricing of the negative externalities emanating from pollution. This report highlights leading literature and empirical findings on carbon trading, amongst others addressing the relevant carbon and related markets, the (lack of) success of carbon trading so far and room for improvement as well as its impact on investments in emission reduction. This report is part of a set of SEO-reports on finance and sustainability. The other reports deal with: Financing the Transition to Sustainable Energy; Innovations in financing environmental and social sustainability; and Sustainable investment.

  2. Permutation Entropy for Random Binary Sequences

    Directory of Open Access Journals (Sweden)

    Lingfeng Liu

    2015-12-01

    Full Text Available In this paper, we generalize the permutation entropy (PE measure to binary sequences, which is based on Shannon’s entropy, and theoretically analyze this measure for random binary sequences. We deduce the theoretical value of PE for random binary sequences, which can be used to measure the randomness of binary sequences. We also reveal the relationship between this PE measure with other randomness measures, such as Shannon’s entropy and Lempel–Ziv complexity. The results show that PE is consistent with these two measures. Furthermore, we use PE as one of the randomness measures to evaluate the randomness of chaotic binary sequences.

  3. Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison

    Directory of Open Access Journals (Sweden)

    Saville Barry J

    2007-09-01

    Full Text Available Abstract Background Ustilago maydis is the basidiomycete fungus responsible for common smut of corn and is a model organism for the study of fungal phytopathogenesis. To aid in the annotation of the genome sequence of this organism, several expressed sequence tag (EST libraries were generated from a variety of U. maydis cell types. In addition to utility in the context of gene identification and structure annotation, the ESTs were analyzed to identify differentially abundant transcripts and to detect evidence of alternative splicing and anti-sense transcription. Results Four cDNA libraries were constructed using RNA isolated from U. maydis diploid teliospores (U. maydis strains 518 × 521 and haploid cells of strain 521 grown under nutrient rich, carbon starved, and nitrogen starved conditions. Using the genome sequence as a scaffold, the 15,901 ESTs were assembled into 6,101 contiguous expressed sequences (contigs; among these, 5,482 corresponded to predicted genes in the MUMDB (MIPS Ustilago maydis database, while 619 aligned to regions of the genome not yet designated as genes in MUMDB. A comparison of EST abundance identified numerous genes that may be regulated in a cell type or starvation-specific manner. The transcriptional response to nitrogen starvation was assessed using RT-qPCR. The results of this suggest that there may be cross-talk between the nitrogen and carbon signalling pathways in U. maydis. Bioinformatic analysis identified numerous examples of alternative splicing and anti-sense transcription. While intron retention was the predominant form of alternative splicing in U. maydis, other varieties were also evident (e.g. exon skipping. Selected instances of both alternative splicing and anti-sense transcription were independently confirmed using RT-PCR. Conclusion Through this work: 1 substantial sequence information has been provided for U. maydis genome annotation; 2 new genes were identified through the discovery of 619

  4. Carbon isotope ratios of atmospheric carbon dioxide

    International Nuclear Information System (INIS)

    Sakai, Hitoshi; Kishima, Noriaki; Tsutaki, Yasuhiro.

    1982-01-01

    The delta 13 C values relative to PDB were measured for carbon dioxide in air samples collected at various parts of Japan and at Mauna Loa Observatory, Hawaii in the periods of 1977 and 1978. The delta 13 C values of the ''clean air'' are -7.6 % at Hawaii and -8.1 per mille Oki and Hachijo-jima islands. These values are definitely lighter than the carbon isotope ratios (-6.9 per mille) obtained by Keeling for clean airs collected at Southern California in 1955 to 1956. The increase in 12 C in atmospheric carbon dioxide is attributed to the input of the anthropogenic light carbon dioxides (combustion of fossil fuels etc.) Taking -7.6 per mille to be the isotope ratio of CO 2 in the present clean air, a simple three box model predicts that the biosphere has decreased rather than increased since 1955, implying that it is acting as the doner of carbon rather than the sink. (author)

  5. Fractionation between inorganic and organic carbon during the Lomagundi (2.22 2.1 Ga) carbon isotope excursion

    Science.gov (United States)

    Bekker, A.; Holmden, C.; Beukes, N. J.; Kenig, F.; Eglinton, B.; Patterson, W. P.

    2008-07-01

    The Lomagundi (2.22-2.1 Ga) positive carbon isotope excursion in shallow-marine sedimentary carbonates has been associated with the rise in atmospheric oxygen, but subsequent studies have demonstrated that the carbon isotope excursion was preceded by the rise in atmospheric oxygen. The amount of oxygen released to the exosphere during the Lomagundi excursion is constrained by the average global fractionation between inorganic and organic carbon, which is poorly characterized. Because dissolved inorganic and organic carbon reservoirs were arguably larger in the Paleoproterozoic ocean, at a time of lower solar luminosity and lower ocean redox state, decoupling between these two variables might be expected. We determined carbon isotope values of carbonate and organic matter in carbonates and shales of the Silverton Formation, South Africa and in the correlative Sengoma Argillite Formation, near the border in Botswana. These units were deposited between 2.22 and 2.06 Ga along the margin of the Kaapvaal Craton in an open-marine deltaic setting and experienced lower greenschist facies metamorphism. The prodelta to offshore marine shales are overlain by a subtidal carbonate sequence. Carbonates exhibit elevated 13C values ranging from 8.3 to 11.2‰ vs. VPDB consistent with deposition during the Lomagundi positive excursion. The total organic carbon (TOC) contents range from 0.01 to 0.6% and δ13C values range from - 24.8 to - 13.9‰. Thus, the isotopic fractionation between organic and carbonate carbon was on average 30.3 ± 2.8‰ ( n = 32) in the shallow-marine environment. The underlying Sengoma shales have highly variable TOC contents (0.14 to 21.94%) and δ13C values (- 33.7 to - 20.8‰) with an average of - 27.0 ± 3.0‰ ( n = 50). Considering that the shales were also deposited during the Lomagundi excursion, and taking δ13C values of the overlying carbonates as representative of the δ13C value of dissolved inorganic carbon during shale deposition, a carbon

  6. The 2016 Kumamoto earthquake sequence.

    Science.gov (United States)

    Kato, Aitaro; Nakamura, Kouji; Hiyama, Yohei

    2016-01-01

    Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An M j 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an M j 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest.

  7. Data selector group sequencer interface

    International Nuclear Information System (INIS)

    Zizka, G.; Turko, B.

    1984-01-01

    A CAMAC-based module for high rate data selection and transfer to Tracor Northern TN-1700 multichannel analysis system is described. The module can select any group of 4096 consecutive addresses of events, in the range of 24 bits. This module solves the problem of connecting a number of time digitizing systems to the memory of a multichannel analyzer. Continuous processing rate up to 200,000 events per second along with the live display make the testing of the above systems very efficient and relatively inexpensive. The module also can be programmed for storing the preset group of addresses into more than one section of the memory. The events are analyzed in each section of the memory during the preset time. Multiple spectra can thus be taken automatically in a sequence

  8. A main sequence for quasars

    Science.gov (United States)

    Marziani, Paola; Dultzin, Deborah; Sulentic, Jack W.; Del Olmo, Ascensión; Negrete, C. A.; Martínez-Aldama, Mary L.; D'Onofrio, Mauro; Bon, Edi; Bon, Natasa; Stirpe, Giovanna M.

    2018-03-01

    The last 25 years saw a major step forward in the analysis of optical and UV spectroscopic data of large quasar samples. Multivariate statistical approaches have led to the definition of systematic trends in observational properties that are the basis of physical and dynamical modeling of quasar structure. We discuss the empirical correlates of the so-called “main sequence” associated with the quasar Eigenvector 1, its governing physical parameters and several implications on our view of the quasar structure, as well as some luminosity effects associated with the virialized component of the line emitting regions. We also briefly discuss quasars in a segment of the main sequence that includes the strongest FeII emitters. These sources show a small dispersion around a well-defined Eddington ratio value, a property which makes them potential Eddington standard candles.

  9. The 2016 Kumamoto earthquake sequence

    Science.gov (United States)

    KATO, Aitaro; NAKAMURA, Kouji; HIYAMA, Yohei

    2016-01-01

    Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An Mj 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an Mj 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest. PMID:27725474

  10. A Main Sequence for Quasars

    Directory of Open Access Journals (Sweden)

    Paola Marziani

    2018-03-01

    Full Text Available The last 25 years saw a major step forward in the analysis of optical and UV spectroscopic data of large quasar samples. Multivariate statistical approaches have led to the definition of systematic trends in observational properties that are the basis of physical and dynamical modeling of quasar structure. We discuss the empirical correlates of the so-called “main sequence” associated with the quasar Eigenvector 1, its governing physical parameters and several implications on our view of the quasar structure, as well as some luminosity effects associated with the virialized component of the line emitting regions. We also briefly discuss quasars in a segment of the main sequence that includes the strongest FeII emitters. These sources show a small dispersion around a well-defined Eddington ratio value, a property which makes them potential Eddington standard candles.

  11. RANDNA: a random DNA sequence generator.

    Science.gov (United States)

    Piva, Francesco; Principato, Giovanni

    2006-01-01

    Monte Carlo simulations are useful to verify the significance of data. Genomic regularities, such as the nucleotide correlations or the not uniform distribution of the motifs throughout genomic or mature mRNA sequences, exist and their significance can be checked by means of the Monte Carlo test. The test needs good quality random sequences in order to work, moreover they should have the same nucleotide distribution as the sequences in which the regularities have been found. Random DNA sequences are also useful to estimate the background score of an alignment, that is a threshold below which the resulting score is merely due to chance. We have developed RANDNA, a free software which allows to produce random DNA or RNA sequences setting both their length and the percentage of nucleotide composition. Sequences having the same nucleotide distribution of exonic, intronic or intergenic sequences can be generated. Its graphic interface makes it possible to easily set the parameters that characterize the sequences being produced and saved in a text format file. The pseudo-random number generator function of Borland Delphi 6 is used, since it guarantees a good randomness, a long cycle length and a high speed. We have checked the quality of sequences generated by the software, by means of well-known tests, both by themselves and versus genuine random sequences. We show the good quality of the generated sequences. The software, complete with examples and documentation, is freely available to users from: http://www.introni.it/en/software.

  12. Weathering controls on mechanisms of carbon storage in grassland soils

    Science.gov (United States)

    Masiello, C.A.; Chadwick, O.A.; Southon, J.; Torn, M.S.; Harden, J.W.

    2004-01-01

    On a sequence of soils developed under similar vegetation, temperature, and precipitation conditions, but with variations in mineralogical properties, we use organic carbon and 14C inventories to examine mineral protection of soil organic carbon. In these soils, 14C data indicate that the creation of slow-cycling carbon can be modeled as occurring through reaction of organic ligands with Al3+ and Fe3+ cations in the upper horizons, followed by sorption to amorphous inorganic Al compounds at depth. Only one of these processes, the chelation Al3+ and Fe3+ by organic ligands, is linked to large carbon stocks. Organic ligands stabilized by this process traverse the soil column as dissolved organic carbon (both from surface horizons and root exudates). At our moist grassland site, this chelation and transport process is very strongly correlated with the storage and long-term stabilization of soil organic carbon. Our 14C results show that the mechanisms of organic carbon transport and storage at this site follow a classic model previously believed to only be significant in a single soil order (Spodosols), and closely related to the presence of forests. The presence of this process in the grassland Alfisol, Inceptisol, and Mollisol soils of this chronosequence suggests that this process is a more significant control on organic carbon storage than previously thought. Copyright 2004 by the American Geophysical Union.

  13. Locomotor sequence learning in visually guided walking

    DEFF Research Database (Denmark)

    Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo

    2016-01-01

    walking. In addition, we determined how age (i.e., healthy young adults vs. children) and biomechanical factors (i.e., walking speed) affected the rate and magnitude of locomotor sequence learning. The results showed that healthy young adults (age 24 ± 5 years, N = 20) could learn a specific sequence...... of step lengths over 300 training steps. Younger children (age 6-10 years, N = 8) have lower baseline performance, but their magnitude and rate of sequence learning was the same compared to older children (11-16 years, N = 10) and healthy adults. In addition, learning capacity may be more limited...... to modify step length from one trial to the next. Our sequence learning paradigm is derived from the serial reaction-time (SRT) task that has been used in upper limb studies. Both random and ordered sequences of step lengths were used to measure sequence-specific and sequence non-specific learning during...

  14. The RNA world, automatic sequences and oncogenetics

    Energy Technology Data Exchange (ETDEWEB)

    Tahir Shah, K

    1993-04-01

    We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. (1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. (2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or ``accept`` other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs.

  15. The RNA world, automatic sequences and oncogenetics

    International Nuclear Information System (INIS)

    Tahir Shah, K.

    1993-04-01

    We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. 1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. 2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or 'accept' other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs

  16. Microbially mediated mineral carbonation

    Science.gov (United States)

    Power, I. M.; Wilson, S. A.; Dipple, G. M.; Southam, G.

    2010-12-01

    Mineral carbonation involves silicate dissolution and carbonate precipitation, which are both natural processes that microorganisms are able to mediate in near surface environments (Ferris et al., 1994; Eq. 1). (Ca,Mg)SiO3 + 2H2CO3 + H2O → (Ca,Mg)CO3 + H2O + H4SiO4 + O2 (1) Cyanobacteria are photoautotrophs with cell surface characteristics and metabolic processes involving inorganic carbon that can induce carbonate precipitation. This occurs partly by concentrating cations within their net-negative cell envelope and through the alkalinization of their microenvironment (Thompson & Ferris, 1990). Regions with mafic and ultramafic bedrock, such as near Atlin, British Columbia, Canada, represent the best potential sources of feedstocks for mineral carbonation. The hydromagnesite playas near Atlin are a natural biogeochemical model for the carbonation of magnesium silicate minerals (Power et al., 2009). Field-based studies at Atlin and corroborating laboratory experiments demonstrate the ability of a microbial consortium dominated by filamentous cyanobacteria to induce the precipitation of carbonate minerals. Phototrophic microbes, such as cyanobacteria, have been proposed as a means for producing biodiesel and other value added products because of their efficiency as solar collectors and low requirement for valuable, cultivable land in comparison to crops (Dismukes et al., 2008). Carbonate precipitation and biomass production could be facilitated using specifically designed ponds to collect waters rich in dissolved cations (e.g., Mg2+ and Ca2+), which would allow for evapoconcentration and provide an appropriate environment for growth of cyanobacteria. Microbially mediated carbonate precipitation does not require large quantities of energy or chemicals needed for industrial systems that have been proposed for rapid carbon capture and storage via mineral carbonation (e.g., Lackner et al., 1995). Therefore, this biogeochemical approach may represent a readily

  17. Welding distortion analysis of multipass joint combination with different sequences using 3D FEM and experiment

    International Nuclear Information System (INIS)

    Manurung, Yupiter H.P.; Lidam, Robert Ngendang; Rahim, M. Ridzwan; Zakaria, M. Yusof; Redza, M. Ridhwan; Sulaiman, M. Shahar; Tham, Ghalib; Abas, Sunhaji K.

    2013-01-01

    This paper presents an investigation of the welding sequence effect on induced angular distortion using FEM and experiments. The specimen of a combined joint geometry was modeled and simulated using Multipass Welding Advisor (MWA) in SYSWELD 2010 based on the thermal-elastic-plastic approach with low manganese carbon steel S3355J2G3 as specimen material and Goldak's double ellipsoid as heat source model. To validate the simulation results, a series of experiments was conducted with two different welding sequences using automated welding process, low carbon steel as parent metal, digital GMAW power source with premixed shielding gas and both-sided clamping technique. Based on the results, it was established that the thermo-elastic-plastic 3D FEM analysis shows good agreement with experimental results and the welding sequence “from outside to inside” induced less angular distortion compared to “from inside to outside”. -- Highlights: • 3D FEM was used to analyze the welding distortion on two different sequences. • Simulation results were validated with experiments using automated welding system. • Simulation results and experiments showed acceptable accuracy. • Welding sequence “outside–inside” showed less distortion than “inside–outside”

  18. Sedimentology and sequence stratigraphy of the Lopingian (Late Permian) coal measures in southwestern China

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hao [School of Geosciences and Surveying Engineering, China University of Mining and Technology, Beijing (China); School of Earth and Environment, University of Leeds (United Kingdom); Shao, Longyi; Hao, Liming; Zhang, Pengfei [School of Geosciences and Surveying Engineering, China University of Mining and Technology, Beijing (China); Glasspool, Ian J. [Department of Geology, Field Museum of Natural History, Chicago, Illinois (United States); Wheeley, James R.; Hilton, Jason [School of Geography, Earth and Environmental Sciences, University of Birmingham (United Kingdom); Wignall, Paul B. [School of Earth and Environment, University of Leeds (United Kingdom); Yi, Tongsheng [Guizhou Bureau of Coal Geological Exploration, Guiyang, Guizhou (China); Zhang, Mingquan [Coal Geology and Prospecting Institute of Yunnan Province, Kunming, Yunnan (China)

    2011-01-01

    The Lopingian coal measures of southwestern China were deposited within a range of facies associations spanning a spectrum of settings from fluvial to marine carbonate platform. The transitional to terrestrial coal measures are dominated by siliciclastics, but they also contain fifteen laterally extensive marine bands (limestone beds and mudstone). These bands act as marker horizons that enable correlation between fully marine and terrestrial facies. Examination of this range of facies and their sedimentology has enabled the development of a high-resolution sequence stratigraphic framework. Set against the established backdrop of second-order Lopingian transgression, sixteen fourth-order sequences and three composite sequences (third-order) are recognized. Results show that, in the composite sequences, peat accumulation in the seaward parts of the study area predominantly correlates with early transgressive sequence sets (TSS), while in more landward areas it correlates with the middle TSS to late highstand sequence sets (HSS). Differences in peat-accumulation regimes within the sequence stratigraphic framework are attributed to variations in subsidence and background siliciclastic input rates in different depositional settings, with these combining to produce differences in the rate of accommodation change. The preservation of coal resources in the middle to late HSS in this area was most likely related to the rise of the regional base level throughout the Lopingian. (author)

  19. Carbon Monoxide Information Center

    Medline Plus

    Full Text Available ... main content Languages 简体中文 English Bahasa Indonesia 한국어 Español ภาษาไทย Tiếng Việt Text Size: Decrease Font Increase ... Monoxide Information Center Carbon Monoxide Information Center En Español The Invisible Killer Carbon monoxide, also known as ...

