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Sample records for s5 ring motifs

  1. 2-[(2,4,4,6,6-Pentachloro-1,3,5,2λ5,4λ5,6λ5-triazatriphosphinin-2-ylazanidyl]pyridinium

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    Safaa A. Ahmed

    2012-02-01

    Full Text Available The title compound, C5H5Cl5N5P3, crystallizes as a zwitterion in which the pyridine N atom is protonated. An S(6 ring motif is formed via an intramolecular C—H...N hydrogen bond. The triazatriphosphinine ring adopts an envelope conformation, with one N atom displaced by 0.145 (1 Å from the other atoms. In the crystal, N—H...N and C—H...N hydrogen bonds link the molecules into centrosymmetric dimers containing one R22(7 ring motif and two R22(8 ring motifs.

  2. 4,4-Dimethyl-3,4-dihydropyrido[2′,3′:3,4]pyrazolo[1,5-a][1,3,5]triazin-2-amine ethanol monosolvateFused heterocyclic systems with s-triazine ring. Part 16. for part 15, see Sachdeva et al. (2010.

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    Lip Lin Koh

    2011-01-01

    Full Text Available In the title compound, C10H12N6·C2H5OH, the planarity of the heterocyclic system is slightly distorted at the triazine ring (r.m.s. deviation = 0.1191 Å, which adopts a conformation best described as intermediate between a flattened twisted boat and a half-boat with the tertiary Csp3 atom at the bow. In the crystal, molecules form centrosymmetric dimers connected by N...H—O and O...H—N hydrogen bonds between the amino group H atom, the ethanol solvent molecule and the triazine N atom, making an R44(12 graph-set motif. The other H atom of the amino group and the H atom on the endocyclic N atom form N...H—N hydrogen bonds with the N atoms of the pyrazole and pyridine rings, respectively, linking the molecules into C(7C(7 chains with the R22(8 binary graph-set motif running along [010].

  3. A ROBUST EIGHT–MEMBERED RING MOTIF IN THE HYDROGEN-BONDED STRUCTURE OF -(PHENYLAMINOPYRIDINIUM- DI(METHANESULFONYLAMIDATE

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    Karna Wijaya

    2002-03-01

    Full Text Available The compound was prepared by dissolving 2-(phenylaminopyridine (0.52 g ; 3.0 mmol and di(methanesulfonylamine (0.51 g; 3.0 mmol in 5 mL methanol. Slow partial evaporation of the solvent at low tempertaure (-30 oC gave a yield of 0.66 g (64% and crystals suitable for X-ray study (m.p. 150-152 oC. The single crystal X-ray result showed that the crystal system was trikline with space group P. The crystal structure of the title compound 2-(phenylaminopyridinium-di(methane-sulfonylamidate forms a robust antidromic ring motif type. The structure testifies to the persistence of the  in question, which was previously detected as a robust supramolecular synthon in 2-aminopyridinium di(benzenesulfonylamidate and in a series of onium di(methane-sulfonylamidates.   Keywords: supramolecule, hydrogen-bond

  4. Hybrid DNA i-motif: Aminoethylprolyl-PNA (pC5) enhance the stability of DNA (dC5) i-motif structure.

    Science.gov (United States)

    Gade, Chandrasekhar Reddy; Sharma, Nagendra K

    2017-12-15

    This report describes the synthesis of C-rich sequence, cytosine pentamer, of aep-PNA and its biophysical studies for the formation of hybrid DNA:aep-PNAi-motif structure with DNA cytosine pentamer (dC 5 ) under acidic pH conditions. Herein, the CD/UV/NMR/ESI-Mass studies strongly support the formation of stable hybrid DNA i-motif structure with aep-PNA even near acidic conditions. Hence aep-PNA C-rich sequence cytosine could be considered as potential DNA i-motif stabilizing agents in vivo conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Remnants of black rings from gravity’s rainbow

    Energy Technology Data Exchange (ETDEWEB)

    Ali, Ahmed Farag [Center for Fundamental Physics, Zewail City of Science and Technology,6th of October City, Giza 12588 (Egypt); Department of Physics, Faculty of Science, Benha University,Benha 13518 (Egypt); Faizal, Mir [Department of Physics and Astronomy, University of Waterloo,Waterloo, Ontario, N2L 3G1 (Canada); Khalil, Mohammed M. [Department of Electrical Engineering, Alexandria University,El-Horreya Rd., Alexandria 12544 (Egypt)

    2014-12-29

    In this paper, we investigate a spinning black ring and a charged black ring in the context of gravity’s rainbow. By incorporating rainbow functions proposed by Amelino-Camelia, et al. in http://dx.doi.org/10.1142/S0217751X97000566 http://dx.doi.org/10.12942/lrr-2013-5 in the metric of the black rings, a considerable modification happens to their thermodynamical properties. We calculate corrections to the temperature, entropy and heat capacity of the black rings. These calculations demonstrate that the behavior of Hawking radiation changes considerably near the Planck scale in gravity’s rainbow, where it is shown that black rings do not evaporate completely and a remnant is left as the black rings evaporate down to Planck scale.

  6. Non-canonical binding interactions of the RNA recognition motif (RRM) domains of P34 protein modulate binding within the 5S ribonucleoprotein particle (5S RNP).

    Science.gov (United States)

    Kamina, Anyango D; Williams, Noreen

    2017-01-01

    RNA binding proteins are involved in many aspects of RNA metabolism. In Trypanosoma brucei, our laboratory has identified two trypanosome-specific RNA binding proteins P34 and P37 that are involved in the maturation of the 60S subunit during ribosome biogenesis. These proteins are part of the T. brucei 5S ribonucleoprotein particle (5S RNP) and P34 binds to 5S ribosomal RNA (rRNA) and ribosomal protein L5 through its N-terminus and its RNA recognition motif (RRM) domains. We generated truncated P34 proteins to determine these domains' interactions with 5S rRNA and L5. Our analyses demonstrate that RRM1 of P34 mediates the majority of binding with 5S rRNA and the N-terminus together with RRM1 contribute the most to binding with L5. We determined that the consensus ribonucleoprotein (RNP) 1 and 2 sequences, characteristic of canonical RRM domains, are not fully conserved in the RRM domains of P34. However, the aromatic amino acids previously described to mediate base stacking interactions with their RNA target are conserved in both of the RRM domains of P34. Surprisingly, mutation of these aromatic residues did not disrupt but instead enhanced 5S rRNA binding. However, we identified four arginine residues located in RRM1 of P34 that strongly impact L5 binding. These mutational analyses of P34 suggest that the binding site for 5S rRNA and L5 are near each other and specific residues within P34 regulate the formation of the 5S RNP. These studies show the unique way that the domains of P34 mediate binding with the T. brucei 5S RNP.

  7. 4-({[6-(4-Chlorobenzyl-4-methyl-5-oxo-4,5-dihydro-1,2,4-triazin-3-yl]sulfanyl}acetyl-3-phenylsydnone

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    Hoong-Kun Fun

    2011-04-01

    Full Text Available In the title syndone (1,2,3-oxadiazol-3-ylium-5-olate compound, C21H16ClN5O4S, the dihedral angle between the benzene and oxadiazole rings is 55.62 (11° and that between the triazine and the chloro-substituted phenyl rings is 82.45 (9°. There is an intramolecular C—H...S hydrogen bond, which generates an S(5 ring motif. In the crystal, inversion dimers linked by pairs of C—H...O hydrogen bonds generate R22(20 loops. The dimers are connected by C—H...N and C—H...O hydrogen bonds.

  8. Ethyl (E-2-(2,7-dimethyl-5-oxo-4H,5H-pyrano[4,3-b]pyran-4-ylideneacetate

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    Oulemda Bassou

    2017-02-01

    Full Text Available In the title compound, C14H14O5, the two heterocyclic rings are coplanar (r.m.s. deviation = 0.008 Å, with the largest deviation from the mean plane being 0.012 (1 Å. The mean plane through the acetate group is inclined slightly with respect to the oxopyrano[4,3-b]pyran-4-yl system, as indicated by the dihedral angle of 1.70 (7° between them. Two intramolecular hydrogen bonds, completing S(6 ring motifs, are observed in the molecule. In the crystal, molecules are linked by weak C—H...O hydrogen bonds involving the same acceptor atom, forming chains propagating along the c-axis direction and enclosing R21(6 ring motifs. The chains are linked via offset π–π interactions [intercentroid distance = 3.622 (1 Å], involving inversion-related oxopyrano[4,3-b]pyran-4-yl ring systems, forming slabs parallel to the bc plane.

  9. 2-Hydroxy-5-nitrobenzaldehyde

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    Şamil Işık

    2009-12-01

    Full Text Available The title compound, C7H5NO4, is essentially planar, with a maximum deviation from the mean plane of 0.0116 (11 Å for the hydroxy O atom. The molecular and crystal structure are stabilized by intra- and intermolecular interactions. An intramolecular O—H...O hydrogen bond generates a six-membered ring, producing an S(6 ring motif. The C—H...O interactions result in the formation of C(5 chains and R22(8 rings forming an approximately planar network parallel to (10overline{1}. These planes are interconnected through π–π interactions [centroid–centroid distance 3.582 (2 Å].

  10. 2-Amino-5-bromopyridinium 2-hydroxybenzoate

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    Ching Kheng Quah

    2010-08-01

    Full Text Available In the title compound, C5H6BrN2+·C7H5O3−, the 2-amino-5-bromopyridinium cation and 2-hydroxybenzoate anion are essentially planar with maximum deviations of 0.020 (1 and 0.018 (2 Å, respectively. The anion is stabilized by an intramolecular O—H...O hydrogen bond, which generates an S(6 ring motif. In the crystal, the cations and anions are linked by N—H...O hydrogen bonds into chains propagating along [010]. The chains contain R22(8 ring motifs. The structure is further stabilized by π–π stacking interactions [centroid–centroid distances = 3.4908 (10 and 3.5927 (10 Å] and also features short Br...O contacts [2.9671 (13 Å].

  11. (1S*,2S*,4R*,5R*-Cyclohexane-1,2,4,5-tetracarboxylic acid

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    Akira Uchida

    2014-01-01

    Full Text Available The title compound, C10H12O8, a prospective raw material for colourless polyimides which are applied to electronic and microelectronic devices, lies about an inversion centre and the cyclohexane ring adopts a chair conformation. Two crystallographycally independent carboxylic acid groups on adjacent C atoms are in equatorial positions, resulting in a mutually trans conformation. In the crystal, O—H...O hydrogen bonds around an inversion centre and a threefold rotoinversion axis, respectively, form an inversion dimer with an R22(8 motif and a trimer with an R33(12 motif.

  12. The crystal structure of 6-(4-chlorophenyl-2-(4-methylbenzylimidazo[2,1-b][1,3,4]thiadiazole-5-carbaldehyde

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    A. Sowmya

    2016-10-01

    Full Text Available In the title imidazo[2,1-b][1,3,4]thiadiazole derivative, C19H14ClN3OS, the 4-methylbenzyl and chlorophenyl rings are inclined to the planar imidazo[2,1-b][1,3,4]thiadiazole moiety (r.m.s. deviation = 0.012 Å by 64.5 (1 and 3.7 (1°, respectively. The molecular structure is primarily stabilized by a strong intramolecular C—H...O hydrogen bond, leading to the formation of a pseudo-seven-membered S(7 ring motif, and a short intramolecular C—H...N contact forming an S(5 ring motif. In the crystal, molecules are linked by pairs of C—H...S hydrogen bonds, forming inversion dimers. The dimers are linked by C—H...O and C—H...π interactions, forming chains propagating along [110].

  13. Homeric Motifs in Cavafy’s Poem »Priam’s Night Journey«

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    Dragica Fabjan Andritsakos

    2016-12-01

    Full Text Available The paper discusses Homeric motifs in ‘Priam’s Night Journey’, a poem by the contemporary Greek poet Constantine P. Cavafy and, more precisely, one of the ten poems composed by Cavafy on mythological themes. The discussion begins by comparing Cavafy’s treatment of a motif from the Iliad, Canto 24 – Priam’s journey to Achilles – with its ancient counterpart. The question of Cavafy’s sources is addressed as well: does the poet draw on the Ancient Greek original or on the Modern Greek translation? The second part of the article analyses in detail those passages which closely lean on the ancient epic, and concludes by illustrating Cavafy’s departure from the myth, which emerges most radically in the close of the poem.

  14. 5-Bromo-4-(3,4-dimethoxyphenylthiazol-2-amine

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    Hazem A. Ghabbour

    2012-06-01

    Full Text Available In the title compound, C11H11BrN2O2S, the thiazole ring makes a dihedral angle of 53.16 (11° with the adjacent benzene ring. The two methoxy groups are slightly twisted from the attached benzene ring with C—O—C—C torsion angles of −9.2 (3 and −5.5 (3°. In the crystal, molecules are linked by a pair of N—H...N hydrogen bonds into an inversion dimer with an R22(8 ring motif. The dimers are further connected by N—H...O hydrogen bonds into a tape along [-110].

  15. 3-Isobutyl-4-phenylsulfanyl-1H-pyrazol-5-ol

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    Tara Shahani

    2011-02-01

    Full Text Available The asymmetric unit of the title compound, C13H16N2OS, contains two independent molecules (A and B. The pyrazole ring [maximum deviations = 0.0049 (17 Å in molecule A and 0.0112 (19 Å in molecule B] makes a dihedral angle of 70.23 (11 and 73.18 (12° with the phenyl ring in molecules A and B, respectively. The isobutyl group in molecule B is disordered over two sets of sites with a ratio of refined occupancies of 0.858 (5:0.142 (5. In the crystal, molecules A and B are linked via a pair of intermolecular N—H...O hydrogen bonds, generating an R22(8 ring motif. These ring motifs are further linked into two-dimensional arrays parallel to the bc plane by intermolecular N—H...O and weak C—H...S hydrogen bonds. The crystal is further stablized by weak π–π interactions [centroid–centroid distances = 3.5698 (13 and 3.5287 (12 Å].

  16. rac-Dimethyl 2-(tert-butylamino-5-oxo-4,5-dihydropyrano[3,2-c]chromene-3,4-dicarboxylate

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    S. Antony Inglebert

    2011-11-01

    Full Text Available The title compound, C20H21NO7, is asymmetric with a chiral centre located in the pyran ring and crystallizes as a racemate. The molecular framework is somewhat bent; the coumarin moiety and the pyran ring are inclined by 7.85 (5°. The molecular structure is characterized by an intramolecular N—H...O hydrogen bond, which generates an S(6 ring motif, and the crystal packing is stabilized by intermolecular C—H...O hydrogen bonds. The 3-carboxylate O atom is involved in both of them, having a bifurcated character.

  17. 4,5,7,8,17-Pentahydroxy-14,18-dimethyl-6-methylene-3,10-dioxapentacyclo[9.8.0.01,7.04,19.013,18]nonadec-14-ene-9,16-dione methanol solvate dihydrate

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    Chin Hoe Teh

    2009-04-01

    Full Text Available The title quassinoid compound, C20H24O9·CH3OH·2H2O, is a natural eurycomanone isolated from the roots of Eurycoma longifolia. The molecules contain a fused five-ring system, with one tetrahydrofuran ring adopting an envelope conformation, one tetrahydropyran-2-one ring in a screw boat conformation, one cyclohexenone ring in a half-chair conformation and two cyclohexane rings in chair conformations. Intramolecular C—H...O interactions generate S(5 ring motifs and an O—H...O interaction generates an S(7 ring motif. In the crystal, molecules are linked via intermolecular O—H...O interactions along the b axis and further stacked along a axis. The absolute configuration of the title compound was inferred from previously solved structures of its analogues.

  18. 1-[3-(2-Benzyloxy-6-hydroxy-4-methylphenyl-5-[3,5-bis(trifluoromethylphenyl]-4,5-dihydro-1H-pyrazol-1-yl]propane-1-one

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    U. H. Patel

    2013-06-01

    Full Text Available In the title compound, C28H24F6N2O3, the mean plane of the central pyrazoline ring forms dihedral angles of 2.08 (9 and 69.02 (16° with the 2-benzyloxy-6-hydroxy-4-methylphenyl and 3,5-bis(trifluoromethylphenyl rings, respectively. The dihedral angle between the mean planes of the pyrazoline and 3,5-bis(trifluoromethylphenyl rings is 68.97 (9°. An intramolecular O—H...N hydrogen bond is observed, which forms an S(6 graph-set motif. In the crystal, pairs of weak C—H...F halogen interactions link the molecules into inversion dimers while molecular chains along [100] are formed by C—H...O contacts.

  19. Benzo[4,5]cyclohepta[1,2-b]fluorene: an isomeric motif for pentacene containing linearly fused five-, six- and seven-membered rings

    KAUST Repository

    Yang, Xuejin

    2016-06-07

    Benzo[4,5]cyclohepta[1,2-b]fluorene (5a), a new π-conjugated polycyclic hydrocarbon containing linearly fused six-, five-, six-, seven- and six-membered rings (C6-C5-C6-C7-C6), was designed and its stable derivatives 5b and 5c were synthesized. With 22 π electrons, 5a is an isomer of pentacene with quinoidal, dipolar ionic and diradical resonance forms. Molecules 5b and 5c were experimentally investigated with cyclic voltammetry, electronic absorption spectroscopy and X-ray crystallographic analysis, and theoretically studied by calculating the NICS value, diradical character and dipole moment. A comparison of 5a–c with pentacene and other pentacene analogues containing linearly fused five- or seven- membered rings was also conducted and discussed. It was found that 5b behaved as a p-type organic semiconductor in solution-processed thin film transistors with field effect mobility of up to 0.025 cm2/Vs.

  20. Benzo[4,5]cyclohepta[1,2-b]fluorene: an isomeric motif for pentacene containing linearly fused five-, six- and seven-membered rings

    KAUST Repository

    Yang, Xuejin; Shi, Xueliang; Aratani, Naoki; Goncalves, Theo; Huang, Kuo-Wei; Yamada, Hiroko; Chi, Chunyan; Miao, Qian

    2016-01-01

    Benzo[4,5]cyclohepta[1,2-b]fluorene (5a), a new π-conjugated polycyclic hydrocarbon containing linearly fused six-, five-, six-, seven- and six-membered rings (C6-C5-C6-C7-C6), was designed and its stable derivatives 5b and 5c were synthesized. With 22 π electrons, 5a is an isomer of pentacene with quinoidal, dipolar ionic and diradical resonance forms. Molecules 5b and 5c were experimentally investigated with cyclic voltammetry, electronic absorption spectroscopy and X-ray crystallographic analysis, and theoretically studied by calculating the NICS value, diradical character and dipole moment. A comparison of 5a–c with pentacene and other pentacene analogues containing linearly fused five- or seven- membered rings was also conducted and discussed. It was found that 5b behaved as a p-type organic semiconductor in solution-processed thin film transistors with field effect mobility of up to 0.025 cm2/Vs.

  1. N′-(3,5-Dibromo-2-hydroxybenzylidene-2-methylbenzohydrazide

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    Chun-Bao Tang

    2010-12-01

    Full Text Available The asymmetric unit of the title compound, C15H12Br2N2O2, contains two independent molecules in which the dihedral angles between the benzene rings are 49.5 (7 and 66.4 (7°. Intramolecular O—H...N hydrogen bonds generate S(6 ring motifs in each molecule. In the crystal, molecules are linked through intermolecular N—H...O hydrogen bonds, forming chains along the b axis.

  2. 2-Hydroxy-5-nitrobenzaldehyde 2,4-dinitrophenylhydrazone

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    Hoong-Kun Fun

    2008-04-01

    Full Text Available In the title compound, C13H9N5O7, one of the nitro groups is twisted away from the attached benzene ring by 16.21 (8°. The dihedral angle between the two benzene rings is 4.63 (1°. The molecular structure is stabilized by intramolecular N—H...O and O—H...N hydrogen bonds which generate an S(6 ring motif. The molecules pack as layers parallel to the ab plane; molecules of adjacent layers are linked into chains along the [101] direction through N—H...O hydrogen bonds.

  3. Ethyl 4′-ethenyl-2′-oxo-4-phenyl-2-(3,4,5-trimethoxyphenylspiro[pyrrolidine-3,3′-indoline]-5-carboxylate monohydrate

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    P. Ramesh

    2008-11-01

    Full Text Available In the title compound, C31H32N2O6·H2O, the pyrrolidine ring adopts an envelope conformation. The ethyl C atoms of the ethoxycabonyl group are disordered over two positions with occupancies of ca 0.80 and 0.20. Intramolecular N—H...O hydrogen bonds form S(5 and S(6 ring motifs. Molecules are linked into a three-dimensional framework by O—H...O, N—H...O and C—H...O hydrogen bonds, and by C—H...π interactions.

  4. Ethyl (E)-2-(2,7-dimethyl-5-oxo-4H,5H-pyrano[4,3-b]pyran-4-ylidene)acetate

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    Oulemda Bassou; Hakima Chicha; Latifa Bouissane; El Mostapha Rakib; Mohamed Saadi; Lahcen El Ammari

    2017-01-01

    In the title compound, C14H14O5, the two heterocyclic rings are coplanar (r.m.s. deviation = 0.008 Å), with the largest deviation from the mean plane being 0.012 (1) Å. The mean plane through the acetate group is inclined slightly with respect to the oxopyrano[4,3-b]pyran-4-yl system, as indicated by the dihedral angle of 1.70 (7)° between them. Two intramolecular hydrogen bonds, completing S(6) ring motifs, are observed in the molecule. In the crystal, molecules are linked by weak C—H...O hy...

  5. (E-2-(5-Chloro-2-hydroxybenzylidene-N-cyclohexylhydrazine-1-carbothioamide

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    Md. Azharul Arafath

    2017-01-01

    Full Text Available In the title compound, C14H18ClN3OS, the phenol ring is almost coplanar with the hydrazinecarbothioamide moiety, making a dihedral angle of 6.92 (8°. The cyclohexane ring has a chair conformation and the conformation about the C=N bond is E. In the crystal, molecules are linked by N—H...O and O—H...S hydrogen bonds, forming inversion dimers with an R22(14 ring motif flanked by two R22(6 ring motifs. The dimers are linked by short Cl...Cl interactions, forming layers parallel to the ab plane.

  6. Crystal structure of ethyl (2S-9-methoxy-2-methyl-4-oxo-3,4,5,6-tetrahydro-2H- 2,6-methanobenzo[g][1,3,5]oxadiazocine-11-carboxylate

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    A. Dhandapani

    2015-02-01

    Full Text Available In the title compound, C15H18N2O5, the methoxyphenyl ring makes a dihedral angle of 84.70 (12° with the mean plane of the tetrahydropyrimidin-2(1H-one ring. Both the pyran and tetrahydropyrimidin-2(1H-one rings have distorted envelope conformations with the carboxylate-substituted C atom as the flap. In the crystal, molecules are linked via pairs of N—H...O hydrogen bonds, forming zigzag chains propagating along [010], which enclose R22(8 ring motifs. The chains are linked by C—H...π interactions, forming a two-dimensional network parallel to (100.

  7. NANOGRAIN DENSITY OUTSIDE SATURN’S A RING

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    Johnson, Robert E. [Engineering Physics, University of Virginia, Charlottesville, VA 22902 (United States); Tseng, Wei-Ling [National Taiwan Normal University, No. 88, Sec. 4, Tingzhou Road, Wenshan District, Taipei 11677, Taiwan (China); Elrod, M. K. [NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Persoon, A. M., E-mail: rej@virginia.edu, E-mail: wltseng@ntnu.edu.tw, E-mail: meredith.k.elrod@nasa.gov, E-mail: ann-persoon@uiowa.edu [Department of Physics and Astronomy, University of Iowa, Iowa City, IA 52242 (United States)

    2017-01-01

    The observed disparity between the radial dependence of the ion and electron densities measured by the Cassini plasma (CAPS) and radio (RPWS) science instruments are used to show that the region between the outer edge of Saturn’s main rings and its tenuous G ring is permeated with small charged grains (nanograins). These grains emanate from the edge of the A ring and from the tenuous F and G rings. This is a region of Saturn’s magnetosphere that is relatively unexplored, but will be a focus of Cassini ’s F ring orbits prior to the end of mission in 2017 September. Confirmation of the grain densities predicted here will enhance our ability to describe the formation and destruction of material in this important region of Saturn’s magnetosphere.

  8. Crystal structure of 3,5-dimethoxy-2-[5-(naphthalen-1-yl-4,5-dihydro-1H-pyrazol-3-yl]phenol

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    Dongsoo Koh

    2015-10-01

    Full Text Available In the title compound, C21H20N2O3, the planes of the benzene ring and the naphthalene ring system are inclined to one another by 70.95°, and by 4.99 (6 and 75.93 (5°, respectively, to the mean plane of the pyrazoline ring. The latter has an envelope conformation with the methine (CH C atom as the flap. There is an intramolecular O—H...N hydrogen bond that forms an S(6 ring motif. In the crystal, molecules are linked by C—H...O hydrogen bonds, forming chains along [100]. The chains are linked via C—H...N hydrogen bonds, forming sheets parallel to the ab plane. The sheets are linked by a series of N—H...π and C—H...π interactions forming a three-dimensional structure.

  9. The special neuraminidase stalk-motif responsible for increased virulence and pathogenesis of H5N1 influenza A virus.

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    Hongbo Zhou

    Full Text Available The variation of highly pathogenic avian influenza H5N1 virus results in gradually increased virulence in poultry, and human cases continue to accumulate. The neuraminidase (NA stalk region of influenza virus varies considerably and may associate with its virulence. The NA stalk region of all N1 subtype influenza A viruses can be divided into six different stalk-motifs, H5N1/2004-like (NA-wt, WSN-like, H5N1/97-like, PR/8-like, H7N1/99-like and H5N1/96-like. The NA-wt is a special NA stalk-motif which was first observed in H5N1 influenza virus in 2000, with a 20-amino acid deletion in the 49(th to 68(th positions of the stalk region. Here we show that there is a gradual increase of the special NA stalk-motif in H5N1 isolates from 2000 to 2007, and notably, the special stalk-motif is observed in all 173 H5N1 human isolates from 2004 to 2007. The recombinant H5N1 virus with the special stalk-motif possesses the highest virulence and pathogenicity in chicken and mice, while the recombinant viruses with the other stalk-motifs display attenuated phenotype. This indicates that the special stalk-motif has contributed to the high virulence and pathogenicity of H5N1 isolates since 2000. The gradually increasing emergence of the special NA stalk-motif in H5N1 isolates, especially in human isolates, deserves attention by all.

  10. 9-(3-Bromo-5-chloro-2-hydroxyphenyl-10-(2-hydroxyethyl-3,6-diphenyl-3,4,9,10-tetrahydroacridine-1,8(2H,5H-dione

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    Mehmet Akkurt

    2014-06-01

    Full Text Available In the title compound, C33H27BrClNO4, the dihydropyridine ring adopts a flattened boat conformation. The molecular conformation is stabilized by an intramolecular O—H...O hydrogen bond, with an S(8 ring motif. In the crystal, O—H...O, C—H...O and C—H...Cl hydrogen bonds, and C—H...π interactions link the molecules, forming a three-dimensional network. In the acridinedione ring system, the two ring C atoms at the 2- and 3-positions, and the C atom at the 6-position and the atoms of the phenyl ring attached to the C atom at the 6-position are disordered over two sets of sites with occupancy ratios of 0.783 (5:0.217 (5 and 0.526 (18:0.474 (18, respectively.

  11. Supramolecular architecture in a co-crystal of the N(7—H tautomeric form of N6-benzoyladenine with adipic acid (1/0.5

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    Robert Swinton Darious

    2016-06-01

    Full Text Available The asymmetric unit of the title co-crystal, C12H9N5O·0.5C6H10O4, consists of one molecule of N6-benzoyladenine (BA and one half-molecule of adipic acid (AA, the other half being generated by inversion symmetry. The dihedral angle between the adenine and phenyl ring planes is 26.71 (7°. The N6-benzoyladenine molecule crystallizes in the N(7—H tautomeric form with three non-protonated N atoms. This tautomeric form is stabilized by intramolecular N—H...O hydrogen bonding between the carbonyl (C=O group and the N(7—H hydrogen atom on the Hoogsteen face of the purine ring, forming an S(7 ring motif. The two carboxyl groups of adipic acid interact with the Watson–Crick face of the BA molecules through O—H...N and N—H...O hydrogen bonds, generating an R22(8 ring motif. The latter units are linked by N—H...N hydrogen bonds, forming layers parallel to (10-5. A weak C—H...O hydrogen bond is also present, linking adipic acid molecules in neighbouring layers, enclosing R22(10 ring motifs and forming a three-dimensional structure. C=O...π and C—H...π interactions are also present in the structure.

  12. Supra-molecular architecture in a co-crystal of the N(7)-H tautomeric form of N (6)-benzoyl-adenine with adipic acid (1/0.5).

    Science.gov (United States)

    Swinton Darious, Robert; Thomas Muthiah, Packianathan; Perdih, Franc

    2016-06-01

    The asymmetric unit of the title co-crystal, C12H9N5O·0.5C6H10O4, consists of one mol-ecule of N (6)-benzoyl-adenine (BA) and one half-mol-ecule of adipic acid (AA), the other half being generated by inversion symmetry. The dihedral angle between the adenine and phenyl ring planes is 26.71 (7)°. The N (6)-benzoyl-adenine mol-ecule crystallizes in the N(7)-H tautomeric form with three non-protonated N atoms. This tautomeric form is stabilized by intra-molecular N-H⋯O hydrogen bonding between the carbonyl (C=O) group and the N(7)-H hydrogen atom on the Hoogsteen face of the purine ring, forming an S(7) ring motif. The two carboxyl groups of adipic acid inter-act with the Watson-Crick face of the BA mol-ecules through O-H⋯N and N-H⋯O hydrogen bonds, generating an R 2 (2)(8) ring motif. The latter units are linked by N-H⋯N hydrogen bonds, forming layers parallel to (10-5). A weak C-H⋯O hydrogen bond is also present, linking adipic acid mol-ecules in neighbouring layers, enclosing R (2) 2(10) ring motifs and forming a three-dimensional structure. C=O⋯π and C-H⋯π inter-actions are also present in the structure.

  13. MIGRATION OF SMALL MOONS IN SATURN's RINGS

    Energy Technology Data Exchange (ETDEWEB)

    Bromley, Benjamin C. [Department of Physics and Astronomy, University of Utah, 115 S 1400 E, Rm 201, Salt Lake City, UT 84112 (United States); Kenyon, Scott J., E-mail: bromley@physics.utah.edu, E-mail: skenyon@cfa.harvard.edu [Smithsonian Astrophysical Observatory, 60 Garden Street, Cambridge, MA 02138 (United States)

    2013-02-20

    The motions of small moons through Saturn's rings provide excellent tests of radial migration models. In theory, torque exchange between these moons and ring particles leads to radial drift. We predict that moons with Hill radii r {sub H} {approx} 2-24 km should migrate through the A ring in 1000 yr. In this size range, moons orbiting in an empty gap or in a full ring eventually migrate at the same rate. Smaller moons or moonlets-such as the propellers-are trapped by diffusion of disk material into corotating orbits, creating inertial drag. Larger moons-such as Pan or Atlas-do not migrate because of their own inertia. Fast migration of 2-24 km moons should eliminate intermediate-size bodies from the A ring and may be responsible for the observed large-radius cutoff of r {sub H} {approx} 1-2 km in the size distribution of the A ring's propeller moonlets. Although the presence of Daphnis (r {sub H} Almost-Equal-To 5 km) inside the Keeler gap challenges this scenario, numerical simulations demonstrate that orbital resonances and stirring by distant, larger moons (e.g., Mimas) may be important factors. For Daphnis, stirring by distant moons seems the most promising mechanism to halt fast migration. Alternatively, Daphnis may be a recent addition to the ring that is settling into a low inclination orbit in {approx}10{sup 3} yr prior to a phase of rapid migration. We provide predictions of observational constraints required to discriminate among possible scenarios for Daphnis.

  14. Synthesis and crystal structures of 5'-phenylspiro[indoline-3, 2'-pyrrolidin]-2-one derivatives

    Directory of Open Access Journals (Sweden)

    Perumal Subbu

    2011-07-01

    Full Text Available Abstract Background The spiro- indole-pyrrolidine ring system is a frequently encountered structural motif in many biologically important and pharmacologically relevant alkaloids. The derivatives of spirooxindole ring systems are used as antimicrobial, antitumour agents and as inhibitors of the human NKI receptor besides being found in a number of alkaloids like horsifiline, spirotryprostatin and (+ elacomine. The recently discovered small-molecule MDM2 inhibitor MI-219 and its analogues are in advanced preclinical development as cancer therapeutics. Results In the crystal structures of the two organic compounds, 4'-Nitro-3',5'-diphenylspiro[indoline-3,2'-pyrrolidin]-2-one and 3'-(4-Methoxyphenyl- 4'-nitro -5'-phenylspiro[indoline-3,2'-pyrrolidin]-2-one, N-H···O hydrogen bonds make the R22 (8 ring motif. Further, the structures are stabilized by intermolecular hydrogen bonds. Conclusion The crystal structures of 4'-Nitro-3',5'-diphenylspiro[indoline-3,2'-pyrrolidin]-2-one and 3'-(4-Methoxyphenyl- 4'-nitro -5'-phenylspiro[indoline-3,2'-pyrrolidin]-2-one have been investigated in detail. In both the compounds, the R22(8 motif is present. Due to the substitution of methoxyphenyl instead of phenyl ring, the entire configuration is inverted with respect to the 2-oxyindole ring.

  15. Crystal structure of (Z-3-benzyloxy-6-[(2-hydroxy-5-methylanilinomethylidene]cyclohexa-2,4-dien-1-one

    Directory of Open Access Journals (Sweden)

    Nadir Ghichi

    2014-09-01

    Full Text Available In the title Schiff base compound, C21H19NO3, the conformation about the C=C bond is Z. The N—H group and carbonyl O atom form an intramolecular N—H...O hydrogen bond with an S(6 ring motif. The benzyloxy ring and the 2-hydroxy-5-methylphenyl ring are inclined to the central six-membered ring by 13.68 (9 and 9.13 (8°, respectively, and to one another by 21.95 (9°. In the crystal, molecules are linked by O—H...O hydrogen bonds, forming helical chains along [010].

  16. 5-Pentyl-4-phenylsulfonyl-1H-pyrazol-3-ol

    Directory of Open Access Journals (Sweden)

    Tara Shahani

    2010-06-01

    Full Text Available In the title compound, C14H18N2O3S, the 1H-pyrazole ring is approximately planar, with a maximum deviation of 0.005 (1 Å. The dihedral angle formed between the 1H-pyrazole and phenyl rings is 79.09 (5°. Pairs of intermolecular N—H...O and O...H...N hydrogen bonds form dimers between neighboring molecules, generating R22(10 ring motifs. These dimers are further linked byintermolecular N—H...O and O—H...N hydrogen bonds into a two-dimensional array parallel to the ac plane. The crystal structure is also stabilized by C—H...π interactions.

  17. N,N-Diethyl-2-[5-(4-methoxybenzylidene-2,4-dioxo-1,3-thiazolidin-3-yl]acetamide

    Directory of Open Access Journals (Sweden)

    Vijayan Viswanathan

    2017-05-01

    Full Text Available In the title compound, C17H20N2O4S, the thiazolidine (r.m.s. deviation = 0.022 Å and phenyl rings (major and minor occupancies are inclined to one another by 6.3 (3 and 10.5 (3°, respectively. The molecular conformation is stabilized by an intramolecular C—H...S interaction. In the crystal, molecules are linked by C—H...O hydrogen bonds, which generate R22(18, R22(24 and R21(7 ring motifs. Aromatic π–π stacking interactions are also observed.

  18. A novel RNA-recognition-motif protein is required for premeiotic G1/S-phase transition in rice (Oryza sativa L..

    Directory of Open Access Journals (Sweden)

    Ken-Ichi Nonomura

    2011-01-01

    Full Text Available The molecular mechanism for meiotic entry remains largely elusive in flowering plants. Only Arabidopsis SWI1/DYAD and maize AM1, both of which are the coiled-coil protein, are known to be required for the initiation of plant meiosis. The mechanism underlying the synchrony of male meiosis, characteristic to flowering plants, has also been unclear in the plant kingdom. In other eukaryotes, RNA-recognition-motif (RRM proteins are known to play essential roles in germ-cell development and meiosis progression. Rice MEL2 protein discovered in this study shows partial similarity with human proline-rich RRM protein, deleted in Azoospermia-Associated Protein1 (DAZAP1, though MEL2 also possesses ankyrin repeats and a RING finger motif. Expression analyses of several cell-cycle markers revealed that, in mel2 mutant anthers, most germ cells failed to enter premeiotic S-phase and meiosis, and a part escaped from the defect and underwent meiosis with a significant delay or continued mitotic cycles. Immunofluorescent detection revealed that T7 peptide-tagged MEL2 localized at cytoplasmic perinuclear region of germ cells during premeiotic interphase in transgenic rice plants. This study is the first report of the plant RRM protein, which is required for regulating the premeiotic G1/S-phase transition of male and female germ cells and also establishing synchrony of male meiosis. This study will contribute to elucidation of similarities and diversities in reproduction system between plants and other species.

  19. (E-4-Amino-N′-(2-hydroxy-5-methylbenzylidenebenzohydrazide

    Directory of Open Access Journals (Sweden)

    Hadi Kargar

    2012-07-01

    Full Text Available The asymmetric unit of the title compound, C15H15N3O2, comprises two crystallographically independent molecules (A and B, each having an E conformation around the C=N bond. In each molecule, there is an intramolecular O—H...N hydrogen bond making an S(6 ring motif. The dihedral angles between the substituted phenyl rings are 17.49 (9 and 10.03 (9°. In the crystal, N—H...O hydrogen bonds link neighbouring independent molecules into infinite chains, of the type –A–B–A–B–, along the a axis, enclosing R21(7 ring motifs. The chains are linked by N—H...O hydrogen bonds and C—H...O interactions, leading to the formation of a three-dimensional network.

  20. Results of de-novo and Motif activity analyses - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us FANTOM... JASPAR) Data file File name: Motifs File URL: ftp://ftp.biosciencedbc.jp/archive/fantom5/datafiles/phase1.3...tabase Database Description Download License Update History of This Database Site Policy | Contact Us Results of de-novo and Motif activity analyses - FANTOM5 | LSDB Archive ...

  1. CompariMotif: quick and easy comparisons of sequence motifs.

    Science.gov (United States)

    Edwards, Richard J; Davey, Norman E; Shields, Denis C

    2008-05-15

    CompariMotif is a novel tool for making motif-motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs. CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/

  2. On commutativity of one-sided s-unital rings

    Directory of Open Access Journals (Sweden)

    H. A. S. Abujabal

    1992-01-01

    Full Text Available The following theorem is proved: Let r=r(y>1, s, and t be non-negative integers. If R is a left s-unital ring satisfies the polynomial identity [xy−xsyrxt,x]=0 for every x,y∈R, then R is commutative. The commutativity of a right s-unital ring satisfying the polynomial identity [xy−yrxt,x]=0 for all x,y∈R, is also proved.

  3. Crystal structure of (1S,3R,8R,10S-2,2-dichloro-10-hydroxy-3,7,7,10-tetramethyltricyclo[6.4.0.01,3]dodecan-9-one

    Directory of Open Access Journals (Sweden)

    Ahmed Benzalim

    2016-05-01

    Full Text Available The asymmetric unit of the title compound, C16H24Cl2O2, contains two independent molecules (A and B which are built from three fused rings, viz. a seven-membered heptane ring, a six-membered cyclohexyl ring bearing a ketone and an alcohol group, and a cyclopropane ring bearing two Cl atoms. In the crystal, the two molecules are linked via two O—H...O hydrogen bonds, forming an A–B dimer with an R22(10 ring motif. The A molecules of these dimers are linked via a C—H...O hydrogen bond, forming chains propagating along the a-axis direction. Both molecules have the same absolute configuration, i.e. 1S,3R,8R,10S, which is based on the synthetic pathway and further confirmed by resonant scattering [Flack parameter = 0.03 (5].

  4. Non-Linear Dynamics of Saturn’s Rings

    Science.gov (United States)

    Esposito, Larry W.

    2015-11-01

    Non-linear processes can explain why Saturn’s rings are so active and dynamic. Ring systems differ from simple linear systems in two significant ways: 1. They are systems of granular material: where particle-to-particle collisions dominate; thus a kinetic, not a fluid description needed. We find that stresses are strikingly inhomogeneous and fluctuations are large compared to equilibrium. 2. They are strongly forced by resonances: which drive a non-linear response, pushing the system across thresholds that lead to persistent states.Some of this non-linearity is captured in a simple Predator-Prey Model: Periodic forcing from the moon causes streamline crowding; This damps the relative velocity, and allows aggregates to grow. About a quarter phase later, the aggregates stir the system to higher relative velocity and the limit cycle repeats each orbit.Summary of Halo Results: A predator-prey model for ring dynamics produces transient structures like ‘straw’ that can explain the halo structure and spectroscopy: This requires energetic collisions (v ≈ 10m/sec, with throw distances about 200km, implying objects of scale R ≈ 20km).Transform to Duffing Eqn : With the coordinate transformation, z = M2/3, the Predator-Prey equations can be combined to form a single second-order differential equation with harmonic resonance forcing.Ring dynamics and history implications: Moon-triggered clumping at perturbed regions in Saturn’s rings creates both high velocity dispersion and large aggregates at these distances, explaining both small and large particles observed there. We calculate the stationary size distribution using a cell-to-cell mapping procedure that converts the phase-plane trajectories to a Markov chain. Approximating the Markov chain as an asymmetric random walk with reflecting boundaries allows us to determine the power law index from results of numerical simulations in the tidal environment surrounding Saturn. Aggregates can explain many dynamic aspects

  5. Multiple TPR motifs characterize the Fanconi anemia FANCG protein.

    Science.gov (United States)

    Blom, Eric; van de Vrugt, Henri J; de Vries, Yne; de Winter, Johan P; Arwert, Fré; Joenje, Hans

    2004-01-05

    The genome protection pathway that is defective in patients with Fanconi anemia (FA) is controlled by at least eight genes, including BRCA2. A key step in the pathway involves the monoubiquitylation of FANCD2, which critically depends on a multi-subunit nuclear 'core complex' of at least six FANC proteins (FANCA, -C, -E, -F, -G, and -L). Except for FANCL, which has WD40 repeats and a RING finger domain, no significant domain structure has so far been recognized in any of the core complex proteins. By using a homology search strategy comparing the human FANCG protein sequence with its ortholog sequences in Oryzias latipes (Japanese rice fish) and Danio rerio (zebrafish) we identified at least seven tetratricopeptide repeat motifs (TPRs) covering a major part of this protein. TPRs are degenerate 34-amino acid repeat motifs which function as scaffolds mediating protein-protein interactions, often found in multiprotein complexes. In four out of five TPR motifs tested (TPR1, -2, -5, and -6), targeted missense mutagenesis disrupting the motifs at the critical position 8 of each TPR caused complete or partial loss of FANCG function. Loss of function was evident from failure of the mutant proteins to complement the cellular FA phenotype in FA-G lymphoblasts, which was correlated with loss of binding to FANCA. Although the TPR4 mutant fully complemented the cells, it showed a reduced interaction with FANCA, suggesting that this TPR may also be of functional importance. The recognition of FANCG as a typical TPR protein predicts this protein to play a key role in the assembly and/or stabilization of the nuclear FA protein core complex.

  6. Dimethyl 4,4′-dihydroxy-3,3′-{[(3aRS,7aRS-2,3,3a,4,5,6,7,7a-octahydro-1H-1,3-benzimidazole-1,3-diyl]bis(methylene}dibenzoate

    Directory of Open Access Journals (Sweden)

    Augusto Rivera

    2011-11-01

    Full Text Available The title compound, C25H30N2O6, has the imidazolidine ring in an envelope conformation. There are two intramolecular O—H...N hydrogen-bond interactions with graph-set motif S(6. The cyclohexane ring adopts a slightly distorted chair conformation. One methyl carboxylate substituent forms a dihedral angle of 12.00 (5° with the plane of the benzene ring, while the other methyl carboxylate group is almost coplanar, making a dihedral angle of 2.26 (9°. In the crystal, pairs of intermolecular C—H...O hydrogen bonds form racemic dimers, corresponding to an R22(18 graph-set motif. Further weak C—H...O interactions generate a chain running along the c axis.

  7. Spectral signature barcodes based on S-shaped Split Ring Resonators (S-SRRs

    Directory of Open Access Journals (Sweden)

    Herrojo Cristian

    2016-01-01

    Full Text Available In this paper, it is shown that S-shaped split ring resonators (S-SRRs are useful particles for the implementation of spectral signature (i.e., a class of radiofrequency barcodes based on coplanar waveguide (CPW transmission lines loaded with such resonant elements. By virtue of its S shape, these resonators are electrically small. Hence S-SRRs are of interest for the miniaturization of the barcodes, since multiple resonators, each tuned at a different frequency, are used for encoding purposes. In particular, a 10-bit barcode occupying 1 GHz spectral bandwidth centered at 2.5 GHz, with dimensions of 9 cm2, is presented in this paper.

  8. Motif-role-fingerprints: the building-blocks of motifs, clustering-coefficients and transitivities in directed networks.

    Directory of Open Access Journals (Sweden)

    Mark D McDonnell

    Full Text Available Complex networks are frequently characterized by metrics for which particular subgraphs are counted. One statistic from this category, which we refer to as motif-role fingerprints, differs from global subgraph counts in that the number of subgraphs in which each node participates is counted. As with global subgraph counts, it can be important to distinguish between motif-role fingerprints that are 'structural' (induced subgraphs and 'functional' (partial subgraphs. Here we show mathematically that a vector of all functional motif-role fingerprints can readily be obtained from an arbitrary directed adjacency matrix, and then converted to structural motif-role fingerprints by multiplying that vector by a specific invertible conversion matrix. This result demonstrates that a unique structural motif-role fingerprint exists for any given functional motif-role fingerprint. We demonstrate a similar result for the cases of functional and structural motif-fingerprints without node roles, and global subgraph counts that form the basis of standard motif analysis. We also explicitly highlight that motif-role fingerprints are elemental to several popular metrics for quantifying the subgraph structure of directed complex networks, including motif distributions, directed clustering coefficient, and transitivity. The relationships between each of these metrics and motif-role fingerprints also suggest new subtypes of directed clustering coefficients and transitivities. Our results have potential utility in analyzing directed synaptic networks constructed from neuronal connectome data, such as in terms of centrality. Other potential applications include anomaly detection in networks, identification of similar networks and identification of similar nodes within networks. Matlab code for calculating all stated metrics following calculation of functional motif-role fingerprints is provided as S1 Matlab File.

  9. [3-(5-Nitro-2-furyl-1-phenyl-1H-pyrazol-4-yl](phenylmethanone

    Directory of Open Access Journals (Sweden)

    Jia Hao Goh

    2010-05-01

    Full Text Available In the title pyrazole compound, C20H13N3O4, an intramolecular C—H...O hydrogen bond generates a seven-membered ring, producing an S(7 ring motif. The essentially planar furan and pyrazole rings [maximum deviations of 0.002 (1 and 0.007 (1 Å, respectively] are coplanar with each other, forming a dihedral angle of 3.06 (10°. The pyrazole ring forms dihedral angles of 8.51 (9 and 56.81 (9° with the two benzene rings. The nitro group is coplanar with the attached furan ring, as indicated by the dihedral angle of 2.5 (3°. In the crystal packing, intermolecular C—H...O hydrogen bonds link adjacent molecules into two-molecule-wide chains along the a axis. The crystal packing is further stabilized by weak intermolecular C—H...π and π–π interactions [centroid–centroid distance = 3.4441 (10 Å].

  10. Crystal structure of 3-methoxy-2-[5-(naphthalen-1-yl-4,5-dihydro-1H-pyrazol-3-yl]phenol

    Directory of Open Access Journals (Sweden)

    Dongsoo Koh

    2015-11-01

    Full Text Available In the title compound, C20H18N2O2, the central pyrazoline ring has an envelope conformation with the atom substituted by the naphthalene ring as the flap. It bridges a benzene ring and a naphthalene ring system which are almost normal to one another, making a dihedral angle of 82.03 (6 °. There is an intramolecular O—H...N hydrogen bond forming an S(6 ring motif. In the crystal, molecules are linked by pairs of N—H...π interactions, forming inversion dimers. There are also C—H...π interactions present and the dimers are linked via C—H...O hydrogen bonds, forming ribbons propagating along the a-axis direction.

  11. Analysis of Degree 5 Chordal Rings for Network Topologies

    DEFF Research Database (Denmark)

    Riaz, M. Tahir; Pedersen, Jens Myrup; Bujnowski, Sławomir

    2011-01-01

    This paper presents an analysis of degree 5 chordal rings, from a network topology point of view. The chordal rings are mainly evaluated with respect to average distance and diameter. We derive approximation expressions for the related ideal graphs, and show that these matches the real chordal...

  12. GRAVITATIONAL ACCRETION OF PARTICLES ONTO MOONLETS EMBEDDED IN SATURN's RINGS

    International Nuclear Information System (INIS)

    Yasui, Yuki; Ohtsuki, Keiji; Daisaka, Hiroshi

    2014-01-01

    Using a local N-body simulation, we examine gravitational accretion of ring particles onto moonlet cores in Saturn's rings. We find that gravitational accretion of particles onto moonlet cores is unlikely to occur in the C ring and probably difficult in the inner B ring as well provided that the cores are rigid water ice. Dependence of particle accretion on ring thickness changes when the radial distance from the planet and/or the density of particles is varied: the former determines the size of the core's Hill radius relative to its physical size, while the latter changes the effect of self-gravity of accreted particles. We find that particle accretion onto high-latitude regions of the core surface can occur even if the rings' vertical thickness is much smaller than the core radius, although redistribution of particles onto the high-latitude regions would not be perfectly efficient in outer regions of the rings such as the outer A ring, where the size of the core's Hill sphere in the vertical direction is significantly larger than the core's physical radius. Our results suggest that large boulders recently inferred from observations of transparent holes in the C ring are not formed locally by gravitational accretion, while propeller moonlets in the A ring would be gravitational aggregates formed by particle accretion onto dense cores. Our results also imply that the main bodies of small satellites near the outer edge of Saturn's rings may have been formed in rather thin rings

  13. GRAVITATIONAL ACCRETION OF PARTICLES ONTO MOONLETS EMBEDDED IN SATURN's RINGS

    Energy Technology Data Exchange (ETDEWEB)

    Yasui, Yuki; Ohtsuki, Keiji [Department of Earth and Planetary Sciences, Kobe University, Kobe 657-8501 (Japan); Daisaka, Hiroshi, E-mail: y.yasui@whale.kobe-u.ac.jp, E-mail: ohtsuki@tiger.kobe-u.ac.jp [Graduate School of Commerce and Management, Hitotsubashi University, Tokyo 186-8601 (Japan)

    2014-12-20

    Using a local N-body simulation, we examine gravitational accretion of ring particles onto moonlet cores in Saturn's rings. We find that gravitational accretion of particles onto moonlet cores is unlikely to occur in the C ring and probably difficult in the inner B ring as well provided that the cores are rigid water ice. Dependence of particle accretion on ring thickness changes when the radial distance from the planet and/or the density of particles is varied: the former determines the size of the core's Hill radius relative to its physical size, while the latter changes the effect of self-gravity of accreted particles. We find that particle accretion onto high-latitude regions of the core surface can occur even if the rings' vertical thickness is much smaller than the core radius, although redistribution of particles onto the high-latitude regions would not be perfectly efficient in outer regions of the rings such as the outer A ring, where the size of the core's Hill sphere in the vertical direction is significantly larger than the core's physical radius. Our results suggest that large boulders recently inferred from observations of transparent holes in the C ring are not formed locally by gravitational accretion, while propeller moonlets in the A ring would be gravitational aggregates formed by particle accretion onto dense cores. Our results also imply that the main bodies of small satellites near the outer edge of Saturn's rings may have been formed in rather thin rings.

  14. Dimethyl trans-3-(4-bromophenyl-2-methylisoxazolidine-4,5-dicarboxylate

    Directory of Open Access Journals (Sweden)

    Orhan Büyükgüngör

    2009-09-01

    Full Text Available In the title compound, C14H16BrNO5, the isoxazolidine ring adopts an envelope conformation, with the N atom at the flap. In the crystal, intermolecular C—H...N and C—H...O hydrogen bonds generate R33(18 ring motifs which are fused into a ribbon-like structure extending along the b axis.

  15. MotifNet: a web-server for network motif analysis.

    Science.gov (United States)

    Smoly, Ilan Y; Lerman, Eugene; Ziv-Ukelson, Michal; Yeger-Lotem, Esti

    2017-06-15

    Network motifs are small topological patterns that recur in a network significantly more often than expected by chance. Their identification emerged as a powerful approach for uncovering the design principles underlying complex networks. However, available tools for network motif analysis typically require download and execution of computationally intensive software on a local computer. We present MotifNet, the first open-access web-server for network motif analysis. MotifNet allows researchers to analyze integrated networks, where nodes and edges may be labeled, and to search for motifs of up to eight nodes. The output motifs are presented graphically and the user can interactively filter them by their significance, number of instances, node and edge labels, and node identities, and view their instances. MotifNet also allows the user to distinguish between motifs that are centered on specific nodes and motifs that recur in distinct parts of the network. MotifNet is freely available at http://netbio.bgu.ac.il/motifnet . The website was implemented using ReactJs and supports all major browsers. The server interface was implemented in Python with data stored on a MySQL database. estiyl@bgu.ac.il or michaluz@cs.bgu.ac.il. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  16. (3R,6S,7aS-3-Phenyl-6-(phenylsulfanylperhydropyrrolo[1,2-c]oxazol-5-one

    Directory of Open Access Journals (Sweden)

    Anthony D. Woolhouse

    2009-05-01

    Full Text Available Molecules of the title compound [systematic name: (2R,5S,7S-2-phenyl-7-phenylsulfanyl-1-aza-3-oxabicyclo[3.3.0]octan-8-one], C18H17NO2S, form high quality crystals even though they are only packed using C—H...O(carbonyl and weak C—H...S interactions. The dihedral angle between the aromatic rings is 85.53 (5°. The fused rings adopt envelope and twist conformations.

  17. 4-[(5-Hydroxy-3-methyl-1-phenyl-1H-pyrazol-4-ylphenylmethyl]-5-methyl-2-phenyl-1H-pyrazol-3(2H-one ethanol hemisolvate

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2009-01-01

    Full Text Available The asymmetric unit of the title compound, C27H24N4O2·0.5C2H6O, comprises two crystallographically independent molecules (A and B with slightly different conformations, and one ethanol molecule of crystallization. Intramolecular C—H...O and O—H...O hydrogen bonds generate six- and eight-membered rings, producing S(6 and S(8 ring motifs, respectively. In molecule A, one of the benzene rings is disordered over two positions, with site-occupancy factors of 0.542 (11 and 0.458 (11. The dihedral angles between the central benzene ring and the two outer benzene rings are 73.88 (9 and 82.6 (2/88.9 (2° in molecule A, and 80.81 (8 and 79.38 (8° in molecule B. In the crystal structure, molecules form infinite one-dimensional chains in the (101 plane. The crystal structure is stabilized by intermolecular O—H...N, N—H...N, N—H...O and C—H...O hydrogen bonds, weak C—H...π and π–π [centroid–centroid = 3.5496 (1 Å] interactions.

  18. Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.

    Science.gov (United States)

    Chiu, Yi-Yuan; Lin, Chun-Yu; Lin, Chih-Ta; Hsu, Kai-Cheng; Chang, Li-Zen; Yang, Jinn-Moon

    2012-01-01

    To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.

  19. 5-GHz passively mode-locked quantum dot ring laser diode at 1.5 μm

    NARCIS (Netherlands)

    Heck, M.J.R.; Renault, A.; Bente, E.A.J.M.; Oei, Y.S.; Smit, M.K.; Eikema, K.S.E.; Ubachs, W.; Anantathanasarn, S.; Nötzel, R.

    2008-01-01

    In this paper we present the first observation of passive mode-locking in a quantum dot (QD) ring laser operating at wavelengths around 1.5 µm. The device consists of an 18-mm long (electrically pumped) ring cavity, corresponding to a 5-GHz roundtrip frequency. The waveguide width is 2 µm. A

  20. (1S,3S,4S-tert-Butyl N-[1-benzyl-3-hydroxy-5-phenyl-4-(picolinamidopentyl]carbamate

    Directory of Open Access Journals (Sweden)

    Jian-Feng Zheng

    2008-07-01

    Full Text Available The title compound, C29H35N3O4, was obtained by the reaction of (2S,4S,5S-tert-butyl N-(4-amino-1-benzyl-3-hydroxy-5-phenylpentylcarbamate and picolinic acid using oxalyl chloride as a chlorinating reagent to activate the carboxyl group. In the crystal structure there are two molecules in the asymmetric unit, which are aligned edge-to-face. In one molecule, the pyridyl ring forms a dihedral angle of 22.0 (1° with the phenyl ring of the terminal benzyl group and 14.3 (1° with the other phenyl ring; in the other molecule, the corresponding angles are 12.1 (1 and 10.6 (1°, respectively. The packing is stabilized by intermolecular hydrogen bonds and C—H...π interactions.

  1. Kopi dan Kakao dalam Kreasi Motif Batik Khas Jember

    Directory of Open Access Journals (Sweden)

    Irfa'ina Rohana Salma

    2015-06-01

    Full Text Available ABSTRAK Batik Jember selama ini identik dengan motif daun tembakau. Visualisasi daun tembakau dalam motif Batik Jember cukup lemah, yaitu kurang berkarakter karena motif yang muncul adalah seperti gambar daun pada umumnya. Oleh karena itu perlu diciptakan desain motif batik khas Jember yang sumber inspirasinya digali dari kekayaan alam lainnya dari Jember yang mempunyai bentuk spesifik dan karakteristik sehingga identitas motif bisa didapatkan dengan lebih kuat. Hasil alam khas Jember tersebut adalah kopi dan kakao. Tujuan penciptaan seni ini adalah untuk menghasilkan motif batik  baru yang mempunyai ciri khas Jember. Metode yang digunakan yaitu pengumpulan data, pengamatan mendalam terhadap objek penciptaan, pengkajian sumber inspirasi, pembuatan desain motif, dan perwujudan menjadi batik. Dari penciptaan seni ini berhasil dikreasikan 6 (enam motif batik yaitu: (1 Motif Uwoh Kopi; (2 Motif Godong Kopi;  (3 Motif Ceplok Kakao; (4 Motif Kakao Raja; (5 Motif Kakao Biru; dan (6 Motif Wiji Mukti. Berdasarkan hasil penilaian “Selera Estetika” diketahui bahwa motif yang paling banyak disukai adalah Motif Uwoh Kopi dan Motif Kakao Raja. Kata kunci: Motif Woh Kopi, Motif Godong Kopi, Motif Ceplok Kakao, Motif Kakao Raja, Motif Kakao Biru, Motif Wiji Mukti ABSTRACTBatik Jember is synonymous with tobacco leaf motif. Tobacco leaf shape is quite weak in the visual appearance characterized as that motif emerges like a picture of leaves in general. Therefore, it is necessary to create a distinctive design motif extracted from other natural resources of Jember that have specific shapes and characteristics that can be obtained as the stronger motif identity. The typical natural resources from Jember are coffee and cocoa. The purpose of the creation of this art is to produce the unique, creative and innovative batik and have specific characteristics of Jember. The method used are data collection, observation of the object, reviewing inspiration sources

  2. Semiconductor ring lasers coupled by a single waveguide

    Science.gov (United States)

    Coomans, W.; Gelens, L.; Van der Sande, G.; Mezosi, G.; Sorel, M.; Danckaert, J.; Verschaffelt, G.

    2012-06-01

    We experimentally and theoretically study the characteristics of semiconductor ring lasers bidirectionally coupled by a single bus waveguide. This configuration has, e.g., been suggested for use as an optical memory and as an optical neural network motif. The main results are that the coupling can destabilize the state in which both rings lase in the same direction, and it brings to life a state with equal powers at both outputs. These are both undesirable for optical memory operation. Although the coupling between the rings is bidirectional, the destabilization occurs due to behavior similar to an optically injected laser system.

  3. 2-Phenyl-7-(4-pyridylmethylamino-1,2,4-triazolo[1,5-a][1,3,5]triazin-5(4H-oneFused heterocyclic systems with s-triazine ring. Part 17. For part 16, see Dolzhenko et al. (2011.

    Directory of Open Access Journals (Sweden)

    Lip Lin Koh

    2011-01-01

    Full Text Available In the title compound, C16H13N7O, the 1,2,4-triazolo[1,5-a][1,3,5]triazine heterocyclic system is essentially planar (r.m.s. deviation = 0.0375 Å. The attached benzene ring lies almost in the mean plane of 1,2,4-triazolo[1,5-a][1,3,5]triazine [dihedral angle = 1.36 (23°], while the pyridine ring is turned out of this plane by the aminomethyl bridge [dihedral angle = 69.22 (9°]. The amino group H atom is involved in intramolecular hydrogen bonding with a triazole N atom. In the crystal, molecules are connected via C(=ONH...N hydrogen bonds into C(11 chains parallel to [100]. The amino group H atom acts as a hydrogen-bond donor, forming an NH...O=C hydrogen bond with the carbonyl O atom, which links the molecules into C(6 chains running along [011] and [01overline{1}].

  4. A new type of Na(+-driven ATP synthase membrane rotor with a two-carboxylate ion-coupling motif.

    Directory of Open Access Journals (Sweden)

    Sarah Schulz

    Full Text Available The anaerobic bacterium Fusobacterium nucleatum uses glutamate decarboxylation to generate a transmembrane gradient of Na⁺. Here, we demonstrate that this ion-motive force is directly coupled to ATP synthesis, via an F₁F₀-ATP synthase with a novel Na⁺ recognition motif, shared by other human pathogens. Molecular modeling and free-energy simulations of the rotary element of the enzyme, the c-ring, indicate Na⁺ specificity in physiological settings. Consistently, activity measurements showed Na⁺ stimulation of the enzyme, either membrane-embedded or isolated, and ATP synthesis was sensitive to the Na⁺ ionophore monensin. Furthermore, Na⁺ has a protective effect against inhibitors targeting the ion-binding sites, both in the complete ATP synthase and the isolated c-ring. Definitive evidence of Na⁺ coupling is provided by two identical crystal structures of the c₁₁ ring, solved by X-ray crystallography at 2.2 and 2.6 Å resolution, at pH 5.3 and 8.7, respectively. Na⁺ ions occupy all binding sites, each coordinated by four amino acids and a water molecule. Intriguingly, two carboxylates instead of one mediate ion binding. Simulations and experiments demonstrate that this motif implies that a proton is concurrently bound to all sites, although Na⁺ alone drives the rotary mechanism. The structure thus reveals a new mode of ion coupling in ATP synthases and provides a basis for drug-design efforts against this opportunistic pathogen.

  5. Structure-based design synthesis of functionalized 3-(5-(s-phenyl)-4H-pyrazol-3-yl)-2H-chromen-2-one motifs and indigenous plant extracts and their antimalarial potential

    Science.gov (United States)

    Olayinka, Ajani; Grace, Olasehinde; Titilope, Dokunmu; Ruth, Diji-Geske; Olabode, Onileere; John, Openibo; Oreoluwa, Oluseye; Tochukwu, Chileke; Ezekiel, Adebiyi

    2018-04-01

    Resistance of the malaria parasite to conventional therapeutic agents calls for increased efforts in antimalarial drug discovery. Current efforts should be targeted at developing safe and affordable new agents to counter the spread of malaria parasites that are resistant to existing therapy. In this study, toxicological and in vivo antiplasmodial properties of 3-(5-(s-phenyl)-4H-pyrazol-3-yl)-42H-chromen-2, Mangifera indica and Tithonia diversifolia in swiss albino mice models, Musmusculus were investigated. 2H-Chromen-2-one also known as coumarin is highly privileged oxygen-containing heterocyclic entity which are present in plant kingdom as secondary metabolites. The maceration technique of crude drug extraction was employed using cold water extraction. Toxicological analysis was carried out using Lorke's method for acute toxicity testing while the chemosuppressive activity was carried out using Peter's four day test on early infection. We also report the synthesis of functionalized 3-(5-(s-phenyl)-4H-pyrazol-3-yl)-2H-chromen-2-one motifs via microwave assisted synthetic approach and isolation of indigenous plant extract in order to investigate their antimalarial efficacy. The condensation reaction of 3-acetylcoumarin with various benzaldehyde derivatives resulted in the formation of 3-[3-acryloyl]-2H-chromen-2-one which was subsequently reaction the hydrazine hydrate via microwave assisted hydrazinolysis to afford the targeted 3-(5-(s-phenyl)-4H-pyrazol-3-yl)-2H-chromen-2-one motifs. The chemical structures were confirmed by analytical data and spectroscopic means such as FT-IR, UV, 1H NMR, 13C NMR and DEPT-135. The microwave assisted reaction was remarkably successful and gave targeted 3-(5-(s-phenyl)-4H-pyrazol-3-yl)-2H-chromen-2-one motifs in higher yields at lesser reaction time compared to conventional heating method. The LD50 of the aqueous extracts of the leaves and stem bark Mangifera indica was established to be ± 707.11 mg/kg b.w., p.o. (body weight

  6. BayesMotif: de novo protein sorting motif discovery from impure datasets.

    Science.gov (United States)

    Hu, Jianjun; Zhang, Fan

    2010-01-18

    Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms. We formulated the protein sorting motif discovery problem as a classification problem and proposed a Bayesian classifier based algorithm (BayesMotif) for de novo identification of a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions. A false positive removal procedure is developed to iteratively remove sequences that are unlikely to contain true motifs so that the algorithm can identify motifs from impure input sequences. Experiments on both implanted motif datasets and real-world datasets showed that the enhanced BayesMotif algorithm can identify anchored sorting motifs from pure or impure protein sequence dataset. It also shows that the false positive removal procedure can help to identify true motifs even when there is only 20% of the input sequences containing true motif instances. We proposed BayesMotif, a novel Bayesian classification based algorithm for de novo discovery of a special category of anchored protein sorting motifs from impure datasets. Compared to conventional motif discovery algorithms such as MEME, our algorithm can find less-conserved motifs with short highly conserved anchors. Our algorithm also has the advantage of easy incorporation of additional meta-sequence features such as hydrophobicity or charge of the motifs which may help to overcome the limitations of

  7. Fluorinated cyclohexanes: Synthesis of amine building blocks of the all-cis 2,3,5,6-tetrafluorocyclohexylamine motif

    Directory of Open Access Journals (Sweden)

    Tetiana Bykova

    2017-04-01

    Full Text Available This paper reports the synthesis of three amine stereoisomers 5a–c of the tetrafluorocyclohexyl ring system, as building blocks for discovery chemistry programmes. The synthesis starts from a Birch reduction of benzonitrile, followed by an in situ methyl iodide quench. The resultant 2,5-cyclohexadiene was progressed via double epoxidations and then hydrofluorination ring opening reactions. The resultant fluorohydrin moieties were then converted to different stereoisomers of the tetrafluorocyclohexyl ring system, and then reductive hydrogenation of the nitrile delivered three amine stereoisomers. It proved necessary to place a methyl group on the cyclohexane ring in order to stabilise the compound against subsequent HF elimination. The two all-cis tetrafluorocyclohexyl isomers 5a and 5b constitute facially polarized cyclohexane rings, with fluorines on the electronegative face and hydrogens on the electropositive face.

  8. Colliding and merging galaxies. II. S0 galaxies with polar rings

    International Nuclear Information System (INIS)

    Schweizer, F.; Whitmore, B.D.; Rubin, V.C.

    1983-01-01

    We first present a detailed optical study of A0136-0801, a 16 1/2 -mag ''spindle'' galaxy girdled by a ring of gas, dust, and young stars. The spindle is a normal S0 disk seen nearly edge-on, as shown by its photometric profile and fast rotation (v/sub rot//sigma/sub v/ = 2.2); a prolate structure seems to be ruled out. The surrounding ring runs over the poles of this S0 disk and serves as a probe of the vertical potential. The ring motions suggest that a massive halo extends far beyond the S0 disk (out to 3R 25 ) and that this halo is more nearly spherical than flat. We then list 22 related galaxies and derive that a few percent of all field S0's possess near-polar rings or disks. We suggest that these structures are due to a second event, most likely the transfer of mass from a companion galaxy during a close encounter and occasionally also the merger of a companion. Although accretion occurs presumably at random angles, polar rings are favored statistically because of their slow differential precession and consequent longevity. Alternate evolutionary schemes are also discussed. Finally, we suggest that M82 may be forming a polar ring from former M81 material, and predict that the ''tilted bulge'' of UGC 7576 is an S0 disk seen nearly edge-on

  9. Resource-saving technology for manufacturing billets for piston’s rings

    Directory of Open Access Journals (Sweden)

    A. N. Krutilin

    2010-10-01

    shortcomings, the proposed process is characterized by a significant reduction of laboriousness, improved working conditions, a significant decreasing of molding materials, decreasing of production areas, complete except flasks and ladles. In the Belarusian National Technical University was developed an improved method of casting immersion [2], schematic diagram of the process was shown in Figure 1. Thin ring single mould (5-10 mm, core sand - made, collect by means of a special device to the blocks. Pouring and filling billets are being when preheated moulds immersing in melt metal through one or more gatings, leaving the outer surface of the mould. Filling billet is directly from the molten pool until its complete solidification, after finishing of billet’s crystallization, non - solidified metal from the gatings goes back into the oven. For a long time, based on experimental investigation are identified optimal technological parameters of the process of casting billets of low-alloyed gray and ductile iron.Through the minimum time between the modification and pouring moulds of melt, graphitized items, in ligatures, have the greatest effect. Crystallization of the alloy is mainly running with the formation of austenite-graphite eutectic, which also has a positive effect on reducing marriage to porosity. Due to the active influence on the rate of solidification and cooling at different periods of the formation of the casting, provides technological process provide to obtaining billets without structurally - free carbides with the requisite level of physical and mechanical properties without the using of energy-intensive heat treatment. Optimal thermal conditions for the formation provide uniformity of hardness on the perimeter of billet. Physical-mechanical properties and microstructure satisfy the technical requirements for piston’s rings. Possibility to obtain a single cast billets of ductile iron with hypoeutectic composition, free shrinkage defects. Significantly

  10. The T-cell receptor beta chain CDR3 region of BV8S1/BJ1S5 transcripts in type 1 diabetes.

    Science.gov (United States)

    Naserke, H E; Durinovic-Bellò, I; Seidel, D; Ziegler, A G

    1996-01-01

    We recently described the T-cell receptor (TCR) beta chain CDR3 motif S-SDRLG-NQPQH (BV8S1-BJ1S5) in an islet-specific T-cell clone (K2.12) from a type 1 diabetic patient (AS). A similar motif (RLGNQ) was also reported in a T-cell clone of non-obese diabetic (NOD) mice by others. In order to determine the frequency of our motif in selected and unselected T-cell populations, we cloned and sequenced the CDR3 region of BV8S1-BJ1S5 transcripts. These transcripts were derived from unstimulated peripheral blood T lymphocytes from two type 1 diabetic patients (AS and FS) and their non-diabetic sibling (WS), as well as from an islet-specific T-cell line of one of the patients. In addition, we compared the structure and composition of the CDR3 region in BV8S1-BJ1S5 transcripts from peripheral blood T cells between the patients and their non-diabetic sibling (>50 sequences each). We found that 30% of the islet-specific T-cell line cDNA clones expressed the entire sequence-motif, whereas it was absent in the clones of unstimulated peripheral blood T cells from both patients and their non-diabetic sibling. The average length of the CDR3 region was shorter in the patients (mean AS 9.9, FS 9.9, versus WS 10.7, p = 0.0037) and the number of inserted nucleotides in N nucleotide addition at the DJ-junction lower (mean AS 3.5, FS 3. 2, versus WS 5.2, P = diabetic sibling. Moreover, the pattern of amino acid usage in the CDR3 region was dissimilar at positions 5 and 6, where polar amino acids predominated in both diabetic siblings. In contrast, basic amino acids are preferentially used at position 5 in the clones of the non-diabetic sibling. These data provide information on the general structure of the TCR(BV8S1-BJ1S5) CDR3 region in type 1 diabetes and may indicate differences in the amino and nucleic acid composition of the TCR beta chain CDR3 region between two type 1 diabetic patients and their non-diabetic sibling.

  11. THE EFFECTS OF CRACKING ON THE SURFACE POTENTIAL OF ICY GRAINS IN SATURN’S E-RING: LABORATORY STUDIES

    Energy Technology Data Exchange (ETDEWEB)

    Bu, Caixia; Bahr, David A.; Dukes, Catherine A.; Baragiola, Raúl A., E-mail: cb8nw@virginia.edu [Laboratory for Astrophysics and Surface Physics, Materials Science and Engineering, University of Virginia, Charlottesville, VA 22904 (United States)

    2016-07-10

    Within Saturn's E-ring, dust grains are coated by water vapor co-released with ice grains from the geyser-like eruptions of Enceladus. These ice-coated grains have intrinsic surface potential and interact synergistically with the ions and electrons of Saturn's magnetospheric plasmas. We perform laboratory experiments to investigate the effects of water-ice growth on the surface potential, using amorphous solid water (ASW) films. We estimate the growth of the surface potential to be ∼ 2.5 mV (Earth) yr{sup 1} and 112 mV yr{sup 1} for E-ring grains at ∼4.5 R {sub s} and 3.95 R {sub s} outside Enceladus’s plume, respectively. In addition, our measurements show that the linear relationship between the surface potential and the film thickness, as described in previous studies, has an upper limit, where the film spontaneously cracks above a porosity-dependent critical thickness. Heating of the cracked films with (and without) deposited charge shows that significant positive (and negative) surface potentials are retained at temperatures above 110 K, contrary to the minimal values (roughly zero) for thin, transparent ASW films. The significant surface potentials observed on micron-scale cracked ice films after thermal cycling, (5–20) V, are consistent with Cassini measurements, which indicate a negative charge of up to 5 V for E-ring dust particles at ∼5 R {sub s}. Therefore, the native grain surface potential resulting from water-vapor coating must be included in modeling studies of interactions between E-ring icy surfaces and Saturn's magnetospheric plasma.

  12. 200 MW S-band traveling wave resonant ring development at IHEP

    Science.gov (United States)

    Zhou, Zu-Sheng; Chi, Yun-Long; Git, Meng-Ping; Pei, Guo-Xi

    2010-03-01

    The resonant-ring is a traveling wave circuit, which is used to produce high peak power with comparatively smaller stored energy. The application to be considered is its use as a high power simulator mainly for testing the klystron ceramic output window, as well as for high power microwave transmission devices. This paper describes the principle of a resonant ring and introduces the structure and property of the newly constructed traveling wave resonant ring at IHEP. Our goal is to produce a 200 MW class resonant ring at 2.856 GHz with a pulse length of 2 μs and repetition rate of 25 Hz. The installation, commissioning and testing of the ring have been completed and a peak power of 200 MW at 3 μs has been achieved. The conditioning results show that all the parameters of the resonant ring reach the design goals.

  13. Motif enrichment tool.

    Science.gov (United States)

    Blatti, Charles; Sinha, Saurabh

    2014-07-01

    The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Tert-butyl 3-oxo-2,3,4,5,6,7-hexahydro-1H-pyrazolo[4,3-c]pyridine-5-carboxylate

    Directory of Open Access Journals (Sweden)

    Tara Shahani

    2010-01-01

    Full Text Available In the title compound, C11H17N3O3, the pyrazole ring is approximately planar, with a maximum deviation of 0.005 (2 Å, and forms a dihedral angle of 5.69 (13° with the plane through the six atoms of the piperidine ring. In the crystal, pairs of intermolecular N—H...O hydrogen bonds form dimers with neighbouring molecules, generating R22(8 ring motifs. These dimers are further linked into two-dimensional arrays parallel to the bc plane by intermolecular N—H...O and C—H...O hydrogen bonds.

  15. Design of low energy ring(s)

    CERN Document Server

    Lachaize, Antoine

    During the last two years, several upgrades of the initial baseline scenario were studied with the aim of increasing the average intensity of ion beams in the accelerator chain of the Beta Beam complex. This is the reason why the Rapid Cycling Synchrotron (RCS) specifications were reconsidered many times [1], [2], [3].General considerations on the optical design were presented at the Beta Beam Task Meetings held at CERN and at Saclay in 2005 [4]. More detailed beam optics studies were performed during the next months. Lattices, RF system parameters, multi-turn injection scheme, fast extraction, closed orbit correction and chromaticity correction systems were proposed for different versions of the RCS [5], [6], [7].Finally, the RCS specifications have stabilized in November 2006 after the fourth Beta Beam Task Meeting when it was decided to fix the maximum magnetic rigidity of ion beams to 14.47 T.m (3.5 GeV equivalent proton energy) and to adopt a ring physical radius of 40 m in order to facilitate injectio...

  16. Crystal structure of 2-methylamino-4-(6-methyl-4-oxo-4H-chromen-3-yl-3-nitropyrano[3,2-c]chromen-5(4H-one with an unknown solvate

    Directory of Open Access Journals (Sweden)

    Rajamani Raja

    2015-09-01

    Full Text Available In the title compound, C23H16N2O7, the mean planes of the two chromene units (r.m.s. deviations = 0.031 and 0.064 Å are almost normal to one another with a dihedral angle of 85.59 (6°. The central six-membered pyran ring has a distorted envelope conformation, with the methine C atom at the flap. There is an intramolecular N—H...O hydrogen bond, which generates an S(6 ring motif. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with an R22(12 ring motif. The dimers are linked by pairs of C—H...O hydrogen bonds, enclosing R22(6 ring motifs, forming zigzag chains along [001]. The chains are linked by a second pair of C—H...O hydrogen bonds, forming slabs parallel to (110. Within the slabs there are C—H...π interactions present. A region of disordered electron density was treated with the SQUEEZE procedure in PLATON [Spek (2015. Acta Cryst. C71, 9–18] following unsuccessful attempts to model it as plausible solvent molecule(s. The given chemical formula and other crystal data do not take into account the unknown solvent molecule(s.

  17. Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation.

    Science.gov (United States)

    Michael, Sushama; Travé, Gilles; Ramu, Chenna; Chica, Claudia; Gibson, Toby J

    2008-02-15

    KEN-box-mediated target selection is one of the mechanisms used in the proteasomal destruction of mitotic cell cycle proteins via the APC/C complex. While annotating the Eukaryotic Linear Motif resource (ELM, http://elm.eu.org/), we found that KEN motifs were significantly enriched in human protein entries with cell cycle keywords in the UniProt/Swiss-Prot database-implying that KEN-boxes might be more common than reported. Matches to short linear motifs in protein database searches are not, per se, significant. KEN-box enrichment with cell cycle Gene Ontology terms suggests that collectively these motifs are functional but does not prove that any given instance is so. Candidates were surveyed for native disorder prediction using GlobPlot and IUPred and for motif conservation in homologues. Among >25 strong new candidates, the most notable are human HIPK2, CHFR, CDC27, Dab2, Upf2, kinesin Eg5, DNA Topoisomerase 1 and yeast Cdc5 and Swi5. A similar number of weaker candidates were present. These proteins have yet to be tested for APC/C targeted destruction, providing potential new avenues of research.

  18. Improved i-motif thermal stability by insertion of anthraquinone monomers

    DEFF Research Database (Denmark)

    Gouda, Alaa S; Amine, Mahasen S.; Pedersen, Erik Bjerregaard

    2017-01-01

    In order to gain insight into how to improve thermal stability of i-motifs when used in the context of biomedical and nanotechnological applications, novel anthraquinone-modified i-motifs were synthesized by insertion of 1,8-, 1,4-, 1,5- and 2,6-disubstituted anthraquinone monomers into the TAA...... loops of a 22mer cytosine-rich human telomeric DNA sequence. The influence of the four anthraquinone linkers on the i-motif thermal stability was investigated at 295 nm and pH 5.5. Anthraquinone monomers modulate the i-motif stability in a position-depending manner and the modulation also depends...... unlocked nucleic acid monomers or twisted intercalating nucleic acid. The 2,6-disubstituted anthraquinone linker replacing T10 enabled a significant increase of i-motif thermal melting by 8.2 °C. A substantial increase of 5.0 °C in i-motif thermal melting was recorded when both A6 and T16 were modified...

  19. N-[(2S-4-Chloro-2-(l-menthyloxy-5-oxo-2,5-dihydro-3-furyl]-l-alanine

    Directory of Open Access Journals (Sweden)

    Kai Yang

    2009-05-01

    Full Text Available The title compound, C17H26ClNO5, was prepared via a tandem asymmetric Michael addition–elimination reaction of (5S-3,4-dichloro-5-(l-menthyloxyfuran-2(5H-one and l-alanine in the presence of potassium hydroxide. The five-membered furanone ring is approximately planar while the six-membered menthyloxy ring adopts a chair conformation. The crystal packing is stabilized by intermolecular O—H...O and N—H...O hydrogen bonds.

  20. 3-Phenyl-6-(2-pyridyl-1,2,4,5-tetrazine

    Directory of Open Access Journals (Sweden)

    Daniel Chartrand

    2008-01-01

    Full Text Available The title compound, C13H9N5, is the first asymmetric diaryl-1,2,4,5-tetrazine to be crystallographically characterized. We have been interested in this motif for incorporation into supramolecular assemblies based on coordination chemistry. The solid state structure shows a centrosymmetric molecule, forcing a positional disorder of the terminal phenyl and pyridyl rings. The molecule is completely planar, unusual for aromatic rings with N atoms in adjacent ortho positions. The stacking observed is very common in diaryltetrazines and is dominated by π stacking [centroid-to-centroid distance between the tetrazine ring and the aromatic ring of an adjacent molecule is 3.6 Å, perpendicular (centroid-to-plane distance of about 3.3 Å].