  20. Arctic carbon cycling

    NARCIS (Netherlands)

    Christensen, Torben R; Rysgaard, SØREN; Bendtsen, JØRGEN; Else, Brent; Glud, Ronnie N; van Huissteden, J.; Parmentier, F.J.W.; Sachs, Torsten; Vonk, J.E.

    2017-01-01

    The marine Arctic is considered a net carbon sink, with large regional differences in uptake rates. More regional modelling and observational studies are required to reduce the uncertainty among current estimates. Robust projections for how the Arctic Ocean carbon sink may evolve in the future are

  1. Carbon trading: Literature overview

    NARCIS (Netherlands)

    Kerste, M.; Weda, J.; Rosenboom, N.

    2010-01-01

    From Pigou and Coase to the Kyoto Protocol, carbon trading has resulted in pricing of the negative externalities emanating from pollution. At the request of Duisenberg school of finance, this report highlights leading literature and empirical findings on ‘carbon trading’, amongst others addressing

  2. Amorphous iron (II) carbonate

    DEFF Research Database (Denmark)

    Sel, Ozlem; Radha, A.V.; Dideriksen, Knud

    2012-01-01

    Abstract The synthesis, characterization and crystallization energetics of amorphous iron (II) carbonate (AFC) are reported. AFC may form as a precursor for siderite (FeCO3). The enthalpy of crystallization (DHcrys) of AFC is similar to that of amorphous magnesium carbonate (AMC) and more...

  3. Modeling Carbon Exchange

    Science.gov (United States)

    Sellers, Piers

    2012-01-01

    Model results will be reviewed to assess different methods for bounding the terrestrial role in the global carbon cycle. It is proposed that a series of climate model runs could be scoped that would tighten the limits on the "missing sink" of terrestrial carbon and could also direct future satellite image analyses to search for its geographical location and understand its seasonal dynamics.

  4. Carbon Capture and Storage

    NARCIS (Netherlands)

    Benson, S.M.; Bennaceur, K.; Cook, P.; Davison, J.; Coninck, H. de; Farhat, K.; Ramirez, C.A.; Simbeck, D.; Surles, T.; Verma, P.; Wright, I.

    2012-01-01

    Emissions of carbon dioxide, the most important long-lived anthropogenic greenhouse gas, can be reduced by Carbon Capture and Storage (CCS). CCS involves the integration of four elements: CO 2 capture, compression of the CO2 from a gas to a liquid or a denser gas, transportation of pressurized CO 2

  5. Carbon monoxide poisoning

    Science.gov (United States)

    ... Animals can also be poisoned by carbon monoxide. People who have pets at home may notice that their animals become ... or unresponsive from carbon monoxide exposure. Often the pets will ... these conditions. This can lead to a delay in getting help.

  6. Many Phases of Carbon

    Indian Academy of Sciences (India)

    According to the electronic configuration of a neutral carbon atom, there are only two unpaired .... coke. Further heating this to 2500°C - 3000°C causes an ordering .... The density of these carbon films is around 1.6-. 1.8 glee, which is less than that of graphite. The electrical conductivity of the films prepared depends on the.

  7. Carbon for sensing devices

    CERN Document Server

    Tagliaferro, Alberto

    2015-01-01

    This book reveals why carbon is playing such an increasingly prominent role as a sensing material. The various steps that transform a raw material in a sensing device are thoroughly presented and critically discussed.  The authors deal with all aspects of carbon-based sensors, starting from the various hybridization and allotropes of carbon, with specific focus on micro and nanosized carbons (e.g., carbon nanotubes, graphene) and their growth processes. The discussion then moves to the role of functionalization and the different routes to achieve it. Finally, a number of sensing applications in various fields are presented, highlighting the connection with the basic properties of the various carbon allotropes.  Readers will benefit from this book’s bottom-up approach, which starts from the local bonding in carbon solids and ends with sensing applications, linking the local hybridization of carbon atoms and its modification by functionalization to specific device performance. This book is a must-have in th...

  8. Capacitance for carbon capture

    International Nuclear Information System (INIS)

    Landskron, Kai

    2018-01-01

    Metal recycling: A sustainable, capacitance-assisted carbon capture and sequestration method (Supercapacitive Swing Adsorption) can turn scrap metal and CO 2 into metal carbonates at an attractive energy cost. (copyright 2018 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

  9. Capacitance for carbon capture

    Energy Technology Data Exchange (ETDEWEB)

    Landskron, Kai [Department of Chemistry, Lehigh University, Bethlehem, PA (United States)

    2018-03-26

    Metal recycling: A sustainable, capacitance-assisted carbon capture and sequestration method (Supercapacitive Swing Adsorption) can turn scrap metal and CO{sub 2} into metal carbonates at an attractive energy cost. (copyright 2018 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

  10. Fly ash carbon passivation

    Science.gov (United States)

    La Count, Robert B; Baltrus, John P; Kern, Douglas G

    2013-05-14

    A thermal method to passivate the carbon and/or other components in fly ash significantly decreases adsorption. The passivated carbon remains in the fly ash. Heating the fly ash to about 500 and 800 degrees C. under inert gas conditions sharply decreases the amount of surfactant adsorbed by the fly ash recovered after thermal treatment despite the fact that the carbon content remains in the fly ash. Using oxygen and inert gas mixtures, the present invention shows that a thermal treatment to about 500 degrees C. also sharply decreases the surfactant adsorption of the recovered fly ash even though most of the carbon remains intact. Also, thermal treatment to about 800 degrees C. under these same oxidative conditions shows a sharp decrease in surfactant adsorption of the recovered fly ash due to the fact that the carbon has been removed. This experiment simulates the various "carbon burnout" methods and is not a claim in this method. The present invention provides a thermal method of deactivating high carbon fly ash toward adsorption of AEAs while retaining the fly ash carbon. The fly ash can be used, for example, as a partial Portland cement replacement in air-entrained concrete, in conductive and other concretes, and for other applications.

  11. Targeted assembly of short sequence reads.

    Directory of Open Access Journals (Sweden)

    René L Warren

    Full Text Available As next-generation sequence (NGS production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled stringently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming genomic mutations, polymorphisms, fusions and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly.

  12. Carbon used in electrotechnology

    International Nuclear Information System (INIS)

    Coulon, M.; Reynvaan, C.; Maire, J.

    1994-01-01

    The carbon is the essential or single component of several materials. After having recalled the general properties of carbon and graphite some traditional processes of fabrication are described and some new products are studied then we tackle the applications with electric current: -electrodes in the electric piles where we use the carbon chemical inertia -coals of electric arc where we use the refractory properties and the low resistivity of graphite -Joule effect where we work on an enough wide field of material resistivity -electric fixed or sliding contacts where in addition to the refractory properties it is its unweldability which makes it indispensable particularly in the brooms for electric motors. The future is good for carbon and its compounds particularly for the new discovered fullerenes, spheric molecules of carbon, the properties of which are bad known (supraconductivity, lubrication, energy storage). 21 refs., 26 figs., 14 tab

  13. Carbonate hosted gold deposit in Tasmania, Australia

    International Nuclear Information System (INIS)

    Abadi, M.H.

    1999-01-01

    Full text: This study uses elemental and isotopic composition of carbonates associated with gold from Henty and Beaconsfield in Tasmania, Australia, to illustrate source of gold-bearing fluids, salinity, temperature and dissolution and reprecipitation of carbonate. The Beaconsfield and Henty gold mines are located in northern and western Tasmania respectively. Gold mineralisation in Beaconsfield occurs within the quartz-carbonate Tasmania Reef (Lower to Middle Palaeozoic sequence, Hills, 1998). The Henty gold mine is located at the base of the Cambrian Tyndall Group (volcano-sedimentary succession, White and McPhie, 1996) close to Henty Fault. Gold in carbonate samples from Henty ranges from 7.7 to 9360 ppm and in Beaconsfield ranges from 0.01 to 434 ppm. The amount of carbonate in samples from Henty and Beaconsfield gold mines varies from approximately 24 to 99.8%. Bivariate plot of Ca relative to total amounts of Mg, Fe and Mn illustrates that the major carbonate minerals at Beaconsfield and Henty gold mines are magnesian ankerite and calcite. The difference in carbonate mineralogy, at Henty and Beaconsfield gold mines, is attributed to the composition of fluids responsible for carbonate alteration. Gold and magnesium in Beaconsfield ankerite are derived from the leaching of Cambrian ultramafic rocks during the Devonian by the passage of meteoric fluids through tectonically affected Ordovician carbonates (Rao and Adabi, 1999). The total concentration of Fe and Mn are low (0.5 to 2%) in Henty and high (1 to 17.5%) in Beaconsfield ankerite, possibly due to oxidising conditions at Henty and reducing conditions at Beaconsfield gold mines during gold mineralisation. Variation of Sr values between Beaconsfield ankerite and Henty calcite is related to dissolution of limestone that increase Sr concentrations in gold mineralising fluids. Na values in both Beaconsfield (20 to 1100 ppm) and Henty carbonates (25 to 1650 ppm) suggest low salinity fluids responsible for gold

  14. Carbon-13 NMR characterization of actinyl(VI) carbonate complexes in aqueous solution

    International Nuclear Information System (INIS)

    Clark, D.L.; Hobart, D.E.; Palmer, P.D.; Sullivan, J.C.; Stout, B.E.

    1992-01-01

    The uranyl(VI) carbonate system has been re-examined using 13 C NMR of 99.9% 13 C-enriched U VI O 2 ( 13 CO 3 ) 3 4- in millimolar concentrations. By careful control of carbonate ion concentration, we have confirmed the existence of the trimer, and observed dynamic equilibrium between the monomer and the timer. In addition, the ligand exchange reaction between free and coordinated carbonate on Pu VI O 2 ( 13 CO 3 ) 3 4- and Am VI O 2 ( 13 CO 3 ) 3 4- systems has been examined by variable temperature 13 C NMR line-broadening techniques 13 C NMR line-broadening techniques. A modified Carr-Purcell-Meiboom-Gill NMR pulse sequence was written to allow for experimental determination of ligand exchange parameters for paramagnetic actinide complexes. Preliminary Eyring analysis has provided activation parameters of ΔG double-dagger 295 = 56 kJ/M, ΔH double-dagger = 38 kJ/M, and ΔS double-dagger = -60 J/M-K for the plutonyl triscarbonate system, suggesting an associative transition state for the plutonyl (VI) carbonate complex self-exchange reaction. Experiments for determination of the activation parameters for the americium (VI) carbonate system are in progress

  15. The Contemporary Carbon Cycle

    Science.gov (United States)

    Houghton, R. A.

    2003-12-01

    The global carbon cycle refers to the exchanges of carbon within and between four major reservoirs: the atmosphere, the oceans, land, and fossil fuels. Carbon may be transferred from one reservoir to another in seconds (e.g., the fixation of atmospheric CO2 into sugar through photosynthesis) or over millennia (e.g., the accumulation of fossil carbon (coal, oil, gas) through deposition and diagenesis of organic matter). This chapter emphasizes the exchanges that are important over years to decades and includes those occurring over the scale of months to a few centuries. The focus will be on the years 1980-2000 but our considerations will broadly include the years ˜1850-2100. Chapter 8.09, deals with longer-term processes that involve rates of carbon exchange that are small on an annual timescale (weathering, vulcanism, sedimentation, and diagenesis).The carbon cycle is important for at least three reasons. First, carbon forms the structure of all life on the planet, making up ˜50% of the dry weight of living things. Second, the cycling of carbon approximates the flows of energy around the Earth, the metabolism of natural, human, and industrial systems. Plants transform radiant energy into chemical energy in the form of sugars, starches, and other forms of organic matter; this energy, whether in living organisms or dead organic matter, supports food chains in natural ecosystems as well as human ecosystems, not the least of which are industrial societies habituated (addicted?) to fossil forms of energy for heating, transportation, and generation of electricity. The increased use of fossil fuels has led to a third reason for interest in the carbon cycle. Carbon, in the form of carbon dioxide (CO2) and methane (CH4), forms two of the most important greenhouse gases. These gases contribute to a natural greenhouse effect that has kept the planet warm enough to evolve and support life (without the greenhouse effect the Earth's average temperature would be -33

  16. Pareto optimal pairwise sequence alignment.

    Science.gov (United States)

    DeRonne, Kevin W; Karypis, George

    2013-01-01

    Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

  17. Hierarchically nested river landform sequences

    Science.gov (United States)

    Pasternack, G. B.; Weber, M. D.; Brown, R. A.; Baig, D.

    2017-12-01

    River corridors exhibit landforms nested within landforms repeatedly down spatial scales. In this study we developed, tested, and implemented a new way to create river classifications by mapping domains of fluvial processes with respect to the hierarchical organization of topographic complexity that drives fluvial dynamism. We tested this approach on flow convergence routing, a morphodynamic mechanism with different states depending on the structure of nondimensional topographic variability. Five nondimensional landform types with unique functionality (nozzle, wide bar, normal channel, constricted pool, and oversized) represent this process at any flow. When this typology is nested at base flow, bankfull, and floodprone scales it creates a system with up to 125 functional types. This shows how a single mechanism produces complex dynamism via nesting. Given the classification, we answered nine specific scientific questions to investigate the abundance, sequencing, and hierarchical nesting of these new landform types using a 35-km gravel/cobble river segment of the Yuba River in California. The nested structure of flow convergence routing landforms found in this study revealed that bankfull landforms are nested within specific floodprone valley landform types, and these types control bankfull morphodynamics during moderate to large floods. As a result, this study calls into question the prevailing theory that the bankfull channel of a gravel/cobble river is controlled by in-channel, bankfull, and/or small flood flows. Such flows are too small to initiate widespread sediment transport in a gravel/cobble river with topographic complexity.

  18. Four-electron deoxygenative reductive coupling of carbon monoxide at a single metal site

    Science.gov (United States)

    Buss, Joshua A.; Agapie, Theodor

    2016-01-01

    Carbon dioxide is the ultimate source of the fossil fuels that are both central to modern life and problematic: their use increases atmospheric levels of greenhouse gases, and their availability is geopolitically constrained. Using carbon dioxide as a feedstock to produce synthetic fuels might, in principle, alleviate these concerns. Although many homogeneous and heterogeneous catalysts convert carbon dioxide to carbon monoxide, further deoxygenative coupling of carbon monoxide to generate useful multicarbon products is challenging. Molybdenum and vanadium nitrogenases are capable of converting carbon monoxide into hydrocarbons under mild conditions, using discrete electron and proton sources. Electrocatalytic reduction of carbon monoxide on copper catalysts also uses a combination of electrons and protons, while the industrial Fischer-Tropsch process uses dihydrogen as a combined source of electrons and electrophiles for carbon monoxide coupling at high temperatures and pressures. However, these enzymatic and heterogeneous systems are difficult to probe mechanistically. Molecular catalysts have been studied extensively to investigate the elementary steps by which carbon monoxide is deoxygenated and coupled, but a single metal site that can efficiently induce the required scission of carbon-oxygen bonds and generate carbon-carbon bonds has not yet been documented. Here we describe a molybdenum compound, supported by a terphenyl-diphosphine ligand, that activates and cleaves the strong carbon-oxygen bond of carbon monoxide, enacts carbon-carbon coupling, and spontaneously dissociates the resulting fragment. This complex four-electron transformation is enabled by the terphenyl-diphosphine ligand, which acts as an electron reservoir and exhibits the coordinative flexibility needed to stabilize the different intermediates involved in the overall reaction sequence. We anticipate that these design elements might help in the development of efficient catalysts for

  19. Sequencing intractable DNA to close microbial genomes.

    Directory of Open Access Journals (Sweden)

    Richard A Hurt

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

  20. Sequencing Intractable DNA to Close Microbial Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Hurt, Jr., Richard Ashley [ORNL; Brown, Steven D [ORNL; Podar, Mircea [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL

    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.