  1. Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d

    Directory of Open Access Journals (Sweden)

    Moffatt Barbara A

    2010-08-01

    Full Text Available Abstract Background Aromatic amino acids play a critical role in protein-glycan interactions. Clusters of surface aromatic residues and their features may therefore be useful in distinguishing glycan-binding sites as well as predicting novel glycan-binding proteins. In this work, a structural bioinformatics approach was used to screen the Protein Data Bank (PDB for coplanar aromatic motifs similar to those found in known glycan-binding proteins. Results The proteins identified in the screen were significantly associated with carbohydrate-related functions according to gene ontology (GO enrichment analysis, and predicted motifs were found frequently within novel folds and glycan-binding sites not included in the training set. In addition to numerous binding sites predicted in structural genomics proteins of unknown function, one novel prediction was a surface motif (W34/W36/W192 in the tobacco pathogenesis-related protein, PR-5d. Phylogenetic analysis revealed that the surface motif is exclusive to a subfamily of PR-5 proteins from the Solanaceae family of plants, and is absent completely in more distant homologs. To confirm PR-5d's insoluble-polysaccharide binding activity, a cellulose-pulldown assay of tobacco proteins was performed and PR-5d was identified in the cellulose-binding fraction by mass spectrometry. Conclusions Based on the combined results, we propose that the putative binding site in PR-5d may be an evolutionary adaptation of Solanaceae plants including potato, tomato, and tobacco, towards defense against cellulose-containing pathogens such as species of the deadly oomycete genus, Phytophthora. More generally, the results demonstrate that coplanar aromatic clusters on protein surfaces are a structural signature of glycan-binding proteins, and can be used to computationally predict novel glycan-binding proteins from 3 D structure.

  2. Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d.

    Science.gov (United States)

    Doxey, Andrew C; Cheng, Zhenyu; Moffatt, Barbara A; McConkey, Brendan J

    2010-08-03

    Aromatic amino acids play a critical role in protein-glycan interactions. Clusters of surface aromatic residues and their features may therefore be useful in distinguishing glycan-binding sites as well as predicting novel glycan-binding proteins. In this work, a structural bioinformatics approach was used to screen the Protein Data Bank (PDB) for coplanar aromatic motifs similar to those found in known glycan-binding proteins. The proteins identified in the screen were significantly associated with carbohydrate-related functions according to gene ontology (GO) enrichment analysis, and predicted motifs were found frequently within novel folds and glycan-binding sites not included in the training set. In addition to numerous binding sites predicted in structural genomics proteins of unknown function, one novel prediction was a surface motif (W34/W36/W192) in the tobacco pathogenesis-related protein, PR-5d. Phylogenetic analysis revealed that the surface motif is exclusive to a subfamily of PR-5 proteins from the Solanaceae family of plants, and is absent completely in more distant homologs. To confirm PR-5d's insoluble-polysaccharide binding activity, a cellulose-pulldown assay of tobacco proteins was performed and PR-5d was identified in the cellulose-binding fraction by mass spectrometry. Based on the combined results, we propose that the putative binding site in PR-5d may be an evolutionary adaptation of Solanaceae plants including potato, tomato, and tobacco, towards defense against cellulose-containing pathogens such as species of the deadly oomycete genus, Phytophthora. More generally, the results demonstrate that coplanar aromatic clusters on protein surfaces are a structural signature of glycan-binding proteins, and can be used to computationally predict novel glycan-binding proteins from 3 D structure.

  3. Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries

    DEFF Research Database (Denmark)

    Nielsen, Jeppe Lund; Schramm, Andreas; Bernhard, Anne E.

    2004-01-01

    for Systems Biology,3 Seattle, Washington, and Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany2 A flow cytometry method was developed for rapid screening and recovery of cloned DNA containing common sequence motifs. This approach, termed fluorescence-activated cell sorting......  FLOW CYTOMETRY-ASSISTED CLONING OF SPECIFIC SEQUENCE MOTIFS FROM COMPLEX 16S RRNA GENE LIBRARIES Jeppe L. Nielsen,1 Andreas Schramm,1,2 Anne E. Bernhard,1 Gerrit J. van den Engh,3 and David A. Stahl1* Department of Civil and Environmental Engineering, University of Washington,1 and Institute......-assisted cloning, was used to recover sequences affiliated with a unique lineage within the Bacteroidetes not abundant in a clone library of environmental 16S rRNA genes.  ...

  4. Identity and functions of CxxC-derived motifs.

    Science.gov (United States)

    Fomenko, Dmitri E; Gladyshev, Vadim N

    2003-09-30

    Two cysteines separated by two other residues (the CxxC motif) are employed by many redox proteins for formation, isomerization, and reduction of disulfide bonds and for other redox functions. The place of the C-terminal cysteine in this motif may be occupied by serine (the CxxS motif), modifying the functional repertoire of redox proteins. Here we found that the CxxC motif may also give rise to a motif, in which the C-terminal cysteine is replaced with threonine (the CxxT motif). Moreover, in contrast to a view that the N-terminal cysteine in the CxxC motif always serves as a nucleophilic attacking group, this residue could also be replaced with threonine (the TxxC motif), serine (the SxxC motif), or other residues. In each of these CxxC-derived motifs, the presence of a downstream alpha-helix was strongly favored. A search for conserved CxxC-derived motif/helix patterns in four complete genomes representing bacteria, archaea, and eukaryotes identified known redox proteins and suggested possible redox functions for several additional proteins. Catalytic sites in peroxiredoxins were major representatives of the TxxC motif, whereas those in glutathione peroxidases represented the CxxT motif. Structural assessments indicated that threonines in these enzymes could stabilize catalytic thiolates, suggesting revisions to previously proposed catalytic triads. Each of the CxxC-derived motifs was also observed in natural selenium-containing proteins, in which selenocysteine was present in place of a catalytic cysteine.

  5. MotifMark: Finding regulatory motifs in DNA sequences.

    Science.gov (United States)

    Hassanzadeh, Hamid Reza; Kolhe, Pushkar; Isbell, Charles L; Wang, May D

    2017-07-01

    The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the specificity of target proteins in binding to these regions are two important steps in understanding the mechanisms of these biological activities. A number of high-throughput technologies have recently emerged that try to quantify the affinity between proteins and DNA motifs. Despite their success, these technologies have their own limitations and fall short in precise characterization of motifs, and as a result, require further downstream analysis to extract useful and interpretable information from a haystack of noisy and inaccurate data. Here we propose MotifMark, a new algorithm based on graph theory and machine learning, that can find binding sites on candidate probes and rank their specificity in regard to the underlying transcription factor. We developed a pipeline to analyze experimental data derived from compact universal protein binding microarrays and benchmarked it against two of the most accurate motif search methods. Our results indicate that MotifMark can be a viable alternative technique for prediction of motif from protein binding microarrays and possibly other related high-throughput techniques.

  6. UKIRAN KERAWANG ACEH GAYO SEBAGAI INSPIRASI PENCIPTAAN MOTIF BATIK KHAS GAYO

    Directory of Open Access Journals (Sweden)

    Irfa ina Rohana Salma

    2016-12-01

    Full Text Available ABSTRAK Industri batik mulai berkembang di Gayo, tetapi belum memiliki motif batik khas daerah. Oleh karena itu perlu diciptakan motif batik khas Gayo, dengan mengambil inspirasi dari ukiran yang terdapat pada rumah tradisional yang biasa disebut ukiran kerawang Gayo. Tujuan penciptaan seni ini adalah untuk menciptakan motif batik yang memiliki ciri khas Gayo. Metode yang digunakan yaitu eksplorasi ide, perancangan, dan perwujudan menjadi motif batik. Dalam kegiatan ini telah diciptakan enam motif batik khas Gayo yaitu: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif Gayo Lurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. Hasil uji kesukaan terhadap motif kepada lima puluh responden menunjukkan bahwa Motif Ceplok Gayo paling banyak dipilih oleh responden yaitu sebesar 19%, sedangkan Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo Lurus 15% dan Motif Gayo Tegak 14%. Rata-rata motif yang dihasilkan mendapatkan apresiasi yang baik dari responden, sehingga semua motif layak diproduksi sebagai batik khas Gayo.Kata kunci: batik Gayo, Motif Ceplok Gayo, Motif Parang Gayo.ABSTRACTBatik industry began to develop in Gayo, but have not had a typical batik motif itself. Therefore, it is necessary to create batik motifs of Gayo, by taking inspiration from the carvings found in traditional houses commonly called kerawang Gayo. The purpose of this art is to create motifs those have a Gayo characteristic. The method used are the idea exploration, design, and motifs embodiment. In this activity has created six Gayo batik motifs, namely: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif GayoLurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. The test results fondness of the motives to fifty respondents indicated that the Motif Ceplok Gayo most preferred by respondents ie 19%, while Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo

  7. 2-(5-Chloro-2-oxoindolin-3-ylidenehydrazinecarbothioamide

    Directory of Open Access Journals (Sweden)

    Viviane Conceição Duarte de Bittencourt

    2014-01-01

    Full Text Available The title molecule, C9H7ClN4OS, is almost planar, with an r.m.s. deviation of 0.034 (2 Å for the mean plane through all the non-H atoms. Intramolecular N—H...O and N—H...N hydrogen bonds form S(6 and S(5 ring motifs, respectively. In the crystal, molecules are assembled into inversion dimers through pairs of co-operative N—H...Cl interactions. These dimers are connected along the b axis by N—H...O and N—H...S hydrogen bonds, generating layers parallel to (103. The layers are further connected along the a axis into a three-dimensional network, through weak π–π stacking interactions [centroid–centroid distance = 3.849 (2 Å].

  8. 25Gb/s 1V-driving CMOS ring modulator with integrated thermal tuning.

    Science.gov (United States)

    Li, Guoliang; Zheng, Xuezhe; Yao, Jin; Thacker, Hiren; Shubin, Ivan; Luo, Ying; Raj, Kannan; Cunningham, John E; Krishnamoorthy, Ashok V

    2011-10-10

    We report a high-speed ring modulator that fits many of the ideal qualities for optical interconnect in future exascale supercomputers. The device was fabricated in a 130 nm SOI CMOS process, with 7.5 μm ring radius. Its high-speed section, employing PN junction that works at carrier-depletion mode, enables 25 Gb/s modulation and an extinction ratio >5 dB with only 1V peak-to-peak driving. Its thermal tuning section allows the device to work in broad wavelength range, with a tuning efficiency of 0.19 nm/mW. Based on microwave characterization and circuit modeling, the modulation energy is estimated ~7 fJ/bit. The whole device fits in a compact 400 μm2 footprint.

  9. Parole, Sintagmatik, dan Paradigmatik Motif Batik Mega Mendung

    Directory of Open Access Journals (Sweden)

    Rudi - Nababan

    2012-04-01

    Full Text Available ABSTRACT   Discussing traditional batik is related a lot to the organization system of fine arts element ac- companying it, either the pattern of the motif or the technique of the making. In this case, the motif of Mega Mendung Cirebon certainly has patterns and rules which are traditionally different from the other motifs in other areas. Through  semiotics analysis especially with Saussure and Pierce concept, it can be traced that batik with Cirebon motif, in this case Mega Mendung motif, has parole and langue system, as unique fine arts language in batik, and structure of visual syntagmatic and paradigmatic. In the context of batik motif as fine arts language, it is surely related to sign system as symbol and icon.       Keywords: visual semiotic, Cirebon’s batik.

  10. 6-Bromo-1,3-di-2-propynyl-1H-imidazo[4,5-b]pyridin-2(3H-one

    Directory of Open Access Journals (Sweden)

    S. Dahmani

    2010-04-01

    Full Text Available The room-temperature reaction of propargyl bromide and 6-bromo-1,3-dihydroimidazo[4,5-b]pyridin-2-one in dimethylformamide yields the title compound, C12H8BrN3O, which features nitrogen-bound propynyl substituents. The imidazopyridine fused ring is almost planar (r.m.s. deviation = 0.011 Å; the propynyl chains point in opposite directions relative to the fused ring. One acetylenic H atom is hydrogen bonded to the carbonyl O atom of an inversion-related molecule, forming a dimer; adjacent dimers are linked by a second acetylene–pyridine C—H...N interaction, forming a layer motif.

  11. RingSys-Scheduler User`s manual. Information terminal for town monitoring; Brukermanual for RingSys-Scheduler. Informasjonsterminal for byovervaaking

    Energy Technology Data Exchange (ETDEWEB)

    Marsteen, L.

    1996-02-01

    This report is a User`s manual. It describes RingSys Scheduler, a computer system for continuous display of time series, public information and static pictures. The computer is connected to a host machine via modem and time series, and public information are automatically updated once an hour. RingSys-Scheduler is PC based. It is developed using Excel`s macro language as well as the asynchronous communication program Dynacomm`s script language. 12 figs.

  12. 3-Phenyl-6-(2-pyrid­yl)-1,2,4,5-tetra­zine

    OpenAIRE

    Chartrand, Daniel; Laverdière, François; Hanan, Garry

    2007-01-01

    The title compound, C13H9N5, is the first asymmetric diaryl-1,2,4,5-tetrazine to be crystallographically characterized. We have been interested in this motif for incorporation into supramolecular assemblies based on coordination chemistry. The solid state structure shows a centrosymmetric molecule, forcing a positional disorder of the terminal phenyl and pyridyl rings. The molecule is completely planar, unusual for aromatic rings with N atoms in adjacent ortho positions. The stacking observed...

  13. Saturn’s ring temperatures at equinox

    Science.gov (United States)

    Spilker, Linda J.; Ferrari, C.; Morishima, R.

    2013-10-01

    Modeling the thermal emission of Saturn's rings is challenging due to the numerous heating sources as well as the structural properties of the disk and of the particles that are closely related. At equinox, however, the main rings are externally heated by Saturn alone and the problem is somewhat simplified. We test the abilities of our current models to reproduce the temperatures observed with the Cassini CIRS instrument around equinox in August 2009. A simple semi-analytic model which includes mutual shadowing effects can mostly explain the radial profile of the equinox ring temperatures, except the model predicts lower temperatures than those observed for the A ring. The temperature variation at a given saturnocentric radius is primarily caused by observational geometry variations relative to Saturn. The observed temperature increases with decreasing Saturn-ring-observer angle. In addition, we found evidence that the leading hemispheres of particles are warmer than the trailing hemispheres at least for the C ring and probably for the A and B rings as well. This is explained if some fraction of particles has spin rates lower than the synchronous rotation rate as predicted by N-body simulations. The spin model for a monolayer ring (Ferrari, C., Leyrat, C., 2006, Astron. Astrophys. 447, 745-760) can fit the temperature variations with spacecraft longitude observed in the C ring with currently known thermal properties and a mixing of slow and fast rotators. The multilayer model (Morishima, R., Salo, H., Ohtsuki, K., 2009, Icarus 201, 634-654) can reproduce the temperatures of the B and C rings but gives A ring temperatures that are significantly lower than those observed as does the simple semi-analytic model. More advanced models which take into account self-gravity wakes may explain the A ring temperature behavior.

  14. ARCHETYPES AND MYTHOLOGICAL MOTIFS: JOHN UPDIKE’S LEGACY REVISITED

    Directory of Open Access Journals (Sweden)

    Loreta Ulvydienė

    2018-04-01

    Full Text Available John Updike is widely considered to be one of the greatest, one of the most popular and sometimes most controversial writers concerned with the American small town and middle-class materialism. A lot of literary critics and researchers observe that Updike’s finest work came from his exploration of ordinary America and from his use of elegant prose, rich with metaphor, to portray the public and private feelings of Americans, their daily rounds of life. In addition, discussing Updike’s individual works a lot of literary critics and researchers have observed the writer’s attempts to re-write myth in “the mythical age”1 of the twentieth century. Naturally enough, as the return to myth is assumed to be a certain feature of the Modernist movement, half a century later since Updike’s famous novel Centaur was penned, it is indispensable to re-examine the writer’s fictional intentions in the usage of myth. More importantly, it is needful to determine whether we can see the mythic elements and realistic details as a continuum or as the contrasted opposites in his so called “historical chronicles”. Updike’s novels and stories are filled with mythological motifs and character archetypes. Thus, the study aims at revisiting John Updike’s creation considering mythological elements and archetypal images of his heroes alongside with heroic masculinity, war, terrorism and American perfectionism.

  15. Mapping the Thermal Inertia of Saturn’s Rings with Cassini CIRS

    Science.gov (United States)

    Brooks, Shawn M.; Spilker, L. J.; PIlorz, S. H.; Showalter, M. R.

    2013-10-01

    We use data from Cassini's Composite Infrared Spectrometer to map out the thermal response of Saturn's ring particles passing through Saturn's shadow and to determine variations in ring thermal inertia. CIRS records far infrared radiation in three separate detectors, each of which covers a distinct wavelength range. In this work, we analyze rings spectra recorded at focal plane 1 (FP1), as its wavelength response (16.7-1000 microns) is well suited to detecting direct thermal emission from Saturn's rings. The thermal budget of the rings is typically dominated by solar radiation. When ring particles enter Saturn’s shadow this source of energy is abruptly cut off with a consequential drop in ring temperature. Likewise, temperatures rebound when particles exit the shadow. To characterize these heating and cooling events, FP1 was repeatedly scanned across the main rings. Each scan was offset from either the ingress or egress shadow boundary by an amount corresponding to a fraction of a Keplerian orbit. By resampling these scans onto a common radial grid, we can map out the rings’ response to the abrupt changes in insolation at shadow ingress and egress. Periods near equinox represent a unique situation. During this time the Sun's disk crosses the ring plane and its rays strike the rings at zero incidence. Solar heating is virtually absent, and thermal radiation from Saturn and sunlight reflected by Saturn dominate the thermal environment. While ring temperature variations at equinox are much more subtle, they represent temperature contrasts that vary at the unique timescale corresponding to variations in Saturn contributions to the rings’ thermal budget. By analyzing CIRS data at a variety of locations and epochs, we will map out thermal inertia across the rings and attempt to tease out structural information about the particles which comprise Saturn’s rings. This presentation will report upon our progress towards these ends. This research was carried out at the

  16. Belisa-Dido’s Suicide: Variations on a Vergilian Motif in Lope de Vega’s Non-Dramatic Works

    Directory of Open Access Journals (Sweden)

    Antonio Sánchez Jiménez

    2018-05-01

    Full Text Available This article examines the theme of the abandoned beloved in four texts by Lope de Vega in which the motif combines subtexts of different origin: on the one hand, a conspicuous biographical key, filtered by literature (Belisa’s and Filis’ attempted suicide; on the other, erudite sources (Dido’s suicide. Analyzing these four texts, dating from Lope’s youth and de senectute periods, we also suggest how Lope could have come up with the idea of combining these strains inspiring himself in an anonymous romance (La desesperada Dido that appears to be the source of the famous De pechos sobre una torre.

  17. Open Sores of a Republic: Injustice and Poverty as Motifs in Alex La Guma’s First Three Novels

    Directory of Open Access Journals (Sweden)

    OGBEIDE, O. Victor

    2013-11-01

    Full Text Available This paper examines injustice and poverty as motifs in Alex La Guma’s first three novels. A motif is a recurrent formal element in a work of art. The foundation of apartheid is injustice which often leads to massive poverty on the part of the non-white community whose members are hapless victims of marginalization and disfranchisement in the Republic of South Africa. The prevalence of the twin forces of injustice and poverty in apartheid South Africa which La Guma artistically portrays in his first three novels confers on them the status of a motif. This, in itself, is a function of the novelist’s deference to realism and artistic relevance. The paper discovers that the unrelenting travesty of justice and the prevalence of destitution which describe so many unsavoury scenes in the novels in focus are due to the non-whites’ lack of meaningful political consciousness which itself is a function of the racist government’s stamp on oppositional discourse. It is this vacuum that the puny and ineffective pockets of individual acts of courage attempt to fill in the three novels to no avail.

  18. On commutativity of right s-unital rings with some polynomial constraints

    International Nuclear Information System (INIS)

    Khan, M.A.

    1994-08-01

    We study the commutativity of certain class of rings, namely rings with unity 1 and right s-unital rings under each of the following properties [yx m - x n f(y)x p ,x]=0, [yx m +x n f(y)x p ,x]=0, where f(t) is a polynomial in t 2 Z[t] varying with pair of ring elements x,y and m,n,p are fixed non-negative integers. Moreover, the results have been extended to the case when m and n depend on the choice of x and y and the ring satisfies the Chacron's Theorem. (author). 14 refs

  19. Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Joshi NV

    2009-01-01

    Full Text Available Abstract Background Regulation of gene expression in Plasmodium falciparum (Pf remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found. Results The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs – the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs – were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS; this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action. Conclusion The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

  20. Hard x-ray measurements of the hot-electron rings in EBT-S

    International Nuclear Information System (INIS)

    Hillis, D.L.

    1982-06-01

    A thorough understanding of the hot electron rings in ELMO Bumpy Torus-Scale (EBT-S) is essential to the bumpy torus concept of plasma production, since the rings provide bulk plasma stability. The hot electrons are produced via electron cyclotron resonant heating using a 28-GHz cw gyrotron, which has operated up to power levels of 200 kW. The parameters of the energetic electron rings are studied via hard x-ray measurement techniques and with diamagnetic pickup coils. The hard x-ray measurements have used collimated NaI(Tl) detectors to determine the electron temperature T/sub e/ and electron density n/sub e/ for the hot electron annulus. Typical values of T/sub e/ are 400 to 500 keV and of n/sub e/ 2 to 5 x 10 11 cm -3 . The total stored energy of a single energetic electron ring as measured by diamagnetic pickup loops approaches approx. 40 J and is in good agreement with that deduced from hard x-ray measurements. By combining the experimental measurements from hard x-rays and the diamagnetic loops, an estimate can be obtained for the volume of a single hot electron ring. The ring volume is determined to be approx. 2.2 litres, and this volume remains approximately constant over the T-mode operating regime. Finally, the power in the electrons scattered out of the ring is measured indirectly by measuring the x-ray radiation produced when those electrons strike the chamber walls. The variation of this radiation with increasing microwave power levels is found to be consistent with classical scattering estimates

  1. Crystal structures and conformations of two Diels–Alder adduct derivatives: 1,8-bis(thiophen-2-yl-14-oxatetracyclo[6.5.1.02,7.09,13]tetradeca-2(7,3,5-trien-10-one and 1,8-diphenyl-14-oxatetracyclo[6.5.1.02,7.09,13] tetradeca-2,4,6-trien-10-one

    Directory of Open Access Journals (Sweden)

    S. Gopinath

    2015-02-01

    Full Text Available The title compounds, C21H16O2S2 (I and C25H20O2 (II, are products of a tandem `pincer' Diels–Alder reaction consisting of [2 + 2] cycloadditions between benzo[c]furan and cyclopentanone. Each comprises a fused tetracyclic ring system containing two five-membered rings (in envelope conformations with the O atom as the flap and six-membered rings (in boat conformations. In addition, two thiophene rings in (I and two phenyl rings in (II are attached to the tetracyclic ring system. The cyclopentanone ring adopts a twisted conformation in (I and an envelope conformation in (II. In (I, the thiophene rings are positionally disordered over two sets of sites, with occupancy ratios of 0.901 (2:0.099 (2 and 0.666 (2:0.334 (2. In (II, the oxygen atom of the cyclopentanone ring is rotationally disordered over two sites with an occupancy ratio of 0.579 (4:0.421 (4. The molecular structure of (I is stabilized by an intramolecular C—H...O hydrogen bond, which generates an S(7 ring motif. In the crystal, the molecules are linked via weak C—H...O hydrogen bonds, which generate R22(16 ring motifs in (I and C(8 chains in (II. In both structures, the crystal packing also features C—H...π interactions. The crystal studied of compound (I was twinned by non-merohedry. The twin component is related by the twin law [−1 0 0 −0.101 1 −0.484 0 0 −1] operated by a twofold rotation axis parallel to the b axis. The structure of (I was refined with a twin scale factor of 0.275 (2.

  2. A Conserved GPG-Motif in the HIV-1 Nef Core Is Required for Principal Nef-Activities.

    Directory of Open Access Journals (Sweden)

    Marta Martínez-Bonet

    Full Text Available To find out new determinants required for Nef activity we performed a functional alanine scanning analysis along a discrete but highly conserved region at the core of HIV-1 Nef. We identified the GPG-motif, located at the 121-137 region of HIV-1 NL4.3 Nef, as a novel protein signature strictly required for the p56Lck dependent Nef-induced CD4-downregulation in T-cells. Since the Nef-GPG motif was dispensable for CD4-downregulation in HeLa-CD4 cells, Nef/AP-1 interaction and Nef-dependent effects on Tf-R trafficking, the observed effects on CD4 downregulation cannot be attributed to structure constraints or to alterations on general protein trafficking. Besides, we found that the GPG-motif was also required for Nef-dependent inhibition of ring actin re-organization upon TCR triggering and MHCI downregulation, suggesting that the GPG-motif could actively cooperate with the Nef PxxP motif for these HIV-1 Nef-related effects. Finally, we observed that the Nef-GPG motif was required for optimal infectivity of those viruses produced in T-cells. According to these findings, we propose the conserved GPG-motif in HIV-1 Nef as functional region required for HIV-1 infectivity and therefore with a potential interest for the interference of Nef activity during HIV-1 infection.

  3. Mechanical loading of the gymnast’s motor system during swings on rings

    Directory of Open Access Journals (Sweden)

    R Serafin

    2008-12-01

    Full Text Available The aim of this work was to identify the mechanical loading of the gymnast’s motor system during forward and backward swings on gymnastic rings. A junior gymnast of the First Class, aged 14, with body mass 53.1 kg and body length 1.61 m, participated in the study. He executed a series of ten cyclic swing movements on rings with his maximum amplitude. Kinematic variables of the gymnast’s centre of mass (COM as well as reaction forces in the cables were measured and synchronized using the SIMI MOTION movement analysis system. Two separate phases of mechanical loading of the motor system have been identified: resistance phase and non resistance phase. In the non resistance phase the gymnast attains similar values of the COM’s momentum but different angular displacements. In the resistance phase the forces acting on the motor system have their maximum. They amount to 5.5 BW for the forward swing and 6.5 BW for the backward swing movement. The maximum rate of change of the force for forward and backward swing is 42.6 BWs-1 and 67.4 BWs-1, respectively. These two variables differentiate the mechanical loading of the gymnast’s motor system between forward and backward swings. The reaction force produced by the gymnast is significantly greater during the execution of forward swings. It seems probable that horizontal displacements of COM may be the factor responsible for reduction of the mechanical loading experienced by the gymnast.

  4. 4-{(E-[2-(4-Iodobutoxybenzylidene]amino}-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H-one

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2010-07-01

    Full Text Available The title Schiff base compound, C22H24IN3O2, adopts an E configuration about the central C=N bond. The pyrazolone ring makes a dihedral angle of 49.68 (10° with its attached phenyl ring. The phenolate plane makes dihedral angles of 16.78 (9 and 50.54 (9°, respectively, with the pyrazolone ring and the terminal phenyl ring. An intramolecular C—H...O hydrogen bond generates an S(6 ring motif. In the crystal structure, an intermolecular C—H...O hydrogen bond is also observed.

  5. The PDZ-binding motif of Yes-associated protein is required for its co-activation of TEAD-mediated CTGF transcription and oncogenic cell transforming activity

    International Nuclear Information System (INIS)

    Shimomura, Tadanori; Miyamura, Norio; Hata, Shoji; Miura, Ryota; Hirayama, Jun; Nishina, Hiroshi

    2014-01-01

    Highlights: •Loss of the PDZ-binding motif inhibits constitutively active YAP (5SA)-induced oncogenic cell transformation. •The PDZ-binding motif of YAP promotes its nuclear localization in cultured cells and mouse liver. •Loss of the PDZ-binding motif inhibits YAP (5SA)-induced CTGF transcription in cultured cells and mouse liver. -- Abstract: YAP is a transcriptional co-activator that acts downstream of the Hippo signaling pathway and regulates multiple cellular processes, including proliferation. Hippo pathway-dependent phosphorylation of YAP negatively regulates its function. Conversely, attenuation of Hippo-mediated phosphorylation of YAP increases its ability to stimulate proliferation and eventually induces oncogenic transformation. The C-terminus of YAP contains a highly conserved PDZ-binding motif that regulates YAP’s functions in multiple ways. However, to date, the importance of the PDZ-binding motif to the oncogenic cell transforming activity of YAP has not been determined. In this study, we disrupted the PDZ-binding motif in the YAP (5SA) protein, in which the sites normally targeted by Hippo pathway-dependent phosphorylation are mutated. We found that loss of the PDZ-binding motif significantly inhibited the oncogenic transformation of cultured cells induced by YAP (5SA). In addition, the increased nuclear localization of YAP (5SA) and its enhanced activation of TEAD-dependent transcription of the cell proliferation gene CTGF were strongly reduced when the PDZ-binding motif was deleted. Similarly, in mouse liver, deletion of the PDZ-binding motif suppressed nuclear localization of YAP (5SA) and YAP (5SA)-induced CTGF expression. Taken together, our results indicate that the PDZ-binding motif of YAP is critical for YAP-mediated oncogenesis, and that this effect is mediated by YAP’s co-activation of TEAD-mediated CTGF transcription

  6. The PDZ-binding motif of Yes-associated protein is required for its co-activation of TEAD-mediated CTGF transcription and oncogenic cell transforming activity

    Energy Technology Data Exchange (ETDEWEB)

    Shimomura, Tadanori; Miyamura, Norio; Hata, Shoji; Miura, Ryota; Hirayama, Jun, E-mail: hirayama.dbio@mri.tmd.ac.jp; Nishina, Hiroshi, E-mail: nishina.dbio@mri.tmd.ac.jp

    2014-01-17

    Highlights: •Loss of the PDZ-binding motif inhibits constitutively active YAP (5SA)-induced oncogenic cell transformation. •The PDZ-binding motif of YAP promotes its nuclear localization in cultured cells and mouse liver. •Loss of the PDZ-binding motif inhibits YAP (5SA)-induced CTGF transcription in cultured cells and mouse liver. -- Abstract: YAP is a transcriptional co-activator that acts downstream of the Hippo signaling pathway and regulates multiple cellular processes, including proliferation. Hippo pathway-dependent phosphorylation of YAP negatively regulates its function. Conversely, attenuation of Hippo-mediated phosphorylation of YAP increases its ability to stimulate proliferation and eventually induces oncogenic transformation. The C-terminus of YAP contains a highly conserved PDZ-binding motif that regulates YAP’s functions in multiple ways. However, to date, the importance of the PDZ-binding motif to the oncogenic cell transforming activity of YAP has not been determined. In this study, we disrupted the PDZ-binding motif in the YAP (5SA) protein, in which the sites normally targeted by Hippo pathway-dependent phosphorylation are mutated. We found that loss of the PDZ-binding motif significantly inhibited the oncogenic transformation of cultured cells induced by YAP (5SA). In addition, the increased nuclear localization of YAP (5SA) and its enhanced activation of TEAD-dependent transcription of the cell proliferation gene CTGF were strongly reduced when the PDZ-binding motif was deleted. Similarly, in mouse liver, deletion of the PDZ-binding motif suppressed nuclear localization of YAP (5SA) and YAP (5SA)-induced CTGF expression. Taken together, our results indicate that the PDZ-binding motif of YAP is critical for YAP-mediated oncogenesis, and that this effect is mediated by YAP’s co-activation of TEAD-mediated CTGF transcription.

  7. Tyrocidine A Analogues Bearing the Planar d-Phe-2-Abz Turn Motif: How Conformation Impacts Bioactivity.

    Science.gov (United States)

    Cameron, Alan J; Edwards, Patrick J B; Harjes, Elena; Sarojini, Vijayalekshmi

    2017-12-14

    The d-Phe-Pro β-turn of the cyclic β-hairpin antimicrobial decapeptide tyrocidine A, (Tyrc A) was substituted with the d-Phe-2-aminobenzoic acid (2-Abz) motif in a synthetic analogue (1). The NMR structure of 1 demonstrated that compound 1 retained the β-hairpin structure of Tyrc A with additional planarity, resulting in approximately 30-fold reduced hemolysis than Tyrc A. Although antibacterial activity was partially compromised, a single Gln to Lys substitution (2) restored activity equivalent to Tyrc A against S. aureus, enhanced activity against two Gram negative strains and maintained the reduced hemeloysis of 1. Analysis by transmission electron microscopy (TEM) suggested a membrane lytic mechanism of action for these peptides. Compound 2 also exhibits nanomolar antifungal activity in synergy with amphotericin B. The d-Phe-2-Abz turn may serve as a tool for the synthesis of structurally predictable β-hairpin libraries. Unlike traditional β-turn motifs such as d-Pro-Gly, both the 2-Abz and d-Phe rings may be further functionalized.

  8. Graphical linking of MO multicenter bond index and VB structures. II-5-c rings and 6-c heterocyclic rings

    International Nuclear Information System (INIS)

    Bollini, Carlos Guido; Giambiagi, Mario; Giambiagi, Myriam Segre de; Figueiredo, Aloysio Paiva de

    2001-02-01

    Through the graphical method proposed it is possible to set a link between an MO multicenter bond index and VB structures. The value of the index depends on the order of the atoms involved if they are more than three. For 5-c rings three basic structures are required; the eventually different values are 12. Unlike the 6-c case it may happen that different pairs of basic structures are used to build the same polygon. For the 6-c rings including heteroatoms the original degeneracy of benzene splits leading eventually to 60 different I ring values. (author)

  9. (3Z-5-Chloro-3-(hydroxyiminoindolin-2-one

    Directory of Open Access Journals (Sweden)

    Bianca Barreto Martins

    2016-10-01

    Full Text Available In the title compound, C8H5ClN2O2 (common name: 5-chloroisatin 3-oxime, the molecular structure deviates slightly from the ideal planarity, with a maximum deviation of 0.0478 (8 Å for the non-H atoms. In the crystal, molecules are linked by N—H...O interactions, building centrosymmetric dimers with graph-set motif R22(8. Additionally, the molecules are connected by pairs of O—H...O interactions into chains along [100] with a C(6 motif. The hydrogen-bonded dimers and chains build a two-dimensional network parallel to (100. The packing also features π–π stacking interactions between benzene rings [centroid–centroid distance = 3.748 (2 Å].

  10. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

    Science.gov (United States)

    Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

    2013-01-01

    The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

  11. A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data.

    Science.gov (United States)

    Tran, Ngoc Tam L; Huang, Chun-Hsi

    2014-02-20

    ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for detecting binding site motifs in ChIP-Seq data. We showed each motif finding Web tool has its own advantages for detecting motifs that other tools may not discover. We recommended the users to use multiple motif finding Web tools that implement different algorithms for obtaining significant motifs, overlapping resemble motifs, and non-overlapping motifs. Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data.

  12. Determination of 5 '-leader sequences from radically disparate strains of porcine reproductive and respiratory syndrome virus reveals the presence of highly conserved sequence motifs

    DEFF Research Database (Denmark)

    Oleksiewicz, M.B.; Bøtner, Anette; Nielsen, Jens

    1999-01-01

    We determined the untranslated 5'-leader sequence for three different isolates of porcine reproductive and respiratory syndrome virus (PRRSV): pathogenic European- and American-types, as well as an American-type vaccine strain. 5'-leader from European- and American-type PRRSV differed in length...... (220 and 190 nt, respectively), and exhibited only approximately 50% nucleotide homology. Nevertheless, highly conserved areas were identified in the leader of all 3 PRRSV isolates, which constitute candidate motifs for binding of protein(s) involved in viral replication. These comparative data provide...

  13. Photochemistry in Saturn’s Ring-Shadowed Atmosphere: Modulation of Hydrocarbons and Aerosols

    Science.gov (United States)

    Edgington, Scott G.; Atreya, Sushil K.; Wilson, Eric H.; Baines, Kevin H.; West, Robert A.; Bjoraker, Gordon L.; Fletcher, Leigh N.; Momary, Tom

    2015-11-01

    Cassini has been orbiting Saturn for over eleven years now. During this epoch, the ring shadow has moved from covering much of the northern hemisphere (the solar inclination was 24 degrees) to covering a large swath south of the equator and it continues to move southward. At Saturn Orbit Insertion in 2004, the projection of the A-ring onto Saturn reached as far as 40N along the central meridian (52N at the terminator). At its maximum extent, the ring shadow can reach as far as 48N/S (58N/S at the terminator). The net effect is that the intensity of both ultraviolet and visible sunlight penetrating through the rings to any particular latitude will vary depending on both Saturn’s axis relative to the Sun and the optical thickness of each ring system. In essence, the rings act like semi-transparent venetian blinds.Our previous work, examined the variation of the solar flux as a function of solar inclination, i.e. for each 7.25-year season at Saturn. Here, we report on the impact of the oscillating ring shadow on the photolysis and production rates of hydrocarbons (acetylene, ethane, propane, and benzene) and phosphine in Saturn’s stratosphere and upper troposphere. The impact of these production and loss rates on the abundance of long-lived photochemical products leading to haze formation are explored. Similarly, we assess their impact on phosphine abundance, a disequilibrium species whose presence in the upper troposphere can be used as a tracer of convective processes in the deeper atmosphere.We will also present our ongoing analysis of Cassini’s datasets that provide an estimate of the evolving haze content of the northern hemisphere and we will begin to assess the implications for dynamical mixing. In particular, we will examine how the now famous hexagonal jet stream acts like a barrier to transport, isolating Saturn’s north polar region from outside transport of photochemically-generated molecules and haze.The research described in this paper was carried

  14. Expression of 5 S rRNA genes linked to 35 S rDNA in plants, their epigenetic modification and regulatory element divergence

    Directory of Open Access Journals (Sweden)

    Garcia Sònia

    2012-06-01

    Full Text Available Abstract Background In plants, the 5S rRNA genes usually occur as separate tandems (S-type arrangement or, less commonly, linked to 35 S rDNA units (L-type. The activity of linked genes remains unknown so far. We studied the homogeneity and expression of 5S genes in several species from family Asteraceae known to contain linked 35 S-5S units. Additionally, their methylation status was determined using bisulfite sequencing. Fluorescence in situ hybridization was applied to reveal the sub-nuclear positions of rDNA arrays. Results We found that homogenization of L-type units went to completion in most (4/6 but not all species. Two species contained major L-type and minor S-type units (termed Ls-type. The linked genes dominate 5S rDNA expression while the separate tandems do not seem to be expressed. Members of tribe Anthemideae evolved functional variants of the polymerase III promoter in which a residing C-box element differs from the canonical angiosperm motif by as much as 30%. On this basis, a more relaxed consensus sequence of a plant C-box: (5’-RGSWTGGGTG-3’ is proposed. The 5S paralogs display heavy DNA methylation similarly as to their unlinked counterparts. FISH revealed the close association of 35 S-5S arrays with nucleolar periphery indicating that transcription of 5S genes may occur in this territory. Conclusions We show that the unusual linked arrangement of 5S genes, occurring in several plant species, is fully compatible with their expression and functionality. This extraordinary 5S gene dynamics is manifested at different levels, such as variation in intrachromosomal positions, unit structure, epigenetic modification and considerable divergence of regulatory motifs.

  15. 4-Methyl-5-phenyl-1H-pyrazol-3-ol

    Directory of Open Access Journals (Sweden)

    Tara Shahani

    2010-07-01

    Full Text Available The title compound, C10H10N2O, crystallizes with two independent molecules in the asymmetric unit, having closely comparable geometries. The dihedral angles between the 1H-pyrazole and benzene rings in the two molecules are 39.57 (14 and 41.95 (13°. The two molecules are each connected to neighbouring molecules by pairs of intermolecular O—H...N hydrogen bonds, forming dimers with R22(8 ring motifs. These dimers are further linked into R44(10 ring motifs by intermolecular N—H...O hydrogen bonds, forming chains along [101]. The crystal structure is further stabilized by a C—H...π interaction.

  16. Black rings

    International Nuclear Information System (INIS)

    Emparan, Roberto; Reall, Harvey S

    2006-01-01

    A black ring is a five-dimensional black hole with an event horizon of topology S 1 x S 2 . We provide an introduction to the description of black rings in general relativity and string theory. Novel aspects of the presentation include a new approach to constructing black ring coordinates and a critical review of black ring microscopics. (topical review)

  17. Genome Analysis of Conserved Dehydrin Motifs in Vascular Plants

    Directory of Open Access Journals (Sweden)

    Ahmad A. Malik

    2017-05-01

    Full Text Available Dehydrins, a large family of abiotic stress proteins, are defined by the presence of a mostly conserved motif known as the K-segment, and may also contain two other conserved motifs known as the Y-segment and S-segment. Using the dehydrin literature, we developed a sequence motif definition of the K-segment, which we used to create a large dataset of dehydrin sequences by searching the Pfam00257 dehydrin dataset and the Phytozome 10 sequences of vascular plants. A comprehensive analysis of these sequences reveals that lysine residues are highly conserved in the K-segment, while the amino acid type is often conserved at other positions. Despite the Y-segment name, the central tyrosine is somewhat conserved, but can be substituted with two other small aromatic amino acids (phenylalanine or histidine. The S-segment contains a series of serine residues, but in some proteins is also preceded by a conserved LHR sequence. In many dehydrins containing all three of these motifs the S-segment is linked to the K-segment by a GXGGRRKK motif (where X can be any amino acid, suggesting a functional linkage between these two motifs. An analysis of the sequences shows that the dehydrin architecture and several biochemical properties (isoelectric point, molecular mass, and hydrophobicity score are dependent on each other, and that some dehydrin architectures are overexpressed during certain abiotic stress, suggesting that they may be optimized for a specific abiotic stress while others are involved in all forms of dehydration stress (drought, cold, and salinity.

  18. 5-Isobutyl-4-phenylsulfonyl-1H-pyrazol-3(2H-one

    Directory of Open Access Journals (Sweden)

    M. Venkatesh

    2010-12-01

    Full Text Available The title compound, C13H16N2O3S, consists of two crystallographically independent molecules with similar geometries and exists in a keto form, the C=O bond lengths being 1.267 (2 and 1.254 (2 Å. In both molecules, the pyrazole rings are approximately planar, with maximum deviations of 0.017 (2 and 0.010 (2 Å, and the dihedral angles between the pyrazole and phenyl rings are 83.63 (11 and 70.07 (12°. In one molecule, an intramolecular C—H...O hydrogen bond with an S(6 ring motif is observed. In the crystal, intermolecular N—H...O and C—H...O hydrogen bonds link the molecules into two-dimensional networks parallel to the ab plane.

  19. (S,Z-3-Phenyl-2-[(1,1,1-trichloro-7-methoxy-2,7-dioxohept-3-en-4-ylamino]propanoic acid monohydrate

    Directory of Open Access Journals (Sweden)

    Alex Fabiani Claro Flores

    2014-02-01

    Full Text Available In the title compound, C17H18Cl3NO5·H2O, intramolecular N—H...O and C—H...Cl hydrogen bonds form S(6 and S(5 ring motifs, respectively. The chiral organic molecule is connected to the solvent water molecule by a short O—H...O hydrogen bond. In the crystal, a weak C—H...Cl interaction connects the organic molecules along [100] while the water molecules act as bridges between the organic molecules in both the [100] and [010] directions, generating layers parallel to the ab plane.

  20. 2-(5-Iodo-2-oxoindolin-3-ylidenehydrazinecarbothioamide including an unknown solvate

    Directory of Open Access Journals (Sweden)

    Viviane Conceição Duarte de Bittencourt

    2014-06-01

    Full Text Available The molecule of the title compound, C9H7IN4OS, is almost planar (r.m.s. deviation = 0.0373 Å. In the molecule, N—H...N and N—H...O hydrogen bonds generate, respectively, S(5 and S(6 ring motifs. In the crystal, molecules are linked via N—H...O hydrogen bonds, forming chains propagating along [010]. These chains are linked via S...I contacts [3.4915 (16 Å], forming sheets lying parallel to (100. A region of disordered electron density, probably a disordered tetrahydrofuran solvent molecule, was treated using the SQUEEZE routine in PLATON [Spek (2009. Acta Cryst. D65, 148–155]. The formula mass and unit-cell characteristics were not taken into account during refinement.

  1. Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase: DAWIDZIAK et al.

    Energy Technology Data Exchange (ETDEWEB)

    Dawidziak, Daria M. [Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville Virginia; Sanchez, Jacint G. [Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville Virginia; Wagner, Jonathan M. [Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville Virginia; Ganser-Pornillos, Barbie K. [Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville Virginia; Pornillos, Owen [Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville Virginia

    2017-07-24

    Tripartite motif (TRIM) proteins comprise a large family of RING-type ubiquitin E3 ligases that regulate important biological processes. An emerging general model is that TRIMs form elongated antiparallel coiled-coil dimers that prevent interaction of the two attendant RING domains. The RING domains themselves bind E2 conjugating enzymes as dimers, implying that an active TRIM ligase requires higher-order oligomerization of the basal coiled-coil dimers. Here, we report crystal structures of the TRIM23 RING domain in isolation and in complex with an E2–ubiquitin conjugate. Our results indicate that TRIM23 enzymatic activity requires RING dimerization, consistent with the general model of TRIM activation.

  2. RNA recognition motif (RRM)-containing proteins in Bombyx mori

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-20

    Mar 20, 2009 ... Recognition Motif (RRM), sometimes referred to as. RNP1, is one of the first identified domains for RNA interaction. RRM is very common ..... Apart from the RRM motif, eIF3-S9 has a Trp-Asp. (WD) repeat domain, Poly (A) ...

  3. Short Arginine Motifs Drive Protein Stickiness in the Escherichia coli Cytoplasm.

    Science.gov (United States)

    Kyne, Ciara; Crowley, Peter B

    2017-09-19

    Although essential to numerous biotech applications, knowledge of molecular recognition by arginine-rich motifs in live cells remains limited. 1 H, 15 N HSQC and 19 F NMR spectroscopies were used to investigate the effects of C-terminal -GR n (n = 1-5) motifs on GB1 interactions in Escherichia coli cells and cell extracts. While the "biologically inert" GB1 yields high-quality in-cell spectra, the -GR n fusions with n = 4 or 5 were undetectable. This result suggests that a tetra-arginine motif is sufficient to drive interactions between a test protein and macromolecules in the E. coli cytoplasm. The inclusion of a 12 residue flexible linker between GB1 and the -GR 5 motif did not improve detection of the "inert" domain. In contrast, all of the constructs were detectable in cell lysates and extracts, suggesting that the arginine-mediated complexes were weak. Together these data reveal the significance of weak interactions between short arginine-rich motifs and the E. coli cytoplasm and demonstrate the potential of such motifs to modify protein interactions in living cells. These interactions must be considered in the design of (in vivo) nanoscale assemblies that rely on arginine-rich sequences.

  4. Interaction of higher plant ribosomal 5S RNAs with ''Xenopus laevis'' transcriptional factor IIIA

    International Nuclear Information System (INIS)

    Barciszewska, M.Z.

    1994-01-01

    In this paper transcriptional factor IIIA (TFIIIA) has been used as a probe for identity of three-dimensional-structure of eukaryotic 5S rRNAs. I was interested in finding a common motif in plant and ''Xenopus'' 5S rRNAs for TFIIIA recognition. I found that the two eukaryotic 5S rRNAs (from wheat germ and lupin seeds) are recognized by ''X. laevis'' TFIIIA and the data clearly suggest that these 5S rRNAs have very similar if not identical three-dimensional structures. Also effects of various conditions on stability of these complexes have been studied. (author). 30 refs, 6 figs, 1 tab

  5. Motif signatures of transcribed enhancers

    KAUST Repository

    Kleftogiannis, Dimitrios

    2017-09-14

    In mammalian cells, transcribed enhancers (TrEn) play important roles in the initiation of gene expression and maintenance of gene expression levels in spatiotemporal manner. One of the most challenging questions in biology today is how the genomic characteristics of enhancers relate to enhancer activities. This is particularly critical, as several recent studies have linked enhancer sequence motifs to specific functional roles. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers genomic code in a more systematic way. To address this problem, we developed a novel computational method, TELS, aimed at identifying predictive cell type/tissue specific motif signatures. We used TELS to compile a comprehensive catalog of motif signatures for all known TrEn identified by the FANTOM5 consortium across 112 human primary cells and tissues. Our results confirm that distinct cell type/tissue specific motif signatures characterize TrEn. These signatures allow discriminating successfully a) TrEn from random controls, proxy of non-enhancer activity, and b) cell type/tissue specific TrEn from enhancers expressed and transcribed in different cell types/tissues. TELS codes and datasets are publicly available at http://www.cbrc.kaust.edu.sa/TELS.

  6. Dicyclohexylammonium 3,5-dinitrobenzoate

    OpenAIRE

    Sohail Saeed; Naghmana Rashid; Rizwan Hussain; Wing-Tak Wong

    2012-01-01

    The asymmetric unit of the title salt, C12H24N+·C7H3N2O6−, contains two cations and two anions. In the crystal, the cations and anions are connected by N—H...O hydrogen bonds, forming a 12-membered ring with an R44(12) graph-set motif. The center of this 12-membered ring coincides with an inversion centre. π–π stacking is observed between parallel benzene rings [centroid–centriod distance = 3.771 (2) &#...

  7. DMINDA: an integrated web server for DNA motif identification and analyses.

    Science.gov (United States)

    Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

    2014-07-01

    DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. 4′-Methyl-14′,19′-dioxa-4′-azaspiro[acenaphthylene-1,5′-tetracyclo[18.4.0.02,6.08,13]tetracosane]-1′(24′,8′,10′,12′,20′,22′-hexaene-2,7′(1H-dione

    Directory of Open Access Journals (Sweden)

    Sibi Narayanan

    2012-12-01

    Full Text Available In the title compound, C33H29NO4, the acenaphthylene ring system is essentially planar (r.m.s. deviation = 0.0290 Å. The pyrrolidine ring adopts a C-envelope conformation with a C atom displaced by 0.671 (2 Å from the mean-plane formed by the remaining ring atoms. The pyrrolidine ring is fused to acenaphthylene ring system making a dihedral angle of 88.0 (7°. In the crystal, molecules are linked into R22(9 dimers via C—H...N and C—H...O hydrogen bonds. Two C atoms act as donors to the same O atom acceptor, resulting in the formation of R21(7 ring motifs. These two motifs combine to form hydrogen-bonded sheets running along the a- and b-axis directions.

  9. 'On Earth as it is in Heaven...' The heavenly sanctuary motif in ...

    African Journals Online (AJOL)

    ... archetype] by Philo) and σκια [shadow] – is studied within the context of Hebrews 8:1–5. The purpose of this investigation is to explore the possible Graeco-Jewish background(s) of the 'heavenly sanctuary' motif in Hebrews 8:5, the presence of its key terminology and some of its intertextual occurrences in, amongst others ...

  10. AtalaphyllineThis paper is dedicated to the late His Royal Highness Prince Mahidol of Songkla for his contributions to the development of medical education in Thailand.

    Directory of Open Access Journals (Sweden)

    Suchada Chantrapromma

    2010-01-01

    Full Text Available The title acridone alkaloid [systematic name: 1,3,5-trihydroxy-2,4-bis(3-methylbut-2-enylacridin-9(10H-one], C23H25NO4, known as atalaphylline, was isolated from Atalantia monophylla Corrêa, a mangrove plant. The molecule contains three fused planar rings with an r.m.s. deviation of 0.026 (2 Å. Both 3-methylbut-2-enyl substituents are in a (−anticlinal conformation. An intramolecular N—H...O hydrogen bond generates an S(5 ring motif, while an intramolecular O—H...O hydrogen bond generates an S(6 ring motif. In the crystal structure, the molecules are linked into screw chains along [010] by intermolecular O—H...O hydrogen bonds. These chains are stacked along the a axis by π–π interactions with centroid–centroid distances of 3.6695 (13 and 3.6696 (13 Å.

  11. The identification of functional motifs in temporal gene expression analysis

    Directory of Open Access Journals (Sweden)

    Michael G. Surette

    2005-01-01

    Full Text Available The identification of transcription factor binding sites is essential to the understanding of the regulation of gene expression and the reconstruction of genetic regulatory networks. The in silico identification of cis-regulatory motifs is challenging due to sequence variability and lack of sufficient data to generate consensus motifs that are of quantitative or even qualitative predictive value. To determine functional motifs in gene expression, we propose a strategy to adopt false discovery rate (FDR and estimate motif effects to evaluate combinatorial analysis of motif candidates and temporal gene expression data. The method decreases the number of predicted motifs, which can then be confirmed by genetic analysis. To assess the method we used simulated motif/expression data to evaluate parameters. We applied this approach to experimental data for a group of iron responsive genes in Salmonella typhimurium 14028S. The method identified known and potentially new ferric-uptake regulator (Fur binding sites. In addition, we identified uncharacterized functional motif candidates that correlated with specific patterns of expression. A SAS code for the simulation and analysis gene expression data is available from the first author upon request.

  12. A General and Simple Diastereoselective Reduction by L-Selectride: Efficient Synthesis of Protected (4S,5S)-Dihydroxy Amides

    OpenAIRE

    Yin; Ye; Yu; Liu

    2010-01-01

    A general approach to (4S,5S)-4-benzyloxy-5-hydroxy-N-(4-methoxybenzyl) amides 10 based on a diastereoselective reduction of (5S,6RS)-6-alkyl-5-benzyloxy-6-hydroxy-2-piperidinones 6 and their tautomeric ring-opened keto amides 7 is described. The reduction with L-Selectride at -20 °C to room temperature afforded the products 10 in excellent yields and moderate to high syn-diastereoselectivities.

  13. A general and simple diastereoselective reduction by L-Selectride: efficient synthesis of protected (4S,5S)-dihydroxy amides.

    Science.gov (United States)

    Yin, Bo; Ye, Dong-Nai; Yu, Kai-Hui; Liu, Liang-Xian

    2010-04-16

    A general approach to (4S,5S)-4-benzyloxy-5-hydroxy-N-(4-methoxybenzyl) amides 10 based on a diastereoselective reduction of (5S,6RS)-6-alkyl-5-benzyloxy-6-hydroxy-2-piperidinones 6 and their tautomeric ring-opened keto amides 7 is described. The reduction with L-Selectride at -20 degrees C to room temperature afforded the products 10 in excellent yields and moderate to high syn-diastereoselectivities.

  14. Dicyclohexylammonium 3,5-dinitrobenzoate

    Directory of Open Access Journals (Sweden)

    Sohail Saeed

    2012-07-01

    Full Text Available The asymmetric unit of the title salt, C12H24N+·C7H3N2O6−, contains two cations and two anions. In the crystal, the cations and anions are connected by N—H...O hydrogen bonds, forming a 12-membered ring with an R44(12 graph-set motif. The center of this 12-membered ring coincides with an inversion centre. π–π stacking is observed between parallel benzene rings [centroid–centriod distance = 3.771 (2 Å].

  15. 11-[(E-Benzylidene]-14-hydroxy-8-phenyl-6-thia-3,13-diazaheptacyclo[13.7.1.19,13.02,9.02,14.03,7.019,23]tetracosa-1(22,15(23,16,18,20-pentaen-10-one

    Directory of Open Access Journals (Sweden)

    Raju Suresh Kumar

    2012-07-01

    Full Text Available In the title compound, C34H28N2O2S, the piperidine ring adopts a chair conformation. One of the pyrrolidine rings adopts an envelope conformation with the methylene C atom at the flap whereas the other pyrrolidine ring and the thiazolidine ring adopt half-chair conformations. The mean plane of the dihydroacenaphthylene ring system [maximum deviation = 0.067 (1 Å] makes dihedral angles of 28.31 (5 and 31.32 (6° with the two terminal benzene rings. An intramolecular O—H...N hydrogen bond forms an S(5 ring motif. In the crystal, molecules are linked by C—H...O and C—H...S hydrogen bonds into layers lying parallel to the ac plane.

  16. Mode-Locked 1.5 um Semiconductor Optical Fiber Ring

    DEFF Research Database (Denmark)

    Pedersen, Niels Vagn; Jakobsen, Kaj Bjarne; Vaa, Michael

    1996-01-01

    The dynamics of a mode-locked SOA fiber ring are investigated experimentally and numerically. Generation of near transform-limited (time-bandwidth product = 0.7) 1.5 um 54 ps FWHM pulses with a peak power of 2.8 mW at a repetition rate of 960 MHz is demonstrated experimentally. The experimental r...

  17. Thermal Stability of Modified i-Motif Oligonucleotides with Naphthalimide Intercalating Nucleic Acids

    DEFF Research Database (Denmark)

    El-Sayed, Ahmed Ali; Pedersen, Erik B.; Khaireldin, Nahid Y.

    2016-01-01

    In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion of naphtha......In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion...... of naphthalimide (1H-benzo[de]isoquinoline-1,3(2H)-dione) as the intercalating nucleic acid. The stabilities of i-motif structures with inserted naphthalimide intercalating nucleotides were studied using UV melting temperatures (Tm) and circular dichroism spectra at different pH values and conditions (crowding...

  18. Annotating RNA motifs in sequences and alignments.

    Science.gov (United States)

    Gardner, Paul P; Eldai, Hisham

    2015-01-01

    RNA performs a diverse array of important functions across all cellular life. These functions include important roles in translation, building translational machinery and maturing messenger RNA. More recent discoveries include the miRNAs and bacterial sRNAs that regulate gene expression, the thermosensors, riboswitches and other cis-regulatory elements that help prokaryotes sense their environment and eukaryotic piRNAs that suppress transposition. However, there can be a long period between the initial discovery of a RNA and determining its function. We present a bioinformatic approach to characterize RNA motifs, which are critical components of many RNA structure-function relationships. These motifs can, in some instances, provide researchers with functional hypotheses for uncharacterized RNAs. Moreover, we introduce a new profile-based database of RNA motifs--RMfam--and illustrate some applications for investigating the evolution and functional characterization of RNA. All the data and scripts associated with this work are available from: https://github.com/ppgardne/RMfam. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Christian J. Michel

    2017-12-01

    Full Text Available A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C 3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X , using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X , in the complete genome of the yeast Saccharomyces cerevisiae. Several properties of X motifs are identified by basic statistics (at the frequency level, and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R . We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae. We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae, but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions. This property is true for all cardinalities of X motifs (from 4 to 20 and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non- X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together

  20. Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Michel, Christian J; Ngoune, Viviane Nguefack; Poch, Olivier; Ripp, Raymond; Thompson, Julie D

    2017-12-03

    A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading) frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X, using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X, in the complete genome of the yeast Saccharomyces cerevisiae . Several properties of X motifs are identified by basic statistics (at the frequency level), and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R. We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae . We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae , but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions). This property is true for all cardinalities of X motifs (from 4 to 20) and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non-X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together, represent the first

  1. 2-[2-Chloro-5-(trifluoromethylphenyl]hexahydropyrimidine monohydrate

    Directory of Open Access Journals (Sweden)

    Reza Kia

    2008-09-01

    Full Text Available The molecule of the title compound, C11H12ClF3N2·H2O, is a substituted hexahydropyrimidine. There are two crystallographically independent molecules (A and B and two water molecules in the asymmetric unit of the title compound. Intermolecular C—H...Cl (× 2, C—H...F, and C—H...N (× 2 hydrogen bonds generate S(5 ring motifs. The dihedral angle between the two benzene rings is 8.17 (11°. The F atoms in molecule B are disordered over four positions with refined site-occupancies of ca 0.35/0.19/0.29/0.17 for the four components. In the crystal structure, molecules are arranged into one-dimensional extended chains along the c axis and are further stacked along the a axis by directed four-membered O—H...O—H interactions, forming two-dimensional networks parallel to the ac plane. The short distances between the centroids of the benzene rings (3.8002–3.8327 Å indicate the existence of π–π interactions. In addition, the crystal structure is further stabilized by N—H...O, O—H...N (× 4, N—H...Cl and C—H...O (× 2 hydrogen-bonding interactions.

  2. A General and Simple Diastereoselective Reduction by L-Selectride: Efficient Synthesis of Protected (4S,5S-Dihydroxy Amides

    Directory of Open Access Journals (Sweden)

    Bo Yin

    2010-04-01

    Full Text Available A general approach to (4S,5S-4-benzyloxy-5-hydroxy-N-(4-methoxybenzyl amides 10 based on a diastereoselective reduction of (5S,6RS-6-alkyl-5-benzyloxy-6-hydroxy-2-piperidinones 6 and their tautomeric ring-opened keto amides 7 is described. The reduction with L-Selectride at -20 °C to room temperature afforded the products 10 in excellent yields and moderate to high syn-diastereoselectivities.

  3. Surface geometry of 5D black holes and black rings

    International Nuclear Information System (INIS)

    Frolov, Valeri P.; Goswami, Rituparno

    2007-01-01

    We discuss geometrical properties of the horizon surface of five-dimensional rotating black holes and black rings. Geometrical invariants characterizing these 3D geometries are calculated. We obtain a global embedding of the 5D rotating black horizon surface into a flat space. We also describe the Kaluza-Klein reduction of the black ring solution (along the direction of its rotation) which, though it is nakedly singular, relates this solution to the 4D metric of a static black hole distorted by the presence of external scalar (dilaton) and vector ('electromagnetic') fields. The properties of the reduced black hole horizon and its embedding in E 3 are briefly discussed

  4. Photochemistry in Saturn’s Ring-Shadowed Atmosphere: Photochemistry and Haze Observations

    Science.gov (United States)

    Edgington, Scott G.; Atreya, Sushil K.; Baines, Kevin H.; West, Robert A.; Bjoraker, Gordon L.; Fletcher, Leigh; Momary, Thomas W.; Wilson, Eric; CIRS, ISS, UVIS, VIMS

    2017-10-01

    After 13 years of observing Saturn, Cassini would have ended nearly a half Saturnian year. During this epoch, the ring shadow has moved from covering much of the northern hemisphere to covering a large swath southern hemisphere. The net effect is that the intensity of both ultraviolet and visible sunlight penetrating through the rings to any particular latitude will vary depending on both Saturn’s axis relative to the Sun and the optical thickness of each ring system. In essence, the rings act like semi-transparent venetian blinds. This effect magnifies the effect due to axial tilt alone and acts to turn off photochemistry and haze generation. This effect is seen in both the presence of a bluish Rayleigh-scattering atmosphere in 2004 in the northern hemisphere and color change to blue in the northern hemisphere.Previous work examined the variation of the solar flux as a function of solar inclination, i.e. for each 7.25-year season at Saturn. We report on the impact of the oscillating ring shadow, in addition to variation due to axial tilt, on photolysis and production rates of hydrocarbons and phosphine in Saturn’s stratosphere and upper troposphere. The impact of these production and loss rates on the abundance of long-lived photochemical products leading to haze formation are explored. We assess their impact on a disequilibrium species whose presence in the upper troposphere can be used as a tracer of convective processes in the deeper atmosphere.We will also present our ongoing analysis of Cassini’s CIRS, UVIS, and VIMS datasets that provide an estimate of the evolving haze content. In particular, we will examine how the region inside Saturn’s famous hexagonal jet stream changes over time from a relatively clear atmosphere to a hazy one. We also explore how the hexagon acts like a barrier to transport, isolating Saturn’s north polar region from outside influences of photochemically-generated molecules and haze.The research described in this paper was

  5. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements

    OpenAIRE

    Huang, Hsi-Yuan; Chien, Chia-Hung; Jen, Kuan-Hua; Huang, Hsien-Da

    2006-01-01

    Numerous regulatory structural motifs have been identified as playing essential roles in transcriptional and post-transcriptional regulation of gene expression. RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs and structural homologs of regulatory RNA motifs can be recognized. The regulatory RNA motifs supported in RegRNA are categorized into several classes: (i) motifs in mRNA 5′-untra...

  6. Identification of sequence motifs significantly associated with antisense activity

    Directory of Open Access Journals (Sweden)

    Peek Andrew S

    2007-06-01

    Full Text Available Abstract Background Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the model to be efficient we must know what properties do not associate significantly and can be omitted from the model. This paper will discuss the results of a randomization procedure to find motifs that associate significantly with either high or low antisense suppression activity, analysis of their properties, as well as the results of support vector machine modelling using these significant motifs as features. Results We discovered 155 motifs that associate significantly with high antisense suppression activity and 202 motifs that associate significantly with low suppression activity. The motifs range in length from 2 to 5 bases, contain several motifs that have been previously discovered as associating highly with antisense activity, and have thermodynamic properties consistent with previous work associating thermodynamic properties of sequences with their antisense activity. Statistical analysis revealed no correlation between a motif's position within an antisense sequence and that sequences antisense activity. Also, many significant motifs existed as subwords of other significant motifs. Support vector regression experiments indicated that the feature set of significant motifs increased correlation compared to all possible motifs as well as several subsets of the significant motifs. Conclusion The thermodynamic properties of the significantly associated motifs support existing data correlating the thermodynamic properties of the antisense oligonucleotide with antisense efficiency, reinforcing our hypothesis that antisense suppression is strongly associated with probe/target thermodynamics, as there are no enzymatic

  7. The positron accumulator ring for the APS

    International Nuclear Information System (INIS)

    Crosbie, E.A.

    1989-01-01

    The Positron Accumulator Ring (PAR) is designed to accumulate and damp positrons from the 450-MeV linac during the 0.5-s cycle time of the injector synchrotron for the APS 7-GeV storage ring. During 0.4 s of each synchrotron cycle, up to 24 linac pulses are injected into the horizontal phase space of the PAR at a 60-Hz rate. Each injected pulse occupies about 1.3 of the circumference of the accumulator ring. After 0.1 s for longitudinal damping, the single accumulated bunch is transferred to one of the 353-MHz buckets of the injector synchrotron RF system. The bunch is accelerated to 7 GeV and transferred to the storage ring, while the PAR accumulates the next bunch of positrons. 2 refs., 3 figs., 2 tabs

  8. The positron accumulator ring for the APS

    International Nuclear Information System (INIS)

    Crosbie, E.A.

    1989-01-01

    The Positron Accumulator Ring (PAR) is designed to accumulate and damp positrons from the 450-MeV linac during the 0.5-s cycle time of the injector synchrotron for the APS 7-GeV storage ring. During 0.4 s of each synchrotron cycle, up to 24 linac pulses are injected into the horizontal phase space of the PAR at a 60-Hz rate. Each injected pulse occupies about 1/3 of the circumference of the accumulator ring. After 0.1 s for longitudinal damping, the single accumulated bunch is transferred to one of the 353-MHz buckets of the injector synchrotron RF system. The bunch is accelerated to 7 GeV and transferred to the storage ring, while the PAR accumulates the next bunch of positrons. 2 refs., 3 figs., 2 tabs

  9. Manufacturing processes of S-shaped temple rings from Vrbno, Central Bohemia

    Czech Academy of Sciences Publication Activity Database

    Ottenwelter, Estelle; Hošek, Jiří; Děd, J.; Štefan, I.

    2012-01-01

    Roč. 64, č. 3 (2012), s. 525-533 ISSN 0323-1267 Institutional research plan: CEZ:AV0Z80020508 Keywords : S-shaped temple rings * Early Middle Ages * Vrbno * tinning * gilding * silver plating Subject RIV: AC - Archeology, Anthropology, Ethnology

  10. Direct AUC optimization of regulatory motifs.

    Science.gov (United States)

    Zhu, Lin; Zhang, Hong-Bo; Huang, De-Shuang

    2017-07-15

    The discovery of transcription factor binding site (TFBS) motifs is essential for untangling the complex mechanism of genetic variation under different developmental and environmental conditions. Among the huge amount of computational approaches for de novo identification of TFBS motifs, discriminative motif learning (DML) methods have been proven to be promising for harnessing the discovery power of accumulated huge amount of high-throughput binding data. However, they have to sacrifice accuracy for speed and could fail to fully utilize the information of the input sequences. We propose a novel algorithm called CDAUC for optimizing DML-learned motifs based on the area under the receiver-operating characteristic curve (AUC) criterion, which has been widely used in the literature to evaluate the significance of extracted motifs. We show that when the considered AUC loss function is optimized in a coordinate-wise manner, the cost function of each resultant sub-problem is a piece-wise constant function, whose optimal value can be found exactly and efficiently. Further, a key step of each iteration of CDAUC can be efficiently solved as a computational geometry problem. Experimental results on real world high-throughput datasets illustrate that CDAUC outperforms competing methods for refining DML motifs, while being one order of magnitude faster. Meanwhile, preliminary results also show that CDAUC may also be useful for improving the interpretability of convolutional kernels generated by the emerging deep learning approaches for predicting TF sequences specificities. CDAUC is available at: https://drive.google.com/drive/folders/0BxOW5MtIZbJjNFpCeHlBVWJHeW8 . dshuang@tongji.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  11. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-01-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

  12. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun

    2013-06-29

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors\\' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

  13. Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires

    DEFF Research Database (Denmark)

    Bergseng, Elin; Dørum, Siri; Arntzen, Magnus Ø.

    2014-01-01

    Celiac disease is caused by intolerance to cereal gluten proteins, and HLA-DQ molecules are involved in the disease pathogenesis by presentation of gluten peptides to CD4+ T cells. The α- or β-chain sharing HLA molecules DQ2.5, DQ2.2, and DQ7.5 display different risks for the disease...... established binding motifs. The binding motif of DQ2.2 was strikingly different from that of DQ2.5 with position P3 being a major anchor having a preference for threonine and serine. This is notable as three recently identified epitopes of gluten recognized by T cells of DQ2.2 celiac patients harbor serine...... at position P3. This study demonstrates that relative quantitative comparison of endogenous peptides sampled from our protein metabolism by HLA molecules provides clues to understand HLA association with disease....

  14. 5-[(E-(2-Hydroxybenzylideneamino]-1H-1,3-benzimidazole-2(3H-thione

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2011-01-01

    Full Text Available There are two molecules in the asymmetric unit of the title compound, C14H11N3OS. In each, the benzimidazole ring system is essentially planar, with maximum deviations of 0.010 (2 and 0.006 (2 Å, and makes dihedral angles of 8.70 (9 and 13.75 (8°, respectively, with the hydroxy-substituted benzene rings. Each molecule adopts an E configuration about the central C=N double bond. In the crystal, the two independent molecules are connected via intermolecular N—H...S hydrogen bonds, forming dimers. Furthermore, the dimers are connected by N—H...O hydrogen bonds into molecular ribbons along the c axis. There is an intramolecular O—H...N hydrogen bond in each molecule, which generates an S(6 ring motif.

  15. Investigations into the construction of the pentasubstituted ring C of Neosurugatoxin – a crystallographic study

    Directory of Open Access Journals (Sweden)

    Alan M. Jones

    2016-01-01

    Full Text Available The crystal structures of three cyclopenta[c]furans with various substituents at the 4-, 5- and 6-positions of the ring system are reported, namely, (±-(3aR,4S,5S,6aS-4-methyl-5-phenylhexahydro-1H-cyclopenta[c]furan-4,5-diol, C14H18O3, (I, (±-(3aR,4S,5S,6aS-4-benzyloxy-4-methyl-5-phenylhexahydro-1H-cyclopenta[c]furan-5-ol, C21H24O3, (II, and (±-(1aR,1bS,4aR,5S,5aR-5-benzyloxy-5-methyl-5a-phenylhexahydro-2H-oxireno[2′,3′:3,4]cyclopenta[1,2-c]furan, C21H22O3, (III. The dominant interaction in (I and (II is an O—H...O hydrogen bond across the bicyclic 5,5-ring system between the non-functionalized hydroxy group and the tetrahydrofuran O atom, which appears to influence the envelope conformations of the fused five-membered rings, whereas in (III, the rings have different conformations. A weak intramolecular C—H...O interaction appears to influence the degree of tilt of the phenyl ring attached to the 5-position and is different in (I compared to (II and (III.

  16. The heptanucleotide motif GAGACGC is a key component of a cis-acting promoter element that is critical for SnSAG1 expression in Sarcocystis neurona.

    Science.gov (United States)

    Gaji, Rajshekhar Y; Howe, Daniel K

    2009-07-01

    The apicomplexan parasite Sarcocystis neurona undergoes a complex process of intracellular development, during which many genes are temporally regulated. The described study was undertaken to begin identifying the basic promoter elements that control gene expression in S. neurona. Sequence analysis of the 5'-flanking region of five S. neurona genes revealed a conserved heptanucleotide motif GAGACGC that is similar to the WGAGACG motif described upstream of multiple genes in Toxoplasma gondii. The promoter region for the major surface antigen gene SnSAG1, which contains three heptanucleotide motifs within 135 bases of the transcription start site, was dissected by functional analysis using a dual luciferase reporter assay. These analyses revealed that a minimal promoter fragment containing all three motifs was sufficient to drive reporter molecule expression, with the presence and orientation of the 5'-most heptanucleotide motif being absolutely critical for promoter function. Further studies should help to identify additional sequence elements important for promoter function and for controlling gene expression during intracellular development by this apicomplexan pathogen.

  17. The MHC motif viewer: a visualization tool for MHC binding motifs

    DEFF Research Database (Denmark)

    Rapin, Nicolas; Hoof, Ilka; Lund, Ole

    2010-01-01

    is hampered by the lack of tools for browsing and comparing specificity of these molecules. We have developed a Web server, MHC Motif Viewer, which allows the display of the binding motif for MHC class I proteins for human, chimpanzee, rhesus monkey, mouse, and swine, as well as HLA-DR protein sequences...

  18. Distributively generated matrix near rings

    International Nuclear Information System (INIS)

    Abbasi, S.J.

    1993-04-01

    It is known that if R is a near ring with identity then (I,+) is abelian if (I + ,+) is abelian and (I,+) is abelian if (I*,+) is abelian [S.J. Abbasi, J.D.P. Meldrum, 1991]. This paper extends these results. We show that if R is a distributively generated near ring with identity then (I,+) is included in Z(R), the center of R, if (I + ,+) is included in Z(M n (R)), the center of matrix near ring M n (R). Furthermore (I,+) is included in Z(R) if (I*,+) is included in Z(M n (R)). (author). 5 refs

  19. 2-Amino-5-bromopyridinium trifluoroacetate

    Directory of Open Access Journals (Sweden)

    Madhukar Hemamalini

    2010-04-01

    Full Text Available In the title compound, C5H6BrN2+·C2F3O2−, the F atoms of the anion are disordered over two sets of sites, with occupancies of 0.59 (2:0.41 (2. In the crystal structure, the anions and cations are linked into a two-dimensional network parallel to (100 by N—H...O and C—H...O hydrogen bonds. Within this network, the N—H...O hydrogen bonds generate R22(8 ring motifs.

  20. Variations in Ring Particle Cooling across Saturn's Rings with Cassini CIRS

    Science.gov (United States)

    Brooks, S. M.; Spilker, L. J.; Pilorz, S.; Edgington, S. G.; Déau, E.; Altobelli, N.

    2010-12-01

    Cassini's Composite Infrared Spectrometer has recorded over two million of spectra of Saturn's rings in the far infrared since arriving at Saturn in 2004. CIRS records far infrared radiation between 10 and 600 cm-1 ( 16.7 and 1000 μ {m} ) at focal plane 1 (FP1), which has a field of view of 3.9 mrad. Thermal emission from Saturn’s rings peaks in this wavelength range. Ring temperatures can be inferred from FP1 data. By tracking how ring temperatures vary, we can determine the thermal inertia of the rings. Previous studies have shown that the rings' thermal inertia, a measure of their response to changes in the thermal environment, varies from ring to ring. Thermal inertia can provide insight into the physical structure of Saturn's ring particles and their regoliths. Low thermal inertia and rapidly changing temperatures are suggestive of ring particles that have more porous or fluffy regoliths or that are riddled with cracks. Solid particles can be expected to have higher thermal inertias. Ferrari et al. (2005) fit thermal inertia values of 5218 {Jm)-2 {K}-1 {s}-1/2 to their B ring data and 6412 {Jm)-2 {K}-1 {s}-1/2 to their C ring data. In this work we focus on CIRS observations of the shadowed portion of Saturn's rings. The rings’ thermal budget is dominated by its absorption of solar radiation. As a result, ring particles abruptly cool as they traverse Saturn's shadow. From these shadow observations we can create cooling curves at specific locations across the rings. We will show that the rings' cooling curves and thus their thermal inertia vary not only from ring to ring, but by location within the individual rings. This research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract with NASA. Copyright 2010 California Institute of Technology. Government sponsorship acknowledged.

  1. MODA: an efficient algorithm for network motif discovery in biological networks.

    Science.gov (United States)

    Omidi, Saeed; Schreiber, Falk; Masoudi-Nejad, Ali

    2009-10-01

    In recent years, interest has been growing in the study of complex networks. Since Erdös and Rényi (1960) proposed their random graph model about 50 years ago, many researchers have investigated and shaped this field. Many indicators have been proposed to assess the global features of networks. Recently, an active research area has developed in studying local features named motifs as the building blocks of networks. Unfortunately, network motif discovery is a computationally hard problem and finding rather large motifs (larger than 8 nodes) by means of current algorithms is impractical as it demands too much computational effort. In this paper, we present a new algorithm (MODA) that incorporates techniques such as a pattern growth approach for extracting larger motifs efficiently. We have tested our algorithm and found it able to identify larger motifs with more than 8 nodes more efficiently than most of the current state-of-the-art motif discovery algorithms. While most of the algorithms rely on induced subgraphs as motifs of the networks, MODA is able to extract both induced and non-induced subgraphs simultaneously. The MODA source code is freely available at: http://LBB.ut.ac.ir/Download/LBBsoft/MODA/

  2. Graphical linking of MO multicenter bond index and VB structures. II-5-c rings and 6-c heterocyclic rings

    CERN Document Server

    Bollini, C G; Giambiagi, M

    2001-01-01

    Through the graphical method proposed it is possible to set a link between an MO multicenter bond index and VB structures. The value of the index depends on the order of the atoms involved if they are more than three. For 5-c rings three basic structures are required; the eventually different values are 12. Unlike the 6-c case it may happen that different pairs of basic structures are used to build the same polygon. For the 6-c rings including heteroatoms the original degeneracy of benzene splits leading eventually to 60 different I sub r sub i sub n sub g values.

  3. Conceptual design of a moving-ring reactor

    International Nuclear Information System (INIS)

    Smith, A.C.; Carlson, G.A.; Ashworth, C.P.

    1986-01-01

    A design of a prototype moving-ring reactor was completed, and a development plan for a pilot reactor is outlined. The fusion fuel is confined in current-carrying rings of magnetically field-reversed plasma (''compact toroids''). The plasma rings, formed by a coaxial plasma gun, undergo adiabatic magnetic compression to ignition temperature while they are being injected into the reactor's burner section. The cylindrical burner chamber is divided into three ''burn stations.'' Separator coils and a slight axial guide field gradient are used to shuttle the ignited toroids rapidly from one burn station to the next, pausing for one-third of the total burn time at each station. Deuterium-tritium- 3 He ice pellets refuel the rings at a rate that maintains constant radiated power. The fusion power per ring is approx. =105.5 MW. The burn time to reach a fusion energy gain of Q = 30 is 5.9 s

  4. Crystal structures of (E-4-[1-(2-carbamothioylhydrazinylideneethyl]phenyl acetate and (E-4-[1-(2-carbamothioylhydrazinylideneethyl]phenyl benzoate

    Directory of Open Access Journals (Sweden)

    Vijayan Viswanathan

    2017-01-01

    Full Text Available In the title compounds, C11H13N3O2S, (I, and C16H15N3O2S, (II, the thiosemicarbazone group adopts an extended conformation. The acetate ester (I crystallizes with two independent molecules in the asymmetric unit. In the benzoate ester (II, the planes of the two aryl rings are inclined to one another by 46.70 (7°. In both compounds, there is a short intramolecular N—H...N contact present, forming an S(5 ring motif. In the crystals of both compounds, molecules are linked via pairs of N—H...S hydrogen bonds, forming dimers with R22(8 ring motifs. The dimers are linked by N—H...S and N—H...O hydrogen bonds, forming slabs parallel to (01-1. In (I, there are N—H...π and C—H...π interactions present within the slabs, while in (II, there are only N—H...π interactions present.

  5. CombiMotif: A new algorithm for network motifs discovery in protein-protein interaction networks

    Science.gov (United States)

    Luo, Jiawei; Li, Guanghui; Song, Dan; Liang, Cheng

    2014-12-01

    Discovering motifs in protein-protein interaction networks is becoming a current major challenge in computational biology, since the distribution of the number of network motifs can reveal significant systemic differences among species. However, this task can be computationally expensive because of the involvement of graph isomorphic detection. In this paper, we present a new algorithm (CombiMotif) that incorporates combinatorial techniques to count non-induced occurrences of subgraph topologies in the form of trees. The efficiency of our algorithm is demonstrated by comparing the obtained results with the current state-of-the art subgraph counting algorithms. We also show major differences between unicellular and multicellular organisms. The datasets and source code of CombiMotif are freely available upon request.

  6. Physiological Responses during Cycling With Oval Chainrings (Q-Ring and Circular Chainrings

    Directory of Open Access Journals (Sweden)

    Alfredo Cordova

    2014-06-01

    Full Text Available The aim of this study was to compare the physiological responses of cyclists using round (C-ring or oval (Q-ring chainrings during an incremental test until exhaustion. Following a randomized design, fourteen male elite cyclists [age (mean ± SD: 21.1 ± 2.1 yr; VO2max: 78.5 ± 5.3 mL·kg-1min-1] performed two incremental maximal tests separated by 48 h (one with C-rings, the other with Q-rings. Starting at 100 W, the workload was increased by 25 W every 3 min until volitional exhaustion. Maximal heart rate, power output and oxygen consumption were compared. Blood lactate was monitored throughout the test. After the incremental test, 4 intermittent 20-s maximal sprints with a 60-s recovery period in between were performed. Maximal isometric voluntary contractions were performed at rest and immediately after each 20-s maximal sprint, and the force and EMG RMS amplitude were recorded from the vastus medialis and vastus lateralis muscles. For the incremental exercise test, no significant differences were found in the maximal power output (P=0.12, oxygen consumption (P=0.39, and heart rate (P=0.32 between Q-rings and C-rings. Throughout the incremental test, lactate levels were comparable when using both the C-rings and Q-rings (P=0.47. During the short sprints, power output was 2.5–6.5% greater for Q-rings than for C-rings (P=0.22. The decline in EMG RMS amplitude observed during the incremental tests was comparable for Q-rings and C-rings (0.42. These findings indicate that the oval chainring design, presented here as “Q-rings”, did not significantly influence the physiological response to an incremental exercise test as compared to a conventional chainring.