  1. Carbon dioxide conversion over carbon-based nanocatalysts.

    Science.gov (United States)

    Khavarian, Mehrnoush; Chai, Siang-Piao; Mohamed, Abdul Rahman

    2013-07-01

    The utilization of carbon dioxide for the production of valuable chemicals via catalysts is one of the efficient ways to mitigate the greenhouse gases in the atmosphere. It is known that the carbon dioxide conversion and product yields are still low even if the reaction is operated at high pressure and temperature. The carbon dioxide utilization and conversion provides many challenges in exploring new concepts and opportunities for development of unique catalysts for the purpose of activating the carbon dioxide molecules. In this paper, the role of carbon-based nanocatalysts in the hydrogenation of carbon dioxide and direct synthesis of dimethyl carbonate from carbon dioxide and methanol are reviewed. The current catalytic results obtained with different carbon-based nanocatalysts systems are presented and how these materials contribute to the carbon dioxide conversion is explained. In addition, different strategies and preparation methods of nanometallic catalysts on various carbon supports are described to optimize the dispersion of metal nanoparticles and catalytic activity.

  2. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    Science.gov (United States)

    de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

  3. cis sequence effects on gene expression

    Directory of Open Access Journals (Sweden)

    Jacobs Kevin

    2007-08-01

    Full Text Available Abstract Background Sequence and transcriptional variability within and between individuals are typically studied independently. The joint analysis of sequence and gene expression variation (genetical genomics provides insight into the role of linked sequence variation in the regulation of gene expression. We investigated the role of sequence variation in cis on gene expression (cis sequence effects in a group of genes commonly studied in cancer research in lymphoblastoid cell lines. We estimated the proportion of genes exhibiting cis sequence effects and the proportion of gene expression variation explained by cis sequence effects using three different analytical approaches, and compared our results to the literature. Results We generated gene expression profiling data at N = 697 candidate genes from N = 30 lymphoblastoid cell lines for this study and used available candidate gene resequencing data at N = 552 candidate genes to identify N = 30 candidate genes with sufficient variance in both datasets for the investigation of cis sequence effects. We used two additive models and the haplotype phylogeny scanning approach of Templeton (Tree Scanning to evaluate association between individual SNPs, all SNPs at a gene, and diplotypes, with log-transformed gene expression. SNPs and diplotypes at eight candidate genes exhibited statistically significant (p cis sequence effects in our study, respectively. Conclusion Based on analysis of our results and the extant literature, one in four genes exhibits significant cis sequence effects, and for these genes, about 30% of gene expression variation is accounted for by cis sequence variation. Despite diverse experimental approaches, the presence or absence of significant cis sequence effects is largely supported by previously published studies.

  4. Multiple tag labeling method for DNA sequencing

    Science.gov (United States)

    Mathies, R.A.; Huang, X.C.; Quesada, M.A.

    1995-07-25

    A DNA sequencing method is described which uses single lane or channel electrophoresis. Sequencing fragments are separated in the lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radioisotope labels. 5 figs.

  5. Exome sequencing and genetic testing for MODY.

    Directory of Open Access Journals (Sweden)

    Stefan Johansson

    Full Text Available Genetic testing for monogenic diabetes is important for patient care. Given the extensive genetic and clinical heterogeneity of diabetes, exome sequencing might provide additional diagnostic potential when standard Sanger sequencing-based diagnostics is inconclusive.The aim of the study was to examine the performance of exome sequencing for a molecular diagnosis of MODY in patients who have undergone conventional diagnostic sequencing of candidate genes with negative results.We performed exome enrichment followed by high-throughput sequencing in nine patients with suspected MODY. They were Sanger sequencing-negative for mutations in the HNF1A, HNF4A, GCK, HNF1B and INS genes. We excluded common, non-coding and synonymous gene variants, and performed in-depth analysis on filtered sequence variants in a pre-defined set of 111 genes implicated in glucose metabolism.On average, we obtained 45 X median coverage of the entire targeted exome and found 199 rare coding variants per individual. We identified 0-4 rare non-synonymous and nonsense variants per individual in our a priori list of 111 candidate genes. Three of the variants were considered pathogenic (in ABCC8, HNF4A and PPARG, respectively, thus exome sequencing led to a genetic diagnosis in at least three of the nine patients. Approximately 91% of known heterozygous SNPs in the target exomes were detected, but we also found low coverage in some key diabetes genes using our current exome sequencing approach. Novel variants in the genes ARAP1, GLIS3, MADD, NOTCH2 and WFS1 need further investigation to reveal their possible role in diabetes.Our results demonstrate that exome sequencing can improve molecular diagnostics of MODY when used as a complement to Sanger sequencing. However, improvements will be needed, especially concerning coverage, before the full potential of exome sequencing can be realized.

  6. Identifying driver mutations in sequenced cancer genomes

    DEFF Research Database (Denmark)

    Raphael, Benjamin J; Dobson, Jason R; Oesper, Layla

    2014-01-01

    High-throughput DNA sequencing is revolutionizing the study of cancer and enabling the measurement of the somatic mutations that drive cancer development. However, the resulting sequencing datasets are large and complex, obscuring the clinically important mutations in a background of errors, nois...... patterns of mutual exclusivity. These techniques, coupled with advances in high-throughput DNA sequencing, are enabling precision medicine approaches to the diagnosis and treatment of cancer....

  7. EGNAS: an exhaustive DNA sequence design algorithm

    Directory of Open Access Journals (Sweden)

    Kick Alfred

    2012-06-01

    Full Text Available Abstract Background The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences. Results The algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented. Conclusions We developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS.

  8. Genome Sequencing and Analysis Conference IV

    Energy Technology Data Exchange (ETDEWEB)

    1993-12-31

    J. Craig Venter and C. Thomas Caskey co-chaired Genome Sequencing and Analysis Conference IV held at Hilton Head, South Carolina from September 26--30, 1992. Venter opened the conference by noting that approximately 400 researchers from 16 nations were present four times as many participants as at Genome Sequencing Conference I in 1989. Venter also introduced the Data Fair, a new component of the conference allowing exchange and on-site computer analysis of unpublished sequence data.

  9. FRESCO: Referential compression of highly similar sequences.

    Science.gov (United States)

    Wandelt, Sebastian; Leser, Ulf

    2013-01-01

    In many applications, sets of similar texts or sequences are of high importance. Prominent examples are revision histories of documents or genomic sequences. Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever-increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, computational requirements for analysis and storage of the sequences are steeply increasing. Compression is a key technology to deal with this challenge. Recently, referential compression schemes, storing only the differences between a to-be-compressed input and a known reference sequence, gained a lot of interest in this field. In this paper, we propose a general open-source framework to compress large amounts of biological sequence data called Framework for REferential Sequence COmpression (FRESCO). Our basic compression algorithm is shown to be one to two orders of magnitudes faster than comparable related work, while achieving similar compression ratios. We also propose several techniques to further increase compression ratios, while still retaining the advantage in speed: 1) selecting a good reference sequence; and 2) rewriting a reference sequence to allow for better compression. In addition,we propose a new way of further boosting the compression ratios by applying referential compression to already referentially compressed files (second-order compression). This technique allows for compression ratios way beyond state of the art, for instance,4,000:1 and higher for human genomes. We evaluate our algorithms on a large data set from three different species (more than 1,000 genomes, more than 3 TB) and on a collection of versions of Wikipedia pages. Our results show that real-time compression of highly similar sequences at high compression ratios is possible on modern hardware.

  10. Responses of Carbon Dynamics to Nitrogen Deposition in Typical Freshwater Wetland of Sanjiang Plain

    Directory of Open Access Journals (Sweden)

    Yang Wang

    2014-01-01

    Full Text Available The effects of nitrogen deposition (N-deposition on the carbon dynamics in typical Calamagrostis angustifolia wetland of Sanjiang Plain were studied by a pot-culture experiment during two continuous plant growing seasons. Elevated atmospheric N-deposition caused significant increases in the aboveground net primary production and root biomass; moreover, a preferential partition of carbon to root was also observed. Different soil carbon fractions gained due to elevated N-deposition and their response intensities followed the sequence of labile carbon > dissolved organic carbon > microbial biomass carbon, and the interaction between N-deposition and flooded condition facilitated the release of different carbon fractions. Positive correlations were found between CO2 and CH4 fluxes and liable carbon contents with N-deposition, and flooded condition also tended to facilitate CH4 fluxes and to inhibit the CO2 fluxes with N-deposition. The increases in soil carbon fractions occurring in the nitrogen treatments were significantly correlated with increases in root, aboveground parts, total biomass, and their carbon uptake. Our results suggested that N-deposition could enhance the contents of active carbon fractions in soil system and carbon accumulation in plant of the freshwater wetlands.

  11. Robustness analysis of chiller sequencing control

    International Nuclear Information System (INIS)

    Liao, Yundan; Sun, Yongjun; Huang, Gongsheng

    2015-01-01

    Highlights: • Uncertainties with chiller sequencing control were systematically quantified. • Robustness of chiller sequencing control was systematically analyzed. • Different sequencing control strategies were sensitive to different uncertainties. • A numerical method was developed for easy selection of chiller sequencing control. - Abstract: Multiple-chiller plant is commonly employed in the heating, ventilating and air-conditioning system to increase operational feasibility and energy-efficiency under part load condition. In a multiple-chiller plant, chiller sequencing control plays a key role in achieving overall energy efficiency while not sacrifices the cooling sufficiency for indoor thermal comfort. Various sequencing control strategies have been developed and implemented in practice. Based on the observation that (i) uncertainty, which cannot be avoided in chiller sequencing control, has a significant impact on the control performance and may cause the control fail to achieve the expected control and/or energy performance; and (ii) in current literature few studies have systematically addressed this issue, this paper therefore presents a study on robustness analysis of chiller sequencing control in order to understand the robustness of various chiller sequencing control strategies under different types of uncertainty. Based on the robustness analysis, a simple and applicable method is developed to select the most robust control strategy for a given chiller plant in the presence of uncertainties, which will be verified using case studies

  12. Multiplexed microsatellite recovery using massively parallel sequencing

    Science.gov (United States)

    Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

  13. Digital Recovery Sequencer - Advanced Concept Ejection Seats

    National Research Council Canada - National Science Library

    Ross, David A; Cotter, Lee; Culhane, David; Press, Matthew J

    2005-01-01

    .... Continued usage of the Analog Sequencer is undesirable due to limitations with respect to its installed life, electronic component obsolescence, flexibility to accommodate seat safety improvements...

  14. Quantitative phenotyping via deep barcode sequencing.

    Science.gov (United States)

    Smith, Andrew M; Heisler, Lawrence E; Mellor, Joseph; Kaper, Fiona; Thompson, Michael J; Chee, Mark; Roth, Frederick P; Giaever, Guri; Nislow, Corey

    2009-10-01

    Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.

  15. Hardware Accelerated Sequence Alignment with Traceback

    Directory of Open Access Journals (Sweden)

    Scott Lloyd

    2009-01-01

    in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.

  16. Multipliers on Generalized Mixed Norm Sequence Spaces

    Directory of Open Access Journals (Sweden)

    Oscar Blasco

    2014-01-01

    Full Text Available Given 1≤p,q≤∞ and sequences of integers (nkk and (nk′k such that nk≤nk′≤nk+1, the generalized mixed norm space ℓℐ(p,q is defined as those sequences (ajj such that ((∑j∈Ik‍|aj|p1/pk∈ℓq where Ik={j∈ℕ0 s.t. nk≤jsequence λ=(λjj to belong to the space of multipliers (ℓℐ(r,s,ℓ(u,v, for different sequences ℐ and of intervals in ℕ0, are determined.

  17. Recursive sequences in first-year calculus

    Science.gov (United States)

    Krainer, Thomas

    2016-02-01

    This article provides ready-to-use supplementary material on recursive sequences for a second-semester calculus class. It equips first-year calculus students with a basic methodical procedure based on which they can conduct a rigorous convergence or divergence analysis of many simple recursive sequences on their own without the need to invoke inductive arguments as is typically required in calculus textbooks. The sequences that are accessible to this kind of analysis are predominantly (eventually) monotonic, but also certain recursive sequences that alternate around their limit point as they converge can be considered.

  18. A measurement of disorder in binary sequences

    Science.gov (United States)

    Gong, Longyan; Wang, Haihong; Cheng, Weiwen; Zhao, Shengmei

    2015-03-01

    We propose a complex quantity, AL, to characterize the degree of disorder of L-length binary symbolic sequences. As examples, we respectively apply it to typical random and deterministic sequences. One kind of random sequences is generated from a periodic binary sequence and the other is generated from the logistic map. The deterministic sequences are the Fibonacci and Thue-Morse sequences. In these analyzed sequences, we find that the modulus of AL, denoted by |AL | , is a (statistically) equivalent quantity to the Boltzmann entropy, the metric entropy, the conditional block entropy and/or other quantities, so it is a useful quantitative measure of disorder. It can be as a fruitful index to discern which sequence is more disordered. Moreover, there is one and only one value of |AL | for the overall disorder characteristics. It needs extremely low computational costs. It can be easily experimentally realized. From all these mentioned, we believe that the proposed measure of disorder is a valuable complement to existing ones in symbolic sequences.

  19. Polynomial sequences generated by infinite Hessenberg matrices

    Directory of Open Access Journals (Sweden)

    Verde-Star Luis

    2017-01-01

    Full Text Available We show that an infinite lower Hessenberg matrix generates polynomial sequences that correspond to the rows of infinite lower triangular invertible matrices. Orthogonal polynomial sequences are obtained when the Hessenberg matrix is tridiagonal. We study properties of the polynomial sequences and their corresponding matrices which are related to recurrence relations, companion matrices, matrix similarity, construction algorithms, and generating functions. When the Hessenberg matrix is also Toeplitz the polynomial sequences turn out to be of interpolatory type and we obtain additional results. For example, we show that every nonderogative finite square matrix is similar to a unique Toeplitz-Hessenberg matrix.

  20. Genomic sequencing of Pleistocene cave bears

    Energy Technology Data Exchange (ETDEWEB)

    Noonan, James P.; Hofreiter, Michael; Smith, Doug; Priest, JamesR.; Rohland, Nadin; Rabeder, Gernot; Krause, Johannes; Detter, J. Chris; Paabo, Svante; Rubin, Edward M.

    2005-04-01

    Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome, the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.

  1. Conducting carbonized polyaniline nanotubes

    International Nuclear Information System (INIS)

    Mentus, Slavko; Ciric-Marjanovic, Gordana; Trchova, Miroslava; Stejskal, Jaroslav

    2009-01-01

    Conducting nitrogen-containing carbon nanotubes were synthesized by the carbonization of self-assembled polyaniline nanotubes protonated with sulfuric acid. Carbonization was carried out in a nitrogen atmosphere at a heating rate of 10 deg. C min -1 up to a maximum temperature of 800 deg. C. The carbonized polyaniline nanotubes which have a typical outer diameter of 100-260 nm, with an inner diameter of 20-170 nm and a length extending from 0.5 to 0.8 μm, accompanied with very thin nanotubes with outer diameters of 8-14 nm, inner diameters 3.0-4.5 nm and length extending from 0.3 to 1.0 μm, were observed by scanning and transmission electron microscopies. Elemental analysis showed 9 wt% of nitrogen in the carbonized product. Conductivity of the nanotubular PANI precursor, amounting to 0.04 S cm -1 , increased to 0.7 S cm -1 upon carbonization. Molecular structure of carbonized polyaniline nanotubes has been analyzed by FTIR and Raman spectroscopies, and their paramagnetic characteristics were compared with the starting PANI nanotubes by EPR spectroscopy.

  2. Conducting carbonized polyaniline nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Mentus, Slavko; Ciric-Marjanovic, Gordana [Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade (Serbia); Trchova, Miroslava; Stejskal, Jaroslav [Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovsky Square 2, 162 06 Prague 6 (Czech Republic)], E-mail: gordana@ffh.bg.ac.rs

    2009-06-17

    Conducting nitrogen-containing carbon nanotubes were synthesized by the carbonization of self-assembled polyaniline nanotubes protonated with sulfuric acid. Carbonization was carried out in a nitrogen atmosphere at a heating rate of 10 deg. C min{sup -1} up to a maximum temperature of 800 deg. C. The carbonized polyaniline nanotubes which have a typical outer diameter of 100-260 nm, with an inner diameter of 20-170 nm and a length extending from 0.5 to 0.8 {mu}m, accompanied with very thin nanotubes with outer diameters of 8-14 nm, inner diameters 3.0-4.5 nm and length extending from 0.3 to 1.0 {mu}m, were observed by scanning and transmission electron microscopies. Elemental analysis showed 9 wt% of nitrogen in the carbonized product. Conductivity of the nanotubular PANI precursor, amounting to 0.04 S cm{sup -1}, increased to 0.7 S cm{sup -1} upon carbonization. Molecular structure of carbonized polyaniline nanotubes has been analyzed by FTIR and Raman spectroscopies, and their paramagnetic characteristics were compared with the starting PANI nanotubes by EPR spectroscopy.

  3. Global carbon inequality

    International Nuclear Information System (INIS)

    Hubacek, Klaus; Baiocchi, Giovanni; Feng, Kuishuang; Munoz Castillo, Raul; Sun, Laixiang; Xue, Jinjun

    2017-01-01

    Global climate change and inequality are inescapably linked both in terms of who contributes climate change and who suffers the consequences. This fact is also partly reflected in two United Nations (UN) processes: on the one hand, the Paris Agreement of the UN Framework Convention on Climate Change under which countries agreed to hold the increase in the global average temperature to below 2 C above pre-industrial levels and, on the other hand, the UN's Sustainable Development Goals aiming to end poverty. These agreements are seen as important foundation to put the world nations on a sustainable pathway. However, how these agreements can be achieved or whether they are even mutually compatible is less clear. We explore the global carbon inequality between and within countries and the carbon implications of poverty alleviation by combining detailed consumer expenditure surveys for different income categories for a wide range of countries with an environmentally extended multi-regional input-output approach to estimate carbon footprints of different household groups, globally, and assess the carbon implications of moving the poorest people out of poverty. Given the current context, increasing income leads to increasing carbon footprints and makes global targets for mitigating greenhouse gases more difficult to achieve given the pace of technological progress and current levels of fossil fuel dependence. We conclude that the huge level of carbon inequality requires a critical discussion of undifferentiated income growth. Current carbon-intensive lifestyles and consumption patterns need to enter the climate discourse to a larger extent. (orig.)