  7. MSDmotif: exploring protein sites and motifs

    Directory of Open Access Journals (Sweden)

    Henrick Kim

    2008-07-01

    Full Text Available Abstract Background Protein structures have conserved features – motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is essential for 3D structure prediction, modelling and drug-design. The Protein Data Bank (PDB is the source of this information however present search tools have limited 3D options to integrate protein sequence with its 3D structure. Results We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database. Novel algorithms for chemical fragments, 3D motifs, ϕ/ψ sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated. The interface provides functionality for visualization, search criteria creation, sequence and 3D multiple alignment options. MSDmotif is an integrated system where a results page is also a search form. A set of motif statistics is available for analysis. This set includes molecule and motif binding statistics, distribution of motif sequences, occurrence of an amino-acid within a motif, correlation of amino-acids side-chain charges within a motif and Ramachandran plots for each residue. The binding statistics are presented in association with properties that include a ligand fragment library. Access is also provided through the distributed Annotation System (DAS protocol. An additional entry point facilitates XML requests with XML responses. Conclusion MSDmotif is unique by combining chemical, sequence and 3D data in a single search engine with a range of search and visualisation options. It provides multiple views of data found in the PDB archive for exploring protein structures.

  8. Alpha - Skew Pi - Armendariz Rings

    Directory of Open Access Journals (Sweden)

    Areej M Abduldaim

    2018-03-01

    Full Text Available In this article we introduce a new concept called Alpha-skew Pi-Armendariz rings (Alpha - S Pi - ARas a generalization of the notion of Alpha-skew Armendariz rings.Another important goal behind studying this class of rings is to employ it in order to design a modern algorithm of an identification scheme according to the evolution of using modern algebra in the applications of the field of cryptography.We investigate general properties of this concept and give examples for illustration. Furthermore, this paperstudy the relationship between this concept and some previous notions related to Alpha-skew Armendariz rings. It clearly presents that every weak Alpha-skew Armendariz ring is Alpha-skew Pi-Armendariz (Alpha-S Pi-AR. Also, thisarticle showsthat the concepts of Alpha-skew Armendariz rings and Alpha-skew Pi- Armendariz rings are equivalent in case R is 2-primal and semiprime ring.Moreover, this paper proves for a semicommutative Alpha-compatible ringR that if R[x;Alpha] is nil-Armendariz, thenR is an Alpha-S Pi-AR. In addition, if R is an Alpha - S Pi -AR, 2-primal and semiprime ring, then N(R[x;Alpha]=N(R[x;Alpha]. Finally, we look forwardthat Alpha-skew Pi-Armendariz rings (Alpha-S Pi-ARbe more effect (due to their properties in the field of cryptography than Pi-Armendariz rings, weak Armendariz rings and others.For these properties and characterizations of the introduced concept Alpha-S Pi-AR, we aspire to design a novel algorithm of an identification scheme.

  9. Study of improvement in 1st ring`s gas-seal; Top ring no gas seal seino kojo no kento

    Energy Technology Data Exchange (ETDEWEB)

    Ando, H; Tateishi, Y; Fujimura, K; Hitosugi, H [Nippon Piston Ring Co. Ltd., Tokyo (Japan)

    1997-10-01

    The authors studied the effect of an angle of 1st ring twist on the amount of blow-by concerning higher speed/higher output engines for motorcycles. As a result, the authors found the twist made the ring restrained in a ring groove of piston , and confirmed its suitable range for blow-by. By means of the developed optimization method, the authors have achieved significant reduction in blow-by at high engine speed. 1 ref., 9 figs., 2 tabs.

  10. Dicyclo-hexyl-ammonium 3,5-dinitro-benzoate.

    Science.gov (United States)

    Saeed, Sohail; Rashid, Naghmana; Hussain, Rizwan; Wong, Wing-Tak

    2012-07-01

    The asymmetric unit of the title salt, C(12)H(24)N(+)·C(7)H(3)N(2)O(6) (-), contains two cations and two anions. In the crystal, the cations and anions are connected by N-H⋯O hydrogen bonds, forming a 12-membered ring with an R(4) (4)(12) graph-set motif. The center of this 12-membered ring coincides with an inversion centre. π-π stacking is observed between parallel benzene rings [centroid-centriod distance = 3.771 (2) Å].

  11. Review article: The mountain motif in the plot of Matthew

    Directory of Open Access Journals (Sweden)

    Gert J. Volschenk

    2010-09-01

    Full Text Available This article reviewed T.L. Donaldson’s book, Jesus on the mountain: A study in Matthean theology, published in 1985 by JSOT Press, Sheffield, and focused on the mountain motif in the structure and plot of the Gospel of Matthew, in addition to the work of Donaldson on the mountain motif as a literary motif and as theological symbol. The mountain is a primary theological setting for Jesus’ ministry and thus is an important setting, serving as one of the literary devices by which Matthew structured and progressed his narrative. The Zion theological and eschatological significance and Second Temple Judaism serve as the historical and theological background for the mountain motif. The last mountain setting (Mt 28:16–20 is the culmination of the three theological themes in the plot of Matthew, namely Christology, ecclesiology and salvation history.

  12. AN N-BODY INTEGRATOR FOR GRAVITATING PLANETARY RINGS, AND THE OUTER EDGE OF SATURN'S B RING

    International Nuclear Information System (INIS)

    Hahn, Joseph M.; Spitale, Joseph N.

    2013-01-01

    A new symplectic N-body integrator is introduced, one designed to calculate the global 360° evolution of a self-gravitating planetary ring that is in orbit about an oblate planet. This freely available code is called epi i nt, and it is distinct from other such codes in its use of streamlines to calculate the effects of ring self-gravity. The great advantage of this approach is that the perturbing forces arise from smooth wires of ring matter rather than discreet particles, so there is very little gravitational scattering and so only a modest number of particles are needed to simulate, say, the scalloped edge of a resonantly confined ring or the propagation of spiral density waves. The code is applied to the outer edge of Saturn's B ring, and a comparison of Cassini measurements of the ring's forced response to simulations of Mimas's resonant perturbations reveals that the B ring's surface density at its outer edge is σ 0 = 195 ± 60 g cm –2 , which, if the same everywhere across the ring, would mean that the B ring's mass is about 90% of Mimas's mass. Cassini observations show that the B ring-edge has several free normal modes, which are long-lived disturbances of the ring-edge that are not driven by any known satellite resonances. Although the mechanism that excites or sustains these normal modes is unknown, we can plant such a disturbance at a simulated ring's edge and find that these modes persist without any damping for more than ∼10 5 orbits or ∼100 yr despite the simulated ring's viscosity ν s = 100 cm 2 s –1 . These simulations also indicate that impulsive disturbances at a ring can excite long-lived normal modes, which suggests that an impact in the recent past by perhaps a cloud of cometary debris might have excited these disturbances, which are quite common to many of Saturn's sharp-edged rings

  13. meso-4,4′-Dimethoxy-2,2′-{[(3aR,7aS-2,3,3a,4,5,6,7,7a-octahydro-1H-benzimidazole-1,3-diyl]bis(methylene}diphenol

    Directory of Open Access Journals (Sweden)

    Augusto Rivera

    2013-07-01

    Full Text Available The title compound, C23H30N2O4, a di-Mannich base derived from 4-methoxyphenol and cis-1,2-diaminecyclohexane, has a perhydrobenzimidazolidine nucleus, in which the cyclohexane ring adopts a chair conformation and the heterocyclic ring has a half-chair conformation with a C—N—C—C torsion angles of −48.14 (15 and −14.57 (16°. The mean plane of the heterocycle makes dihedral angles of 86.29 (6 and 78.92 (6° with the pendant benzene rings. The molecular structure of the title compound shows the presence of two interactions between the N atoms of the imidazolidine ring and the hydroxyl groups through intramolecular O—H...N hydrogen bonds with graph-set motif S(6. The unobserved lone pairs of the N atoms are presumed to be disposed in a syn conformation, being only the second example of an exception to the typical `rabbit-ears' effect in 1,2-diamines.

  14. Structural and functional analysis of a FeoB A143S G5 loop mutant explains the accelerated GDP release rate.

    Science.gov (United States)

    Guilfoyle, Amy P; Deshpande, Chandrika N; Vincent, Kimberley; Pedroso, Marcelo M; Schenk, Gerhard; Maher, Megan J; Jormakka, Mika

    2014-05-01

    GTPases (G proteins) hydrolyze the conversion of GTP to GDP and free phosphate, comprising an integral part of prokaryotic and eukaryotic signaling, protein biosynthesis and cell division, as well as membrane transport processes. The G protein cycle is brought to a halt after GTP hydrolysis, and requires the release of GDP before a new cycle can be initiated. For eukaryotic heterotrimeric Gαβγ proteins, the interaction with a membrane-bound G protein-coupled receptor catalyzes the release of GDP from the Gα subunit. Structural and functional studies have implicated one of the nucleotide binding sequence motifs, the G5 motif, as playing an integral part in this release mechanism. Indeed, a Gαs G5 mutant (A366S) was shown to have an accelerated GDP release rate, mimicking a G protein-coupled receptor catalyzed release state. In the present study, we investigate the role of the equivalent residue in the G5 motif (residue A143) in the prokaryotic membrane protein FeoB from Streptococcus thermophilus, which includes an N-terminal soluble G protein domain. The structure of this domain has previously been determined in the apo and GDP-bound states and in the presence of a transition state analogue, revealing conformational changes in the G5 motif. The A143 residue was mutated to a serine and analyzed with respect to changes in GTPase activity, nucleotide release rate, GDP affinity and structural alterations. We conclude that the identity of the residue at this position in the G5 loop plays a key role in the nucleotide release rate by allowing the correct positioning and hydrogen bonding of the nucleotide base. © 2014 FEBS.

  15. N-Butoxycarbonyl-5-oxo-l-proline ethyl ester

    Directory of Open Access Journals (Sweden)

    P. Rajalakshmi

    2013-04-01

    Full Text Available The molecular structure of the title compound, C12H19NO5, may be visualized as made up of two nearly perpendicular planes [dihedral angle = 87.39 (12°] and its crystal structure is a good example of C—H...O interactions assuming significance in optimizing supramolecular aggregation in crystals in a molecule which is severely imbalanced in terms of donors to acceptor atoms. The pyrrolidine ring adopts a (3T2 twist conformation with puckering parameters Q = 0.2630 (4 Å and ϕ = 59 (9°. The crystal structure features R24(10 and R34(26 ring motifs formed by four weak C—H...O interactions, leading to supramolecular sheets lying parallel to the bc plane.

  16. Phyloproteomic Analysis of 11780 Six-Residue-Long Motifs Occurrences

    Directory of Open Access Journals (Sweden)

    O. V. Galzitskaya

    2015-01-01

    Full Text Available How is it possible to find good traits for phylogenetic reconstructions? Here, we present a new phyloproteomic criterion that is an occurrence of simple motifs which can be imprints of evolution history. We studied the occurrences of 11780 six-residue-long motifs consisting of two randomly located amino acids in 97 eukaryotic and 25 bacterial proteomes. For all eukaryotic proteomes, with the exception of the Amoebozoa, Stramenopiles, and Diplomonadida kingdoms, the number of proteins containing the motifs from the first group (one of the two amino acids occurs once at the terminal position made about 20%; in the case of motifs from the second (one of two amino acids occurs one time within the pattern and third (the two amino acids occur randomly groups, 30% and 50%, respectively. For bacterial proteomes, this relationship was 10%, 27%, and 63%, respectively. The matrices of correlation coefficients between numbers of proteins where a motif from the set of 11780 motifs appears at least once in 9 kingdoms and 5 phyla of bacteria were calculated. Among the correlation coefficients for eukaryotic proteomes, the correlation between the animal and fungi kingdoms (0.62 is higher than between fungi and plants (0.54. Our study provides support that animals and fungi are sibling kingdoms. Comparison of the frequencies of six-residue-long motifs in different proteomes allows obtaining phylogenetic relationships based on similarities between these frequencies: the Diplomonadida kingdoms are more close to Bacteria than to Eukaryota; Stramenopiles and Amoebozoa are more close to each other than to other kingdoms of Eukaryota.

  17. 1,4a-Dimethyl-6-methyl-ene-5-(5,5,6,6-tetra-cyano-2-methyl-cyclo-hex-2-enylmeth-yl)deca-hydro-naphthalene-1-carboxylic acid: a trans-communic acid derivative.

    Science.gov (United States)

    Rejouani, Nezha; Auhmani, Aziz; Ait Itto, My Youssef; Benharref, Ahmed; Daran, Jean-Claude

    2008-01-18

    In the search for cancer chemopreventive agents, we have studied the Diels-Alder reaction of trans-communic acid with tetra-cyano-ethyl-ene in the presence of SiO(2) as catalyst. The title cycloadduct, C(26)H(30)N(4)O(2), was obtained in 75% yield. The mol-ecules are arranged in pairs through O-H⋯O hydrogen bonds, forming an R(2) (2)(8) ring motif. Both the fused cyclohexyl rings adopt a chair conformation, whereas the nonfused ring adopts a half-chair conformation.

  18. Statistical tests to compare motif count exceptionalities

    Directory of Open Access Journals (Sweden)

    Vandewalle Vincent

    2007-03-01

    Full Text Available Abstract Background Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required. Results We develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops. Conclusion The exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use.

  19. Analisis Peranan Franchisor Terhadap Suksesnya Bisnis Franchise Pada Mc. Donald’s Cabang Ring Road Medan

    OpenAIRE

    Simarmata, Leonardo

    2012-01-01

    Tujuan penelitian ini adalah untuk mengetahui dan menganalisis peranan franchisor dalam promotion, support service, training, control system dan communication terhadap suksesnya bisnis franchise pada Mc Donald’s Cabang Ring Road Medan. Pengumpulan data primer diperoleh dengan cara memberikan daftar pertanyaan (questionaire) dan melakukan wawancara (interview) secara mendalam (depth interview) kepada pemilik usaha M. Donald’s Cabang Ring Road Medan. Teknik analisis data penelitian ini ad...

  20. Thomson's Jumping Ring over a Long Coil

    Science.gov (United States)

    Jeffery, Rondo N.; Amiri, Farhang

    2018-01-01

    The classic jumping ring apparatus consists of a coil with an iron core that extends out of the coil. A copper or aluminum ring placed over the iron core jumps upward when AC power is applied to the coil. In this paper we will examine a modified design of the jumping ring apparatus, called the "long-coil design." It allows the ring to…

  1. FY2017 status report: Model 9975 O-ring fixture long-term leak performance

    Energy Technology Data Exchange (ETDEWEB)

    Daugherty, W. L. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2017-07-27

    A series of experiments to monitor the aging performance of Viton® GLT and GLT-S O-rings used in the Model 9975 shipping package has been ongoing since 2004 at the Savannah River National Laboratory. One approach has been to periodically evaluate the leak performance of O-rings being aged in mock-up 9975 Primary Containment Vessels (PCVs) at elevated temperature. Other methods such as compression-stress relaxation (CSR) tests and field surveillance are also on-going to evaluate O-ring behavior. Seventy tests using PCV mock-ups with GLT O-rings were assembled and heated to temperatures ranging from 200 to 450 ºF. They were leak-tested initially and have been tested periodically to determine if they continue to meet the leak-tightness criterion defined in ANSI standard N14.5-97. Due to material substitution, a smaller test matrix with fourteen additional tests was initiated in 2008 with GLT-S O-rings heated to temperatures ranging from 200 to 400 ºF. Leak test failures have been experienced in all of the GLT O-ring fixtures aging at 350 ºF and higher temperatures, and in 8 fixtures aging at 300 ºF. The 300 °F GLT O-ring fixtures failed after 2.8 to 5.7 years at temperature. The remaining GLT O-ring fixtures aging at 300 ºF were retired from testing following more than 5 years at temperature without failure. No failures have yet been observed in GLT O-ring fixtures aging at 200 ºF for 9 to 10.5 years, or in GLT O-ring fixtures aging at 270 ºF for 5.7 years. These aging temperatures bound O-ring temperatures anticipated during normal storage in K-Area Complex (KAC). Leak test failures have been experienced in all of the GLT-S O-ring fixtures aging at 300 ºF and above. No failures have yet been observed in GLT-S O-ring fixtures aging at 200 and 250 ºF for 6.9 to 7.5 years. Data from the O-ring fixtures are generally consistent with results from compression stress relaxation testing, and provide confidence in the predictive models based on those results

  2. Prestressed Ring Beam in the Church of St. Peter’s and Paul’s in Bodzanow, Design and Realization

    Science.gov (United States)

    Szydlowski, Rafal; Labuzek, Barbara; Turcza, Monika

    2017-10-01

    The present trend in architecture is designing thin. slender and spacious architectural forms. It has become the reason for searching for new solutions and finding new ways of use of the existing construction ones. Recently, the first time in Poland, the post-tensioning has been used in realization of church building. In the Church of St. Peter’s and Paul’s in Bodzanow (near Cracow) was designed circumferential ring beam post-tensioned with 4 unbounded tendons to transfer peripheral tensile forces from the roof. Thanks to the use of a prestressed ring beam hidden in the wall, large cross-section of roof girders was possible to be avoided, as well as a massive reinforced concrete ring or additional steel tie-rods. The paper presents the applied solutions in details with the theoretical calculated results as well as the results of prestressing measured in site during tensioning of tendons. Based on presented results some conclusions have been drawn.

  3. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed

    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 applications require mining of motifs in one very long sequence (i.e., in the order of several gigabytes). For this case, there exist statistical approaches that are fast but inaccurate; or combinatorial methods that are sound and complete. Unfortunately, existing combinatorial methods are serial and very slow. Consequently, they are limited to very short sequences (i.e., a few megabytes), small alphabets (typically 4 symbols for DNA sequences), and restricted types of motifs. This paper presents ACME, a combinatorial method for extracting motifs from a single very long sequence. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution. It also decomposes the search space in a smart way that allows scalability to thousands of processors with more than 90% speedup. ACME is the only method that: (i) scales to gigabyte-long sequences; (ii) handles large alphabets; (iii) supports interesting types of motifs with minimal additional cost; and (iv) is optimized for a variety of architectures such as multi-core systems, clusters in the cloud, and supercomputers. ACME reduces the extraction time for an exact-length query from 4 hours to 7 minutes on a typical workstation; handles 3 orders of magnitude longer sequences; and scales up to 16, 384 cores on a supercomputer. Copyright is held by the owner/author(s).

  4. Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Hanke, S.; Hinsby, A. M.

    2008-01-01

    set of 481 unique phosphotyrosine (Tyr(P)) peptides by sequence similarity to known ligands of the Src homology 2 (SH2) and the phosphotyrosine binding (PTB) domains. From 20 clusters we extracted 16 known and four new interaction motifs. Using quantitative mass spectrometry we pulled down Tyr......(P)-specific binding partners for peptides corresponding to the extracted motifs. We confirmed numerous previously known interaction motifs and found 15 new interactions mediated by phosphosites not previously known to bind SH2 or PTB. Remarkably, a novel hydrophobic N-terminal motif ((L/V/I)(L/V/I)pY) was identified...

  5. Record of the Solar Activity and of Other Geophysical Phenomenons in Tree Ring

    Science.gov (United States)

    Rigozo, Nivaor Rodolfo

    1999-01-01

    Tree ring studies are usually used to determine or verify climatic factors which prevail in a given place or region and may cause tree ring width variations. Few studies are dedicated to the geophysical phenomena which may underlie these tree ring width variations. In order to look for periodicities which may be associated to the solar activity and/or to other geophysical phenomena which may influence tree ring growth, a new interactive image analysis method to measure tree ring width was developed and is presented here. This method makes use of a computer and a high resolution flatbed scanner; a program was also developed in Interactive Data Language (IDL 5.0) to study ring digitized images and transform them into time series. The main advantage of this method is the tree ring image interactive analysis without needing complex and high cost instrumentation. Thirty-nine samples were collected: 12 from Concordia - S. C., 9 from Canela - R. S., 14 from Sao Francisco de Paula - R. S., one from Nova Petropolis - R. S., 2 from Sao Martinho da Serra - R. S. e one from Chile. Fit functions are applied to ring width time series to obtain the best long time range trend (growth rate of every tree) curves and are eliminated through a standardization process that gives the tree ring index time series from which is performed spectral analysis by maximum entropy method and iterative regression. The results obtained show periodicities close to 11 yr, 22 yr Hale solar cycles and 5.5 yr for all sampling locations 52 yr and Gleissberg cycles for Concordia - S. C. and Chile samples. El Nino events were also observed with periods around 4 e 7 yr.

  6. The 5s25p2 - (5s25p5d + 5s5p3 + 5s25p6s + 5s25p7s) transitions in Sb II and 5s25p - (5s5p2 + 5s2nl) transitions in Sb III

    International Nuclear Information System (INIS)

    Arcimowicz, B.; Joshi, Y.N.; Kaufman, V.

    1989-01-01

    The spectrum of antimony was photographed in the 575-2300 A region (1A 10 -10 m) using a hollow cathode and a triggered spark source. The analysis of the 5s 2 5p 2 - (5s 2 5p5d + 5s5p 3 + 5s 2 5p6s + 5s 2 5p7s) transitions in Sb II spectrum was revised and interpreted on the basis of multiconfiguration interaction calculations. Accurate wavelength measurements of Sb III lines lead to a revised ground-state 5s 2 5p 2 P interval value of 6574.5 cm -1 . (author). 15 refs., 9 tabs., 1 fig

  7. (E-Methyl 3-(3,4-dimethoxyphenyl-2-[(1,3-dioxoisoindolin-2-ylmethyl]acrylate

    Directory of Open Access Journals (Sweden)

    D. Kannan

    2012-04-01

    Full Text Available In the title compound, C21H19NO6, the isoindole ring system is essentially planar [maximum deviation = 0.019 (2 Å for the N atom] and is oriented at a dihedral angle of 51.3 (1° with respect to the benzene ring. The two methoxy groups are almost coplanar with the attached benzene ring [C—O—C—C = 3.7 (4 and 4.3 (4°]. The molecular conformation is stabilized by an intramolecular C—H...O hydrogen bond, which generates an S(9 ring motif. In the crystal, molecules are linked through bifurcated C—H...(O,O hydrogen bonds having R12(5 ring motifs, forming chains along the b-axis direction. The crystal packing is further stabilzed by π–π interactions [centriod–centroid distance = 3.463 (1 Å].

  8. (E)-Methyl 3-(3,4-dimeth-oxy-phen-yl)-2-[(1,3-dioxoisoindolin-2-yl)meth-yl]acrylate.

    Science.gov (United States)

    Kannan, D; Bakthadoss, M; Lakshmanan, D; Murugavel, S

    2012-04-01

    In the title compound, C(21)H(19)NO(6), the isoindole ring system is essentially planar [maximum deviation = 0.019 (2) Å for the N atom] and is oriented at a dihedral angle of 51.3 (1)° with respect to the benzene ring. The two meth-oxy groups are almost coplanar with the attached benzene ring [C-O-C-C = 3.7 (4) and 4.3 (4)°]. The mol-ecular conformation is stabilized by an intra-molecular C-H⋯O hydrogen bond, which generates an S(9) ring motif. In the crystal, mol-ecules are linked through bifurcated C-H⋯(O,O) hydrogen bonds having R(1) (2)(5) ring motifs, forming chains along the b-axis direction. The crystal packing is further stabilzed by π-π inter-actions [centriod-centroid distance = 3.463 (1) Å].

  9. (1S*,2S*,5R*,8S*,11S*,14R*,17S*,20R*-14-Methyl-6-methylene-10,16,18-trioxahexacyclo[12.5.1.15,8.01,11.02,8.017,20]henicosane-7,9-dione: natural diterpenoid macrocalyxoformin B

    Directory of Open Access Journals (Sweden)

    Hao Shi

    2008-01-01

    Full Text Available The title compound, C20H24O5, isolated from Rabdosia var. lophanthoides Hara, is built up from six fused rings. Cyclohexane ring A adopts a chair conformation, ring B exists in a screw-boat conformation and ring C adopts a boat conformation; the three five-membered rings D, E and F adopt envelope conformations.

  10. Structural Analysis of the Bacterial Proteasome Activator Bpa in Complex with the 20S Proteasome.

    Science.gov (United States)

    Bolten, Marcel; Delley, Cyrille L; Leibundgut, Marc; Boehringer, Daniel; Ban, Nenad; Weber-Ban, Eilika

    2016-12-06

    Mycobacterium tuberculosis harbors proteasomes that recruit substrates for degradation through an ubiquitin-like modification pathway. Recently, a non-ATPase activator termed Bpa (bacterial proteasome activator) was shown to support an alternate proteasomal degradation pathway. Here, we present the cryo-electron microscopy (cryo-EM) structure of Bpa in complex with the 20S core particle (CP). For docking into the cryo-EM density, we solved the X-ray structure of Bpa, showing that it forms tight four-helix bundles arranged into a 12-membered ring with a 40 Å wide central pore and the C-terminal helix of each protomer protruding from the ring. The Bpa model was fitted into the cryo-EM map of the Bpa-CP complex, revealing its architecture and striking symmetry mismatch. The Bpa-CP interface was resolved to 3.5 Å, showing the interactions between the C-terminal GQYL motif of Bpa and the proteasome α-rings. This docking mode is related to the one observed for eukaryotic activators with features specific to the bacterial complex. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Electronic de-multipliers II (ring-shape systems)

    International Nuclear Information System (INIS)

    Raievski, V.

    1948-09-01

    This report describes a new type of ring-shape fast electronic counter (de-multiplier) with a resolution capacity equivalent to the one made by Regener (Rev. of Scientific Instruments USA 1946, 17, 180-89) but requiring two-times less electronic valves. This report follows the general description of electronic de-multipliers made by J. Ailloud (CEA--001). The ring comprises 5 flip-flop circuits with two valves each. The different elements of the ring are calculated with enough details to allow the transfer of this calculation to different valve types. (J.S.)

  12. The Runt domain of AML1 (RUNX1) binds a sequence-conserved RNA motif that mimics a DNA element.

    Science.gov (United States)

    Fukunaga, Junichi; Nomura, Yusuke; Tanaka, Yoichiro; Amano, Ryo; Tanaka, Taku; Nakamura, Yoshikazu; Kawai, Gota; Sakamoto, Taiichi; Kozu, Tomoko

    2013-07-01

    AML1 (RUNX1) is a key transcription factor for hematopoiesis that binds to the Runt-binding double-stranded DNA element (RDE) of target genes through its N-terminal Runt domain. Aberrations in the AML1 gene are frequently found in human leukemia. To better understand AML1 and its potential utility for diagnosis and therapy, we obtained RNA aptamers that bind specifically to the AML1 Runt domain. Enzymatic probing and NMR analyses revealed that Apt1-S, which is a truncated variant of one of the aptamers, has a CACG tetraloop and two stem regions separated by an internal loop. All the isolated aptamers were found to contain the conserved sequence motif 5'-NNCCAC-3' and 5'-GCGMGN'N'-3' (M:A or C; N and N' form Watson-Crick base pairs). The motif contains one AC mismatch and one base bulged out. Mutational analysis of Apt1-S showed that three guanines of the motif are important for Runt binding as are the three guanines of RDE, which are directly recognized by three arginine residues of the Runt domain. Mutational analyses of the Runt domain revealed that the amino acid residues used for Apt1-S binding were similar to those used for RDE binding. Furthermore, the aptamer competed with RDE for binding to the Runt domain in vitro. These results demonstrated that the Runt domain of the AML1 protein binds to the motif of the aptamer that mimics DNA. Our findings should provide new insights into RNA function and utility in both basic and applied sciences.

  13. [Personal motif in art].

    Science.gov (United States)

    Gerevich, József

    2015-01-01

    One of the basic questions of the art psychology is whether a personal motif is to be found behind works of art and if so, how openly or indirectly it appears in the work itself. Analysis of examples and documents from the fine arts and literature allow us to conclude that the personal motif that can be identified by the viewer through symbols, at times easily at others with more difficulty, gives an emotional plus to the artistic product. The personal motif may be found in traumatic experiences, in communication to the model or with other emotionally important persons (mourning, disappointment, revenge, hatred, rivalry, revolt etc.), in self-searching, or self-analysis. The emotions are expressed in artistic activity either directly or indirectly. The intention nourished by the artist's identity (Kunstwollen) may stand in the way of spontaneous self-expression, channelling it into hidden paths. Under the influence of certain circumstances, the artist may arouse in the viewer, consciously or unconsciously, an illusionary, misleading image of himself. An examination of the personal motif is one of the important research areas of art therapy.

  14. 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

  15. Temporal motifs in time-dependent networks

    International Nuclear Information System (INIS)

    Kovanen, Lauri; Karsai, Márton; Kaski, Kimmo; Kertész, János; Saramäki, Jari

    2011-01-01

    Temporal networks are commonly used to represent systems where connections between elements are active only for restricted periods of time, such as telecommunication, neural signal processing, biochemical reaction and human social interaction networks. We introduce the framework of temporal motifs to study the mesoscale topological–temporal structure of temporal networks in which the events of nodes do not overlap in time. Temporal motifs are classes of similar event sequences, where the similarity refers not only to topology but also to the temporal order of the events. We provide a mapping from event sequences to coloured directed graphs that enables an efficient algorithm for identifying temporal motifs. We discuss some aspects of temporal motifs, including causality and null models, and present basic statistics of temporal motifs in a large mobile call network

  16. Current’s Fluctuations through Molecular Wires Composed of Thiophene Rings

    Directory of Open Access Journals (Sweden)

    Judith Helena Ojeda Silva

    2018-04-01

    Full Text Available We study theoretically the electronic transport and quantum fluctuations in single-molecule systems using thiophene rings as integrated elementary functions, as well as the dependence of these properties with the increase of the coupled rings, i.e., as a quantum wire. In order to analyze the current flow through these molecular systems, the thiophene rings are considered to be connected to metal contacts, which, in general terms, will be related to the application of voltages (bias voltages or gate voltages to generate non-equilibrium behavior between the contacts. Due to the nonlinear behavior that is generated when said voltages are applied, it is possible to observe quantum fluctuations in the transport properties of these molecular wires. For the calculation of the transport properties, we applied a tight-binding approach using the Landauer–Büttiker formalism and the Fischer–Lee relationship, by means of a semi-analytic Green’s function method within a real-space renormalization (decimation procedure. Our results showed an excellent agreement with results using a tight-binding model with a minimal number of parameters reported so far for these molecular systems.

  17. Mouse nucleolin binds to 4.5S RNAH, a small noncoding RNA

    International Nuclear Information System (INIS)

    Hirose, Yutaka; Harada, Fumio

    2008-01-01

    4.5S RNAH is a rodent-specific small noncoding RNA that exhibits extensive homology to the B1 short interspersed element. Although 4.5S RNAH is known to associate with cellular poly(A)-terminated RNAs and retroviral genomic RNAs, its function remains unclear. In this study, we analyzed 4.5S RNAH-binding proteins in mouse nuclear extracts using gel mobility shift and RNA-protein UV cross-linking assays. We found that at least nine distinct polypeptides (p170, p110, p93, p70, p48, p40, p34, p20, and p16.5) specifically interacted with 4.5S RNAHin vitro. Using anti-La antibody, p48 was identified as mouse La protein. To identify the other 4.5S RNAH-binding proteins, we performed expression cloning from a mouse cDNA library and obtained cDNA clones derived from nucleolin mRNA. We identified p110 as nucleolin using nucleolin-specific antibodies. UV cross-linking analysis using various deletion mutants of nucleolin indicated that the third of four tandem RNA recognition motifs is a major determinant for 4.5S RNAH recognition. Immunoprecipitation of nucleolin from the subcellular fractions of mouse cell extracts revealed that a portion of the endogenous 4.5S RNAH was associated with nucleolin and that this complex was located in both the nucleoplasm and nucleolus

  18. Robustness and backbone motif of a cancer network regulated by miR-17-92 cluster during the G1/S transition.

    Directory of Open Access Journals (Sweden)

    Lijian Yang

    Full Text Available Based on interactions among transcription factors, oncogenes, tumor suppressors and microRNAs, a Boolean model of cancer network regulated by miR-17-92 cluster is constructed, and the network is associated with the control of G1/S transition in the mammalian cell cycle. The robustness properties of this regulatory network are investigated by virtue of the Boolean network theory. It is found that, during G1/S transition in the cell cycle process, the regulatory networks are robustly constructed, and the robustness property is largely preserved with respect to small perturbations to the network. By using the unique process-based approach, the structure of this network is analyzed. It is shown that the network can be decomposed into a backbone motif which provides the main biological functions, and a remaining motif which makes the regulatory system more stable. The critical role of miR-17-92 in suppressing the G1/S cell cycle checkpoint and increasing the uncontrolled proliferation of the cancer cells by targeting a genetic network of interacting proteins is displayed with our model.

  19. Magnetic and structural properties of an octanuclear Cu(II) S=1/2 mesoscopic ring: Susceptibility and NMR measurements

    International Nuclear Information System (INIS)

    Lascialfari, A.; Jang, Z. H.; Borsa, F.; Gatteschi, D.; Cornia, A.; Rovai, D.; Caneschi, A.; Carretta, P.

    2000-01-01

    Magnetic susceptibility, 1 H NMR and 63 Cu NMR-NQR experiments on two slightly different species of the molecular S=1/2 antiferromagnetic (AF) ring Cu8, [Cu 8 (dmpz) 8 (OH) 8 ]·2C 5 H 5 N (Cu8P) and [Cu 8 (dmpz) 8 (OH) 8 ]·2C 5 H 5 NO 2 (Cu8N), are presented. The magnetic energy levels are calculated exactly for an isotropic Heisenberg model Hamiltonian in zero magnetic field. From the magnetic susceptibility measurements we estimate the AF exchange coupling constant J∼1000 K and the resulting gap Δ∼500 K between the S T =0 ground state and the S T =1 first excited state. The 63,65 Cu NQR spectra indicate the presence of four crystallographically inequivalent copper nuclei in each ring. From the combination of the 63 Cu NQR spectra and of the 63 Cu NMR spectra at high magnetic field, we estimate the quadrupole coupling constant v Q of each site and the average asymmetry parameter η of the electric-field gradient tensor. The nuclear spin-lattice relaxation rate (NSLR) decreases exponentially on decreasing temperature for all nuclei investigated. The gap parameter extracted from 63 Cu NQR-NSLR is the same as for the susceptibility while a smaller value is obtained from the 63 Cu NMR-NSLR in an external magnetic field of 8.2 T. (c) 2000 The American Physical Society

  20. Trimethyl 3,3′,3′′-(benzene-1,3,5-triyltripropynoate

    Directory of Open Access Journals (Sweden)

    Felix Katzsch

    2016-04-01

    Full Text Available In the title compound, C18H12O6, the alkyne bonds are distorted, featuring bond angles around the C—C[triple-bond]C—C group of 173.6 (1/179.0 (1, 178.1 (1/178.4 (1 and 174.9 (1/175.9 (1°, and the ester groups make angles of 3.5 (1, 13.8 (1 and 14.5 (1° with the central benzene ring. In the crystal, molecules are connected in layers parallel to (131 by weak C—H...O hydrogen bonds, giving rise to a system of hydrogen-bonded ring motifs with graph sets R22(14 and R44(22. The layers are linked by C—H...O and C—H...π contacts.

  1. 2-[(E-(2S,5R-2-Isopropyl-5-methylcyclohexylidene]-N-methylhydrazine-1-carbothioamide

    Directory of Open Access Journals (Sweden)

    Adriano Bof de Oliveira

    2016-03-01

    Full Text Available There are two molecules in the asymmetric unit of the title compound, C12H23N3S, which are linked by two strong N—H...S hydrogen bonds, building a non-centrosymmetric dimer with graph-set motif R22(8. The molecules are further connected by N—H...S interactions into a two-dimensional hydrogen-bonded polymeric structure along the [001] direction. The absolute structure is based on the refinement of the Flack parameter.

  2. Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus)

    Science.gov (United States)

    Suntronpong, Aorarat; Thapana, Watcharaporn; Twilprawat, Panupon; Prakhongcheep, Ornjira; Somyong, Suthasinee; Muangmai, Narongrit; Surin Peyachoknagul; Srikulnath, Kornsorn

    2017-01-01

    Abstract Among teleost fishes, Asian swamp eel (Monopterus albus Zuiew, 1793) possesses the lowest chromosome number, 2n = 24. To characterize the chromosome constitution and investigate the genome organization of repetitive sequences in M. albus, karyotyping and chromosome mapping were performed with the 18S – 28S rRNA gene, telomeric repeats, microsatellite repeat motifs, and Rex retroelements. The 18S – 28S rRNA genes were observed to the pericentromeric region of chromosome 4 at the same position with large propidium iodide and C-positive bands, suggesting that the molecular structure of the pericentromeric regions of chromosome 4 has evolved in a concerted manner with amplification of the 18S – 28S rRNA genes. (TTAGGG)n sequences were found at the telomeric ends of all chromosomes. Eight of 19 microsatellite repeat motifs were dispersedly mapped on different chromosomes suggesting the independent amplification of microsatellite repeat motifs in M. albus. Monopterus albus Rex1 (MALRex1) was observed at interstitial sites of all chromosomes and in the pericentromeric regions of most chromosomes whereas MALRex3 was scattered and localized to all chromosomes and MALRex6 to several chromosomes. This suggests that these retroelements were independently amplified or lost in M. albus. Among MALRexs (MALRex1, MALRex3, and MALRex6), MALRex6 showed higher interspecific sequence divergences from other teleost species in comparison. This suggests that the divergence of Rex6 sequences of M. albus might have occurred a relatively long time ago. PMID:29093797

  3. Physiological Responses during Cycling With Oval Chainrings (Q-Ring) and Circular Chainrings.

    Science.gov (United States)

    Cordova, Alfredo; Latasa, Iban; Seco, Jesus; Villa, Gerardo; Rodriguez-Falces, Javier

    2014-05-01

    The aim of this study was to compare the physiological responses of cyclists using round (C-ring) or oval (Q-ring) chainrings during an incremental test until exhaustion. Following a randomized design, twelve male elite cyclists [age (mean ± SD): 21.1 ± 2.1 yr; VO2max: 78.1 ± 5.3 mL·kg(-1)min(-1)] performed two incremental maximal tests separated by 48 h (one with C-rings, the other with Q-rings). Starting at 100 W, the workload was increased by 25 W every 3 min until volitional exhaustion. Maximal heart rate, power output and oxygen consumption were compared. Blood lactate was monitored throughout the test. After the incremental test, 4 intermittent 20-s maximal sprints with a 60-s recovery period in between were performed. Maximal isometric voluntary contractions were performed at rest and immediately after each 20-s maximal sprint, and the force and EMG RMS amplitude were recorded from the vastus medialis and vastus lateralis muscles. For the incremental exercise test, no significant differences were found in the maximal power output (P=0.12), oxygen consumption (P=0.39), and heart rate (P=0.32) between Q-rings and C-rings. Throughout the incremental test, lactate levels were comparable when using both the C-rings and Q-rings (P=0.47). During the short sprints, power output was 2.5-6.5% greater for Q-rings than for C-rings (P=0.22). The decline in EMG RMS amplitude observed during the incremental tests was comparable for Q-rings and C-rings (0.42). These findings indicate that the oval chainring design, presented here as "Q-rings", did not significantly influence the physiological response to an incremental exercise test as compared to a conventional chainring. Key pointsDuring the incremental exercise test, no significant differences were found in power output, oxygen consumption or heart rate between oval "Q-rings" and conventional chainrings.Over the course of the incremental test, blood lactate levels were comparable for the oval "Q-rings" and

  4. Benzo[1,2-b:4,5-b’]dithiophene-Pyrido[3,4-b]pyrazine Small-Molecule Donors for Bulk Heterojunction Solar Cells

    KAUST Repository

    Wolf, Jannic Sebastian; Babics, Maxime; Wang, Kai; Saleem, Qasim; Liang, Ru-Ze; Hansen, Michael Ryan; Beaujuge, Pierre

    2016-01-01

    We report on the synthesis, material properties and BHJ solar cell characteristics of a set of π-conjugated small-molecule (SM) donors composed of benzo[1,2-b:4,5-b′]dithiophene (BDT) and pyrido[3,4-b]pyrazine (PP) units – examining the perspectives of alkyl-substituted PP acceptor motifs in SM designs. In these systems (SM1-4), both the type of side chains derived from the PP motifs and the presence of ring-substituents on BDT critically impact (i) molecular packing, and (ii) thin-film morphologies and charge transport in BHJ solar cells. With the appropriate side-chain pattern, the ring-substituted analogue SM4 stands out: achieving efficiencies of ca. 6.5% with PC71BM, and fine-scale morphologies comparable to those obtained with some of the best-performing polymer donors in BHJ solar cells. 1H-1H DQ-SQ NMR analyses are used to examine the distinct self-assembly pattern of SM4, expected to factor into the development of the BHJ morphology.

  5. Benzo[1,2-b:4,5-b’]dithiophene-Pyrido[3,4-b]pyrazine Small-Molecule Donors for Bulk Heterojunction Solar Cells

    KAUST Repository

    Wolf, Jannic Sebastian

    2016-01-22

    We report on the synthesis, material properties and BHJ solar cell characteristics of a set of π-conjugated small-molecule (SM) donors composed of benzo[1,2-b:4,5-b′]dithiophene (BDT) and pyrido[3,4-b]pyrazine (PP) units – examining the perspectives of alkyl-substituted PP acceptor motifs in SM designs. In these systems (SM1-4), both the type of side chains derived from the PP motifs and the presence of ring-substituents on BDT critically impact (i) molecular packing, and (ii) thin-film morphologies and charge transport in BHJ solar cells. With the appropriate side-chain pattern, the ring-substituted analogue SM4 stands out: achieving efficiencies of ca. 6.5% with PC71BM, and fine-scale morphologies comparable to those obtained with some of the best-performing polymer donors in BHJ solar cells. 1H-1H DQ-SQ NMR analyses are used to examine the distinct self-assembly pattern of SM4, expected to factor into the development of the BHJ morphology.

  6. 5-Imino-3,4-diphenyl-1H-pyrrol-2-one

    Science.gov (United States)

    Bulatov, Evgeny; Chulkova, Tatiana; Haukka, Matti

    2014-01-01

    The title compound, C16H12N2O, exists in the crystalline state as the 5-imino-3,4-di­phenyl­-1H-pyrrol-2-one tautomer. The dihedral angles between the pyrrole and phenyl rings are 35.3 (2) and 55.3 (2)°. In the crystal, inversion dimers linked by pairs of N—H⋯N hydrogen bonds generate a graph-set motif of R 2 2(8) via N—H⋯N hydrogen bonds. PMID:24764881

  7. 5-Imino-3,4-diphenyl-1H-pyrrol-2-one

    Directory of Open Access Journals (Sweden)

    Evgeny Bulatov

    2014-02-01

    Full Text Available The title compound, C16H12N2O, exists in the crystalline state as the 5-imino-3,4-diphenyl-1H-pyrrol-2-one tautomer. The dihedral angles between the pyrrole and phenyl rings are 35.3 (2 and 55.3 (2°. In the crystal, inversion dimers linked by pairs of N—H...N hydrogen bonds generate a graph-set motif of R22(8 via N—H...N hydrogen bonds.

  8. Crystal structure of (E)-3-fluoro-N-((5-nitrothiophen-2-yl)methylene)aniline

    Energy Technology Data Exchange (ETDEWEB)

    Karataş, Şadiye; Tanak, Hasan, E-mail: hasantanak@gmail.com [Amasya University, Department of Physics, Faculty of Arts and Sciences (Turkey); Ağar, Ayşen Alaman [Ondokuz Mayıs University, Department of Chemistry, Faculty of Arts and Sciences (Turkey)

    2016-05-15

    The structure of the title compound C{sub 11}H{sub 7}FN{sub 2}O{sub 2}S was characterized by single crystal X-ray diffraction. The compound crystallizes in the monoclinic space group P2{sub 1}/n with Z = 12, i.e. with three molecules in asymmetric unit. The molecules are not planar: the dihedral angles between the planes of thiophene and the benzene rings are 42.3(3)°, 42.0(3)°, and 48.9(2)°. In the crystal, intermolecular C–H···F interactions link the molecules through R{sub 2}{sup 2} (14) ring motif. The crystal packing is also stabilized by π···π interactions.

  9. Polarization Studies for the eRHIC Electron Storage Ring

    Energy Technology Data Exchange (ETDEWEB)

    Gianfelice-Wendt, Eliana [Fermilab; Tepikian, S. [Brookhaven

    2018-04-01

    A hadron/lepton collider with polarized beams has been under consideration by the scientific community since some years, in the U.S. and Europe. Among the various proposals, those by JLAB and BNL with polarized electron and proton beams are currently under closer study in the U.S. Experimenters call for the simultaneous storage of electron bunches with both spin helicity. In the BNL based Ring-Ring design, electrons are stored at top energy in a ring to be accommodated in the existing RHIC tunnel. The transversely polarized electron beam is injected into the storage ring at variable energies, between 5 and 18 GeV. Polarization is brought into the longitudinal direction at the IP by a couple of spin rotators. In this paper results of first studies of the attainable beam polarization level and lifetime in the storage ring at 18 GeV are presented.

  10. (E)-Methyl 3-(3,4-dimeth­oxy­phen­yl)-2-[(1,3-dioxoisoindolin-2-yl)meth­yl]acrylate

    Science.gov (United States)

    Kannan, D.; Bakthadoss, M.; Lakshmanan, D.; Murugavel, S.

    2012-01-01

    In the title compound, C21H19NO6, the isoindole ring system is essentially planar [maximum deviation = 0.019 (2) Å for the N atom] and is oriented at a dihedral angle of 51.3 (1)° with respect to the benzene ring. The two meth­oxy groups are almost coplanar with the attached benzene ring [C—O—C—C = 3.7 (4) and 4.3 (4)°]. The mol­ecular conformation is stabilized by an intra­molecular C—H⋯O hydrogen bond, which generates an S(9) ring motif. In the crystal, mol­ecules are linked through bifurcated C—H⋯(O,O) hydrogen bonds having R 1 2(5) ring motifs, forming chains along the b-axis direction. The crystal packing is further stabilzed by π–π inter­actions [centriod–centroid distance = 3.463 (1) Å]. PMID:22589965

  11. Evolutionarily conserved bias of amino-acid usage refines the definition of PDZ-binding motif

    Directory of Open Access Journals (Sweden)

    Launey Thomas

    2011-06-01

    Full Text Available Abstract Background The interactions between PDZ (PSD-95, Dlg, ZO-1 domains and PDZ-binding motifs play central roles in signal transductions within cells. Proteins with PDZ domains bind to PDZ-binding motifs almost exclusively when the motifs are located at the carboxyl (C- terminal ends of their binding partners. However, it remains little explored whether PDZ-binding motifs show any preferential location at the C-terminal ends of proteins, at genome-level. Results Here, we examined the distribution of the type-I (x-x-S/T-x-I/L/V or type-II (x-x-V-x-I/V PDZ-binding motifs in proteins encoded in the genomes of five different species (human, mouse, zebrafish, fruit fly and nematode. We first established that these PDZ-binding motifs are indeed preferentially present at their C-terminal ends. Moreover, we found specific amino acid (AA bias for the 'x' positions in the motifs at the C-terminal ends. In general, hydrophilic AAs were favored. Our genomics-based findings confirm and largely extend the results of previous interaction-based studies, allowing us to propose refined consensus sequences for all of the examined PDZ-binding motifs. An ontological analysis revealed that the refined motifs are functionally relevant since a large fraction of the proteins bearing the motif appear to be involved in signal transduction. Furthermore, co-precipitation experiments confirmed two new protein interactions predicted by our genomics-based approach. Finally, we show that influenza virus pathogenicity can be correlated with PDZ-binding motif, with high-virulence viral proteins bearing a refined PDZ-binding motif. Conclusions Our refined definition of PDZ-binding motifs should provide important clues for identifying functional PDZ-binding motifs and proteins involved in signal transduction.

  12. Near the horizon of 5D black rings

    International Nuclear Information System (INIS)

    Loran, Farhang; Soltanpanahi, Hesam

    2009-01-01

    For the five dimensional N = 2 black rings, we study the supersymmetry enhancement and identify the global supergroup of the near horizon geometry. We show that the global part of the supergroup is OSp(4*|2) x U(1) which is similar to the small black string. We show that results obtained by applying the entropy function formalism, the c-extremization approach and the Brown-Henneaux method to the black ring solution are in agreement with the microscopic entropy calculation.

  13. Continuously tunable S and C+L bands ultra wideband erbium-doped fiber ring laser

    International Nuclear Information System (INIS)

    Wang, Q; Yu, Q X

    2009-01-01

    This paper presents an ultra wideband tunable silica-based erbium doped fiber ring laser (EDFRL) that can be continuously tuned in S and C+L bands from 1475 to 1619 nm. It is the first time that a fiber ring laser's tuning range reaches 144 nm using a standard silica-based C-band erbium-doped fiber as gain media. In the laser configuration two isolators are used in the fiber loop for suppressing the ASE in C-band and elevating the lasing gain in S-band. As a result the available lasing wavelength is extended toward the shorter wavelength of the gain bandwidth. The optimized erbium-doped fiber length, output coupling ratio and pumping laser power have been obtained through experimental study. This ring fiber laser has simple configuration, low threshold, flat laser spectral distribution and high signal-to-ASE-noise ratio. The laser will have many potential applications in fiber sensor wavelength interrogation, high-resolution spectroscopy and fiber optic communications

  14. Functional Characterization of the Apple RING E3 Ligase MdMIEL1 in Transgenic Arabidopsis

    Directory of Open Access Journals (Sweden)

    Jianping AN

    2017-03-01

    Full Text Available E3 ubiquitin ligases are involved in various physiological processes, and they play pivotal roles in growth and development. In this study, we identified a previously unknown gene in the apple fruit (Malus × domestica and named it MdMIEL1. The MdMIEL1 gene encoded a protein that contained a zinc-finger domain at its N-terminus and a RING-finger motif at its C-terminus. To investigate MdMIEL1 functions, we generated transgenic Arabidopsis lines expressing the MdMIEL1 gene under the control of the Cauliflower mosaic virus 35S promoter. Interestingly, ectopic expression of MdMIEL1 in Arabidopsis produced multiple phenotypes, including early germination, early flowering and a lateral root number increase relative to wild-type plants. Further analysis indicated that MdMIEL1 regulated lateral root initiation by increasing auxin accumulation in the roots. In a word, these results suggest that, MdMIEL1 as a novel RING-finger ubiquitin ligase influences plant growth and development, and highlight that MdMIEL1 regulates lateral root growth.

  15. Large-scale discovery of promoter motifs in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Thomas A Down

    2007-01-01

    Full Text Available A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes.

  16. MHC motif viewer

    DEFF Research Database (Denmark)

    Rapin, Nicolas Philippe Jean-Pierre; Hoof, Ilka; Lund, Ole

    2008-01-01

    . Algorithms that predict which peptides MHC molecules bind have recently been developed and cover many different alleles, but the utility of these algorithms is hampered by the lack of tools for browsing and comparing the specificity of these molecules. We have, therefore, developed a web server, MHC motif....... A special viewing feature, MHC fight, allows for display of the specificity of two different MHC molecules side by side. We show how the web server can be used to discover and display surprising similarities as well as differences between MHC molecules within and between different species. The MHC motif...

  17. Methyl 2-({6-[(1-methoxy-2-methyl-1-oxopropan-2-ylcarbamoyl]pyridin-2-yl}formamido-2-methylpropanoate

    Directory of Open Access Journals (Sweden)

    Abdel-Galil E. Amr

    2012-05-01

    Full Text Available In the title compound, C17H23N3O6, the two methoxycarbonyl C—O—C=O planes are inclined at dihedral angles of 5.3 (4 and 83.9 (4° with respect to the central pyridine ring. An intramolecular N—H...O hydrogen bond generates an S(5 ring motif. In the crystal, molecules are linked into a chain along the c axis via C—H...O hydrogen bonds.

  18. Motif discovery in ranked lists of sequences

    DEFF Research Database (Denmark)

    Nielsen, Morten Muhlig; Tataru, Paula; Madsen, Tobias

    2016-01-01

    Motif analysis has long been an important method to characterize biological functionality and the current growth of sequencing-based genomics experiments further extends its potential. These diverse experiments often generate sequence lists ranked by some functional property. There is therefore...... advantage of the regular expression feature, including enrichments for combinations of different microRNA seed sites. The method is implemented and made publicly available as an R package and supports high parallelization on multi-core machinery....... a growing need for motif analysis methods that can exploit this coupled data structure and be tailored for specific biological questions. Here, we present an exploratory motif analysis tool, Regmex (REGular expression Motif EXplorer), which offers several methods to evaluate the correlation of motifs...

  19. RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

    Science.gov (United States)

    Castro-Mondragon, Jaime Abraham; Jaeger, Sébastien; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

    2017-07-27

    Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant TFBM collections. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools, and highlights biologically relevant variations of similar motifs. We also ran a large-scale application to cluster ∼11 000 motifs from 24 entire databases, showing that matrix-clustering correctly groups motifs belonging to the same TF families, and drastically reduced motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Magnetic and structural properties of an octanuclear Cu(II) S=1/2 mesoscopic ring: Susceptibility and NMR measurements

    Energy Technology Data Exchange (ETDEWEB)

    Lascialfari, A. [Department of Physics ' ' A. Volta' ' and Unita INFM, University of Pavia, Via Bassi 6, I-27100 Pavia, (Italy); Jang, Z. H. [Ames Laboratory and Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011 (United States); Borsa, F. [Department of Physics ' ' A. Volta' ' and Unita INFM, University of Pavia, Via Bassi 6, I-27100 Pavia, (Italy); Ames Laboratory and Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011 (United States); Gatteschi, D. [Department of Chemistry, University of Florence, Via Maragliano 77, I-50144 Florence, (Italy); Cornia, A. [Department of Chemistry, University of Modena, Via Campi 183, I-41100 Modena, (Italy); Rovai, D. [Department of Chemistry, University of Florence, Via Maragliano 77, I-50144 Florence, (Italy); Caneschi, A. [Department of Chemistry, University of Florence, Via Maragliano 77, I-50144 Florence, (Italy); Carretta, P. [Department of Physics ' ' A. Volta' ' and Unita INFM, University of Pavia, Via Bassi 6, I-27100 Pavia, (Italy)

    2000-03-01

    Magnetic susceptibility, {sup 1}H NMR and {sup 63}Cu NMR-NQR experiments on two slightly different species of the molecular S=1/2 antiferromagnetic (AF) ring Cu8, [Cu{sub 8}(dmpz){sub 8}(OH){sub 8}]{center_dot}2C{sub 5}H{sub 5}N (Cu8P) and [Cu{sub 8}(dmpz){sub 8}(OH){sub 8}]{center_dot}2C{sub 5}H{sub 5}NO{sub 2} (Cu8N), are presented. The magnetic energy levels are calculated exactly for an isotropic Heisenberg model Hamiltonian in zero magnetic field. From the magnetic susceptibility measurements we estimate the AF exchange coupling constant J{approx}1000 K and the resulting gap {delta}{approx}500 K between the S{sub T}=0 ground state and the S{sub T}=1 first excited state. The {sup 63,65}Cu NQR spectra indicate the presence of four crystallographically inequivalent copper nuclei in each ring. From the combination of the {sup 63}Cu NQR spectra and of the {sup 63}Cu NMR spectra at high magnetic field, we estimate the quadrupole coupling constant v{sub Q} of each site and the average asymmetry parameter {eta} of the electric-field gradient tensor. The nuclear spin-lattice relaxation rate (NSLR) decreases exponentially on decreasing temperature for all nuclei investigated. The gap parameter extracted from {sup 63}Cu NQR-NSLR is the same as for the susceptibility while a smaller value is obtained from the {sup 63}Cu NMR-NSLR in an external magnetic field of 8.2 T. (c) 2000 The American Physical Society.

  1. The phase structure of higher-dimensional black rings and black holes

    International Nuclear Information System (INIS)

    Emparan, Roberto; Harmark, Troels; Niarchos, Vasilis; Obers, Niels A.; RodrIguez, Maria J.

    2007-01-01

    We construct an approximate solution for an asymptotically flat, neutral, thin rotating black ring in any dimension D ≥ 5 by matching the near-horizon solution for a bent boosted black string, to a linearized gravity solution away from the horizon. The rotating black ring solution has a regular horizon of topology S 1 x S D-3 and incorporates the balancing condition of the ring as a zero-tension condition. For D = 5 our method reproduces the thin ring limit of the exact black ring solution. For D ≥ 6 we show that the black ring has a higher entropy than the Myers-Perry black hole in the ultra-spinning regime. By exploiting the correspondence between ultra-spinning black holes and black membranes on a two-torus, we take steps towards qualitatively completing the phase diagram of rotating blackfolds with a single angular momentum. We are led to propose a connection between MP black holes and black rings, and between MP black holes and black Saturns, through merger transitions involving two kinds of 'pinched' black holes. More generally, the analogy suggests an infinite number of pinched black holes of spherical topology leading to a complicated pattern of connections and mergers between phases

  2. Deciphering functional glycosaminoglycan motifs in development.

    Science.gov (United States)

    Townley, Robert A; Bülow, Hannes E

    2018-03-23

    Glycosaminoglycans (GAGs) such as heparan sulfate, chondroitin/dermatan sulfate, and keratan sulfate are linear glycans, which when attached to protein backbones form proteoglycans. GAGs are essential components of the extracellular space in metazoans. Extensive modifications of the glycans such as sulfation, deacetylation and epimerization create structural GAG motifs. These motifs regulate protein-protein interactions and are thereby repsonsible for many of the essential functions of GAGs. This review focusses on recent genetic approaches to characterize GAG motifs and their function in defined signaling pathways during development. We discuss a coding approach for GAGs that would enable computational analyses of GAG sequences such as alignments and the computation of position weight matrices to describe GAG motifs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  3. Structural and thermodynamic aspects of the dissociation of cyclopentadienyl rings from homoleptic cyclopentadienyl early transition metal, cerium, and thorium derivatives

    International Nuclear Information System (INIS)

    Peng Bin; Cheng Feng; Li Qianshu; Xie Yaoming; King, R. Bruce; Schaefer, Henry F.

    2011-01-01

    Graphical abstract: Density functional theory indicates that for Cp 4 M the S 4 structures are saddle points and the minima have C 1 symmetry with all η 5 -Cp rings for M = Ce and Th, three η 5 -Cp rings and one η 5 -Cp ring for M = Zr, and two η 5 -Cp rings and two η 5 -Cp rings for M = Ti and Hf. The dissociation energies for Cp 4 M → Cp 3 M + Cp · increase in the sequence Ti 3h structures with all η 5 -Cp rings are genuine minima for most of the Cp 3 M compounds except for Cp 3 Ti, which has a Cs symmetry minimum with two η 5 -Cp rings and one η 2 -Cp ring. The dissociation energies for Cp 3 M → Cp 2 M + Cp · increase in the sequence V 4 M the S 4 structures are saddle points. → The minima for Cp 4 M have all η 5 -Cp rings for M = Ce and Th, three η 5 -Cp rings and one η 1 -Cp ring for M = Zr, and two η 5 -Cp rings and two η 5 -Cp rings for M = Ti and Hf. → The dissociation energies for Cp 4 M → Cp 3 M + Cp · increase in the sequence Ti 3h structures with all η 5 -Cp rings are genuine minima for all of the Cp 3 M compounds except for Cp 3 Ti. → The dissociation energies for Cp 3 M → Cp 2 M + Cp · increase in the sequence V 4 M (M = Ti, Zr, Ce, Hf, Th), Cp 3 M (M = Sc, Y, most lanthanides, Ti, Zr, Hf, Th), and Cp 2 M (M = Ti, V). Density functional theory shows that the Cp 4 M structures with unusual S 4 symmetry are saddle points for the d-block metals Ti, Zr, Hf but genuine minima for the f-block metals Ce and Th. The true equilibrium Cp 4 M geometries have C 1 symmetry with two η 5 -Cp rings and two η 1 -Cp rings for M = Ti and Hf but three η 5 -Cp rings and one η 1 -Cp ring for M = Zr. The dissociation energies for Cp 4 M → Cp 3 M + Cp · are substantial and in the order Ti 3h structures with all η 5 -Cp rings are genuine minima for most of the Cp 3 M compounds except for Cp 3 Ti, which has a C s symmetry minimum with two η 5 -Cp rings and one η 2 -Cp ring, and Cp 3 V, which has two η 5 -Cp rings and one η 1 -Cp ring

  4. Fitness for synchronization of network motifs

    DEFF Research Database (Denmark)

    Vega, Y.M.; Vázquez-Prada, M.; Pacheco, A.F.

    2004-01-01

    We study the synchronization of Kuramoto's oscillators in small parts of networks known as motifs. We first report on the system dynamics for the case of a scale-free network and show the existence of a non-trivial critical point. We compute the probability that network motifs synchronize, and fi...... that the fitness for synchronization correlates well with motifs interconnectedness and structural complexity. Possible implications for present debates about network evolution in biological and other systems are discussed....

  5. Tree rings and radiocarbon calibration

    International Nuclear Information System (INIS)

    Barbetti, M.

    1999-01-01

    Only a few kinds of trees in Australia and Southeast Asia are known to have growth rings that are both distinct and annual. Those that do are therefore extremely important to climatic and isotope studies. In western Tasmania, extensive work with Huon pine (Lagarostrobos franklinii) has shown that many living trees are more than 1,000 years old, and that their ring widths are sensitive to temperature, rainfall and cloud cover (Buckley et al. 1997). At the Stanley River there is a forest of living (and recently felled) trees which we have sampled and measured. There are also thousands of subfossil Huon pine logs, buried at depths less than 5 metres in an area of floodplain extending over a distance of more than a kilometre with a width of tens of metres. Some of these logs have been buried for 50,000 years or more, but most of them belong to the period between 15,000 years and the present. In previous expeditions in the 1980s and 1990s, we excavated and sampled about 350 logs (Barbetti et al. 1995; Nanson et al. 1995). By measuring the ring-width patterns, and matching them between logs and living trees, we have constructed a tree-ring dated chronology from 571 BC to AD 1992. We have also built a 4254-ring floating chronology (placed by radiocarbon at ca. 3580 to 7830 years ago), and an earlier 1268-ring chronology (ca. 7,580 to 8,850 years ago). There are many individuals, or pairs of logs which match and together span several centuries, at 9,000 years ago and beyond

  6. Multiband Split-Ring Resonator Based Planar Inverted-F Antenna for 5G Applications

    Directory of Open Access Journals (Sweden)

    Muhammad Kamran Ishfaq

    2017-01-01

    Full Text Available 5G, the fifth generation of wireless communications, is focusing on multiple frequency bands, such as 6 GHz, 10 GHz, 15 GHz, 28 GHz, and 38 GHz, to achieve high data rates up to 10 Gbps or more. The industry demands multiband antennas to cover these distant frequency bands, which is a task much more challenging. In this paper, we have designed a novel multiband split-ring resonator (SRR based planar inverted-F antenna (PIFA for 5G applications. It is composed of a PIFA, an inverted-L parasitic element, a rectangular shaped parasitic element, and a split-ring resonator (SRR etched on the top plate of the PIFA. The basic PIFA structure resonates at 6 GHz. An addition of a rectangular shaped parasitic element produces a resonance at 15 GHz. The introduction of a split-ring resonator produces a band notch at 8 GHz, and a resonance at 10 GHz, while the insertion of an inverted-L shaped parasitic element further enhances the impedance bandwidth in the 10 GHz band. The frequency bands covered, each with more than 1 GHz impedance bandwidth, are 6 GHz (5–7 GHz, 10 GHz (9–10.8 GHz, and 15 GHz (14-15 GHz, expected for inclusion in next-generation wireless communications, that is, 5G. The design is simulated using Ansys Electromagnetic Suite 17 simulation software package. The simulated and the measured results are compared and analyzed which are generally in good agreement.

  7. Aplikasi Ornamen Khas Maluku untuk Pengembangan Desain Motif Batik

    Directory of Open Access Journals (Sweden)

    Masiswo Masiswo

    2016-04-01

    Full Text Available ABSTRAKMaluku memiliki banyak ragam hias budaya warisan nilai leluhur berupa ornamen etnis yang merupakan kesenian dan keterampilan kerajinan. Hasil warisan tersebut sampai saat ini masih lestari hidup serta dapat dinikmati sebagai konsumsi rohani yang memuaskan manusia. Berkaitan dengan keberlangsungan nilai-nilai tradisi etnis yang berwujud pada ornamen-ornamen daerah Maluku, maka dikembangkan untuk kebutuhan manusia berupa motif batik pada kain. Pengembangan ornamen ini lebih menekankan pada representasi akan bentuk-bentuk ornamen yang diterapkan pada kerajinan batik berupa motif khas Maluku. Pengembangan alternatif desain motif batik dibuat tiga variasi yang bersumber dari ornamen khas Maluku dibuat prototipe produknya dan diuji ketahanan luntur warnanya. Hasil uji ketahanan luntur warna terhadap gosokan basah dari tiga prototipe produk berpredikat baik sekali terdapat pada “Motif Siwa” dan predikat baik pada motif “Siwa Talang” dan motif “Matahari Siwa Talang”.Kata kunci: desain, Maluku, motif batik, ornamenABSTRACTMaluku has much decorative ancestral cultural heritage value in the form of ornament ethnic arts and crafts skills. The result of the legacy is still sustainable living can be enjoyed as well as satisfying spiritual human consumption.Related to the sustainability of traditional values in the form of ethnic ornaments Maluku, it was developed for human needs in the form of batik cloth . The development of these ornaments will be more emphasis on the representation forms of ornamentation that is applied to a batik motif Maluku. Development of alternative design motif made three variations. The development of three alternative design motifs derived from the Maluku ornaments made and tested a prototype product color fastness. The test results of color fastness to wet rubbing of the three prototypes are excellent products predicated on the "Motif Siwa" and a good rating on the motif "Siwa Talang" and motif "Matahari Siwa

  8. The limits of de novo DNA motif discovery.

    Directory of Open Access Journals (Sweden)

    David Simcha

    Full Text Available A major challenge in molecular biology is reverse-engineering the cis-regulatory logic that plays a major role in the control of gene expression. This program includes searching through DNA sequences to identify "motifs" that serve as the binding sites for transcription factors or, more generally, are predictive of gene expression across cellular conditions. Several approaches have been proposed for de novo motif discovery-searching sequences without prior knowledge of binding sites or nucleotide patterns. However, unbiased validation is not straightforward. We consider two approaches to unbiased validation of discovered motifs: testing the statistical significance of a motif using a DNA "background" sequence model to represent the null hypothesis and measuring performance in predicting membership in gene clusters. We demonstrate that the background models typically used are "too null," resulting in overly optimistic assessments of significance, and argue that performance in predicting TF binding or expression patterns from DNA motifs should be assessed by held-out data, as in predictive learning. Applying this criterion to common motif discovery methods resulted in universally poor performance, although there is a marked improvement when motifs are statistically significant against real background sequences. Moreover, on synthetic data where "ground truth" is known, discriminative performance of all algorithms is far below the theoretical upper bound, with pronounced "over-fitting" in training. A key conclusion from this work is that the failure of de novo discovery approaches to accurately identify motifs is basically due to statistical intractability resulting from the fixed size of co-regulated gene clusters, and thus such failures do not necessarily provide evidence that unfound motifs are not active biologically. Consequently, the use of prior knowledge to enhance motif discovery is not just advantageous but necessary. An implementation of

  9. A Compact 5.5 GHz Band-Rejected UWB Antenna Using Complementary Split Ring Resonators

    Directory of Open Access Journals (Sweden)

    M. M. Islam

    2014-01-01

    Full Text Available A band-removal property employing microwave frequencies using complementary split ring resonators (CSRRs is applied to design a compact UWB antenna wishing for the rejection of some frequency band, which is meanwhile exercised by the existing wireless applications. The reported antenna comprises optimization of a circular radiating patch, in which slotted complementary SRRs are implanted. It is printed on low dielectric FR4 substrate material fed by a partial ground plane and a microstrip line. Validated results exhibit that the reported antenna shows a wide bandwidth covering from 3.45 to more than 12 GHz, with a compact dimension of 22 × 26 mm2, and VSWR < 2, observing band elimination of 5.5 GHz WLAN band.

  10. A novel fibronectin binding motif in MSCRAMMs targets F3 modules.

    Directory of Open Access Journals (Sweden)

    Sabitha Prabhakaran

    Full Text Available BBK32 is a surface expressed lipoprotein and fibronectin (Fn-binding microbial surface component recognizing adhesive matrix molecule (MSCRAMM of Borrelia burgdorferi, the causative agent of Lyme disease. Previous studies from our group showed that BBK32 is a virulence factor in experimental Lyme disease and located the Fn-binding region to residues 21-205 of the lipoprotein.Studies aimed at identifying interacting sites between BBK32 and Fn revealed an interaction between the MSCRAMM and the Fn F3 modules. Further analysis of this interaction showed that BBK32 can cause the aggregation of human plasma Fn in a similar concentration-dependent manner to that of anastellin, the superfibronectin (sFn inducing agent. The resulting Fn aggregates are conformationally distinct from plasma Fn as indicated by a change in available thermolysin cleavage sites. Recombinant BBK32 and anastellin affect the structure of Fn matrices formed by cultured fibroblasts and inhibit endothelial cell proliferation similarly. Within BBK32, we have located the sFn-forming activity to a region between residues 160 and 175 which contains two sequence motifs that are also found in anastellin. Synthetic peptides mimicking these motifs induce Fn aggregation, whereas a peptide with a scrambled sequence motif was inactive, suggesting that these motifs represent the sFn-inducing sequence.We conclude that BBK32 induces the formation of Fn aggregates that are indistinguishable from those formed by anastellin. The results of this study provide evidence for how bacteria can target host proteins to manipulate host cell activities.

  11. Some Aspects of Ring Theory

    CERN Document Server

    Herstein, IN

    2011-01-01

    S. Amitsur: Associative rings with identities.- I.N. Herstein: Topics in ring theory.- N. Jacobson: Representation theory of Jordan algebras.- I. Kaplansky: The theory of homological dimension.- D. Buchsbaum: Complexes in local ring theory.- P.H. Cohn: Two topics in ring theory.- A.W. Goldie: Non-commutative localisation.

  12. (4bS,8aS-1-Isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octahydrophenanthren-2-yl acetate

    Directory of Open Access Journals (Sweden)

    Radouane Oubabi

    2014-03-01

    Full Text Available The hemisynthesis of the title compound, C22H32O2, was carried out through direct acetylation reaction of the naturally occurring diterpene totarol [systematic name: (4bS,8aS-4b,8,8-trimethyl-1-propan-2-yl-5,6,7,8a,9,10-hexahydrophenanthren-2-ol]. The molecule is built up from three fused six membered rings, one saturated and two unsaturated. The central unsaturated ring has a half-chair conformation, whereas the other unsaturated ring displays a chair conformation. The absolute configuration is deduced from the chemical pathway. The value of the Hooft parameter [−0.10 (6] allowed this absolute configuration to be confirmed.

  13. Chemokine (C-C motif) receptor 5-using envelopes predominate in dual/mixed-tropic HIV from the plasma of drug-naive individuals.

    Science.gov (United States)

    Irlbeck, David M; Amrine-Madsen, Heather; Kitrinos, Kathryn M; Labranche, Celia C; Demarest, James F

    2008-07-31

    HIV-1 utilizes CD4 and either chemokine (C-C motif) receptor 5 (CCR5) or chemokine (C-X-C motif) receptor 4 (CXCR4) to gain entry into host cells. Small molecule CCR5 antagonists are currently being developed for the treatment of HIV-1 infection. Because HIV-1 may also use CXCR4 for entry, the use of CCR5 entry inhibitors is controversial for patients harboring CCR5-using and CXCR4-using (dual/mixed-tropic) viruses. The goal of the present study was to determine the proportion of CCR5-tropic and CXCR4-tropic viruses in dual/mixed-tropic virus isolates from drug-naïve patients and the phenotypic and genotypic relationships of viruses that use CCR5 or CXCR4 or both. Fourteen antiretroviral-naive HIV-1-infected patients were identified as having population coreceptor tropism readout of dual/mixed-tropic viruses. Intrapatient comparisons of coreceptor tropism and genotype of env clones were conducted on plasma virus from each patient. Population HIV-1 envelope tropism and susceptibility to the CCR5 entry inhibitor, aplaviroc, were performed using the Monogram Biosciences Trofile Assay. Twelve env clones from each patient were analyzed for coreceptor tropism, aplaviroc sensitivity, genotype, and intrapatient phylogenetic relationships. Viral populations from antiretroviral-naive patients with dual/mixed-tropic virus are composed primarily of CCR5-tropic env clones mixed with those that use both coreceptors (R5X4-tropic) and, occasionally, CXCR4-tropic env clones. Interestingly, the efficiency of CXCR4 use by R5X4-tropic env clones varied with their genetic relationships to CCR5-tropic env clones from the same patient. These data show that the majority of viruses in these dual/mixed-tropic populations use CCR5 and suggest that antiretroviral-naive patients may benefit from combination therapy that includes CCR5 entry inhibitors.

  14. Weyl Exceptional Rings in a Three-Dimensional Dissipative Cold Atomic Gas (Author’s Manuscript)

    Science.gov (United States)

    2017-01-27

    in a dissipative system with particle gain and loss, we discover a new type of topological ring, dubbed Weyl exceptional ring consisting of...valued. On the other hand , the Chern number is zero when the surface S does not enclose any part of the ring even when it is located inside it...k)〉 and Ãθ(k) = i〈ũθ(k)|∂kuθ(k)〉, where 〈ũθ(k)| is the normalized left eigenstate of H [i.e., 〈ũθ(k)|H(k) = 〈ũθ(k)|Eθ(k) and 〈ũθ(k)|uθ(k)〉 = 1

  15. Motif statistics and spike correlations in neuronal networks

    International Nuclear Information System (INIS)

    Hu, Yu; Shea-Brown, Eric; Trousdale, James; Josić, Krešimir

    2013-01-01

    Motifs are patterns of subgraphs of complex networks. We studied the impact of such patterns of connectivity on the level of correlated, or synchronized, spiking activity among pairs of cells in a recurrent network of integrate and fire neurons. For a range of network architectures, we find that the pairwise correlation coefficients, averaged across the network, can be closely approximated using only three statistics of network connectivity. These are the overall network connection probability and the frequencies of two second order motifs: diverging motifs, in which one cell provides input to two others, and chain motifs, in which two cells are connected via a third intermediary cell. Specifically, the prevalence of diverging and chain motifs tends to increase correlation. Our method is based on linear response theory, which enables us to express spiking statistics using linear algebra, and a resumming technique, which extrapolates from second order motifs to predict the overall effect of coupling on network correlation. Our motif-based results seek to isolate the effect of network architecture perturbatively from a known network state. (paper)

  16. Mode-locked 1.5 micrometers semiconductor optical amplifier fiber ring

    DEFF Research Database (Denmark)

    Pedersen, Niels V.; Jakobsen, Kaj Bjarne; Vaa, Michael

    1996-01-01

    The dynamics of a mode-locked SOA fiber ring are investigated experimentally and numerically. Generation of near transform-limited (time-bandwidth product=0.7) 1.5 μm 54 ps FWHM pulses with a peak power of 2.8 mW at a repetition rate of 960 MHz is demonstrated experimentally. The experimental...... results agree well with the simulation results obtained using a transmission line laser model (TLLM) model, Both experiments and numerical simulations show how the RF power and the detuning affect the pulsewidth...

  17. Bayesian centroid estimation for motif discovery.

    Science.gov (United States)

    Carvalho, Luis

    2013-01-01

    Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.

  18. Bayesian centroid estimation for motif discovery.

    Directory of Open Access Journals (Sweden)

    Luis Carvalho

    Full Text Available Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.

  19. White Ring; White ring

    Energy Technology Data Exchange (ETDEWEB)

    Aoki, H.; Yuzawa, H. [Nikken Sekkei Ltd., Osaka (Japan)

    1998-01-05

    White Ring is a citizen`s gymnasium used for figure skating and short track speed skating games of 18th Winter Olympic Games in 1998. White Ring is composed of a main-arena and a sub-arena. For the main-arena with an area 41mtimes66m, an ice link can be made by disengaging the potable floor and by flowing brine in the bridged polystyrene pipes embedded in the concrete floor. Due to the fortunate groundwater in this site, well water is used for the outside air treatment energy in 63% during heating and in 35% during cooling. Ammonia is used as a cooling medium for refrigerating facility. For the heating of audience area in the large space, heat load from the outside is reduced by enhancing the heat insulation performance of the roof of arena. The audience seats are locally heated using heaters. For the White Ring, high quality environment is realized for games through various functions of the large-scale roof of the large space. Success of the big event was expected. 15 figs., 4 tabs.

  20. (1R,4R,6S,7R-5,5-Dibromo-1,4,8,8-tetramethyltricyclo[5.4.1.04,6]dodecan-12-one

    Directory of Open Access Journals (Sweden)

    Mohamed Zaki

    2014-05-01

    Full Text Available The title compound, C16H24Br2O, was synthesized from the reaction of β-himachalene (3,5,5,9-tetramethyl-2,4a,5,6,7,8-hexahydro-1H-benzocycloheptene, which was isolated from Atlas cedar (Cedrus atlantica. The asymmetric unit contains two independent molecules with similar conformations. Each molecule is built up from two fused seven-membered rings and an additional three-membered ring. In both molecules, one of the seven-membered rings has a chair conformation, whereas the other displays a screw-boat conformation.

  1. Propellers in Saturn's rings

    Science.gov (United States)

    Sremcevic, M.; Stewart, G. R.; Albers, N.; Esposito, L. W.

    2013-12-01

    Theoretical studies and simulations have demonstrated the effects caused by objects embedded in planetary rings. Even if the objects are too small to be directly observed, each creates a much larger gravitational imprint on the surrounding ring material. These strongly depend on the mass of the object and range from "S" like propeller-shaped structures for about 100m-sized icy bodies to the opening of circumferential gaps as in the case of the embedded moons Pan and Daphnis and their corresponding Encke and Keeler Gaps. Since the beginning of the Cassini mission many of these smaller objects (~data from Cassini Ultraviolet Imaging Spectrograph (UVIS) and Imaging Science Subsystem (ISS) experiments. We show evidence that B ring seems to harbor two distinct populations of propellers: "big" propellers covering tens of degrees in azimuth situated in the densest part of B ring, and "small" propellers in less dense inner B ring that are similar in size and shape to known A ring propellers. The population of "big" propellers is exemplified with a single object which is observed for 5 years of Cassini data. The object is seen as a very elongated bright stripe (40 degrees wide) in unlit Cassini images, and dark stripe in lit geometries. In total we report observing the feature in images at 18 different epochs between 2005 and 2010. In UVIS occultations we observe this feature as an optical depth depletion in 14 out of 93 occultation cuts at corrotating longitudes compatible with imaging data. Combining the available Cassini data we infer that the object is a partial gap located at r=112,921km embedded in the high optical depth region of the B ring. The gap moves at Kepler speed appropriate for its radial location. Radial offsets of the gap locations in UVIS occultations are consistent with an asymmetric propeller shape. The asymmetry of the observed shape is most likely a consequence of the strong surface mass density gradient, as the feature is located at an edge between

  2. 5-(5-Bromo-2-methoxyphenyl-2-fluoropyridine

    Directory of Open Access Journals (Sweden)

    Muhammad Adeel

    2012-09-01

    Full Text Available In the title compound, C12H9BrFNO, the dihedral angle between the aromatic rings is 51.39 (5°; the C atom of the methoxy group is close to being coplanar with its attached ring (r.m.s. deviation = 0.0172 Å] and is oriented away from the pyridine ring. In the crystal, molecules interact by van der Waals forces.

  3. N,N-Diethylanilinium 2,4-dioxo-5-(2,4,6-trinitrophenyl-1,2,3,4-tetrahydropyrimidin-6-olate

    Directory of Open Access Journals (Sweden)

    Manickam Buvaneswari

    2011-12-01

    Full Text Available In the crystal structure of the title molecular salt, C10H16N+·C10H4N5O9−, the components are linked through a N—H...O hydrogen bonds. R22(8 ring motifs are formed between inversion-related barbiturate residues. Two intramoleculer N—H...O hydrogen bonds are observed in the anion. The dihedral angle between 2,4,6-trinitrophenyl and barbiturate rings is 53.6 (2°. The N,N-diethylamine substituent is disordered and was modeled as two geometrically equivalent conformers with occupancies of 0.737 (2 and 0.273 (2.

  4. N-{(2S-3-Hydroxy-4-[(5-methyl-1,3,4-thiadiazol-2-ylsulfanyl]-1-phenyl-2-butyl}-4-methylbenzenesulfonamide

    Directory of Open Access Journals (Sweden)

    Claudia R. B. Gomes

    2011-09-01

    Full Text Available The thiadiazoyl and sulfonyl-benzene rings in the title compound, C20H23N3O3S3, are aligned to the same side of the molecule, forming a twisted `U' shape [dihedral angle = 77.6 (5°]. The benzyl-benzene ring is orientated in the opposite direction from the molecule but projects approximately along the same axis as the other rings [dihedral angle between benzene rings = 28.2 (5°] so that, overall, the molecule has a flattened shape. The hydroxy and amine groups are almost syn which enables the formation of intermolecular hydroxy-OH...N(thiadiazoyl and amine-H...O(sulfonyl hydrogen bonds leading to a supramolecular chain aligned along the a axis.

  5. CONTEMPORARY USAGE OF TRADITIONAL TURKISH MOTIFS IN PRODUCT DESIGNS

    Directory of Open Access Journals (Sweden)

    Tulay Gumuser

    2012-12-01

    Full Text Available The aim of this study is to identify the traditional Turkish motifs and its relations among present industrial designs. Traditional Turkish motifs played a very important role in 16th century onwards. The arts of the Ottoman Empire were used because of their symbolic meanings and unique styles. When we examine these motifs we encounter; Tiger Stripe, Three Spot (Çintemani, Rumi, Hatayi, Penç, Cloud, Crescent, Star, Crown, Hyacinth, Tulip and Carnation motifs. Nowadays, Turkish designers have begun to use these traditional Turkish motifs in their designs so as to create differences and awareness in the world design. The examples of these industrial designs, using the Turkish motifs, have survived and have Ottoman heritage and historical value. In this study, the Turkish motifs will be examined along with their focus on contemporary Turkish industrial designs used today.