  4. Design of Long Period Pseudo-Random Sequences from the Addition of -Sequences over

    Directory of Open Access Journals (Sweden)

    Ren Jian

    2004-01-01

    Full Text Available Pseudo-random sequence with good correlation property and large linear span is widely used in code division multiple access (CDMA communication systems and cryptology for reliable and secure information transmission. In this paper, sequences with long period, large complexity, balance statistics, and low cross-correlation property are constructed from the addition of -sequences with pairwise-prime linear spans (AMPLS. Using -sequences as building blocks, the proposed method proved to be an efficient and flexible approach to construct long period pseudo-random sequences with desirable properties from short period sequences. Applying the proposed method to , a signal set is constructed.

  5. Carbon Ion Therapy

    DEFF Research Database (Denmark)

    Bassler, Niels; Hansen, David Christoffer; Herrmann, Rochus

    On the importance of choice of target size for selective boosting of hypoxic tumor subvolumina in carbon ion therapy Purpose: Functional imaging methods in radiotherapy are maturing and can to some extent uncover radio resistant structures found within a tumour entity. Selective boost of identified...... effect. All cell lines investigated here did not reach an OER of 1, even for the smaller structures, which may indicate that the achievable dose average LET of carbon ions is too low, and heavier ions than carbon may be considered for functional LET-painting....

  6. Radiolytic carbon gasification

    International Nuclear Information System (INIS)

    Shennan, J.V.

    1980-01-01

    A vast body of knowledge has been accumulated over the past thirty years related to the radiolytic oxidation of the graphite moderator in carbon dioxide cooled Reactors. In the last ten years the dominance of the internal pore structure of the graphite in controlling the rate of carbon gasification has been steadily revealed. The object of this paper is to sift the large body of evidence and show how internal gas composition and hence carbon gasification is controlled by the virgin pore structure and the changes in pore structure brought about by progressive radiolytic oxidation. (author)

  7. Controls on declining carbon balance with leaf age among 10 woody species in Australian woodland: do leaves have zero daily net carbon balances when they die?

    Science.gov (United States)

    Reich, Peter B; Falster, Daniel S; Ellsworth, David S; Wright, Ian J; Westoby, Mark; Oleksyn, Jacek; Lee, Tali D

    2009-01-01

    * Here, we evaluated how increased shading and declining net photosynthetic capacity regulate the decline in net carbon balance with increasing leaf age for 10 Australian woodland species. We also asked whether leaves at the age of their mean life-span have carbon balances that are positive, zero or negative. * The net carbon balances of 2307 leaves on 53 branches of the 10 species were estimated. We assessed three-dimensional architecture, canopy openness, photosynthetic light response functions and dark respiration rate across leaf age sequences on all branches. We used YPLANT to estimate light interception and to model carbon balance along the leaf age sequences. * As leaf age increased to the mean life-span, increasing shading and declining photosynthetic capacity each separately reduced daytime carbon gain by approximately 39% on average across species. Together, they reduced daytime carbon gain by 64% on average across species. * At the age of their mean life-span, almost all leaves had positive daytime carbon balances. These per leaf carbon surpluses were of a similar magnitude to the estimated whole-plant respiratory costs per leaf. Thus, the results suggest that a whole-plant economic framework, including respiratory costs, may be useful in assessing controls on leaf longevity.

  8. Acid mine drainage neutralization in a pilot sequencing batch reactor using limestone from a paper and pulp industry

    CSIR Research Space (South Africa)

    Vadapalli, VRK

    2015-10-01

    Full Text Available This study investigated the implications of using two grades of limestone from a paper and pulp industry for neutralization of acid mine drainage (AMD) in a pilot sequencing batch reactor (SBR). In this regard, two grades of calcium carbonate were...

  9. Sol-gel coatings on carbon/carbon composites

    International Nuclear Information System (INIS)

    Sim, S.M.; Krabill, R.M.; Dalzell, W.J. Jr.; Chu, P.Y.; Clark, D.E.

    1986-01-01

    The need for structural materials that can withstand severe environments up to 4000 0 F has promulgated the investigation of sol-gel derived ceramic and composite coatings on carbon/carbon composite materials. Alumina and zirconia sols have been deposited via thermophoresis on carbon/carbon substrates

  10. Compressing DNA sequence databases with coil

    Directory of Open Access Journals (Sweden)

    Hendy Michael D

    2008-05-01

    Full Text Available Abstract Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

  11. Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

    Directory of Open Access Journals (Sweden)

    Marta Brozynska

    Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

  12. Metabolic diversity and ecological niches of Achromatium populations revealed with single-cell genomic sequencing

    Directory of Open Access Journals (Sweden)

    Muammar eMansor

    2015-08-01

    Full Text Available Large, sulfur-cycling, calcite-precipitating bacteria in the genus Achromatium represent a significant proportion of bacterial communities near sediment-water interfaces throughout the world. Our understanding of their potentially crucial roles in calcium, carbon, sulfur, nitrogen, and iron cycling is limited because they have not been cultured or sequenced using environmental genomics approaches to date. We utilized single-cell genomic sequencing to obtain one incomplete and two nearly complete draft genomes for Achromatium collected at Warm Mineral Springs, FL. Based on 16S rRNA gene sequences, the three cells represent distinct and relatively distant Achromatium populations (91-92% identity. The draft genomes encode key genes involved in sulfur and hydrogen oxidation; oxygen, nitrogen and polysulfide respiration; carbon and nitrogen fixation; organic carbon assimilation and storage; chemotaxis; twitching motility; antibiotic resistance; and membrane transport. Known genes for iron and manganese energy metabolism were not detected. The presence of pyrophosphatase and vacuolar (V-type ATPases, which are generally rare in bacterial genomes, suggests a role for these enzymes in calcium transport, proton pumping, and/or energy generation in the membranes of calcite-containing inclusions.

  13. Hypervelocity technology carbon/carbon testing

    Science.gov (United States)

    Anselmo, John V.; Kretz, Lawrence O.

    The paper describes the procedures used at the Structures Test Laboratory of the Wright Laboratory's Flight Dynamics Directorate to test a carbon/carbon hot structure representing a typical hypersonic gliding body, and presents the results of tests. The forebody was heated to 1371 C over 13 test runs, using radiant quartz lamps; a vertical shear force of 5.34 kN was introduced to the nose at a stabilized temperature of 816 C. Test data were collected using prototype high-temperature strain gages, in-house-designed high-temperature extensometers, conventional strain gages, and thermocouples. Video footage was taken of all test runs. Test runs were successfully completed up to 1371 C with flight typical thermal gradients at heating rates up to 5.56 C/sec. Results showed that, overall, the termal test control systems performed as predicted and that test temperatures and thermal gradients were achieved to within about 5 percent in most cases.

  14. Porous carbons prepared by direct carbonization of MOFs for supercapacitors

    Science.gov (United States)

    Yan, Xinlong; Li, Xuejin; Yan, Zifeng; Komarneni, Sridhar

    2014-07-01

    Three porous carbons were prepared by direct carbonization of HKUST-1, MOF-5 and Al-PCP without additional carbon precursors. The carbon samples obtained by carbonization at 1073 K were characterized by XRD, TEM and N2 physisorption techniques followed by testing for electrochemical performance. The BET surface areas of the three carbons were in the range of 50-1103 m2/g. As electrode materials for supercapacitor, the MOF-5 and Al-PCP derived carbons displayed the ideal capacitor behavior, whereas the HKUST-1 derived carbon showed poor capacitive behavior at various sweep rates and current densities. Among those carbon samples, Al-PCP derived carbons exhibited highest specific capacitance (232.8 F/g) in 30% KOH solution at the current density of 100 mA/g.

  15. Carbon aerogels; Les aerogels de carbone

    Energy Technology Data Exchange (ETDEWEB)

    Berthon-Fabry, S.; Achard, P

    2003-06-15

    The carbon aerogel is a nano-porous material at open porosity, electrical conductor. The aerogels morphology is variable in function of the different synthesis parameters. This characteristic offers to the aerogels a better adaptability to many applications: electrodes (super condensers, fuel cells). The author presents the materials elaboration and their applications. It provides also the research programs: fundamental research, realization of super-condenser electrodes, fuel cells electrodes, gas storage materials and opaque materials for thermal insulation. (A.L.B.)

  16. Carbon Monoxide Information Center

    Medline Plus

    Full Text Available ... Unites States die every year from accidental non-fire related CO poisoning associated with consumer products, including ... CO Blogs Research & Statistics JANUARY 07, 2016 Non-Fire Carbon Monoxide Deaths Associated with the Use of ...

  17. Carbon Monoxide Information Center

    Medline Plus

    Full Text Available ... On Safety Blogs: CO Safety More CO Blogs Research & Statistics JANUARY 07, 2016 Non-Fire Carbon Monoxide ... Related Links Recalls Safety Education Regulations, Laws & Standards Research & Statistics Business & Manufacturing Small Business Resources OnSafety Blogs ...

  18. Clean Carbon Communism

    African Journals Online (AJOL)

    Administrator

    2008-05-07

    May 7, 2008 ... failure are especially dire for the downtrodden masses in the most vulnerable societies. ... that carbon trading has become exceedingly profitable for polluting .... 1 : Energy industries (renewable - / non-renewable sources).

  19. Carbon Monoxide Information Center

    Medline Plus

    Full Text Available ... Community Outreach Resource Center Toy Recall Statistics CO Poster Contest Pool Safely Business & Manufacturing Business & Manufacturing Business ... Featured Resources CPSC announces winners of carbon monoxide poster contest Video View the blog Clues You Can ...

  20. Carbonation of cerium oxychloride

    International Nuclear Information System (INIS)

    Peterson, E.J.; Onstott, E.I.; Bowman, M.G.

    1977-01-01

    Cerous carbonates can be used in thermochemical cycles for H production if the resulting ceric oxides can be converted back into cerous carbonates. One way is to reduce and hydrolyze ceric oxide with HCl to produce CeOCl and then to carbonate it. The reaction 3CeOCl + 3CO 2 + 8H 2 O → CeCl 3 (aq) + Ce 2 (CO 3 ) 3 . 8H 2 O was found to occur in aqueous medium if the final CeCl 3 content is low. Carbonation of CeOCl could also be conducted in acetone --H 2 O . CeClCO 3 . 3H 2 O was decomposed and characterized. The reactions which can be used for water splitting are discussed briefly

  1. Occult carbon monoxide poisoning.

    Science.gov (United States)

    Kirkpatrick, J N

    1987-01-01

    A syndrome of headache, fatigue, dizziness, paresthesias, chest pain, palpitations and visual disturbances was associated with chronic occult carbon monoxide exposure in 26 patients in a primary care setting. A causal association was supported by finding a source of carbon monoxide in a patient's home, workplace or vehicle; results of screening tests that ruled out other illnesses; an abnormally high carboxyhemoglobin level in 11 of 14 patients tested, and abatement or resolution of symptoms when the source of carbon monoxide was removed. Exposed household pets provided an important clue to the diagnosis in some cases. Recurrent occult carbon monoxide poisoning may be a frequently overlooked cause of persistent or recurrent headache, fatigue, dizziness, paresthesias, abdominal pain, diarrhea and unusual spells.

  2. Carbon Monoxide Information Center

    Medline Plus

    Full Text Available ... Import Surveillance International Recall Guidance Civil and Criminal Penalties Federal Court Orders & ... 07, 2016 Non-Fire Carbon Monoxide Deaths Associated with the Use of Consumer Products 2012 ...

  3. From Carbon to Buckypaper

    Indian Academy of Sciences (India)

    hedral, connected by covalent bonds, and forms a 3-dimensional network. The rigid .... increasing number of applications in various sectors [15, 16, 17]. 1. .... [9] Bill Howard, (30 July 2013), BMW i3: Cheap, mass-produced carbon fiber.

  4. Carbon Monoxide Information Center

    Medline Plus

    Full Text Available ... Statistics JANUARY 07, 2016 Non-Fire Carbon Monoxide Deaths Associated with the Use of Consumer Products 2012 Annual Estimates OCTOBER 13, 2015 Incidents, Deaths, and In-Depth Investigations Associated with Non-Fire ...

  5. Carbon Monoxide Information Center

    Medline Plus

    Full Text Available ... Safety Blogs: CO Safety More CO Blogs Research & Statistics JANUARY 07, 2016 Non-Fire Carbon Monoxide Deaths ... 2011 Annual Estimates View All CO-Related Injury Statistics and Technical Reports Related Links Recalls Safety Education ...

  6. Carbon Monoxide Information Center

    Medline Plus

    Full Text Available ... CONSUMER PRODUCT SAFETY COMMISSION Search CPSC Search Menu Home Recalls Recall List CPSC Recall API Recall Lawsuits ... and Bans Report an Unsafe Product Consumers Businesses Home Safety Education Safety Education Centers Carbon Monoxide Information ...

  7. Carbon Monoxide Nonattainment Areas

    Data.gov (United States)

    U.S. Environmental Protection Agency — This data layer identifies areas in the U.S. where air pollution levels have not met the National Ambient Air Quality Standards (NAAQS) for Carbon Monoxide and have...

  8. Step out - Step in Sequencing Games

    NARCIS (Netherlands)

    Musegaas, M.; Borm, P.E.M.; Quant, M.

    2014-01-01

    In this paper a new class of relaxed sequencing games is introduced: the class of Step out - Step in sequencing games. In this relaxation any player within a coalition is allowed to step out from his position in the processing order and to step in at any position later in the processing order.

  9. Step out-step in sequencing games

    NARCIS (Netherlands)

    Musegaas, Marieke; Borm, Peter; Quant, Marieke

    2015-01-01

    In this paper a new class of relaxed sequencing games is introduced: the class of Step out–Step in sequencing games. In this relaxation any player within a coalition is allowed to step out from his position in the processing order and to step in at any position later in the processing order. First,

  10. Enhanced throughput for infrared automated DNA sequencing

    Science.gov (United States)

    Middendorf, Lyle R.; Gartside, Bill O.; Humphrey, Pat G.; Roemer, Stephen C.; Sorensen, David R.; Steffens, David L.; Sutter, Scott L.

    1995-04-01

    Several enhancements have been developed and applied to infrared automated DNA sequencing resulting in significantly higher throughput. A 41 cm sequencing gel (31 cm well- to-read distance) combines high resolution of DNA sequencing fragments with optimized run times yielding two runs per day of 500 bases per sample. A 66 cm sequencing gel (56 cm well-to-read distance) produces sequence read lengths of up to 1000 bases for ds and ss templates using either T7 polymerase or cycle-sequencing protocols. Using a multichannel syringe to load 64 lanes allows 16 samples (compatible with 96-well format) to be visualized for each run. The 41 cm gel configuration allows 16,000 bases per day (16 samples X 500 bases/sample X 2 ten hour runs/day) to be sequenced with the advantages of infrared technology. Enhancements to internal labeling techniques using an infrared-labeled dATP molecule (Boehringer Mannheim GmbH, Penzberg, Germany; Sequenase (U.S. Biochemical) have also been made. The inclusion of glycerol in the sequencing reactions yields greatly improved results for some primer and template combinations. The inclusion of (alpha) -Thio-dNTP's in the labeling reaction increases signal intensity two- to three-fold.

  11. Thread extraction for polyadic instruction sequences

    NARCIS (Netherlands)

    Bergstra, J.; Middelburg, C.

    2011-01-01

    In this paper, we study the phenomenon that instruction sequences are split into fragments which somehow produce a joint behaviour. In order to bring this phenomenon better into the picture, we formalize a simple mechanism by which several instruction sequence fragments can produce a joint

  12. Genome sequence of Lactobacillus rhamnosus ATCC 8530.

    Science.gov (United States)

    Pittet, Vanessa; Ewen, Emily; Bushell, Barry R; Ziola, Barry

    2012-02-01

    Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for probiotics. We became interested in L. rhamnosus isolate ATCC 8530 in relation to beer spoilage and hops resistance. We report here the genome sequence of this isolate, along with a brief comparison to other available L. rhamnosus genome sequences.

  13. Genome Sequence of Lactobacillus rhamnosus ATCC 8530

    OpenAIRE

    Pittet, Vanessa; Ewen, Emily; Bushell, Barry R.; Ziola, Barry

    2012-01-01

    Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for probiotics. We became interested in L. rhamnosus isolate ATCC 8530 in relation to beer spoilage and hops resistance. We report here the genome sequence of this isolate, along with a brief comparison to other available L. rhamnosus genome sequences.

  14. Question-answer sequences in survey interviews

    NARCIS (Netherlands)

    Dijkstra, W.; Ongena, Y.P.