  6. RNA motif search with data-driven element ordering.

    Science.gov (United States)

    Rampášek, Ladislav; Jimenez, Randi M; Lupták, Andrej; Vinař, Tomáš; Brejová, Broňa

    2016-05-18

    In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNAs. The problem is NP-hard and is traditionally solved by backtracking algorithms. We have designed a new algorithm for RNA motif search and implemented a new motif search tool RNArobo. The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. A typical RNA motif consists of multiple elements and the running time of the algorithm is highly dependent on their ordering. By approaching the element ordering problem in a principled way, we demonstrate more than 100-fold speedup of the search for complex motifs compared to previously published tools. We have developed a new method for RNA motif search that allows for a significant speedup of the search of complex motifs that include pseudoknots. Such speed improvements are crucial at a time when the rate of DNA sequencing outpaces growth in computing. RNArobo is available at http://compbio.fmph.uniba.sk/rnarobo .

  7. Mechanism for activation of the growth factor-activated AGC kinases by turn motif phosphorylation

    DEFF Research Database (Denmark)

    Hauge, Camilla; Antal, Torben L; Hirschberg, Daniel

    2007-01-01

    investigated the role of the third, so-called turn motif phosphate, also located in the tail, in the AGC kinases PKB, S6K, RSK, MSK, PRK and PKC. We report cooperative action of the HM phosphate and the turn motif phosphate, because it binds a phosphoSer/Thr-binding site above the glycine-rich loop within...

  8. Supra-molecular hydrogen-bonding patterns in the N(9)-H protonated and N(7)-H tautomeric form of an N(6) -benzoyl-adenine salt: N (6)-benzoyl-adeninium nitrate.

    Science.gov (United States)

    Karthikeyan, Ammasai; Jeeva Jasmine, Nithianantham; Thomas Muthiah, Packianathan; Perdih, Franc

    2016-02-01

    In the title molecular salt, C12H10N5O(+)·NO3 (-), the adenine unit has an N (9)-protonated N(7)-H tautomeric form with non-protonated N(1) and N(3) atoms. The dihedral angle between the adenine ring system and the phenyl ring is 51.10 (10)°. The typical intra-molecular N(7)-H⋯O hydrogen bond with an S(7) graph-set motif is also present. The benzoyl-adeninium cations also form base pairs through N-H⋯O and C-H⋯N hydrogen bonds involving the Watson-Crick face of the adenine ring and the C and O atoms of the benzoyl ring of an adjacent cation, forming a supra-molecular ribbon with R 2 (2)(9) rings. Benzoyl-adeninum cations are also bridged by one of the oxygen atoms of the nitrate anion, which acts as a double acceptor, forming a pair of N-H⋯O hydrogen bonds to generate a second ribbon motif. These ribbons together with π-π stacking inter-actions between the phenyl ring and the five- and six-membered adenine rings of adjacent mol-ecules generate a three-dimensional supra-molecular architecture.

  9. Crystal structure of 2-cyano-N-(furan-2-ylmethyl-3-(3-nitrophenylpropanamide

    Directory of Open Access Journals (Sweden)

    Shivanna Subhadramma

    2015-08-01

    Full Text Available In the title compound, C15H11N3O4, the acetamide group is inclined to the furan ring by 66.5 (1°. The dihedral angle between the furan ring and the benzene ring is 66.8 (1°. In the crystal, molecules are linked by pairs of N—H...N hydrogen bonds, forming inversion dimers with an R22(12 ring motif. The dimers are linked via two pairs of C—H...O hydrogen bonds to the same acceptor oxygen atom, enclosing R21(6 ring motifs, forming chains along the [101] direction.

  10. SUMO-interacting motifs of human TRIM5α are important for antiviral activity.

    Directory of Open Access Journals (Sweden)

    Gloria Arriagada

    2011-04-01

    Full Text Available Human TRIM5α potently restricts particular strains of murine leukemia viruses (the so-called N-tropic strains but not others (the B- or NB-tropic strains during early stages of infection. We show that overexpression of SUMO-1 in human 293T cells, but not in mouse MDTF cells, profoundly blocks N-MLV infection. This block is dependent on the tropism of the incoming virus, as neither B-, NB-, nor the mutant R110E of N-MLV CA (a B-tropic switch are affected by SUMO-1 overexpression. The block occurred prior to reverse transcription and could be abrogated by large amounts of restricted virus. Knockdown of TRIM5α in 293T SUMO-1-overexpressing cells resulted in ablation of the SUMO-1 antiviral effects, and this loss of restriction could be restored by expression of a human TRIM5α shRNA-resistant plasmid. Amino acid sequence analysis of human TRIM5α revealed a consensus SUMO conjugation site at the N-terminus and three putative SUMO interacting motifs (SIMs in the B30.2 domain. Mutations of the TRIM5α consensus SUMO conjugation site did not affect the antiviral activity of TRIM5α in any of the cell types tested. Mutation of the SIM consensus sequences, however, abolished TRIM5α antiviral activity against N-MLV. Mutation of lysines at a potential site of SUMOylation in the CA region of the Gag gene reduced the SUMO-1 block and the TRIM5α restriction of N-MLV. Our data suggest a novel aspect of TRIM5α-mediated restriction, in which the presence of intact SIMs in TRIM5α, and also the SUMO conjugation of CA, are required for restriction. We propose that at least a portion of the antiviral activity of TRIM5α is mediated through the binding of its SIMs to SUMO-conjugated CA.

  11. A Woman Voice in an Epic: Tracing Gendered Motifs in Anne Vabarna's Peko

    Directory of Open Access Journals (Sweden)

    Andreas Kalkun

    2008-12-01

    Full Text Available In the article the gendered motifs found in Anne Vabarna’s Seto epic Peko are analysed. Besides the narrative telling of the life of the male hero, the motives regarding eating, refusing to eat or offering food, and the aspect of the female body or its control deserve to be noticed. These scenes do not communicate the main plot, they are often related to minor characters of the epic and slow down the narrative, but at the same time they clearly carry artistic purpose and meaning. I consider these motifs, present in the liminal parts of the epic, to be the dominant symbols of the epic where the author’s feminine world is being exposed. Observing these motifs of Peko in the context of Seto religious worldview, the life of Anne Vabarna and the social position of Seto women, the symbols become eloquent and informative.

  12. Crystal structure of bromidobis(naphthalen-1-ylantimony(III

    Directory of Open Access Journals (Sweden)

    Omar bin Shawkataly

    2014-10-01

    Full Text Available In the title compound, [SbBr(C10H72], the SbIII atom has a distorted trigonal–pyramidal coordination geometry and the planes of the two naphthalene ring systems make a dihedral angle of 80.26 (18°. An intramolecular C—H...Br hydrogen bond forms an S(5 ring motif. In the crystal, weak C—H...Br interactions link the molecules into helical chains along the b-axis direction.

  13. APOCALYPTIC MOTIFS IN THE CYCLE OF STORIES BY M.A. BULGAKOV «NOTES OF A YOUNG DOCTOR»

    Directory of Open Access Journals (Sweden)

    Evgeniy Igorevich Erokhov

    2015-10-01

    Full Text Available The motif analysis of a cycle of stories by M.A. Bulgakov «Notes of a Young Doctor» from the point of view of their apocalyptic problematics was first performed in this article. To identify apocalyptic motifs the method of motif analysis, developed by B.M. Gasparov, was used which will also help to prove the interpenetration of motifs in the cycle of stories. The result of the research work is the identification of apocalyptic motifs which are manifested in the experiences of the main character and the events taking place around him and passing through the prism of physician’s perception of the world. Our identified motifs show that the stories in the cycle are united not only thematically and with the help of the image of the main character, but with the help of the motifs which reflect interpenetration of apocalyptic motifs in the stories of one cycle. There are the following apocalyptic motifs in the cycle of stories by Bulgakov: diseases, darkness (as part of the landscape, resurrection from the dead and beast. They all belong to the biblical type which is allocated on the basis of the associative bond of these motifs with the biblical texts.

  14. Implications of Liebig’s law of the minimum for tree-ring reconstructions of climate

    Science.gov (United States)

    Stine, A. R.; Huybers, P.

    2017-11-01

    A basic principle of ecology, known as Liebig’s Law of the Minimum, is that plant growth reflects the strongest limiting environmental factor. This principle implies that a limiting environmental factor can be inferred from historical growth and, in dendrochronology, such reconstruction is generally achieved by averaging collections of standardized tree-ring records. Averaging is optimal if growth reflects a single limiting factor and noise but not if growth also reflects locally variable stresses that intermittently limit growth. In this study a collection of Arctic tree ring records is shown to follow scaling relationships that are inconsistent with the signal-plus-noise model of tree growth but consistent with Liebig’s Law acting at the local level. Also consistent with law-of-the-minimum behavior is that reconstructions based on the least-stressed trees in a given year better-follow variations in temperature than typical approaches where all tree-ring records are averaged. Improvements in reconstruction skill occur across all frequencies, with the greatest increase at the lowest frequencies. More comprehensive statistical-ecological models of tree growth may offer further improvement in reconstruction skill.

  15. Modelling of the ring current in Saturn's magnetosphere

    Directory of Open Access Journals (Sweden)

    G. Giampieri

    2004-01-01

    Full Text Available The existence of a ring current inside Saturn's magnetosphere was first suggested by Smith et al. (1980 and Ness et al. (1981, 1982, in order to explain various features in the magnetic field observations from the Pioneer 11 and Voyager 1 and 2 spacecraft. Connerney et al. (1983 formalized the equatorial current model, based on previous modelling work of Jupiter's current sheet and estimated its parameters from the two Voyager data sets. Here, we investigate the model further, by reconsidering the data from the two Voyager spacecraft, as well as including the Pioneer 11 flyby data set.

    First, we obtain, in closed form, an analytic expression for the magnetic field produced by the ring current. We then fit the model to the external field, that is the difference between the observed field and the internal magnetic field, considering all the available data. In general, through our global fit we obtain more accurate parameters, compared to previous models. We point out differences between the model's parameters for the three flybys, and also investigate possible deviations from the axial and planar symmetries assumed in the model. We conclude that an accurate modelling of the Saturnian disk current will require taking into account both of the temporal variations related to the condition of the magnetosphere, as well as non-axisymmetric contributions due to local time effects.

    Key words. Magnetospheric physics (current systems; planetary magnetospheres; plasma sheet

  16. Analisis Unsur Matematika pada Motif Sulam Usus

    Directory of Open Access Journals (Sweden)

    Fredi Ganda Putra

    2017-12-01

    Full Text Available Based on interviews with researchers sources said that the beginning of the intestine embroidery is an art of genuine crafts. Called the intestine embroidery because this technique is a technique of combining a strand of cloth resembling the intestine formed according to the pattern by means of embroidered using a thread. Intestinal embroidery techniques were originally used to create a cover of the women's customary wardrobe of Lampung or often referred to as bebe. But not many people in Lampung, especially people who live in Lampung are still many who do not know and recognize the intestine embroidery because most only know tapis only characteristic of Lampung, besides that there are other cultural results that is embroidered intestine. There are still many who do not know that the intestine motif there is a knowledge of mathematics. The researcher's problem formulation is whether there are mathematical elements contained in the intestine embroidery motif based on the concept of geometry. The purpose of this study is to determine whether there are elements of mathematics contained in the intestine motif based on the concept of geometry. Subjects in this study consisted of 4 people obtained by purposive sampling technique. From the results of data analysis conducted by using descriptive analysis and discussion as follows: (1 Intestinal embroidery motif contains the meaning of mathematics and culture or often called Etnomatematika. On the meaning of culture there is a link between the embroidery intestine with a culture that has been there before as the existence of cultural linkage between Hindu belief Buddhism and there are similarities of motifs and decorative patterns contained in the motif embroidery intestine with ornamental variety in Indonesia. (2 The relationship between the intestine with mathematical motifs there are elements of mathematics such as geometry elements in the form of geometry of dimension one and dimension two, and the

  17. Examination techniques for non-magnetic rings

    International Nuclear Information System (INIS)

    Metala, M.J.; Kilpatrick, N.L.; Frank, W.W.

    1990-01-01

    Until the introduction of 18Mn18Cr rings a few years ago, most non-magnetic steel rings for generator rotors were made from 18Mn5Cr alloy steel, which is highly susceptible to stress corrosion cracking in the presence of water. This, the latest in a series of papers on the subject of non-magnetic rings by the authors' company, provides a discussion of nondestructive examination of 18Mn5Cr rings for stress corrosion distress. With rings on the rotor, fluorescent penetrant, ultrasonic and special visual techniques are applied. With rings off the rotor, the fluorescent penetrant technique is used, with and without stress enhancement

  18. The PEP electron-positron ring

    International Nuclear Information System (INIS)

    Rees, J.R.

    1988-01-01

    The first stage of the positron-electron-proton (PEP) colliding-beam system which has been under joint study by a Lawrence Berkeley Laboratory-Stanford Linear Accelerator Center team for the past two years, will be the electron-positron storage ring. The physics justification for the e + e/sup minus/ ring is summarized briefly and the proposed facility is described. The ring will have six arcs having gross radii of about 220 m and six interaction regions located at the centers of straight sections about 130 m long. The longitudinal distance left free for experimental apparatus at the intersection regions will be 20 m. The range of operating beam energies will be from 5 GeV to 15 GeV. The design luminosity at 15 GeV will be 10 32 cm/sup minus 2/s/sup minus 1/, and the luminosity will vary approximately as the square of the beam energy. Alternative methods under consideration for adjusting the beam cross-section are discussed. The designs of the storage ring subsystems and of the conventional facilities including the experimental halls at the interaction regions are described

  19. On P-coherent endomorphism rings

    Indian Academy of Sciences (India)

    A ring is called right -coherent if every principal right ideal is finitely presented. Let M R be a right -module. We study the -coherence of the endomorphism ring of M R . It is shown that is a right -coherent ring if and only if every endomorphism of M R has a pseudokernel in add M R ; S is a left -coherent ring if and ...

  20. Chemicals from Biomass: Combining Ring-Opening Tautomerization and Hydrogenation Reactions to Produce 1,5-Pentanediol from Furfural.

    Science.gov (United States)

    Brentzel, Zachary J; Barnett, Kevin J; Huang, Kefeng; Maravelias, Christos T; Dumesic, James A; Huber, George W

    2017-04-10

    A process for the synthesis of 1,5-pentanediol (1,5-PD) with 84 % yield from furfural is developed, utilizing dehydration/hydration, ring-opening tautomerization, and hydrogenation reactions. Although this process has more reaction steps than the traditional direct hydrogenolysis of tetrahydrofurfuryl alcohol (THFA), techno-economic analyses demonstrate that this process is the economically preferred route for the synthesis of biorenewable 1,5-PD. 2-Hydroxytetrahydropyran (2-HY-THP) is the key reaction pathway intermediate that allows for a decrease in the minimum selling price of 1,5-PD. The reactivity of 2-HY-THP is 80 times greater than that of THFA over a bimetallic hydrogenolysis catalyst. This enhanced reactivity is a result of the ring-opening tautomerization to 5-hydoxyvaleraldehyde and subsequent hydrogenation to 1,5-PD. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Fifth Interim Status Report: Model 9975 PCV O-Ring Fixture Long-Term Leak Performance

    International Nuclear Information System (INIS)

    Daugherty, W.; Hoffman, E.

    2010-01-01

    A series of experiments to monitor the aging performance of Viton reg. GLT O-rings used in the Model 9975 package has been ongoing for six years at the Savannah River National Laboratory. Sixty-seven mock-ups of 9975 Primary Containment Vessels (PCVs) were assembled and heated to temperatures ranging from 200 to 450 F. They were leak-tested initially and have been tested at nominal six month intervals to determine if they meet the criterion of leaktightness defined in ANSI standard N14.5-97. Fourteen additional tests were initiated in 2008 with GLT-S O-rings heated to temperatures ranging from 200 to 400 F. High temperature aging continues for 36 GLT O-ring fixtures at 200--350 F. Room temperature leak test failures have been experienced in 5 of the GLT O-ring fixtures aging at 300 and 350 F, and in all 3 of the GLT O-ring fixtures aging at higher temperatures. No failures have yet been observed in GLT O-ring fixtures aging at 200 F for 30--48 months, which is still bounding to O-ring temperatures during storage in KAMS. High temperature aging continues for 6 GLT-S O-ring fixtures at 200--300 F. Room temperature leak test failures have been experienced in all 8 of the GLT-S O-ring fixtures aging at 350 and 400 F. No failures have yet been observed in GLT-S O-ring fixtures aging at 200 or 300 F for 19 months. For O-ring fixtures that have failed the room temperature leak test and been disassembled, the O-rings displayed a compression set ranging from 51--95%. This is significantly greater than seen to date for packages inspected during KAMS field surveillance (23% average). For GLT O-rings, service life based on the room temperature leak rate criterion is comparable to that predicted by compression stress relaxation (CSR) data at higher temperatures (350--400 F). While there are no comparable failure data yet at aging temperatures below 300 F, extrapolations of the data for GLT O-rings suggests that CSR model predictions provide a conservative prediction of service

  2. Through the Portal: Viking Motifs Incorporated in the Romanesque Style in Telemark, Norway

    Directory of Open Access Journals (Sweden)

    Kristine Ødeby

    2013-09-01

    Full Text Available This paper presents the results of an analysis of motifs identified on six carved wooden Romanesque portal panels from the Norwegian county of Telemark. The findings suggest that animal motifs in the Late Viking style survived long into the Late Medieval period and were reused on these medieval portals. Stylistically, late expressions of Viking animal art do not differ a great deal from those of the subsequent Romanesque style. However, their symbolical differences are considered to be significant. The motifs themselves, and the issue of whether the Romanesque style adopted motifs from pre-Christian art, have attracted less attention. The motif portraying Sigurd slaying the dragon is considered in depth. It will be suggested that Sigurd, serving as a mediator between the old and the new beliefs when he appeared in late Viking contexts, was given a new role when portrayed in Christian art. Metaphor and liminality are a central part of this paper, and the theories of Alfred Gell and Margrete Andås suggest that the portal itself affects those who pass through it, and that the iconography is meaningful from a liminal perspective.

  3. Dragon polya spotter: Predictor of poly(A) motifs within human genomic DNA sequences

    KAUST Repository

    Kalkatawi, Manal M.

    2011-11-15

    Motivation: Recognition of poly(A) signals in mRNA is relatively straightforward due to the presence of easily recognizable polyadenylic acid tail. However, the task of identifying poly(A) motifs in the primary genomic DNA sequence that correspond to poly(A) signals in mRNA is a far more challenging problem. Recognition of poly(A) signals is important for better gene annotation and understanding of the gene regulation mechanisms. In this work, we present one such poly(A) motif prediction method based on properties of human genomic DNA sequence surrounding a poly(A) motif. These properties include thermodynamic, physico-chemical and statistical characteristics. For predictions, we developed Artificial Neural Network and Random Forest models. These models are trained to recognize 12 most common poly(A) motifs in human DNA. Our predictors are available as a free web-based tool accessible at http://cbrc.kaust.edu.sa/dps. Compared with other reported predictors, our models achieve higher sensitivity and specificity and furthermore provide a consistent level of accuracy for 12 poly(A) motif variants. The Author(s) 2011. Published by Oxford University Press. All rights reserved.

  4. 7α-Methoxycarbonyl-6,7,8,14-tetrahydro-6,14-endo-ethenothebaine

    Directory of Open Access Journals (Sweden)

    Mustafa Odabaşoğlu

    2009-04-01

    Full Text Available In the molecule of the title compound, C23H27NO5, the furan ring adopts an envelope conformation. Intramolecular C—H...O interactions result in the formation of S(5 and S(6 motifs. In the crystal structure, weak intermolecular C—H...O hydrogen bonds link the molecules through C(6 and C(8 chains along the [100] and [010] directions, generating a two-dimensional network.

  5. BERKELEY: ALS ring

    International Nuclear Information System (INIS)

    Anon.

    1993-01-01

    Everybody at Lawrence Berkeley Laboratory's Center for Beam Physics is pleased with the rapid progress in commissioning LBL's Advanced Light Source (ALS) electron storage ring, the foundation for this third-generation synchrotron radiation facility. Designed for a maximum current of 400 mA, the ALS storage ring reached 407 mA just 24 days after storing the first beam on 16 March. ALS construction as a US Department of Energy (DOE) national user facility to provide high-brightness vacuum ultra-violet and soft x-ray radiation began in October 1987. One technical requirement marking project completion was to accumulate a 50-mA current in the storage ring. The ALS passed this milestone on 24 March, a week ahead of the official deadline. Once injected, the electron beam decays quasi-exponentially primarily because of interactions with residual gas molecules in the storage-ring vacuum chamber. Eventually, when the pressure in the vacuum chamber with beam decreases toward the expected operating level of 1 nano Torr, it will only be necessary to refill the storage ring at intervals of four to eight hours. At present the vacuum is improving rapidly as surfaces are irradiated (scrubbed) by the synchrotron radiation itself. At 100 mA, beam lifetime was about one hour (9 April)

  6. Triadic motifs in the dependence networks of virtual societies

    Science.gov (United States)

    Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-06-01

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

  7. Triadic motifs in the dependence networks of virtual societies.

    Science.gov (United States)

    Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-06-10

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

  8. Southwestern (U.S.A. Archaeological Tree-Ring Dating: 1930-1942

    Directory of Open Access Journals (Sweden)

    Stephen E. Nash

    1997-11-01

    Full Text Available Dendrochronology, the science of assigning precise and accurate calendar dates to annual growth rings in trees (Stokes and Smiley 1968, was the first independent dating technique available to prehistorians. Ar­chaeological tree-ring dating came of age at a time when North American archaeologists concerned them­selves primarily with time/space systematics (Willey and Sabloff 1980 and yet had no absolute and inde­pendent dating techniques available to guide their analyses. Histories of archaeology typically have not considered the development of archaeological tree-ring dating in detail. Willey and Sabloff (1980:12 devote one paragraph to the development of Southwestern archaeological tree-ring dating, as does Steibing (1993:261. Trigger (1989:305 considers dendrochronology (in the sense of the Douglass method only in light of radiocarbon dating. Textbooks and regional histories of archaeology do a little better in their treat­ment of dendrochronology, though discussions typically focus on the interpretation of tree-ring dates and not on the developmental history of the technique itself (e.g. Cordell 1984:88-90; Fagan 1991:129-133; Lyon 1996:46; Michels 1973:116; Thomas 1979:190-194. Scott (1966:9 argues that 'the story of the discovery of archaeological tree-ring dating by A E. Douglass and others has been told and retold and is now familiar to scientists and laymen alike'. I beg to differ.

  9. Inhomogeneous molecular ring around the B[e] supergiant LHA 120-S 73

    Science.gov (United States)

    Kraus, M.; Cidale, L. S.; Arias, M. L.; Maravelias, G.; Nickeler, D. H.; Torres, A. F.; Borges Fernandes, M.; Aret, A.; Curé, M.; Vallverdú, R.; Barbá, R. H.

    2016-10-01

    line profile is strongly variable in both width and shape and resembles of those seen in non-radially pulsating stars. A proper determination of the real underlying stellar rotation velocity is hence not possible. Conclusions: The existence of multiple stable and clumpy rings of alternating density recalls ring structures around planets. Although there is currently insufficient observational evidence, it is tempting to propose a scenario with one (or more) minor bodies or planets revolving around LHA 120-S 73 and stabilizing the ring system, in analogy to the shepherd moons in planetary systems. Based on observations: (1) with the 1.52-m and 2.2-m telescopes at the European Southern Observatory (La Silla, Chile), under the programme 076.D-0609(A) and under the agreement with the Observatório Nacional-MCT (Brazil); (2) at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the NSF on behalf of the Gemini partnership: the National Science Foundation (United States), the Science and Technology Facilities Council (United Kingdom), the National Research Council (Canada), CONICYT (Chile), the Australian Research Council (Australia), Ministério da Ciência, Tecnologia e Inovação (Brazil) and Ministerio de Ciencia, Tecnología e Innovación Productiva (Argentina), under the programmes GS-2004B-Q-54, GS-2010B-Q-31, and GS-2012B-Q-90; (3) at Complejo Astronómico El Leoncito operated under agreement between the Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina and the National Universities of La Plata, Córdoba and San Juan (Visiting Astronomer: A.F.T.); and (4) with the du Pont Telescope at Las Campanas Observatory, Chile, under the programme CNTAC 2008-02 (Visiting Astronomer: R.B. and A.F.T.).Presented spectroscopic data are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http

  10. 4-Benzyl-6-bromo-2-(4-chlorophenyl)-4H-imidazo[4,5-b]pyridine

    OpenAIRE

    Selma Bourichi; Youssef Kandri Rodi; Jerry P. Jasinski; Manpreet Kaur; Younes Ouzidan; El Mokhtar Essassi

    2017-01-01

    In the title compound, C19H13BrClN3, the chlorophenyl ring occupies an equatorial position with respect to the mean plane of the imidazopyridine unit, while the other phenyl ring is twisted by 4.1 (2)° with respect to the mean plane of the imidazopyridine unit. In the crystal, pairwise C—H...Br interactions link the molecules into dimers, forming an R22(16) ring motif. In addition, weak π–π stacking interactions stabilize the crystal packing.

  11. 4-Benzyl-6-bromo-2-(4-chlorophenyl-4H-imidazo[4,5-b]pyridine

    Directory of Open Access Journals (Sweden)

    Selma Bourichi

    2017-06-01

    Full Text Available In the title compound, C19H13BrClN3, the chlorophenyl ring occupies an equatorial position with respect to the mean plane of the imidazopyridine unit, while the other phenyl ring is twisted by 4.1 (2° with respect to the mean plane of the imidazopyridine unit. In the crystal, pairwise C—H...Br interactions link the molecules into dimers, forming an R22(16 ring motif. In addition, weak π–π stacking interactions stabilize the crystal packing.

  12. 2-Amino-4-(4-bromophenyl-8-trifluoromethyl-3,4-dihydropyrimido[1,2-a][1,3,5]triazin-6(5H-onePart 13 in the series `Fused heterocyclic systems with an s-triazine ring'. For Part 12, see Dolzhenko et al. (2008b.

    Directory of Open Access Journals (Sweden)

    Anton V. Dolzhenko

    2009-04-01

    Full Text Available The title compound, C13H9BrF3N5O, crystallizes with two independent molecules in the asymmetric unit. The pyrimidine rings of the molecules are planar [maximum deviations 0.053 (3 and 0.012 (3 Å], while the triazine rings adopt flattened half-boat conformations with the p-bromophenyl rings in the flagpole positions. The crystal packing is stabilized by a three-dimensional network of intermolecular N—H...N, N—H...O and N—H...F hydrogen bonds.

  13. Design status of the 2.5 GeV National Synchrotron Light Source x-ray ring

    International Nuclear Information System (INIS)

    Krinsky, S.; Blumberg, L.; Bittner, J.; Galayda, J.; Heese, R.; Schuchman, J.C.; van Steenbergen, A.

    1979-01-01

    The present state of the design of the 2.5 GeV electron storage ring for the National Synchrotron Light Source is described. This ring will serve as a dedicated source of synchrotron radiation in the wavelength range 0.1 A to 30 A. While maintaining the basic high brigtness features of the eariler developed lattice structure, recent work resulted in a more economical magnet system, is simplified chromaticity corrections, and improved distribution of the X-ray beam lines. In addition, the adequacy of the dynamic aperture for stable betatron oscillations has been verified for a variety of betatron tunes

  14. The crystal structure of 2-[5-(dimethylaminonaphthalene-1-sulfonamido]phenyl 5-(dimethylaminonaphthalene-1-sulfonate

    Directory of Open Access Journals (Sweden)

    Kittipong Chainok

    2015-10-01

    Full Text Available The complete molecule of the title compound, C30H29N3O5S2, is generated by a crystallographic twofold axis: the O atom and NH group attached to the central benzene ring are statistically disordered. The dihedral angle between the naphthalene ring system and the central benzene ring is 52.99 (6°, while the pendant naphthalene ring systems subtend a dihedral angle of 68.17 (4°. An intramolecular C—H...O hydrogen bond closes an S(6 ring. In the crystal, the molecules are linked by weak C—H...O hydrogen bonds.

  15. The BsaHI restriction-modification system: Cloning, sequencing and analysis of conserved motifs

    Directory of Open Access Journals (Sweden)

    Roberts Richard J

    2008-05-01

    Full Text Available Abstract Background Restriction and modification enzymes typically recognise short DNA sequences of between two and eight bases in length. Understanding the mechanism of this recognition represents a significant challenge that we begin to address for the BsaHI restriction-modification system, which recognises the six base sequence GRCGYC. Results The DNA sequences of the genes for the BsaHI methyltransferase, bsaHIM, and restriction endonuclease, bsaHIR, have been determined (GenBank accession #EU386360, cloned and expressed in E. coli. Both the restriction endonuclease and methyltransferase enzymes share significant similarity with a group of 6 other enzymes comprising the restriction-modification systems HgiDI and HgiGI and the putative HindVP, NlaCORFDP, NpuORFC228P and SplZORFNP restriction-modification systems. A sequence alignment of these homologues shows that their amino acid sequences are largely conserved and highlights several motifs of interest. We target one such conserved motif, reading SPERRFD, at the C-terminal end of the bsaHIR gene. A mutational analysis of these amino acids indicates that the motif is crucial for enzymatic activity. Sequence alignment of the methyltransferase gene reveals a short motif within the target recognition domain that is conserved among enzymes recognising the same sequences. Thus, this motif may be used as a diagnostic tool to define the recognition sequences of the cytosine C5 methyltransferases. Conclusion We have cloned and sequenced the BsaHI restriction and modification enzymes. We have identified a region of the R. BsaHI enzyme that is crucial for its activity. Analysis of the amino acid sequence of the BsaHI methyltransferase enzyme led us to propose two new motifs that can be used in the diagnosis of the recognition sequence of the cytosine C5-methyltransferases.

  16. Efficient motif finding algorithms for large-alphabet inputs

    Directory of Open Access Journals (Sweden)

    Pavlovic Vladimir

    2010-10-01

    Full Text Available Abstract Background We consider the problem of identifying motifs, recurring or conserved patterns, in the biological sequence data sets. To solve this task, we present a new deterministic algorithm for finding patterns that are embedded as exact or inexact instances in all or most of the input strings. Results The proposed algorithm (1 improves search efficiency compared to existing algorithms, and (2 scales well with the size of alphabet. On a synthetic planted DNA motif finding problem our algorithm is over 10× more efficient than MITRA, PMSPrune, and RISOTTO for long motifs. Improvements are orders of magnitude higher in the same setting with large alphabets. On benchmark TF-binding site problems (FNP, CRP, LexA we observed reduction in running time of over 12×, with high detection accuracy. The algorithm was also successful in rapidly identifying protein motifs in Lipocalin, Zinc metallopeptidase, and supersecondary structure motifs for Cadherin and Immunoglobin families. Conclusions Our algorithm reduces computational complexity of the current motif finding algorithms and demonstrate strong running time improvements over existing exact algorithms, especially in important and difficult cases of large-alphabet sequences.

  17. Diethyl 2,2-bis(3,5-di-tert-butyl-4-hydroxybenzylmalonate

    Directory of Open Access Journals (Sweden)

    Tao Zeng

    2012-02-01

    Full Text Available The title molecule, C37H56O6, possesses twofold symmetry, with the twofold axis passing through the quaternary C atom. In the crystal, neighbouring molecules are linked via O—H...O hydrogen bonds involving the phenol OH group and the carbonyl O atom, forming chains propagating in [101]. Within these chains, rings are formed with an R22(20 motif. There are also C—H...O interactions present within the rings.

  18. Tricuspid annuloplasty with the MC3 ring and septal plication technique.

    Science.gov (United States)

    Isomura, Tadashi; Hirota, Masanori; Hoshino, Joji; Fukada, Yasuhisa; Kondo, Taichi; Takahashi, Yu

    2015-01-01

    Functional tricuspid regurgitation is caused by annular dilation mainly in the posterior annulus. However, ring annuloplasty does not always prevent the recurrence of tricuspid regurgitation due to dilation of the septal annulus. We developed a septal plication technique with a 3-dimensional MC3 ring. Between 2006 and 2011, 76 patients (male/female 30/46; mean age 68 ± 11 years) with functional tricuspid regurgitation received tricuspid ring annuloplasty. After placement of the annular sutures, the 3 commissural ring portions were fixed on the equivalent commissures to plicate the anterior and posterior annulus. The end of the septal ring portion was fixed at the optimal annular position to obtain minimal tricuspid regurgitation. All patients were followed-up for a mean of 47 ± 18 months; the longest duration was 79 months. Although there was no operative death, one patient died of sepsis during hospitalization (hospital mortality 1.3%). After implantation of the MC3 ring (mean size 31.0 ± 3.3 mm), additional edge-to-edge sutures were required for minor leakage in 5 (7%) patients. The degree of tricuspid regurgitation was significantly reduced at discharge (0.5 ± 0.6) and midterm (0.6 ± 0.6) compared to 2.5 ± 0.7 before the operation (p tricuspid ring annuloplasty with a 3-dimensional MC3 ring. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  19. RMOD: a tool for regulatory motif detection in signaling network.

    Directory of Open Access Journals (Sweden)

    Jinki Kim

    Full Text Available Regulatory motifs are patterns of activation and inhibition that appear repeatedly in various signaling networks and that show specific regulatory properties. However, the network structures of regulatory motifs are highly diverse and complex, rendering their identification difficult. Here, we present a RMOD, a web-based system for the identification of regulatory motifs and their properties in signaling networks. RMOD finds various network structures of regulatory motifs by compressing the signaling network and detecting the compressed forms of regulatory motifs. To apply it into a large-scale signaling network, it adopts a new subgraph search algorithm using a novel data structure called path-tree, which is a tree structure composed of isomorphic graphs of query regulatory motifs. This algorithm was evaluated using various sizes of signaling networks generated from the integration of various human signaling pathways and it showed that the speed and scalability of this algorithm outperforms those of other algorithms. RMOD includes interactive analysis and auxiliary tools that make it possible to manipulate the whole processes from building signaling network and query regulatory motifs to analyzing regulatory motifs with graphical illustration and summarized descriptions. As a result, RMOD provides an integrated view of the regulatory motifs and mechanism underlying their regulatory motif activities within the signaling network. RMOD is freely accessible online at the following URL: http://pks.kaist.ac.kr/rmod.

  20. “Direct modulation of a hybrid III-V/Si DFB laser with MRR filtering for 22.5-Gb/s error-free dispersion-uncompensated transmission over 2.5-km SSMF

    DEFF Research Database (Denmark)

    Cristofori, Valentina; Da Ros, Francesco; Ding, Yunhong

    2016-01-01

    Error-free and penalty-free transmission over 2.5 km SSMF of a 22.5 Gb/s data signal from a directly modulated hybrid III-V/Si DFB laser is achieved by enhancing the dispersion tolerance using a silicon micro-ring resonator....

  1. Comparing CTH simulations and experiments on explosively loaded rings

    Science.gov (United States)

    Braithwaite, C. H.; Aydelotte, Brady; Collins, Adam; Thadhani, Naresh; Williamson, David Martin

    2012-03-01

    A series of experiments were conducted on explosively loaded metallic rings for the purpose of studying fragmentation. In addition to the collection of fragments for analysis, the radial velocity of the expanding ring was measured with photon Doppler velocimetry (PDV) and the arrangement was imaged using high speed photography. Both the ring material and the material used as the explosive container were altered and the results compared with simulations performed in CTH. Good agreement was found between the simulations and the experiments. The maximum radial velocity attained was approximately 380 m/s, which was achieved through loading with a 5g PETN based charge.

  2. Disparate requirements for the Walker A and B ATPase motifs ofhuman RAD51D in homologous recombination

    Energy Technology Data Exchange (ETDEWEB)

    Wiese, Claudia; Hinz, John M.; Tebbs, Robert S.; Nham, Peter B.; Urbin, Salustra S.; Collins, David W.; Thompson, Larry H.; Schild, David

    2006-04-21

    In vertebrates, homologous recombinational repair (HRR) requires RAD51 and five RAD51 paralogs (XRCC2, XRCC3, RAD51B, RAD51C, and RAD51D) that all contain conserved Walker A and B ATPase motifs. In human RAD51D we examined the requirement for these motifs in interactions with XRCC2 and RAD51C, and for survival of cells in response to DNA interstrand crosslinks. Ectopic expression of wild type human RAD51D or mutants having a non-functional A or B motif was used to test for complementation of a rad51d knockout hamster CHO cell line. Although A-motif mutants complement very efficiently, B-motif mutants do not. Consistent with these results, experiments using the yeast two- and three-hybrid systems show that the interactions between RAD51D and its XRCC2 and RAD51C partners also require a functional RAD51D B motif, but not motif A. Similarly, hamster Xrcc2 is unable to bind to the non-complementing human RAD51D B-motif mutants in co-immunoprecipitation assays. We conclude that a functional Walker B motif, but not A motif, is necessary for RAD51D's interactions with other paralogs and for efficient HRR. We present a model in which ATPase sites are formed in a bipartite manner between RAD51D and other RAD51 paralogs.

  3. SOT1, a pentatricopeptide repeat protein with a small MutS-related domain, is required for correct processing of plastid 23S-4.5S rRNA precursors in Arabidopsis thaliana.

    Science.gov (United States)

    Wu, Wenjuan; Liu, Sheng; Ruwe, Hannes; Zhang, Delin; Melonek, Joanna; Zhu, Yajuan; Hu, Xupeng; Gusewski, Sandra; Yin, Ping; Small, Ian D; Howell, Katharine A; Huang, Jirong

    2016-03-01

    Ribosomal RNA processing is essential for plastid ribosome biogenesis, but is still poorly understood in higher plants. Here, we show that SUPPRESSOR OF THYLAKOID FORMATION1 (SOT1), a plastid-localized pentatricopeptide repeat (PPR) protein with a small MutS-related domain, is required for maturation of the 23S-4.5S rRNA dicistron. Loss of SOT1 function leads to slower chloroplast development, suppression of leaf variegation, and abnormal 23S and 4.5S processing. Predictions based on the PPR motif sequences identified the 5' end of the 23S-4.5S rRNA dicistronic precursor as a putative SOT1 binding site. This was confirmed by electrophoretic mobility shift assay, and by loss of the abundant small RNA 'footprint' associated with this site in sot1 mutants. We found that more than half of the 23S-4.5S rRNA dicistrons in sot1 mutants contain eroded and/or unprocessed 5' and 3' ends, and that the endonucleolytic cleavage product normally released from the 5' end of the precursor is absent in a sot1 null mutant. We postulate that SOT1 binding protects the 5' extremity of the 23S-4.5S rRNA dicistron from exonucleolytic attack, and favours formation of the RNA structure that allows endonucleolytic processing of its 5' and 3' ends. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  4. Enhanced thermal and mechanical properties of PLA/MoS2 nanocomposites synthesized via the in-situ ring-opening polymerization

    Science.gov (United States)

    Chen, Pengpeng; Liang, Xiao; Xu, Ying; Zhou, Yifeng; Nie, Wangyan

    2018-05-01

    In this work, MoS2 nanosheets were employed to reinforce PLA. In order to promote the homogeneous dispersion of MoS2 in PLA and form a strong interface between MoS2 and PLA, the MoS2 nanosheets were firstly modified by mercapto-ethylamine, and then functionalized with PLA chains through ring-opening polymerization of poly(L-lactide). The XRD, XPS, TGA and 1H NMR characterizations confirmed the successful amino and PLA functionalization of MoS2 nanosheets. The obtained MoS2-g-PLA nanosheets were then introduced to reinforce PLA. SEM images displayed that the MoS2-g-PLA nanosheets were dispersed in PLA matrix uniformly. TGA results showed that initial decomposition temperature was improved from 275.6 °C to 334.8 °C with 0.5 wt% of MoS2-g-PLA nanosheets. The storage modulus of PLA/MoS2-g-PLA-0.5 wt% in the glass state and rubber state were both greatly enhanced compared with neat PLA.

  5. Synthesis and Biological Evaluation of Novel Benzimidazole Derivatives Bearing a Heterocyclic Ring at 4/5 Position

    International Nuclear Information System (INIS)

    Wubulikasimu, Reyila; Yang, Yanbing; Xue, Fei; Luo, Xianjin; Shao, Dongping; Li, Yuhuan; Gao, Rongmei; Ye, Weidong

    2013-01-01

    A series of novel benzimidazole derivatives bearing a heterocyclic ring as oxadiazole (21-32), thiadiazole (33-34), triazole (35-36) were synthesized and evaluated for their activities against Coxsackie virus B3 and B6 in Vero cells. Compounds 21-26, 31-36 with moieties of 2'-pyridyl, 3'-pyridyl and 4'-pyridyl at the 2-position and oxadiazoles, thiadiazole, or triazole substituent at the 4- or 5-position generally displayed activities against CVB3 and CVB6. Especially compound 24 (IC 50 = 1.08 μg/mL, SI = 61.7 against CVB3) was the promising candidate as lead compound for anti-enteroviral drug. It was observed in the incorporation of heterocyclic rings in benzimidazole at the 5-position could enhance their biological activities

  6. Accumulator ring design for the NSNS project

    International Nuclear Information System (INIS)

    Weng, W.T.; Alessi, J.; Beebe-Wang, J.