    2006-01-01

    Interaction analysis was used to analyze a total of 14,265 question-answer sequences of (Q-A Sequences) 80 questions that originated from two face-to-face and three telephone surveys. The analysis was directed towards the causes and effects of particular interactional problems. Our results showed

  15. Trace maps for arbitrary substitution sequences

    International Nuclear Information System (INIS)

    Avishai, Y.

    1993-01-01

    The discovery of quasi-crystals and their 1-dimensional modeling have led to a deep mathematical study of Schroedinger operators with an arbitrary deterministic potential sequence. In this work we address this problem and find trace maps for an arbitrary substitution sequence. our trace maps have lower dimensionality than those of Kolar and Nori, which make them quite attractive for actual applications. (authors)

  16. Stochastic modelling of daily rainfall sequences

    NARCIS (Netherlands)

    Buishand, T.A.

    1977-01-01

    Rainfall series of different climatic regions were analysed with the aim of generating daily rainfall sequences. A survey of the data is given in I, 1. When analysing daily rainfall sequences one must be aware of the following points:
    a. Seasonality. Because of seasonal variation

  17. Learning of Sensory Sequences in Cerebellar Patients

    Science.gov (United States)

    Frings, Markus; Boenisch, Raoul; Gerwig, Marcus; Diener, Hans-Christoph; Timmann, Dagmar

    2004-01-01

    A possible role of the cerebellum in detecting and recognizing event sequences has been proposed. The present study sought to determine whether patients with cerebellar lesions are impaired in the acquisition and discrimination of sequences of sensory stimuli of different modalities. A group of 26 cerebellar patients and 26 controls matched for…

  18. On peculiar Šindel sequences

    Czech Academy of Sciences Publication Activity Database

    Křížek, Michal; Somer, L.

    2010-01-01

    Roč. 17, č. 2 (2010), s. 129-140 ISSN 0972-5555 R&D Projects: GA AV ČR(CZ) IAA100190803 Institutional research plan: CEZ:AV0Z10190503 Keywords : quadratic residue * Chinese remainder theorem * primitive Šindel sequences * Prague clock sequence Subject RIV: BA - General Mathematics http://www.pphmj.com/abstract/5095.htm

  19. Protecting genomic sequence anonymity with generalization lattices.

    Science.gov (United States)

    Malin, B A

    2005-01-01

    Current genomic privacy technologies assume the identity of genomic sequence data is protected if personal information, such as demographics, are obscured, removed, or encrypted. While demographic features can directly compromise an individual's identity, recent research demonstrates such protections are insufficient because sequence data itself is susceptible to re-identification. To counteract this problem, we introduce an algorithm for anonymizing a collection of person-specific DNA sequences. The technique is termed DNA lattice anonymization (DNALA), and is based upon the formal privacy protection schema of k -anonymity. Under this model, it is impossible to observe or learn features that distinguish one genetic sequence from k-1 other entries in a collection. To maximize information retained in protected sequences, we incorporate a concept generalization lattice to learn the distance between two residues in a single nucleotide region. The lattice provides the most similar generalized concept for two residues (e.g. adenine and guanine are both purines). The method is tested and evaluated with several publicly available human population datasets ranging in size from 30 to 400 sequences. Our findings imply the anonymization schema is feasible for the protection of sequences privacy. The DNALA method is the first computational disclosure control technique for general DNA sequences. Given the computational nature of the method, guarantees of anonymity can be formally proven. There is room for improvement and validation, though this research provides the groundwork from which future researchers can construct genomics anonymization schemas tailored to specific datasharing scenarios.

  20. Occupational Sequences: Auto Engines 1. AT 121.

    Science.gov (United States)

    Korb, A. W.; And Others

    In an attempt to individualize an automotive course, the Vocational-Technical Division of Northern Montana College has developed Occupational Sequences for an engine rebuilding course. Occupational Sequences, a learning or teaching aid, is an analysis of numbered operations involved in engine rebuilding. Job sheets, included in the book, provide a…

  1. Sequencing Events: Exploring Art and Art Jobs.

    Science.gov (United States)

    Stephens, Pamela Geiger; Shaddix, Robin K.

    2000-01-01

    Presents an activity for upper-elementary students that correlates the actions of archaeologists, patrons, and artists with the sequencing of events in a logical order. Features ancient Egyptian art images. Discusses the preparation of materials, motivation, a pre-writing activity, and writing a story in sequence. (CMK)

  2. Wijsman Orlicz Asymptotically Ideal -Statistical Equivalent Sequences

    Directory of Open Access Journals (Sweden)

    Bipan Hazarika

    2013-01-01

    in Wijsman sense and present some definitions which are the natural combination of the definition of asymptotic equivalence, statistical equivalent, -statistical equivalent sequences in Wijsman sense. Finally, we introduce the notion of Cesaro Orlicz asymptotically -equivalent sequences in Wijsman sense and establish their relationship with other classes.

  3. Nitrogen chronology of massive main sequence stars

    NARCIS (Netherlands)

    Köhler, K.; Borzyszkowski, M.; Brott, I.; Langer, N.; de Koter, A.

    2012-01-01

    Context. Rotational mixing in massive main sequence stars is predicted to monotonically increase their surface nitrogen abundance with time. Aims. We use this effect to design a method for constraining the age and the inclination angle of massive main sequence stars, given their observed luminosity,

  4. Massively parallel sequencing of forensic STRs

    DEFF Research Database (Denmark)

    Parson, Walther; Ballard, David; Budowle, Bruce

    2016-01-01

    The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that...

  5. Novel algorithms for protein sequence analysis

    NARCIS (Netherlands)

    Ye, Kai

    2008-01-01

    Each protein is characterized by its unique sequential order of amino acids, the so-called protein sequence. Biology”s paradigm is that this order of amino acids determines the protein”s architecture and function. In this thesis, we introduce novel algorithms to analyze protein sequences. Chapter 1

  6. Cyprinus carpio Genome sequencing and assembly

    NARCIS (Netherlands)

    Kolder, I.C.R.M.; Plas-Duivesteijn, van der Suzanne J.; Tan, G.; Wiegertjes, G.; Forlenza, M.; Guler, A.T.; Travin, D.Y.; Nakao, M.; Moritomo, T.; Irnazarow, I.; Jansen, H.J.

    2013-01-01

    Sequencing of the common carp (Cyprinus carpio carpio Linnaeus, 1758) genome, with the objective of establishing carp as a model organism to supplement the closely related zebrafish (Danio rerio). The sequenced individual is a homozygous female (by gynogenesis) of R3 x R8 carp, the heterozygous

  7. Sequence Comparison: Close and Open problems

    NARCIS (Netherlands)

    Lenzini, Gabriele; Cerrai, P.; Freguglia, P.

    Comparing sequences is a very important activity both in computer science and in a many other areas as well. For example thank to text editors, everyone knows the particular instance of a sequence comparison problem knonw as ``string mathcing problem''. It consists in searching a given work

  8. Pig genome sequence - analysis and publication strategy

    DEFF Research Database (Denmark)

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

    2010-01-01

    preferentially selected for sequencing. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement the data have been released into public sequence repositories (Genbank/EMBL, NCBI/Ensembl trace repositories) in a timely manner and in advance of publication. CONCLUSIONS...

  9. Swab-to-Sequence: Real-time Data Analysis Platform for the Biomolecule Sequencer

    Data.gov (United States)

    National Aeronautics and Space Administration — DNA was successfully sequenced on the ISS in 2016, but the DNA sequenced was prepared on the ground. With FY’16 IRAD funds, the same team developed a...

  10. From Sequence to Morphology - Long-Range Correlations in Complete Sequenced Genomes

    NARCIS (Netherlands)

    T.A. Knoch (Tobias)

    2004-01-01

    textabstractThe largely unresolved sequential organization, i.e. the relations within DNA sequences, and its connection to the three-dimensional organization of genomes was investigated by correlation analyses of completely sequenced chromosomes from Viroids, Archaea, Bacteria, Arabidopsis

  11. Applications for alliform carbon

    Energy Technology Data Exchange (ETDEWEB)

    Gogotsi, Yury; Mochalin, Vadym; McDonough, IV, John Kenneth; Simon, Patrice; Taberna, Pierre Louis

    2017-02-21

    This invention relates to novel applications for alliform carbon, useful in conductors and energy storage devices, including electrical double layer capacitor devices and articles incorporating such conductors and devices. Said alliform carbon particles are in the range of 2 to about 20 percent by weight, relative to the weight of the entire electrode. Said novel applications include supercapacitors and associated electrode devices, batteries, bandages and wound healing, and thin-film devices, including display devices.

  12. Occult Carbon Monoxide Poisoning

    OpenAIRE

    Kirkpatrick, John N.

    1987-01-01

    A syndrome of headache, fatigue, dizziness, paresthesias, chest pain, palpitations and visual disturbances was associated with chronic occult carbon monoxide exposure in 26 patients in a primary care setting. A causal association was supported by finding a source of carbon monoxide in a patient's home, workplace or vehicle; results of screening tests that ruled out other illnesses; an abnormally high carboxyhemoglobin level in 11 of 14 patients tested, and abatement or resolution of symptoms ...

  13. States and carbon

    International Nuclear Information System (INIS)

    Criqui, Patrick; Faraco, Benoit; Grandjean, Alain

    2009-01-01

    The climate challenge appeals to an unprecedented mutation of our societies. From north to south, all our life styles will have to be changed from dwelling, to transport and feeding. These changes will have sense only at a worldwide scale and will impact our way of development. How can we reduce our energy consumption and greenhouse impact with answering everyone's essential needs at the same time? How can we invent a carbon-free economy in the North and preserve the big socio-economical equilibria at the same time? How can we get rid of poverty in the South without compromising the well-being of the future generations with an increase of CO 2 emissions? Such difficulties cannot be overcome without innovations in terms of public policies. This book takes stock of the new possible instruments and policies at the global scale and involving fiscality, standards, investments and social justice. Content: 1 - the carbon threat: a changing climate and energies becoming scarce (the climate threat, an increasing energy insecurity); carbon and modern economy (human greenhouse gas emissions, a carbon-free well-being); governments and carbon control (a global challenge requiring an international control, the experiments era from Rio to the present day, the challenge of the state in front of the carbon threat); 2 - the political instruments of environment: standards as first instruments of climate public policies (standards efficiency in some sectors, standards limitations, standards and innovation); emissions quotas and market instruments (Kyoto protocol and CO 2 market, the future of 'cap and trade' and of individual and regional quotas); carbon tax, fiscal instruments and new regulations (carbon tax as an alternative or a complement, other fiscal and para-fiscal instruments, new regulation instruments); investing in climate (managing the transition, governments as transition administrators). (J.S)

  14. Tradeable carbon permits

    International Nuclear Information System (INIS)

    Koutstaal, P.R.

    1995-01-01

    The research project on tradeable carbon permits has focused on three elements. First of all, the practical implications of designing a system of tradeable emission permits for reducing CO2 has been studied. In the second part, the consequences of introducing a system of tradeable carbon permits for entry barriers have been considered. Finally, the institutional requirements and welfare effects of coordination of CO2 abatement in a second-best world have been examined

  15. Complete genome sequence of Halanaerobium praevalens type strain (GSLT)

    Energy Technology Data Exchange (ETDEWEB)

    Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Chertkov, Olga [Los Alamos National Laboratory (LANL); Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kannan, K. Palani [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute

    2011-01-01

    Halanaerobium praevalens Zeikus et al. 1984 is the type species of the genus Halanaero- bium, which in turn is the type genus of the family Halanaerobiaceae. The species is of inter- est because it is able to reduce a variety of nitro-substituted aromatic compounds at a high rate, and because of its ability to degrade organic pollutants. The strain is also of interest be- cause it functions as a hydrolytic bacterium, fermenting complex organic matter and produc- ing intermediary metabolites for other trophic groups such as sulfate-reducing and methano- genic bacteria. It is further reported as being involved in carbon removal in the Great Salt Lake, its source of isolation. This is the first completed genome sequence of a representative of the genus Halanaerobium and the second genome sequence from a type strain of the fami- ly Halanaerobiaceae. The 2,309,262 bp long genome with its 2,110 protein-coding and 70 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  16. Complete genome sequence of Rhodospirillum rubrum type strain (S1).

    Science.gov (United States)

    Munk, A Christine; Copeland, Alex; Lucas, Susan; Lapidus, Alla; Del Rio, Tijana Glavina; Barry, Kerrie; Detter, John C; Hammon, Nancy; Israni, Sanjay; Pitluck, Sam; Brettin, Thomas; Bruce, David; Han, Cliff; Tapia, Roxanne; Gilna, Paul; Schmutz, Jeremy; Larimer, Frank; Land, Miriam; Kyrpides, Nikos C; Mavromatis, Konstantinos; Richardson, Paul; Rohde, Manfred; Göker, Markus; Klenk, Hans-Peter; Zhang, Yaoping; Roberts, Gary P; Reslewic, Susan; Schwartz, David C

    2011-07-01

    Rhodospirillum rubrum (Esmarch 1887) Molisch 1907 is the type species of the genus Rhodospirillum, which is the type genus of the family Rhodospirillaceae in the class Alphaproteobacteria. The species is of special interest because it is an anoxygenic phototroph that produces extracellular elemental sulfur (instead of oxygen) while harvesting light. It contains one of the most simple photosynthetic systems currently known, lacking light harvesting complex 2. Strain S1(T) can grow on carbon monoxide as sole energy source. With currently over 1,750 PubMed entries, R. rubrum is one of the most intensively studied microbial species, in particular for physiological and genetic studies. Next to R. centenum strain SW, the genome sequence of strain S1(T) is only the second genome of a member of the genus Rhodospirillum to be published, but the first type strain genome from the genus. The 4,352,825 bp long chromosome and 53,732 bp plasmid with a total of 3,850 protein-coding and 83 RNA genes were sequenced as part of the DOE Joint Genome Institute Program DOEM 2002.

  17. Comprehensive Genetic Database of Expressed Sequence Tags for Coccolithophorids

    Science.gov (United States)

    Ranji, Mohammad; Hadaegh, Ahmad R.

    Coccolithophorids are unicellular, marine, golden-brown, single-celled algae (Haptophyta) commonly found in near-surface waters in patchy distributions. They belong to the Phytoplankton family that is known to be responsible for much of the earth reproduction. Phytoplankton, just like plants live based on the energy obtained by Photosynthesis which produces oxygen. Substantial amount of oxygen in the earth's atmosphere is produced by Phytoplankton through Photosynthesis. The single-celled Emiliana Huxleyi is the most commonly known specie of Coccolithophorids and is known for extracting bicarbonate (HCO3) from its environment and producing calcium carbonate to form Coccoliths. Coccolithophorids are one of the world's primary producers, contributing about 15% of the average oceanic phytoplankton biomass to the oceans. They produce elaborate, minute calcite platelets (Coccoliths), covering the cell to form a Coccosphere and supplying up to 60% of the bulk pelagic calcite deposited on the sea floors. In order to understand the genetics of Coccolithophorid and the complexities of their biochemical reactions, we decided to build a database to store a complete profile of these organisms' genomes. Although a variety of such databases currently exist, (http://www.geneservice.co.uk/home/) none have yet been developed to comprehensively address the sequencing efforts underway by the Coccolithophorid research community. This database is called CocooExpress and is available to public (http://bioinfo.csusm.edu) for both data queries and sequence contribution.

  18. Complete genome sequence of Desulfomicrobium baculatum type strain (XT)

    Energy Technology Data Exchange (ETDEWEB)

    Copeland, Alex; Spring, Stefan; Goker, Markus; Schneider, Susanne; Lapidus, Alla; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C; Meincke, Linda; Sims, David; Brettin, Thomas; Detter, John C; Han, Cliff; Chain, Patrick; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C; Lucas, Susan

    2009-05-20

    Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain XT is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6percent (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  19. Nucleotide sequence preservation of human mitochondrial DNA

    International Nuclear Information System (INIS)

    Monnat, R.J. Jr.; Loeb, L.A.

    1985-01-01

    Recombinant DNA techniques have been used to quantitate the amount of nucleotide sequence divergence in the mitochondrial DNA population of individual normal humans. Mitochondrial DNA was isolated from the peripheral blood lymphocytes of five normal humans and cloned in M13 mp11; 49 kilobases of nucleotide sequence information was obtained from 248 independently isolated clones from the five normal donors. Both between- and within-individual differences were identified. Between-individual differences were identified in approximately = to 1/200 nucleotides. In contrast, only one within-individual difference was identified in 49 kilobases of nucleotide sequence information. This high degree of mitochondrial nucleotide sequence homogeneity in human somatic cells is in marked contrast to the rapid evolutionary divergence of human mitochondrial DNA and suggests the existence of mechanisms for the concerted preservation of mammalian mitochondrial DNA sequences in single organisms

  20. Snake Genome Sequencing: Results and Future Prospects.

    Science.gov (United States)

    Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K

    2016-12-01

    Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  1. Sequencing Cyclic Peptides by Multistage Mass Spectrometry

    Science.gov (United States)

    Mohimani, Hosein; Yang, Yu-Liang; Liu, Wei-Ting; Hsieh, Pei-Wen; Dorrestein, Pieter C.; Pevzner, Pavel A.

    2012-01-01

    Some of the most effective antibiotics (e.g., Vancomycin and Daptomycin) are cyclic peptides produced by non-ribosomal biosynthetic pathways. While hundreds of biomedically important cyclic peptides have been sequenced, the computational techniques for sequencing cyclic peptides are still in their infancy. Previous methods for sequencing peptide antibiotics and other cyclic peptides are based on Nuclear Magnetic Resonance spectroscopy, and require large amount (miligrams) of purified materials that, for most compounds, are not possible to obtain. Recently, development of mass spectrometry based methods has provided some hope for accurate sequencing of cyclic peptides using picograms of materials. In this paper we develop a method for sequencing of cyclic peptides by multistage mass spectrometry, and show its advantages over single stage mass spectrometry. The method is tested on known and new cyclic peptides from Bacillus brevis, Dianthus superbus and Streptomyces griseus, as well as a new family of cyclic peptides produced by marine bacteria. PMID:21751357

  2. Snake Genome Sequencing: Results and Future Prospects

    Directory of Open Access Journals (Sweden)

    Harald M. I. Kerkkamp

    2016-12-01

    Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  3. Sequencing and comparing whole mitochondrial genomes ofanimals

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  4. Carbon based prosthetic devices

    Energy Technology Data Exchange (ETDEWEB)

    Devlin, D.J.; Carroll, D.W.; Barbero, R.S.; Archuleta, T. [Los Alamos National Lab., NM (US); Klawitter, J.J.; Ogilvie, W.; Strzepa, P. [Ascension Orthopedics (US); Cook, S.D. [Tulane Univ., New Orleans, LA (US). School of Medicine

    1998-12-31

    This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The project objective was to evaluate the use of carbon/carbon-fiber-reinforced composites for use in endoprosthetic devices. The application of these materials for the metacarpophalangeal (MP) joints of the hand was investigated. Issues concerning mechanical properties, bone fixation, biocompatibility, and wear are discussed. A system consisting of fiber reinforced materials with a pyrolytic carbon matrix and diamond-like, carbon-coated wear surfaces was developed. Processes were developed for the chemical vapor infiltration (CVI) of pyrolytic carbon into porous fiber preforms with the ability to tailor the outer porosity of the device to provide a surface for bone in-growth. A method for coating diamond-like carbon (DLC) on the articulating surface by plasma-assisted chemical vapor deposition (CVD) was developed. Preliminary results on mechanical properties of the composite system are discussed and initial biocompatibility studies were performed.

  5. Recent development of carbon nanotube

    Energy Technology Data Exchange (ETDEWEB)

    Yamabe, Tokio [Div. of Molecular Engineering, Kyoto Univ. (Japan); [Inst. for Fundamental Chemistry, Kyoto (Japan)

    1995-03-15

    Recent developments of carbon nanotubes are reviewed. Analytical solutions for the electronic structure of carbon nanotube on the basis of thight-binding approximation are presented and interpreted using the concepts of crystal orbital. The electronic properties of actual carbon nanotubes are presented. The electronic structures of carbon nanotubes in the presence of magnetic fiels are also summerized. (orig.)

  6. Method for synthesizing carbon nanotubes

    Science.gov (United States)

    Fan, Hongyou

    2012-09-04

    A method for preparing a precursor solution for synthesis of carbon nanomaterials, where a polar solvent is added to at least one block copolymer and at least one carbohydrate compound, and the precursor solution is processed using a self-assembly process and subsequent heating to form nanoporous carbon films, porous carbon nanotubes, and porous carbon nanoparticles.

  7. Carbon allocation in forest ecosystems

    Science.gov (United States)

    Creighton M. Litton; James W. Raich; Michael G. Ryan

    2007-01-01

    Carbon allocation plays a critical role in forest ecosystem carbon cycling. We reviewed existing literature and compiled annual carbon budgets for forest ecosystems to test a series of hypotheses addressing the patterns, plasticity, and limits of three components of allocation: biomass, the amount of material present; flux, the flow of carbon to a component per unit...

  8. Carbon dioxide as chemical feedstock

    National Research Council Canada - National Science Library

    Aresta, M

    2010-01-01

    ... Dioxide as an Inert Solvent for Chemical Syntheses 15 Alessandro Galia and Giuseppe Filardo Introduction 15 Dense Carbon Dioxide as Solvent Medium for Chemical Processes 15 Enzymatic Catalysis in Dense Carbon Dioxide 18 Other Reactions in Dense Carbon Dioxide 19 Polymer Synthesis in Supercritical Carbon Dioxide 20 Chain Polymerizations: Synt...

  9. Divide and conquer: enriching environmental sequencing data.

    Directory of Open Access Journals (Sweden)

    Anne Bergeron

    2007-09-01

    Full Text Available In environmental sequencing projects, a mix of DNA from a whole microbial community is fragmented and sequenced, with one of the possible goals being to reconstruct partial or complete genomes of members of the community. In communities with high diversity of species, a significant proportion of the sequences do not overlap any other fragment in the sample. This problem will arise not only in situations with a relatively even distribution of many species, but also when the community in a particular environment is routinely dominated by the same few species. In the former case, no genomes may be assembled at all, while in the latter case a few dominant species in an environment will always be sequenced at high coverage to the detriment of coverage of the greater number of sparse species.Here we show that, with the same global sequencing effort, separating the species into two or more sub-communities prior to sequencing can yield a much higher proportion of sequences that can be assembled. We first use the Lander-Waterman model to show that, if the expected percentage of singleton sequences is higher than 25%, then, under the uniform distribution hypothesis, splitting the community is always a wise choice. We then construct simulated microbial communities to show that the results hold for highly non-uniform distributions. We also show that, for the distributions considered in the experiments, it is possible to estimate quite accurately the relative diversity of the two sub-communities.Given the fact that several methods exist to split microbial communities based on physical properties such as size, density, surface biochemistry, or optical properties, we strongly suggest that groups involved in environmental sequencing, and expecting high diversity, consider splitting their communities in order to maximize the information content of their sequencing effort.

  10. Lower Cretaceous paleo-Vertisols and sedimentary interrelationships in stacked alluvial sequences, Utah, USA

    Science.gov (United States)

    Joeckel, R. M.; Ludvigson, G. A.; Kirkland, J. I.

    2017-11-01

    The Yellow Cat Member of the Cedar Mountain Formation in Poison Strip, Utah, USA, consists of stacked, erosionally bounded alluvial sequences dominated by massive mudstones (lithofacies Fm) with paleo-Vertisols. Sediment bodies within these sequences grade vertically and laterally into each other at pedogenic boundaries, across which color, texture, and structures (sedimentary vs. pedogenic) change. Slickensides, unfilled (sealed) cracks, carbonate-filled cracks, and deeper cracks filled with sandstone; the latter features suggest thorough desiccation during aridification. Thin sandstones (Sms) in some sequences, typically as well as laminated to massive mudstones (Flm) with which they are interbedded in some cases, are interpreted as avulsion deposits. The termini of many beds of these lithofacies curve upward, parallel to nearby pedogenic slickensides, as the features we call ;turnups.; Turnups are overlain or surrounded by paleosols, but strata sheltered underneath beds with turnups retain primary sedimentary fabrics. Turnups were produced by movement along slickensides during pedogenesis, by differential compaction alongside pre-existing gilgai microhighs, or by a combination of both. Palustrine carbonates (lithofacies C) appear only in the highest or next-highest alluvial sequences, along with a deep paleo-Vertisol that exhibits partially preserved microrelief at the base of the overlying Poison Strip Member. The attributes of the Yellow Cat Member suggest comparatively low accommodation, slow accumulation, long hiatuses in clastic sedimentation, and substantial time intervals of subaerial exposure and pedogenesis; it appears to be distinct among the members of the Cedar Mountain Formation in these respects.

  11. Sequence Matters but How Exactly? A Method for Evaluating Activity Sequences from Data

    Science.gov (United States)

    Doroudi, Shayan; Holstein, Kenneth; Aleven, Vincent; Brunskill, Emma

    2016-01-01

    How should a wide variety of educational activities be sequenced to maximize student learning? Although some experimental studies have addressed this question, educational data mining methods may be able to evaluate a wider range of possibilities and better handle many simultaneous sequencing constraints. We introduce Sequencing Constraint…

  12. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    DEFF Research Database (Denmark)

    de Souza, S J; Camargo, A A; Briones, M R

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central ...

  13. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

    Science.gov (United States)

    Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

    2017-07-01

    PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

  14. Biostratigraphy and sequence stratigraphy of the Sarvak Formation at Fahliyan Anticline (South of Yasuj)

    International Nuclear Information System (INIS)

    Ahmadi, A.; Vaziri-Moghaddam, A.; Sayrafian, A.; Taheri, A.

    2016-01-01

    In this study, bio stratigraphy, depositional environment and sequence stratigraphy of the Sarvak Formation at Fahliyan Anticline was studied. 8 species of benthic foraminifera (4 genera) and 8 species of planktonic foraminifera (11 genera) in the study area were recognized. 6 biozones have been recognized by distribution of the foraminifera, which in stratigraphic order are: Favusella washitensis Zone, Orbitolina-Alveolinids Assemblage Zone, Rudist debris Zone, Oligostegina flood Zone, Whiteinella archaeocretacea Zone and Helvetoglobotruncana helvetica Zone. On the basis of these, the age of Albian–Turonian was considered for the Sarvak Formation. Based on petrography and analysis of microfacies features 9 different microfacies types have been recognized, which can be grouped into 3 depositional environments: lagoon, shoal and open marine. The Sarvak Formation represents sedimentation on a carbonate ramp. Sequence stratigraphy analysis led to identification of 4 third-order sequences.

  15. Carbon Monoxide Poisoning

    Directory of Open Access Journals (Sweden)

    Kamal Mishra

    2016-01-01

    Full Text Available Introduction: Carbon monoxide is known as the silent killer, being colorless, odourless, and tasteless. Initially non-irritating, it is very difficult for people to detect Carbon monoxide is a product of incomplete combustion of organic matter due to insufficient oxygen supply that prevents complete oxidation of carbon to C02. During World War II, Nazis used gas vans to kill an estimated over 700,000 prisoners by carbon monoxide poisoning. This method was also used in the gas chambers ofseveral death camps. The true number of incidents of carbon monoxide poisoning is unknown, since many non-lethal exposures go undetected From the available data, carbon monoxide poisoning is the most common cause of injury and death due to poisoning worldwide. Clinical features and management: The signs of carbon monoxide poisoning vary with concentration and length of exposure. Subtle cardiovascular or neurobehavioural effects occur at low concentration. The onset of chronic poisoning is usually insidious and easily mistaken for viral prodrome, depression, or gastroenteritis in children. The classic sign of carbon monoxide poisoning which is actually more often seen in the dead than the living is appearing red-cheeked and healthy. Cherry pink colour develops in nails, skin and mucosa. In acute poisoning, common abnormalities of posture and tone are cogwheel rigidity, opisthotonus, spasticity or flaccidity and seizures. Retinal haemorrhages and the classic cherry red skin colour are seldom seen. Different people andpopulations may have different carbon monoxide tolerance levels. On average, exposures at 100ppm or greater is dangerous to human health. Treatment and prevention: The mainstay of treatment is 100% oxygen administration until the COHb level is normal When the patient is stable enough to be transported, hyperbaric oxygen (HBOT should be considered This treatment is safe and well tolerated Public education about the danger of carbon monoxide, with

  16. Nanoporous metal-carbon composite

    Science.gov (United States)

    Worsley, Marcus A.; Satcher, Joe; Kucheyev, Sergei; Charnvanichborikarn, Supakit; Colvin, Jeffrey; Felter, Thomas; Kim, Sangil; Merrill, Matthew; Orme, Christine

    2017-12-19

    Described here is a metal-carbon composite, comprising (a) a porous three-dimensional scaffold comprising one or more of carbon nanotubes, graphene and graphene oxide, and (b) metal nanoparticles disposed on said porous scaffold, wherein the metal-carbon composite has a density of 1 g/cm.sup.3 or less, and wherein the metal nanoparticles account for 1 wt. % or more of the metal-carbon composite. Also described are methods for making the metal-carbon composite.

  17. Bromine isotopic signature facilitates de novo sequencing of peptides in free-radical-initiated peptide sequencing (FRIPS) mass spectrometry.

    Science.gov (United States)

    Nam, Jungjoo; Kwon, Hyuksu; Jang, Inae; Jeon, Aeran; Moon, Jingyu; Lee, Sun Young; Kang, Dukjin; Han, Sang Yun; Moon, Bongjin; Oh, Han Bin

    2015-02-01

    We recently showed that free-radical-initiated peptide sequencing mass spectrometry (FRIPS MS) assisted by the remarkable thermochemical stability of (2,2,6,6-tetramethyl-piperidin-1-yl)oxyl (TEMPO) is another attractive radical-driven peptide fragmentation MS tool. Facile homolytic cleavage of the bond between the benzylic carbon and the oxygen of the TEMPO moiety in o-TEMPO-Bz-C(O)-peptide and the high reactivity of the benzylic radical species generated in •Bz-C(O)-peptide are key elements leading to extensive radical-driven peptide backbone fragmentation. In the present study, we demonstrate that the incorporation of bromine into the benzene ring, i.e. o-TEMPO-Bz(Br)-C(O)-peptide, allows unambiguous distinction of the N-terminal peptide fragments from the C-terminal fragments through the unique bromine doublet isotopic signature. Furthermore, bromine substitution does not alter the overall radical-driven peptide backbone dissociation pathways of o-TEMPO-Bz-C(O)-peptide. From a practical perspective, the presence of the bromine isotopic signature in the N-terminal peptide fragments in TEMPO-assisted FRIPS MS represents a useful and cost-effective opportunity for de novo peptide sequencing. Copyright © 2015 John Wiley & Sons, Ltd.

  18. IRAS colors of carbon stars - An optical spectroscopic test

    International Nuclear Information System (INIS)

    Cohen, M.; Wainscoat, R.J.; Walker, H.J.; Volk, K.; Schwartz, D.E.

    1989-01-01

    Optical spectra are obtained of 57 photographic counterparts to IRAS sources not previously studied spectroscopically, and expected on the basis of their IRAS colors to be M or C type stars. Confirmed carbon stars are found only in a restricted range of 12-25 index, and constitute a striking vertical sequence in the 12-25-60 micron color-color diagram. This sequence is in accord with evolutionary models for AGB stars that convert M into C stars by dredge-up, and follow loops in the color-color plane. Optically visible and optically invisible carbon stars occupy different color-color locations consistent with their representations of different evolutionary states in the life of relatively low-mass stars. 16 refs

  19. Carbon foam/hydroxyapatite coating for carbon/carbon composites: Microstructure and biocompatibility

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Leilei, E-mail: zhangleilei1121@aliyun.com; Li, Hejun; Li, Kezhi; Zhang, Shouyang; Lu, Jinhua; Li, Wei; Cao, Sheng; Wang, Bin

    2013-12-01

    To improve the surface biocompatibility of carbon/carbon composites, a carbon foam/hydroxyapatite coating was applied using a combination method of slurry procedure and ultrasound-assisted electrochemical deposition procedure. The morphology, microstructure and chemical composition of the coating were investigated by scanning electron microscopy, energy dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, Raman spectroscopy and X-ray diffraction. The biocompatibility of the carbon foam/hydroxyapatite coating was investigated by osteoblast-like MG63 cell culture tests. The results showed that the carbon foam could provide a large number of pores on the surface of carbon/carbon composites. The hydroxyapatite crystals could infiltrate into the pores and form the carbon foam/hydroxyapatite coating. The coating covered the carbon/carbon composites fully and uniformly with slice morphology. The cell response tests showed that the MG63 cells on carbon foam/hydroxyapatite coating had a better cell adhesion and cell proliferation than those on uncoated carbon/carbon composites. The carbon foam/hydroxyapatite coatings were cytocompatible and were beneficial to improve the biocompatibility. The approach presented here may be exploited for fabrication of carbon/carbon composite implant surfaces.

  20. Carbon foam/hydroxyapatite coating for carbon/carbon composites: Microstructure and biocompatibility

    International Nuclear Information System (INIS)

    Zhang, Leilei; Li, Hejun; Li, Kezhi; Zhang, Shouyang; Lu, Jinhua; Li, Wei; Cao, Sheng; Wang, Bin

    2013-01-01

    To improve the surface biocompatibility of carbon/carbon composites, a carbon foam/hydroxyapatite coating was applied using a combination method of slurry procedure and ultrasound-assisted electrochemical deposition procedure. The morphology, microstructure and chemical composition of the coating were investigated by scanning electron microscopy, energy dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, Raman spectroscopy and X-ray diffraction. The biocompatibility of the carbon foam/hydroxyapatite coating was investigated by osteoblast-like MG63 cell culture tests. The results showed that the carbon foam could provide a large number of pores on the surface of carbon/carbon composites. The hydroxyapatite crystals could infiltrate into the pores and form the carbon foam/hydroxyapatite coating. The coating covered the carbon/carbon composites fully and uniformly with slice morphology. The cell response tests showed that the MG63 cells on carbon foam/hydroxyapatite coating had a better cell adhesion and cell proliferation than those on uncoated carbon/carbon composites. The carbon foam/hydroxyapatite coatings were cytocompatible and were beneficial to improve the biocompatibility. The approach presented here may be exploited for fabrication of carbon/carbon composite implant surfaces.

  1. Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir.

    Science.gov (United States)

    Freedman, Adam J E; Tan, BoonFei; Thompson, Janelle R

    2017-06-01

    Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 , harbor a 'deep carbonated biosphere' with carbon cycling potential. We sampled subsurface fluids from scCO 2 -water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  2. Global carbon inequality

    Energy Technology Data Exchange (ETDEWEB)

    Hubacek, Klaus [University of Maryland, Department of Geographical Sciences, College Park, MD (United States); Masaryk University, Department of Environmental Studies, Brno (Czech Republic); Baiocchi, Giovanni [University of Maryland, Department of Geographical Sciences, College Park, MD (United States); University of Maryland, Department of Economics, College Park, MD (United States); Feng, Kuishuang [University of Maryland, Department of Geographical Sciences, College Park, MD (United States); Munoz Castillo, Raul [University of Maryland, Department of Geographical Sciences, College Park, MD (United States); Interamerican Development Bank, Washington, DC (United States); Sun, Laixiang [University of Maryland, Department of Geographical Sciences, College Park, MD (United States); SOAS, University of London, London (United Kingdom); International Institute for Applied Systems Analysis (IIASA), Laxenburg (Austria); Xue, Jinjun [Nagoya University, Graduate School of Economics, Nagoya (Japan); Hubei University of Economics, Wuhan (China)

    2017-12-01

    Global climate change and inequality are inescapably linked both in terms of who contributes climate change and who suffers the consequences. This fact is also partly reflected in two United Nations (UN) processes: on the one hand, the Paris Agreement of the UN Framework Convention on Climate Change under which countries agreed to hold the increase in the global average temperature to below 2 C above pre-industrial levels and, on the other hand, the UN's Sustainable Development Goals aiming to end poverty. These agreements are seen as important foundation to put the world nations on a sustainable pathway. However, how these agreements can be achieved or whether they are even mutually compatible is less clear. We explore the global carbon inequality between and within countries and the carbon implications of poverty alleviation by combining detailed consumer expenditure surveys for different income categories for a wide range of countries with an environmentally extended multi-regional input-output approach to estimate carbon footprints of different household groups, globally, and assess the carbon implications of moving the poorest people out of poverty. Given the current context, increasing income leads to increasing carbon footprints and makes global targets for mitigating greenhouse gases more difficult to achieve given the pace of technological progress and current levels of fossil fuel dependence. We conclude that the huge level of carbon inequality requires a critical discussion of undifferentiated income growth. Current carbon-intensive lifestyles and consumption patterns need to enter the climate discourse to a larger extent. (orig.)

  3. Carbon-14 waste management

    International Nuclear Information System (INIS)

    Bush, R.P.

    1984-01-01

    As part of their research programme on Radioactive Waste Management, the Commission of the European Communities has provided financial support for a detailed study of wastes containing 14 C and the options for their management. The main results of this study are outlined. Carbon-14 is formed by neutron activation reactions in core materials and is therefore present in a variety of waste streams both at reactors and at reprocessing plants. Data on the production and release of 14 C from various reactor systems are presented. A possible management strategy for 14 C might be reduction of 14 N impurity levels in core materials, but only reductions of about a factor of five in arisings could be achieved in this way. The key problem in 14 C management is its retention in off-gas streams, particularly in the dissolver off-gas stream at reprocessing plants. In this stream the nuclide is present as carbon dioxide and is extensively isotopically diluted by the carbon dioxide content of the air. Processes for trapping 14 C from these off-gases must be integrated with the other processes in the overall off-gas treatment system, and should provide for conversion to a stable solid compound of carbon, suitable for subsequent immobilization and disposal. Three trapping processes that convert carbon dioxide into insoluble carbonates can be identified: the double alkali (NaOH/Ca(OH) 2 ) process, the direct calcium hydroxide slurry process, and the barium ocathydrate gas/solid process. Calcium or barium carbonates, produced in the above processes, could probably be incorporated into satisfactory immobilized waste forms. However, the stability of such waste forms to prolonged irradiation and to leaching remains to be investigated. (author)

  4. Carbon dioxide and climate

    International Nuclear Information System (INIS)

    1991-10-01

    Global climate change is a serious environmental concern, and the US has developed ''An Action Agenda'' to deal with it. At the heart of the US effort is the US Global Change Research Program (USGCRP), which has been developed by the Committee on Earth and Environmental Sciences (CEES) of the Federal Coordinating Council for Sciences, Engineering, and Technology (FCCSET). The USGCRP will provide the scientific basis for sound policy making on the climate-change issue. The DOE contribution to the USGCRP is the Carbon Dioxide Research Program, which now places particular emphasis on the rapid improvement of the capability to predict global and regional climate change. DOE's Carbon Dioxide Research Program has been addressing the carbon dioxide-climate change connection for more than twelve years and has provided a solid scientific foundation for the USGCRP. The expansion of the DOE effort reflects the increased attention that the Department has placed on the issue and is reflected in the National Energy Strategy (NES) that was released in 1991. This Program Summary describes projects funded by the Carbon Dioxide Research Program during FY 1991 and gives a brief overview of objectives, organization, and accomplishments. The Environmental Sciences Division of the Office of Health and Environmental Research, Office of Energy Research supports a Carbon Dioxide Research Program to determine the scientific linkage between the rise of greenhouse gases in the atmosphere, especially carbon dioxide, and climate and vegetation change. One facet is the Core CO 2 Program, a pioneering program that DOE established more than 10 years ago to understand and predict the ways that fossil-fuel burning could affect atmospheric CO 2 concentration, global climate, and the Earth's biosphere. Major research areas are: global carbon cycle; climate detection and models of climate change; vegetation research; resource analysis; and, information and integration

  5. MRI contrast enhancement using Magnetic Carbon Nanoparticles

    Science.gov (United States)

    Chaudhary, Rakesh P.; Kangasniemi, Kim; Takahashi, Masaya; Mohanty, Samarendra K.; Koymen, Ali R.; Department of Physics, University of Texas at Arlington Team; University of Texas Southwestern Medical Center Team

    2014-03-01

    In recent years, nanotechnology has become one of the most exciting forefront fields in cancer diagnosis and therapeutics such as drug delivery, thermal therapy and detection of cancer. Here, we report development of core (Fe)-shell (carbon) nanoparticles with enhanced magnetic properties for contrast enhancement in MRI imaging. These new classes of magnetic carbon nanoparticles (MCNPs) are synthesized using a bottom-up approach in various organic solvents, using the electric plasma discharge generated in the cavitation field of an ultrasonic horn. Gradient echo MRI images of well-dispersed MCNP-solutions (in tube) were acquired. For T2 measurements, a multi echo spin echo sequence was performed. From the slope of the 1/T2 versus concentration plot, the R2 value for different CMCNP-samples was measured. Since MCNPs were found to be extremely non-reactive, and highly absorbing in NIR regime, development of carbon-based MRI contrast enhancement will allow its simultaneous use in biomedical applications. We aim to localize the MCNPs in targeted tissue regions by external DC magnetic field, followed by MRI imaging and subsequent photothermal therapy.

  6. Investigating Interactions between the Silica and Carbon Cycles during Precipitation and Early Diagenesis of Authigenic Clay/Carbonate-Mineral Associations in the Carbonate Rock Record

    Science.gov (United States)

    McKenzie, J. A.; Francisca Martinez Ruiz, F.; Sanchez-Roman, M.; Anjos, S.; Bontognali, T. R. R.; Nascimento, G. S.; Vasconcelos, C.

    2017-12-01

    The study of authigenic clay/carbonate-mineral associations within carbonate sequences has important implications for the interpretation of scientific problems related with rock reservoir properties, such as alteration of potential porosity and permeability. More specifically, when clay minerals are randomly distributed within the carbonate matrix, it becomes difficult to predict reservoir characteristics. In order to understand this mineral association in the geological record, we have undertaken a comparative study of specially designed laboratory experiments with modern environments, where clay minerals have been shown to precipitate together with a range of carbonate minerals, including calcite, Mg-calcite and dolomite. Two modern dolomite-forming environments, the Coorong lakes, South Australia and Brejo do Espinho Rio de Janeiro, Brazil, were selected for this investigation. For comparative evaluation, enrichment microbial culture experiments, using natural pore water from Brejo do Espinho as the growth medium to promote mineral precipitation, were performed under both aerobic and anaerobic conditions. To establish the environmental parameters and biological processes facilitating the dual mineral association, the experimental samples have been compared with the natural minerals using HRTEM measurements. The results demonstrate that the clay and carbonate minerals apparently do not co-precipitate, but the precipitation of the different minerals in the same sample has probably occurred under different environmental conditions with variable chemistries, e.g., hypersalinity versus normal salinity resulting from the changing ratio of evaporation versus precipitation. Thus, the investigated mineral association is not a product of diagenetic processes but of sequential in situ precipitation processes related to changes in the silica and carbon availability. Implications for ancient carbonate formations will be presented and discussed in the context of a specific

  7. Measurement of carbon capture efficiency and stored carbon leakage

    Science.gov (United States)

    Keeling, Ralph F.; Dubey, Manvendra K.

    2013-01-29

    Data representative of a measured carbon dioxide (CO.sub.2) concentration and of a measured oxygen (O.sub.2) concentration at a measurement location can be used to determine whether the measured carbon dioxide concentration at the measurement location is elevated relative to a baseline carbon dioxide concentration due to escape of carbon dioxide from a source associated with a carbon capture and storage process. Optionally, the data can be used to quantify a carbon dioxide concentration increase at the first location that is attributable to escape of carbon dioxide from the source and to calculate a rate of escape of carbon dioxide from the source by executing a model of gas-phase transport using at least the first carbon dioxide concentration increase. Related systems, methods, and articles of manufacture are also described.

  8. A comparative evaluation of sequence classification programs

    Directory of Open Access Journals (Sweden)

    Bazinet Adam L

    2012-05-01

    Full Text Available Abstract Background A fundamental problem in modern genomics is to taxonomically or functionally classify DNA sequence fragments derived from environmental sampling (i.e., metagenomics. Several different methods have been proposed for doing this effectively and efficiently, and many have been implemented in software. In addition to varying their basic algorithmic approach to classification, some methods screen sequence reads for ’barcoding genes’ like 16S rRNA, or various types of protein-coding genes. Due to the sheer number and complexity of methods, it can be difficult for a researcher to choose one that is well-suited for a particular analysis. Results We divided the very large number of programs that have been released in recent years for solving the sequence classification problem into three main categories based on the general algorithm they use to compare a query sequence against a database of sequences. We also evaluated the performance of the leading programs in each category on data sets whose taxonomic and functional composition is known. Conclusions We found significant variability in classification accuracy, precision, and resource consumption of sequence classification programs when used to analyze various metagenomics data sets. However, we observe some general trends and patterns that will be useful to researchers who use sequence classification programs.

  9. CATEGORIZATION OF EVENT SEQUENCES FOR LICENSE APPLICATION

    Energy Technology Data Exchange (ETDEWEB)

    G.E. Ragan; P. Mecheret; D. Dexheimer

    2005-04-14

    The purposes of this analysis are: (1) Categorize (as Category 1, Category 2, or Beyond Category 2) internal event sequences that may occur before permanent closure of the repository at Yucca Mountain. (2) Categorize external event sequences that may occur before permanent closure of the repository at Yucca Mountain. This includes examining DBGM-1 seismic classifications and upgrading to DBGM-2, if appropriate, to ensure Beyond Category 2 categorization. (3) State the design and operational requirements that are invoked to make the categorization assignments valid. (4) Indicate the amount of material put at risk by Category 1 and Category 2 event sequences. (5) Estimate frequencies of Category 1 event sequences at the maximum capacity and receipt rate of the repository. (6) Distinguish occurrences associated with normal operations from event sequences. It is beyond the scope of the analysis to propose design requirements that may be required to control radiological exposure associated with normal operations. (7) Provide a convenient compilation of the results of the analysis in tabular form. The results of this analysis are used as inputs to the consequence analyses in an iterative design process that is depicted in Figure 1. Categorization of event sequences for permanent retrieval of waste from the repository is beyond the scope of this analysis. Cleanup activities that take place after an event sequence and other responses to abnormal events are also beyond the scope of the analysis.

  10. Exploration of noncoding sequences in metagenomes.

    Directory of Open Access Journals (Sweden)

    Fabián Tobar-Tosse

    Full Text Available Environment-dependent genomic features have been defined for different metagenomes, whose genes and their associated processes are related to specific environments. Identification of ORFs and their functional categories are the most common methods for association between functional and environmental features. However, this analysis based on finding ORFs misses noncoding sequences and, therefore, some metagenome regulatory or structural information could be discarded. In this work we analyzed 23 whole metagenomes, including coding and noncoding sequences using the following sequence patterns: (G+C content, Codon Usage (Cd, Trinucleotide Usage (Tn, and functional assignments for ORF prediction. Herein, we present evidence of a high proportion of noncoding sequences discarded in common similarity-based methods in metagenomics, and the kind of relevant information present in those. We found a high density of trinucleotide repeat sequences (TRS in noncoding sequences, with a regulatory and adaptive function for metagenome communities. We present associations between trinucleotide values and gene function, where metagenome clustering correlate with microorganism adaptations and kinds of metagenomes. We propose here that noncoding sequences have relevant information to describe metagenomes that could be considered in a whole metagenome analysis in order to improve their organization, classification protocols, and their relation with the environment.

  11. CATEGORIZATION OF EVENT SEQUENCES FOR LICENSE APPLICATION

    International Nuclear Information System (INIS)

    G.E. Ragan; P. Mecheret; D. Dexheimer

    2005-01-01

    The purposes of this analysis are: (1) Categorize (as Category 1, Category 2, or Beyond Category 2) internal event sequences that may occur before permanent closure of the repository at Yucca Mountain. (2) Categorize external event sequences that may occur before permanent closure of the repository at Yucca Mountain. This includes examining DBGM-1 seismic classifications and upgrading to DBGM-2, if appropriate, to ensure Beyond Category 2 categorization. (3) State the design and operational requirements that are invoked to make the categorization assignments valid. (4) Indicate the amount of material put at risk by Category 1 and Category 2 event sequences. (5) Estimate frequencies of Category 1 event sequences at the maximum capacity and receipt rate of the repository. (6) Distinguish occurrences associated with normal operations from event sequences. It is beyond the scope of the analysis to propose design requirements that may be required to control radiological exposure associated with normal operations. (7) Provide a convenient compilation of the results of the analysis in tabular form. The results of this analysis are used as inputs to the consequence analyses in an iterative design process that is depicted in Figure 1. Categorization of event sequences for permanent retrieval of waste from the repository is beyond the scope of this analysis. Cleanup activities that take place after an event sequence and other responses to abnormal events are also beyond the scope of the analysis

  12. On site DNA barcoding by nanopore sequencing.

    Directory of Open Access Journals (Sweden)

    Michele Menegon

    Full Text Available Biodiversity research is becoming increasingly dependent on genomics, which allows the unprecedented digitization and understanding of the planet's biological heritage. The use of genetic markers i.e. DNA barcoding, has proved to be a powerful tool in species identification. However, full exploitation of this approach is hampered by the high sequencing costs and the absence of equipped facilities in biodiversity-rich countries. In the present work, we developed a portable sequencing laboratory based on the portable DNA sequencer from Oxford Nanopore Technologies, the MinION. Complementary laboratory equipment and reagents were selected to be used in remote and tough environmental conditions. The performance of the MinION sequencer and the portable laboratory was tested for DNA barcoding in a mimicking tropical environment, as well as in a remote rainforest of Tanzania lacking electricity. Despite the relatively high sequencing error-rate of the MinION, the development of a suitable pipeline for data analysis allowed the accurate identification of different species of vertebrates including amphibians, reptiles and mammals. In situ sequencing of a wild frog allowed us to rapidly identify the species captured, thus confirming that effective DNA barcoding in the field is possible. These results open new perspectives for real-time-on-site DNA sequencing thus potentially increasing opportunities for the understanding of biodiversity in areas lacking conventional laboratory facilities.

  13. Comparison of two Next Generation sequencing platforms for full genome sequencing of Classical Swine Fever Virus

    DEFF Research Database (Denmark)

    Fahnøe, Ulrik; Pedersen, Anders Gorm; Höper, Dirk

    2013-01-01

    to the consensus sequence. Additionally, we got an average sequence depth for the genome of 4000 for the Iontorrent PGM and 400 for the FLX platform making the mapping suitable for single nucleotide variant (SNV) detection. The analysis revealed a single non-silent SNV A10665G leading to the amino acid change D......Next Generation Sequencing (NGS) is becoming more adopted into viral research and will be the preferred technology in the years to come. We have recently sequenced several strains of Classical Swine Fever Virus (CSFV) by NGS on both Genome Sequencer FLX (GS FLX) and Iontorrent PGM platforms...

  14. Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

    Directory of Open Access Journals (Sweden)

    Jian eWu

    2012-11-01

    Full Text Available Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome.

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

    Science.gov (United States)

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

    2017-10-01

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

  16. Diffusion-weighted MR imaging findings in carbon monoxide poisoning

    International Nuclear Information System (INIS)

    Teksam, M.; Casey, S.O.; Michel, E.; Liu, H.; Truwit, C.L.

    2002-01-01

    Diffusion-weighted MR imaging (DWI) of two patients with carbon monoxide (CO) poisoning demonstrated white matter and cortical hyperintensities. In one patient, the changes on the FLAIR sequence were more subtle than those on DWI. The DWI abnormality in this patient represented true restriction. In the second patient, repeated exposure to CO caused restricted diffusion. DWI may be helpful for earlier identification of the changes of acute CO poisoning. (orig.)

  17. Computer simulation of replacement sequences in copper

    International Nuclear Information System (INIS)

    Schiffgens, J.O.; Schwartz, D.W.; Ariyasu, R.G.; Cascadden, S.E.

    1978-01-01

    Results of computer simulations of , , and replacement sequences in copper are presented, including displacement thresholds, focusing energies, energy losses per replacement, and replacement sequence lengths. These parameters are tabulated for six interatomic potentials and shown to vary in a systematic way with potential stiffness and range. Comparisons of results from calculations made with ADDES, a quasi-dynamical code, and COMENT, a dynamical code, show excellent agreement, demonstrating that the former can be calibrated and used satisfactorily in the analysis of low energy displacement cascades. Upper limits on , , and replacement sequences were found to be approximately 10, approximately 30, and approximately 14 replacements, respectively. (author)

  18. Whole-genome sequencing of veterinary pathogens

    DEFF Research Database (Denmark)

    Ronco, Troels

    -electrophoresis and single-locus sequencing has been widely used to characterize such types of veterinary pathogens. However, DNA sequencing techniques have become fast and cost effective in recent years and whole-genome sequencing data provide a much higher discriminative power and reproducibility than any...... genetic background. This indicates that dairy cows can be natural carriers of S. aureus subtypes that in certain cases lead to CM. A group of isolates that mostly belonged to ST151 carried three pathogenicity islands that were primarily found in this group. The prevalence of resistance genes was generally...

  19. Spreadsheet macros for coloring sequence alignments.

    Science.gov (United States)

    Haygood, M G

    1993-12-01

    This article describes a set of Microsoft Excel macros designed to color amino acid and nucleotide sequence alignments for review and preparation of visual aids. The colored alignments can then be modified to emphasize features of interest. Procedures for importing and coloring sequences are described. The macro file adds a new menu to the menu bar containing sequence-related commands to enable users unfamiliar with Excel to use the macros more readily. The macros were designed for use with Macintosh computers but will also run with the DOS version of Excel.

  20. Tensor products of higher almost split sequences

    OpenAIRE

    Pasquali, Andrea

    2015-01-01

    We investigate how the higher almost split sequences over a tensor product of algebras are related to those over each factor. Herschend and Iyama gave a precise criterion for when the tensor product of an $n$-representation finite algebra and an $m$-representation finite algebra is $(n+m)$-representation finite. In this case we give a complete description of the higher almost split sequences over the tensor product by expressing every higher almost split sequence as the mapping cone of a suit...

  1. Arbitrarily accurate twin composite π -pulse sequences

    Science.gov (United States)

    Torosov, Boyan T.; Vitanov, Nikolay V.

    2018-04-01

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

  2. Modeling of Prepregs during Automated Draping Sequences

    DEFF Research Database (Denmark)

    Krogh, Christian; Glud, Jens Ammitzbøll; Jakobsen, Johnny

    2017-01-01

    algorithm used to generate target points on the mold which are used as input to a draping sequence planner. The draping sequence planner prescribes the displacement history for each gripper in the drape tool and these displacements are then applied to each gripper in a transient model of the draping...... sequence. The model is based on a transient finite element analysis with the material’s constitutive behavior currently being approximated as linear elastic orthotropic. In-plane tensile and bias-extension tests as well as bending tests are conducted and used as input for the model. The virtual draping...

  3. Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

    Directory of Open Access Journals (Sweden)

    Joern Toedling

    Full Text Available Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.

  4. Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform

    Directory of Open Access Journals (Sweden)

    Shan Wei

    2018-05-01

    Full Text Available Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples’ genomic DNA in under three hours, including library preparation and sequencing. This novel method shows great promise as a clinical diagnostic test for applications requiring rapid short-read DNA sequencing.

  5. Carbon nanotubes field-effect transistor for rapid detection of DHA

    International Nuclear Information System (INIS)

    Nguyen Thi Thuy; Nguyen Duc Chien; Mai Anh Tuan

    2012-01-01

    This paper presents the development of DNA sensor based on a network carbon nanotubes field effect transistor (CNTFETs) for Escherichia coli bacteria detection. The DNA sequences were immobilized on single-walled carbon nanotubes of transistor CNTFETs by using absorption. The hybridization of the DNA probe sequences and complementary DNA strands was detected by electrical conductance change from the electron doping by DNA hybridization directly on the carbon nanotubes leading to the change in the metal-CNTs barrier energy through the modulation of the electrode work function of carbon nanotubes field effect transistor. The results showed that the response time of DNA sensor was approximately 1 min and the sensitivity of DNA sensor was at 0.565 μA/nM; the detection limit of the sensor was about 1 pM of E. coli bacteria sample. (author)

  6. Synthesis and Characterization Carbon Nanotubes Doped Carbon Aerogels

    Science.gov (United States)

    Xu, Yuelong; Yan, Meifang; Liu, Zhenfa

    2017-12-01

    Polycondensation of phloroglucinol, resorcinol and formaldehyde with carbon nanotube (CNT) as the additives, using sodium carbonate as the catalyst, leads to the formation of CNT - doped carbon aerogels. The structure of carbon aerogels (CAs) with carbon nanotubes (CNTs) were characterized by X-ray diffraction and scanning electron microscopy. The specific surface area, pore size distribution and pore volume were measured by surface area analyzer. The results show that when the optimum doping dosage is 5%, the specific surface area of CNT - doped carbon aerogel is up to 665 m2 g-1 and exhibit plentiful mesoporous.

  7. Carbon fuel particles used in direct carbon conversion fuel cells

    Science.gov (United States)

    Cooper, John F.; Cherepy, Nerine

    2012-10-09

    A system for preparing particulate carbon fuel and using the particulate carbon fuel in a fuel cell. Carbon particles are finely divided. The finely dividing carbon particles are introduced into the fuel cell. A gas containing oxygen is introduced into the fuel cell. The finely divided carbon particles are exposed to carbonate salts, or to molten NaOH or KOH or LiOH or mixtures of NaOH or KOH or LiOH, or to mixed hydroxides, or to alkali and alkaline earth nitrates.

  8. Carbon Fuel Particles Used in Direct Carbon Conversion Fuel Cells

    Science.gov (United States)

    Cooper, John F.; Cherepy, Nerine

    2008-10-21

    A system for preparing particulate carbon fuel and using the particulate carbon fuel in a fuel cell. Carbon particles are finely divided. The finely dividing carbon particles are introduced into the fuel cell. A gas containing oxygen is introduced into the fuel cell. The finely divided carbon particles are exposed to carbonate salts, or to molten NaOH or KOH or LiOH or mixtures of NaOH or KOH or LiOH, or to mixed hydroxides, or to alkali and alkaline earth nitrates.

  9. Probabilistic Motor Sequence Yields Greater Offline and Less Online Learning than Fixed Sequence.

    Science.gov (United States)

    Du, Yue; Prashad, Shikha; Schoenbrun, Ilana; Clark, Jane E

    2016-01-01

    It is well acknowledged that motor sequences can be learned quickly through online learning. Subsequently, the initial acquisition of a motor sequence is boosted or consolidated by offline learning. However, little is known whether offline learning can drive the fast learning of motor sequences (i.e., initial sequence learning in the first training session). To examine offline learning in the fast learning stage, we asked four groups of young adults to perform the serial reaction time (SRT) task with either a fixed or probabilistic sequence and with or without preliminary knowledge (PK) of the presence of a sequence. The sequence and PK were manipulated to emphasize either procedural (probabilistic sequence; no preliminary knowledge (NPK)) or declarative (fixed sequence; with PK) memory that were found to either facilitate or inhibit offline learning. In the SRT task, there were six learning blocks with a 2 min break between each consecutive block. Throughout the session, stimuli followed the same fixed or probabilistic pattern except in Block 5, in which stimuli appeared in a random order. We found that PK facilitated the learning of a fixed sequence, but not a probabilistic sequence. In addition to overall learning measured by the mean reaction time (RT), we examined the progressive changes in RT within and between blocks (i.e., online and offline learning, respectively). It was found that the two groups who performed the fixed sequence, regardless of PK, showed greater online learning than the other two groups who performed the probabilistic sequence. The groups who performed the probabilistic sequence, regardless of PK, did not display online learning, as indicated by a decline in performance within the learning blocks. However, they did demonstrate remarkably greater offline improvement in RT, which suggests that they are learning the probabilistic sequence offline. These results suggest that in the SRT task, the fast acquisition of a motor sequence is driven

  10. Carbon Partitioning in Green Algae (Chlorophyta and the Enolase Enzyme

    Directory of Open Access Journals (Sweden)

    Jürgen E. W. Polle

    2014-08-01

    Full Text Available The exact mechanisms underlying the distribution of fixed carbon within photoautotrophic cells, also referred to as carbon partitioning, and the subcellular localization of many enzymes involved in carbon metabolism are still unknown. In contrast to the majority of investigated green algae, higher plants have multiple isoforms of the glycolytic enolase enzyme, which are differentially regulated in higher plants. Here we report on the number of gene copies coding for the enolase in several genomes of species spanning the major classes of green algae. Our genomic analysis of several green algae revealed the presence of only one gene coding for a glycolytic enolase [EC 4.2.1.11]. Our predicted cytosolic localization would require export of organic carbon from the plastid to provide substrate for the enolase and subsequent re-import of organic carbon back into the plastids. Further, our comparative sequence study of the enolase and its 3D-structure prediction may suggest that the N-terminal extension found in green algal enolases could be involved in regulation of the enolase activity. In summary, we propose that the enolase represents one of the crucial regulatory bottlenecks in carbon partitioning in green algae.

  11. [Review of lime carbon sink.

    Science.gov (United States)

    Liu, Li Li; Ling, Jiang Hua; Tie, Li; Wang, Jiao Yue; Bing, Long Fei; Xi, Feng Ming

    2018-01-01

    Under the background of "missing carbon sink" mystery and carbon capture and storage (CCS) technology development, this paper summarized the lime material flow process carbon sink from the lime carbonation principles, impact factors, and lime utilization categories in chemical industry, metallurgy industry, construction industry, and lime kiln ash treatment. The results showed that the lime carbonation rate coefficients were mainly impacted by materials and ambient conditions; the lime carbon sink was mainly in chemical, metallurgy, and construction industries; and current researches focused on the mechanisms and impact factors for carbonation, but their carbon sequestration calculation methods had not been proposed. Therefore, future research should focus on following aspects: to establish a complete system of lime carbon sequestration accounting method in view of material flow; to calculate lime carbon sequestration in both China and the world and explain their offset proportion of CO 2 emission from lime industrial process; to analyze the contribution of lime carbon sequestration to missing carbon sink for clarifying part of missing carbon sinks; to promote the development of carbon capture and storage technology and provide some scientific bases for China's international negotiations on climate change.

  12. Low-weight Impact Behaviour of Carbon Fibre Reinforced Methyl Methacrylate Nanocomposites

    Directory of Open Access Journals (Sweden)

    Virginija Jankauskaitė

    2015-06-01

    Full Text Available Inthis study, the carbon fibre reinforced methyl methacrylate (CF/MMA compositetoecap for safety shoes was manufactured to increase the energy absorptioncapacity during impact. Different types of nanofillers such as organic andinorganic nanotubes, unmodified and organically modified nanoclays were appliedto modify matrix impact properties. The drop-weight impact tests of thenanocomposite toecap were performed with respect to nanofiller nature andcarbon fibre stacking sequence. It was found that the most influence on thestiffness and impact damage of the carbon fibre methyl methacrylatenanocomposite toecaps besides stacking sequence show organic and inorganic nanotubesor unmodified nanoclay.DOI: http://dx.doi.org/10.5755/j01.ms.21.2.7075

  13. Application of carbon isotope stratigraphy to late miocene shallow marine sediments, new zealand.

    Science.gov (United States)

    Loutit, T S; Kennett, J P

    1979-06-15

    A distinct (0.5 per mil) carbon-13/carbon-12 isotopic shift in the light direction has been identified in a shallow marine sedimentary sequence of Late Miocene age at Blind River, New Zealand, and correlated with a similar shift in Late Miocene Deep Sea Drilling Project sequences throughout the Indo-Pacific. A dated piston core provides an age for the shift of 6.2 +/- 0.1 million years. Correlations based on the carbon isotopic change require a revision of the previously established magnetostratigraphy at Blind River. The carbon shift at Blind River occurs between 6.2 and 6.3 +/- 0.1 million years before present. A new chronology provides an age for the evolutionary first appearance datum of Globorotalia conomiozea at 6.1 +/- 0.1 million years, the beginning of a distinct latest Miocene cooling event associated with the Kapitean stage at 6.2 +/- 0.1 million years, and the beginning of a distinct shallowing of water depths at 6.1 +/- 0.1 million years. The Miocene-Pliocene boundary as recognized in New Zealand is now dated at 5.3 +/- 0.1 million years. Extension of carbon isotope stratigraphy to other shallow Late Miocene sequences should provide an important datum for international correlation of Late Miocene shallow and deep marine sequences.

  14. Flexible Carbon Aerogels

    Directory of Open Access Journals (Sweden)

    Marina Schwan

    2016-09-01

    Full Text Available Carbon aerogels are highly porous materials with a large inner surface area. Due to their high electrical conductivity they are excellent electrode materials in supercapacitors. Their brittleness, however, imposes certain limitations in terms of applicability. In that context, novel carbon aerogels with varying degree of flexibility have been developed. These highly porous, light aerogels are characterized by a high surface area and possess pore structures in the micrometer range, allowing for a reversible deformation of the aerogel network. A high ratio of pore size to particle size was found to be crucial for high flexibility. For dynamic microstructural analysis, compression tests were performed in-situ within a scanning electron microscope allowing us to directly visualize the microstructural flexibility of an aerogel. The flexible carbon aerogels were found to withstand between 15% and 30% of uniaxial compression in a reversible fashion. These findings might stimulate further research and new application fields directed towards flexible supercapacitors and batteries.

  15. The Carbon Trading Game

    International Nuclear Information System (INIS)

    Fouquet, Roger

    2003-12-01

    In response to the Kyoto Protocol, an international market for carbon dioxide tradable permits is likely to be created. Two of the key issues involved are explaining the concepts of tradable permits to industrialists, policy-makers and the man on the street, and anticipating how the market will evolve. A simple game of the market for carbon dioxide tradable permits has been developed and used that can help deal with both issues. As a pedagogical tool, this game benefits from simplicity (just a few pieces of paper are needed) and enables students to grasp the concepts and remember them through the intensity and fun of a trading 'pit'. The experiences also provide substantial insights into the evolution of the carbon dioxide permit market, particularly related to the evolution of trade volume, permit prices and country strategies

  16. Densities of carbon foils

    International Nuclear Information System (INIS)

    Stoner, J.O. Jr.

    1991-01-01

    The densities of arc-evaporated carbon target foils have been measured by several methods. The density depends upon the method used to measure it; for the same surface density, values obtained by different measurement techniques may differ by fifty percent or more. The most reliable density measurements are by flotation, yielding a density of 2.01±0.03 g cm -3 , and interferometric step height with the surface density known from auxiliary measurements, yielding a density of 2.61±0.4 g cm -3 . The difference between these density values mayy be due in part to the compressive stresses that carbon films have while still on their substrates, uncertainties in the optical calibration of surface densities of carbon foils, and systematic errors in step-height measurements. Mechanical thickness measurements by micrometer caliper are unreliable due to nonplanarity of these foils. (orig.)

  17. Carbon Monoxide Poisoning

    Directory of Open Access Journals (Sweden)

    Alisa Wray

    2016-07-01

    Full Text Available Audience: This oral boards case is appropriate for all emergency medicine learners (residents, interns, and medical students. Introduction: Carbon monoxide (CO is a colorless and odorless gas that typically results from combustion. It binds hemoglobin, dissociating oxygen, causing headache, weakness, confusion and possible seizure or coma. Pulse oxygen levels may be falsely elevated. Practitioners should maintain a high index of suspicion for carbon monoxide poisoning. If caught early CO poisoning is reversible with oxygen or hyperbaric oxygen therapy. Objectives: The learner will assess a patient with altered mental status and weakness, ultimately identifying that the patient has carbon monoxide poisoning. The learner will treat the patient with oxygen and admit/transfer the patient for hyperbaric oxygenation. Method: Oral boards case

  18. Optimization of a sequence of reactors

    DEFF Research Database (Denmark)

    Vidal, Rene Victor Valqui

    1991-01-01

    Concerns the optimal production of sulphuric acid in a sequence of reactors. Using a suitable approximation to the objective function, this problem can easily be solved using the maximum principle. A numerical example documents the applicability of the suggested approach...

  19. Fluency First: Reversing the Traditional ESL Sequence.

    Science.gov (United States)

    MacGowan-Gilhooly, Adele

    1991-01-01

    Describes an ESL department's whole language approach to writing and reading, replacing its traditional grammar-based ESL instructional sequence. Reports the positive quantitative and qualitative results of the first three years of using the new approach. (KEH)

  20. Expressed sequence tags (ESTs) and single nucleotide ...

    African Journals Online (AJOL)

    SERVER

    2008-02-19

    Feb 19, 2008 ... the discovery of the DNA, a new area of modern plant biotechnology begun. In plant ... Marker Assisted Breeding and Sequence Tagged Sites. (STS) are all in use in modern ...... and behaviour in the honey bee. Genome Res.