    1997-01-01

    The goal of the proposed National Spallation Neutron Source (NSNS) is to provide a short pulse proton beam of about 0.5 μs with average beam power of 1 MW. To achieve such purpose, a proton storage ring operated at 60 Hz with 1 x 10 14 protons per pulse at 1 GeV is required. The Accumulator Ring (AR) receives 1 msec long H - beam bunches of 28 mA from a 1 GeV linac. Scope and design performance goals of the AR are presented, other possible technological choices and design options considered, but not adopted, are also briefly reviewed

  7. Crystal structure of diethyl 2-amino-6-[(thiophen-3-ylethynyl]azulene-1,3-dicarboxylate

    Directory of Open Access Journals (Sweden)

    Sebastian Förster

    2015-03-01

    Full Text Available The title compound, C22H19NO4S, has an almost planar geometry supported by intramolecular N—H...O and C—H...O hydrogen bonds. The thiophene ring is inclined to the azulene ring by 4.85 (16°, while the ethoxycarbonyl groups are inclined to the azulene ring by 7.0 (2 and 5.7 (2°. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with an R22(12 ring motif. The dimers are linked via C—H...π interactions, forming sheets parallel to (10-1.

  8. 2-Hydroxy-16-[(E-4-methylbenzylidene]-13-(4-methylphenyl-12-phenyl-1,11-diazapentacyclo[12.3.1.02,10.03,8.010,14]octadeca-3(8,4,6-triene-9,15-dione

    Directory of Open Access Journals (Sweden)

    Raju Suresh Kumar

    2010-08-01

    Full Text Available In the title compound, C37H32N2O3, an intramolecular O—H...N hydrogen bond generates a five-membered ring, producing an S(5 motif. The piperidone ring adopts a half-chair conformation. The two fused pyrrolidine rings have similar envelope conformations. The interplanar angles between the benzene rings A/B and C/D are 75.68 (7 and 30.22 (6°, respectively. In the crystal structure, adjacent molecules are interconnected into chains propagating along the [010] direction via intermolecular C—H...O hydrogen bonds. Further stabilization is provided by weak C—H...π interactions.

  9. DNA motif alignment by evolving a population of Markov chains.

    Science.gov (United States)

    Bi, Chengpeng

    2009-01-30

    Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov chain Monte Carlo (MCMC) method such as Gibbs motif samplers has been widely employed to solve the de novo motif-finding problem through sequence local alignment. Nonetheless, the MCMC-based motif samplers still suffer from local maxima like EM. Therefore, as a prerequisite for finding good local alignments, these motif algorithms are often independently run a multitude of times, but without information exchange between different chains. Hence it would be worth a new algorithm design enabling such information exchange. This paper presents a novel motif-finding algorithm by evolving a population of Markov chains with information exchange (PMC), each of which is initialized as a random alignment and run by the Metropolis-Hastings sampler (MHS). It is progressively updated through a series of local alignments stochastically sampled. Explicitly, the PMC motif algorithm performs stochastic sampling as specified by a population-based proposal distribution rather than individual ones, and adaptively evolves the population as a whole towards a global maximum. The alignment information exchange is accomplished by taking advantage of the pooled motif site distributions. A distinct method for running multiple independent Markov chains (IMC) without information exchange, or dubbed as the IMC motif algorithm, is also devised to compare with its PMC counterpart. Experimental studies demonstrate that the performance could be improved if pooled information were used to run a population of motif samplers. The new PMC algorithm was able to improve the convergence and outperformed other popular algorithms tested using simulated and biological motif sequences.

  10. (S,S,S,S-Nebivolol hydrochloride hemihydrate

    Directory of Open Access Journals (Sweden)

    Yoann Rousselin

    2012-12-01

    Full Text Available The asymmetric unit of the title hydrated salt, C22H26F2NO4+·Cl−·0.5H2O, consists of an (S,S,S,S-nebivolol {nebivol = bis[2-(6-fluoro-3,4-dihydro-2H-1-benzopyran-2-yl-2-hydroxyethyl]ammonium} cation, a chloride anion and a half-occupancy water molecule. The dihedral angle between the mean planes of the benzene rings is 50.34 (12°. The pyran rings adopt half-chair conformations. The crystal packing features O—H...O hydrogen bonds and weak N—H...Cl, O—H...Cl, and O—H...Cl interactions, producing layers along (010.

  11. Alignment for new Subaru ring

    International Nuclear Information System (INIS)

    Zhang, Ch.; Matsui, S.; Hashimoto, S.

    1999-01-01

    The New SUBARU is a synchrotron light source being constructed at the SPring-8 site. The main facility is a 1.5 GeV electron storage ring that provides light beam in the region from VUV to soft X-ray using SPring-8's 1 GeV linac as an injector. The ring, with a circumference of about 119 meters, is composed of six bending cells. Each bending cell has two normal dipoles of 34 degree and one inverse dipole of -8 degree. The ring has six straight sections: two very long straight sections for a 11-m long undulator and an optical klystron, four short straight sections for a 2.3-m undulator, a super-conducting wiggler, rf cavity and injection, etc. The magnets of the storage ring are composed of 12 dipoles (BMs), 6 invert dipoles (BIs), 56 quadrupoles and 44 sextupoles, etc. For the magnet alignment, positions of the dipoles (the BMs and BIs) are determined by network survey method. The multipoles, which are mounted on girders between the dipoles, are aligned with a laser-CCD camera system. This article presents the methodology used to position the different components and particularly to assure the precise alignment of the multipoles. (authors)

  12. Proceedings of the 5. International Conference on Nuclear Physics at Storage Rings

    International Nuclear Information System (INIS)

    Calen, H.; Ekstroem, C.

    2003-01-01

    The 5th International Conference on Nuclear Physics at Storage Rings, STORI '02, was organized jointly by The Svedberg Laboratory and the Department of Radiation Sciences, Uppsala University. The STORI '02 conference brought together physicists from a diverse international research community connected by the common technology of storage rings reviewing the topics of current interest in nuclear physics research with stored, cooled ion beams and electron beams. Specifically, the scientific programme of STORI '02 focused on new results from a wide variety of experimental projects at existing stored-beam facilities, on progress in associated theoretical issues, and on discussions of new facilities and experimental techniques. The STORI '02 conference also included a number of review talks on physics in neighbouring fields, e.g., atomic physics at storage rings, physics with stored particles in ion traps, crystalline ion beams. The conference programme was composed of six plenary sessions and a poster session. The meeting was attended by 77 registered participants from 11 countries. The presentations included 12 invited review talks, 27 oral contributions and seven posters. These proceedings contain the written versions of most of the presented talks and posters. They have been slightly regrouped as compared to the order of presentation in the conference program in order to group together the papers according to subject, e.g., the poster papers have been placed within the corresponding subject block. All have been separately indexed

  13. Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins

    Science.gov (United States)

    Chatterjee, Raghunath; Zhao, Jianfei; He, Ximiao; Shlyakhtenko, Andrey; Mann, Ishminder; Waterfall, Joshua J.; Meltzer, Paul; Sathyanarayana, B. K.; FitzGerald, Peter C.; Vinson, Charles

    2012-01-01

    Previously, we identified 8-bps long DNA sequences (8-mers) that localize in human proximal promoters and grouped them into known transcription factor binding sites (TFBS). We now examine split 8-mers consisting of two 4-mers separated by 1-bp to 30-bps (X4-N1-30-X4) to identify pairs of TFBS that localize in proximal promoters at a precise distance. These include two overlapping TFBS: the ETS⇔ETS motif (C/GCCGGAAGCGGAA) and the ETS⇔CRE motif (C/GCGGAAGTGACGTCAC). The nucleotides in bold are part of both TFBS. Molecular modeling shows that the ETS⇔CRE motif can be bound simultaneously by both the ETS and the B-ZIP domains without protein-protein clashes. The electrophoretic mobility shift assay (EMSA) shows that the ETS protein GABPα and the B-ZIP protein CREB preferentially bind to the ETS⇔CRE motif only when the two TFBS overlap precisely. In contrast, the ETS domain of ETV5 and CREB interfere with each other for binding the ETS⇔CRE. The 11-mer (CGGAAGTGACG), the conserved part of the ETS⇔CRE motif, occurs 226 times in the human genome and 83% are in known regulatory regions. In vivo GABPα and CREB ChIP-seq peaks identified the ETS⇔CRE as the most enriched motif occurring in promoters of genes involved in mRNA processing, cellular catabolic processes, and stress response, suggesting that a specific class of genes is regulated by this composite motif. PMID:23050235

  14. A putative SUMO interacting motif in the B30.2/SPRY domain of rhesus macaque TRIM5α important for NF-κB/AP-1 signaling and HIV-1 restriction

    Directory of Open Access Journals (Sweden)

    Marie-Édith Nepveu-Traversy

    2016-01-01

    Full Text Available TRIM5α from the rhesus macaque (TRIM5αRh is a restriction factor that shows strong activity against HIV-1. TRIM5αRh binds specifically to HIV-1 capsid (CA through its B30.2/PRYSPRY domain shortly after entry of the virus into the cytoplasm. Recently, three putative SUMO interacting motifs (SIMs have been identified in the PRYSPRY domain of human and macaque TRIM5α. However, structural modeling of this domain suggested that two of them were buried in the hydrophobic core of the protein, implying that interaction with SUMO was implausible, while the third one was not relevant to restriction. In light of these results, we re-analyzed the TRIM5αRh PRYSPRY sequence and identified an additional putative SIM (435VIIC438 which we named SIM4. This motif is exposed at the surface of the PRYSPRY domain, allowing potential interactions with SUMO or SUMOylated proteins. Introducing a double mutation in SIM4 (V435K, I436K did not alter stability, unlike mutations in SIM1. SIM4-mutated TRIM5αRh failed to bind HIV-1CA and lost the ability to restrict this virus. Accordingly, SIM4 undergoes significant variation among primates and substituting this motif with naturally occurring SIM4 variants affected HIV-1 restriction by TRIM5αRh, suggesting a direct role in capsid recognition. Interestingly, SIM4-mutated TRIM5αRh also failed to activate NF-κB and AP-1-mediated transcription. Although there is no direct evidence that SIM4 is involved in direct interaction with SUMO or a SUMOylated protein, mutating this motif strongly reduced co-localization of TRIM5αRh with SUMO-1 and with PML, a SUMOylated nuclear protein. In conclusion, this new putative SIM is crucial for both direct interaction with incoming capsids and for NF-κB/AP-1 signaling. We speculate that the latter function is mediated by interactions of SIM4 with a SUMOylated protein involved in the NF-κB/AP-1 signaling pathways.

  15. DNA motif elucidation using belief propagation.

    Science.gov (United States)

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-09-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k=8∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM.

  16. CD3 gamma contains a phosphoserine-dependent di-leucine motif involved in down-regulation of the T cell receptor

    DEFF Research Database (Denmark)

    Dietrich, J; Hou, X; Wegener, A M

    1994-01-01

    -regulation of the TCR. Furthermore, analysis of a series of CD3 gamma truncation mutants indicated that in addition to S126 phosphorylation a motif C-terminal of S126 was required for TCR down-regulation. Point mutation analyses confirmed this observation and demonstrated that a membrane-proximal di-leucine motif (L131......, indicating that the TCR was down-regulated by endocytosis via clathrin coated pits. Based on the present results and previously published observations on intracellular receptor sorting, a general model for intracellular sorting of receptors containing di-leucine- or tyrosine-based motifs is proposed....

  17. Molecular pathogenesis of H5 highly pathogenic avian influenza: the role of the haemagglutinin cleavage site motif

    Science.gov (United States)

    Luczo, Jasmina M.; Stambas, John; Durr, Peter A.; Michalski, Wojtek P.

    2015-01-01

    Summary The emergence of H5N1 highly pathogenic avian influenza has caused a heavy socio‐economic burden through culling of poultry to minimise human and livestock infection. Although human infections with H5N1 have to date been limited, concerns for the pandemic potential of this zoonotic virus have been greatly intensified following experimental evidence of aerosol transmission of H5N1 viruses in a mammalian infection model. In this review, we discuss the dominance of the haemagglutinin cleavage site motif as a pathogenicity determinant, the host‐pathogen molecular interactions driving cleavage activation, reverse genetics manipulations and identification of residues key to haemagglutinin cleavage site functionality and the mechanisms of cell and tissue damage during H5N1 infection. We specifically focus on the disease in chickens, as it is in this species that high pathogenicity frequently evolves and from which transmission to the human population occurs. With >75% of emerging infectious diseases being of zoonotic origin, it is necessary to understand pathogenesis in the primary host to explain spillover events into the human population. © 2015 The Authors. Reviews in Medical Virology published by John Wiley & Sons Ltd. PMID:26467906

  18. TOPDOM: database of conservatively located domains and motifs in proteins.

    Science.gov (United States)

    Varga, Julia; Dobson, László; Tusnády, Gábor E

    2016-09-01

    The TOPDOM database-originally created as a collection of domains and motifs located consistently on the same side of the membranes in α-helical transmembrane proteins-has been updated and extended by taking into consideration consistently localized domains and motifs in globular proteins, too. By taking advantage of the recently developed CCTOP algorithm to determine the type of a protein and predict topology in case of transmembrane proteins, and by applying a thorough search for domains and motifs as well as utilizing the most up-to-date version of all source databases, we managed to reach a 6-fold increase in the size of the whole database and a 2-fold increase in the number of transmembrane proteins. TOPDOM database is available at http://topdom.enzim.hu The webpage utilizes the common Apache, PHP5 and MySQL software to provide the user interface for accessing and searching the database. The database itself is generated on a high performance computer. tusnady.gabor@ttk.mta.hu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  19. 2-Amino-4-methoxy-6-methylpyrimidinium hydrogen phthalate

    Directory of Open Access Journals (Sweden)

    Ramalingam Sangeetha

    2016-05-01

    Full Text Available In the hydrogen phthalate anion of the title molecular salt, C6H10N3O+·C8H5O4−, the dihedral angles formed by the benzene ring and the mean planes of the –COOH and –COO− groups are 16.1 (3 and 19.8 (3°, respectively. There is an intramolecular O—H...O hydrogen bond in the anion generating an S(7 ring motif. In the crystal, the protonated N atom of the pyrimidinium ring and the 2-amino group of the cation are hydrogen bonded to the carboxylate O atoms of the anion via a pair of N—H...O hydrogen bonds, forming an R22(8 ring motif. The ion pairs are further connected via N—H...O and C—H...O hydrogen bonds, forming ribbons parallel to the [01-1] direction. The ribbons are linked by off-set π–π stacking interactions [intercentroid distances = 3.8279 (16 and 3.6074 (15 Å], forming a three-dimensional structure.

  20. Heterocyclic organobismuth (III) compounds containing an eight-membered ring: Inhibitory effects on cell cycle progression.

    Science.gov (United States)

    Iuchi, Katsuya; Yagura, Tatsuo

    2018-03-21

    We previously showed that heterocyclic organobismuth compounds have excellent antimicrobial and antitumor potential. These compounds structurally consist of either six- or eight-membered rings. Previous research has shown that bi-chlorodibenzo[c,f][1,5]thiabismocine (Compound 3), an eight-membered ring, induced G 2 /M arrest via inhibition of tubulin polymerization in HeLa cells. Additionally, N-tert-butyl-bi-chlorodi-benzo[c,f][1,5]azabismocine (Compound 1), another eight-membered ring, exhibited higher cytotoxicity than Compound 3 against several cancer cell lines, including HeLa and K562. Finally, bi-chlorophenothiabismin-S,S-dioxide (Compound 5), a six-membered ring, exhibited lower antitumor activity than eight-membered ring compounds. In this study, we investigated the antimitotic activity of Compounds 1 and 5 in HeLa cells. At low concentrations, (0.1 and 0.25 μM), Compound 1 inhibited cell growth and arrested the cell cycle in mitosis. However, 0.5 μM Compound 1 exhibited no antimitotic activity. Conversely, Compound 5 weakly inhibited cell growth and did not markedly arrest the cell cycle. Flow cytometry showed that Compound 1 arrested the cell cycle at G 2 /M, resulting in apoptosis. Compound 1 inhibited tubulin polymerization as revealed by a cell-free assay, and both Compounds 1 and 3 inhibited microtubule spindle formation and chromosome alignment during prometaphase. These results suggest that eight-membered ring-containing organobismuth compounds can induce mitotic arrest by perturbing spindle dynamics. Copyright © 2018. Published by Elsevier Ltd.

  1. (E-1-(2,4-Dinitrophenyl-2-(3-ethoxy-4-hydroxybenzylidenehydrazine

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2014-01-01

    Full Text Available The molecule of the title hydrazine derivative, C15H14N4O6, is essentially planar, the dihedral angle between the substituted benzene rings being 2.25 (9°. The ethoxy and hydroxy groups are almost coplanar with their bound benzene ring [r.m.s. deviation = 0.0153 (2 Å for the ten non-H atoms]. Intramolecular N—H...O and O—H...Oethoxy hydrogen bonds generate S(6 and S(5 ring motifs, respectively. In the crystal, molecules are linked by O—H...Onitro hydrogen bonds into chains propagating in [010]. Weak aromatic π–π interactions, with centroid–centroid distances of 3.8192 (19 and 4.0491 (19 Å, are also observed.

  2. C-C motif ligand 5 promotes migration of prostate cancer cells in the prostate cancer bone metastasis microenvironment.

    Science.gov (United States)

    Urata, Satoko; Izumi, Kouji; Hiratsuka, Kaoru; Maolake, Aerken; Natsagdorj, Ariunbold; Shigehara, Kazuyoshi; Iwamoto, Hiroaki; Kadomoto, Suguru; Makino, Tomoyuki; Naito, Renato; Kadono, Yoshifumi; Lin, Wen-Jye; Wufuer, Guzailinuer; Narimoto, Kazutaka; Mizokami, Atsushi

    2018-03-01

    Chemokines and their receptors have key roles in cancer progression. The present study investigated chemokine activity in the prostate cancer bone metastasis microenvironment. Growth and migration of human prostate cancer cells were assayed in cocultures with bone stromal cells. The migration of LNCaP cells significantly increased when co-cultured with bone stromal cells isolated from prostate cancer bone metastases. Cytokine array analysis of conditioned medium from bone stromal cell cultures identified CCL5 as a concentration-dependent promoter of LNCaP cell migration. The migration of LNCaP cells was suppressed when C-C motif ligand 5 (CCL5) neutralizing antibody was added to cocultures with bone stromal cells. Knockdown of androgen receptor with small interfering RNA increased the migration of LNCaP cells compared with control cells, and CCL5 did not promote the migration of androgen receptor knockdown LNCaP. Elevated CCL5 secretion in bone stromal cells from metastatic lesions induced prostate cancer cell migration by a mechanism consistent with CCL5 activity upstream of androgen receptor signaling. © 2017 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

  3. Almost ring theory

    CERN Document Server

    2003-01-01

    This book develops thorough and complete foundations for the method of almost etale extensions, which is at the basis of Faltings' approach to p-adic Hodge theory. The central notion is that of an "almost ring". Almost rings are the commutative unitary monoids in a tensor category obtained as a quotient V-Mod/S of the category V-Mod of modules over a fixed ring V; the subcategory S consists of all modules annihilated by a fixed ideal m of V, satisfying certain natural conditions. The reader is assumed to be familiar with general categorical notions, some basic commutative algebra and some advanced homological algebra (derived categories, simplicial methods). Apart from these general prerequisites, the text is as self-contained as possible. One novel feature of the book - compared with Faltings' earlier treatment - is the systematic exploitation of the cotangent complex, especially for the study of deformations of almost algebras.

  4. DXD Motif-Dependent and -Independent Effects of the Chlamydia trachomatis Cytotoxin CT166

    Directory of Open Access Journals (Sweden)

    Miriam Bothe

    2015-02-01

    Full Text Available The Gram-negative, intracellular bacterium Chlamydia trachomatis causes acute and chronic urogenital tract infection, potentially leading to infertility and ectopic pregnancy. The only partially characterized cytotoxin CT166 of serovar D exhibits a DXD motif, which is important for the enzymatic activity of many bacterial and mammalian type A glycosyltransferases, leading to the hypothesis that CT166 possess glycosyltransferase activity. CT166-expressing HeLa cells exhibit actin reorganization, including cell rounding, which has been attributed to the inhibition of the Rho-GTPases Rac/Cdc42. Exploiting the glycosylation-sensitive Ras(27H5 antibody, we here show that CT166 induces an epitope change in Ras, resulting in inhibited ERK and PI3K signaling and delayed cell cycle progression. Consistent with the hypothesis that these effects strictly depend on the DXD motif, CT166 with the mutated DXD motif causes neither Ras-ERK inhibition nor delayed cell cycle progression. In contrast, CT166 with the mutated DXD motif is still capable of inhibiting cell migration, suggesting that CT166 with the mutated DXD motif cannot be regarded as inactive in any case. Taken together, CT166 affects various fundamental cellular processes, strongly suggesting its importance for the intracellular survival of chlamydia.

  5. Crystal structure of 5-[(4-carboxybenzyloxy]isophthalic acid

    Directory of Open Access Journals (Sweden)

    Md. Serajul Haque Faizi

    2016-08-01

    Full Text Available The molecular shape of the title compound, C16H12O7, is bent around the central CH2—O bond. The two benzene rings are almost perpendicular to one another, making a dihedral angle of 87.78 (7°. In the crystal, each molecule is linked to three others by three pairs of O—H...O hydrogen bonds, forming undulating sheets parallel to the bc plane and enclosing R22(8 ring motifs. The sheets are linked by C—H...O hydrogen bonds and C—H...π interactions, forming a three-dimensional network.

  6. Mutations in the putative zinc-binding motif of UL52 demonstrate a complex interdependence between the UL5 and UL52 subunits of the human herpes simplex virus type 1 helicase/primase complex.

    Science.gov (United States)

    Chen, Yan; Carrington-Lawrence, Stacy D; Bai, Ping; Weller, Sandra K

    2005-07-01

    Herpes simplex virus type 1 (HSV-1) encodes a heterotrimeric helicase-primase (UL5/8/52) complex. UL5 contains seven motifs found in helicase superfamily 1, and UL52 contains conserved motifs found in primases. The contributions of each subunit to the biochemical activities of the complex, however, remain unclear. We have previously demonstrated that a mutation in the putative zinc finger at UL52 C terminus abrogates not only primase but also ATPase, helicase, and DNA-binding activities of a UL5/UL52 subcomplex, indicating a complex interdependence between the two subunits. To test this hypothesis and to further investigate the role of the zinc finger in the enzymatic activities of the helicase-primase, a series of mutations were constructed in this motif. They differed in their ability to complement a UL52 null virus: totally defective, partial complementation, and potentiating. In this study, four of these mutants were studied biochemically after expression and purification from insect cells infected with recombinant baculoviruses. All mutants show greatly reduced primase activity. Complementation-defective mutants exhibited severe defects in ATPase, helicase, and DNA-binding activities. Partially complementing mutants displayed intermediate levels of these activities, except that one showed a wild-type level of helicase activity. These data suggest that the UL52 zinc finger motif plays an important role in the activities of the helicase-primase complex. The observation that mutations in UL52 affected helicase, ATPase, and DNA-binding activities indicates that UL52 binding to DNA via the zinc finger may be necessary for loading UL5. Alternatively, UL5 and UL52 may share a DNA-binding interface.

  7. Automatic annotation of protein motif function with Gene Ontology terms

    Directory of Open Access Journals (Sweden)

    Gopalakrishnan Vanathi

    2004-09-01

    Full Text Available Abstract Background Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, amuch needed and importanttask is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results This paperpresents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifsis viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association isfound to be a very useful feature. We take advantageof the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correctassociation. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. Conclusions In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about thefunctions of newly discovered candidate protein motifs.

  8. Verification of the MOTIF code version 3.0

    International Nuclear Information System (INIS)

    Chan, T.; Guvanasen, V.; Nakka, B.W.; Reid, J.A.K.; Scheier, N.W.; Stanchell, F.W.

    1996-12-01

    As part of the Canadian Nuclear Fuel Waste Management Program (CNFWMP), AECL has developed a three-dimensional finite-element code, MOTIF (Model Of Transport In Fractured/ porous media), for detailed modelling of groundwater flow, heat transport and solute transport in a fractured rock mass. The code solves the transient and steady-state equations of groundwater flow, solute (including one-species radionuclide) transport, and heat transport in variably saturated fractured/porous media. The initial development was completed in 1985 (Guvanasen 1985) and version 3.0 was completed in 1986. This version is documented in detail in Guvanasen and Chan (in preparation). This report describes a series of fourteen verification cases which has been used to test the numerical solution techniques and coding of MOTIF, as well as demonstrate some of the MOTIF analysis capabilities. For each case the MOTIF solution has been compared with a corresponding analytical or independently developed alternate numerical solution. Several of the verification cases were included in Level 1 of the International Hydrologic Code Intercomparison Project (HYDROCOIN). The MOTIF results for these cases were also described in the HYDROCOIN Secretariat's compilation and comparison of results submitted by the various project teams (Swedish Nuclear Power Inspectorate 1988). It is evident from the graphical comparisons presented that the MOTIF solutions for the fourteen verification cases are generally in excellent agreement with known analytical or numerical solutions obtained from independent sources. This series of verification studies has established the ability of the MOTIF finite-element code to accurately model the groundwater flow and solute and heat transport phenomena for which it is intended. (author). 20 refs., 14 tabs., 32 figs

  9. Suppressing band gap of MoS{sub 2} by the incorporation of four- and eight-membered rings

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Liyan; Zhang, Tingting, E-mail: ttzhang@hytc.edu.cn [Huaiyin Normal University, School of Physics and Electronic & Electrical Engineering, and Jiangsu Key Laboratory of Modern Measurement Technology and Intelligent Systems (China)

    2015-05-15

    A stable planar allotrope of MoS{sub 2}, formed by introducing four- and eight-membered rings into its hexagonal network (H468), is identified to be a narrow direct-band-gap semiconductor by first principle calculations, which is remarkably different from the large band gap semiconductor of conventional MoS{sub 2} and also the zero band gap allotrope consisting of four- and eight-membered rings (H48) only. The medium-sized direct band gap indicates that H468 would find applications in nanoelectronics and near-infrared optoelectronic devices. Furthermore, the distinctive simulated scanning tunneling microscope images under positive and negative biases might be a unique characteristic for the experimental identification of such an allotrope of MoS{sub 2}.

  10. An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers.

    Science.gov (United States)

    Wang, Rang Jian; Gao, Xiang Feng; Kong, Xiang Rui; Yang, Jun

    2016-01-01

    Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait 'cultivar processing-property'. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10(-5), which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property.

  11. Purification and functional motifs of the recombinant ATPase of orf virus.

    Science.gov (United States)

    Lin, Fong-Yuan; Chan, Kun-Wei; Wang, Chi-Young; Wong, Min-Liang; Hsu, Wei-Li

    2011-10-01

    Our previous study showed that the recombinant ATPase encoded by the A32L gene of orf virus displayed ATP hydrolysis activity as predicted from its amino acids sequence. This viral ATPase contains four known functional motifs (motifs I-IV) and a novel AYDG motif; they are essential for ATP hydrolysis reaction by binding ATP and magnesium ions. The motifs I and II correspond with the Walker A and B motifs of the typical ATPase, respectively. To examine the biochemical roles of these five conserved motifs, recombinant ATPases of five deletion mutants derived from the Taiping strain were expressed and purified. Their ATPase functions were assayed and compared with those of two wild type strains, Taiping and Nantou isolated in Taiwan. Our results showed that deletions at motifs I-III or IV exhibited lower activity than that of the wild type. Interestingly, deletion of AYDG motif decreased the ATPase activity more significantly than those of motifs I-IV deletions. Divalent ions such as magnesium and calcium were essential for ATPase activity. Moreover, our recombinant proteins of orf virus also demonstrated GTPase activity, though weaker than the original ATPase activity. Copyright © 2011 Elsevier Inc. All rights reserved.

  12. Generation of stable mixed-compact-toroid rings by inducing plasma currents in strong E rings

    International Nuclear Information System (INIS)

    Jayakumar, R.; Taggart, D.P.; Parker, M.R.; Fleischmann, H.H.

    1989-01-01

    In the RECE-Christa device, hybrid-type compact toroid rings are generated by inducing large toroidal plasma currents I rho in strong electron rings using a thin induction coil positioned along the ring axis. Starting from field-reversal values δ ο = 50 - 120 percent of the original pure fast-electron ring, the induced plasma current I rho raises δ to a maximum value of up to 240 percent with I rho contributing more than 50 percent of the total ring current. Quite interestingly, the generated hybrid compact toroid configurations appear gross-stable during the full I rho pulse length (half-amplitude width about 100 μs)

  13. Requirement for asparagine in the aquaporin NPA sequence signature motifs for cation exclusion

    DEFF Research Database (Denmark)

    Wree, Dorothea; Wu, Binghua; Zeuthen, Thomas

    2011-01-01

    Two highly conserved NPA motifs are a hallmark of the aquaporin (AQP) family. The NPA triplets form N-terminal helix capping structures with the Asn side chains located in the centre of the water or solute-conducting channel, and are considered to play an important role in AQP selectivity. Although...... interchangeable at both NPA sites without affecting protein expression or water, glycerol and methylamine permeability. However, other mutations in the NPA region led to reduced permeability (S186C and S186D), to nonfunctional channels (N64D), or even to lack of protein expression (S186A and S186T). Using...... electrophysiology, we found that an analogous mammalian AQP1 N76S mutant excluded protons and potassium ions, but leaked sodium ions, providing an argument for the overwhelming prevalence of Asn over other amino acids. We conclude that, at the first position in the NPA motifs, only Asn provides efficient helix cap...

  14. Discovery Of B Ring Propellers In Cassini UVIS, And ISS

    Science.gov (United States)

    Sremcevic, Miodrag; Stewart, G. R.; Albers, N.; Esposito, L. W.

    2012-10-01

    We present evidence for the existence of propellers in Saturn's B ring by combining data from Cassini Ultraviolet Imaging Spectrograph (UVIS) and Imaging Science Subsystem (ISS) experiments. We identify two propeller populations: (1) tens of degrees wide propellers in the dense B ring core, and (2) smaller, more A ring like, propellers populating the inner B ring. The prototype of the first population is an object observed at 18 different epochs between 2005 and 2010. The ubiquitous propeller "S" shape is seen both in UVIS occultations as an optical depth depletion and in ISS as a 40 degrees wide bright stripe in unlit geometries and dark in lit geometries. Combining the available Cassini data we infer that the object is a partial gap embedded in the high optical depth region of the B ring. The gap moves at orbital speed consistent with its radial location. From the radial separation of the propeller wings we estimate that the embedded body, which causes the propeller structure, is about 1.5km in size located at a=112,921km. The UVIS occultations indicate an asymmetric propeller "S" shape. Since the object is located at an edge between high and relatively low optical depth, this asymmetry is most likely a consequence of the strong surface mass density gradient. We estimate that there are possibly dozen up to 100 other propeller objects in Saturn's B ring. The location of the discovered body, at an edge of a dense ringlet within the B ring, suggests a novel mechanism for the up to now illusive B ring irregular large-scale structure of alternating high and low optical depth ringlets. We propose that this B ring irregular structure may have its cause in the presence of many embedded bodies that shepherd the individual B ring ringlets.

  15. [(4S,5S-2,2-Dimethyl-1,3-dioxolane-4,5-diyl]bis[N-(thiophen-2-ylmethylidenemethanamine

    Directory of Open Access Journals (Sweden)

    Yan Jiang

    2012-02-01

    Full Text Available In the title compound, C17H20N2O2S2, the five-membered heterocycle exhibits an envelope conformation and the molecular chirality and configuration are well preserved from l-tartaric acid. The dihedral angle between the two thiophene rings is 17.0 (2°. In the crystal, molecules are linked by C—H...O and C—H...S hydrogen interactions, which are effective in the stabilization of the crystal structure.

  16. Topological rings

    CERN Document Server

    Warner, S

    1993-01-01

    This text brings the reader to the frontiers of current research in topological rings. The exercises illustrate many results and theorems while a comprehensive bibliography is also included. The book is aimed at those readers acquainted with some very basic point-set topology and algebra, as normally presented in semester courses at the beginning graduate level or even at the advanced undergraduate level. Familiarity with Hausdorff, metric, compact and locally compact spaces and basic properties of continuous functions, also with groups, rings, fields, vector spaces and modules, and with Zorn''s Lemma, is also expected.

  17. An experimental test of a fundamental food web motif.

    Science.gov (United States)

    Rip, Jason M K; McCann, Kevin S; Lynn, Denis H; Fawcett, Sonia

    2010-06-07

    Large-scale changes to the world's ecosystem are resulting in the deterioration of biostructure-the complex web of species interactions that make up ecological communities. A difficult, yet crucial task is to identify food web structures, or food web motifs, that are the building blocks of this baroque network of interactions. Once identified, these food web motifs can then be examined through experiments and theory to provide mechanistic explanations for how structure governs ecosystem stability. Here, we synthesize recent ecological research to show that generalist consumers coupling resources with different interaction strengths, is one such motif. This motif amazingly occurs across an enormous range of spatial scales, and so acts to distribute coupled weak and strong interactions throughout food webs. We then perform an experiment that illustrates the importance of this motif to ecological stability. We find that weak interactions coupled to strong interactions by generalist consumers dampen strong interaction strengths and increase community stability. This study takes a critical step by isolating a common food web motif and through clear, experimental manipulation, identifies the fundamental stabilizing consequences of this structure for ecological communities.

  18. Multi scale analysis of ITER pre-compression rings

    Energy Technology Data Exchange (ETDEWEB)

    Park, Ben, E-mail: ben.park@sener.es [SENER Ingeniería y Sistemas S.A., Barcelona (Spain); Foussat, Arnaud [ITER Organization, St. Paul-Lez-Durance (France); Rajainmaki, Hannu [Fusion for Energy, Barcelona (Spain); Knaster, Juan [IFMIF, Aomori (Japan)

    2013-10-15

    Highlights: • A multi-scale analysis approach employing various scales of ABAQUS FEM models have been used to calculate the response and performance of the rings. • We have studied the effects of various defects on the performance of the rings under the operating temperatures and loading that will be applied to the PCRs. • The multi scale analysis results are presented here. -- Abstract: The Pre-compression Rings of ITER (PCRs) represent one of the largest and most highly stressed composite structures ever designed for long term operation at 4 K. Six rings, each 5 m in diameter and 337 mm × 288 mm in cross-section, will be manufactured from S2 fiber-glass/epoxy composite and installed three at the top and three at the bottom of the eighteen D shaped toroidal field (TF) coils to apply a total centripetal pre-load of 70 MN per TF coil. The composite rings will be fabricated with a high content (65% by volume) of S2 fiber-glass in an epoxy resin matrix. During the manufacture emphasis will be placed on obtaining a structure with a very low void content and minimal presence of critical defects, such as delaminations. This paper presents a unified framework for the multi-scale analysis of the composite structure of the PCRs. A multi-scale analysis approach employing various scales of ABAQUS FEM models and other analysis tools have been used to calculate the response and performance of the rings over the design life of the structure. We have studied the effects of various defects on the performance of the rings under the operating temperatures and loading that will be applied to the PCRs. The results are presented here.

  19. Two-dimensional hydrogen-bonded polymers in the crystal structures of the ammonium salts of phenoxyacetic acid, (4-fluorophenoxyacetic acid and (4-chloro-2-methylphenoxyacetic acid

    Directory of Open Access Journals (Sweden)

    Graham Smith

    2014-12-01

    Full Text Available The structures of the ammonium salts of phenoxyacetic acid, NH4+·C8H6O3−, (I, (4-fluorophenoxyacetic acid, NH4+·C8H5FO3−, (II, and the herbicidally active (4-chloro-2-methylphenoxyacetic acid (MCPA, NH4+·C9H8ClO3−·0.5H2O, (III have been determined. All have two-dimensional layered structures based on inter-species ammonium N—H...O hydrogen-bonding associations, which give core substructures consisting primarily of conjoined cyclic motifs. The crystals of (I and (II are isomorphous with the core comprising R12(5, R12(4 and centrosymmetric R42(8 ring motifs, giving two-dimensional layers lying parallel to (100. In (III, the water molecule of solvation lies on a crystallographic twofold rotation axis and bridges two carboxyl O atoms in an R44(12 hydrogen-bonded motif, creating two R43(10 rings, which together with a conjoined centrosymmetric R42(8 ring incorporating both ammonium cations, generate two-dimensional layers lying parallel to (100. No π–π ring associations are present in any of the structures.

  20. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit; Bajic, Vladimir B.; Kaushik, Dinesh

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  1. Nuclear localization of the dehydrin OpsDHN1 is determined by histidine-rich motif

    Science.gov (United States)

    Hernández-Sánchez, Itzell E.; Maruri-López, Israel; Ferrando, Alejandro; Carbonell, Juan; Graether, Steffen P.; Jiménez-Bremont, Juan F.

    2015-01-01

    The cactus OpsDHN1 dehydrin belongs to a large family of disordered and highly hydrophilic proteins known as Late Embryogenesis Abundant (LEA) proteins, which accumulate during the late stages of embryogenesis and in response to abiotic stresses. Herein, we present the in vivo OpsDHN1 subcellular localization by N-terminal GFP translational fusion; our results revealed a cytoplasmic and nuclear localization of the GFP::OpsDHN1 protein in Nicotiana benthamiana epidermal cells. In addition, dimer assembly of OpsDHN1 in planta using a Bimolecular Fluorescence Complementation (BiFC) approach was demonstrated. In order to understand the in vivo role of the histidine-rich motif, the OpsDHN1-ΔHis version was produced and assayed for its subcellular localization and dimer capability by GFP fusion and BiFC assays, respectively. We found that deletion of the OpsDHN1 histidine-rich motif restricted its localization to cytoplasm, but did not affect dimer formation. In addition, the deletion of the S-segment in the OpsDHN1 protein affected its nuclear localization. Our data suggest that the deletion of histidine-rich motif and S-segment show similar effects, preventing OpsDHN1 from getting into the nucleus. Based on these results, the histidine-rich motif is proposed as a targeting element for OpsDHN1 nuclear localization. PMID:26442018

  2. Nuclear localization of the dehydrin OpsDHN1 is determined by histidine-rich motif

    Directory of Open Access Journals (Sweden)

    Itzell Euridice Hernández-Sánchez

    2015-09-01

    Full Text Available The cactus OpsDHN1 dehydrin belongs to a large family of disordered and highly hydrophilic proteins known as Late Embryogenesis Abundant (LEA proteins, which accumulate during the late stages of embryogenesis and in response to abiotic stresses. Herein, we present the in vivo OpsDHN1 subcellular localization by N-terminal GFP translational fusion; our results revealed a cytoplasmic and nuclear localization of the GFP::OpsDHN1 protein in Nicotiana benthamiana epidermal cells. In addition, dimer assembly of OpsDHN1 in planta using a Bimolecular Fluorescence Complementation (BiFC approach was demonstrated. In order to understand the in vivo role of the histidine-rich motif, the OpsDHN1-ΔHis version was produced and assayed for its subcellular localization and dimer capability by GFP fusion and BiFC assays, respectively. We found that deletion of the OpsDHN1 histidine-rich motif restricted its localization to cytoplasm, but did not affect dimer formation. In addition, the deletion of the S-segment in the OpsDHN1 protein affected its nuclear localization. Our data suggest that the deletion of histidine-rich motif and S-segment show similar effects, preventing OpsDHN1 from getting into the nucleus. Based on these results, the histidine rich motif is proposed as a targeting element for OpsDHN1 nuclear localization.

  3. Mechanisms of zero-lag synchronization in cortical motifs.

    Directory of Open Access Journals (Sweden)

    Leonardo L Gollo

    2014-04-01

    Full Text Available Zero-lag synchronization between distant cortical areas has been observed in a diversity of experimental data sets and between many different regions of the brain. Several computational mechanisms have been proposed to account for such isochronous synchronization in the presence of long conduction delays: Of these, the phenomenon of "dynamical relaying"--a mechanism that relies on a specific network motif--has proven to be the most robust with respect to parameter mismatch and system noise. Surprisingly, despite a contrary belief in the community, the common driving motif is an unreliable means of establishing zero-lag synchrony. Although dynamical relaying has been validated in empirical and computational studies, the deeper dynamical mechanisms and comparison to dynamics on other motifs is lacking. By systematically comparing synchronization on a variety of small motifs, we establish that the presence of a single reciprocally connected pair--a "resonance pair"--plays a crucial role in disambiguating those motifs that foster zero-lag synchrony in the presence of conduction delays (such as dynamical relaying from those that do not (such as the common driving triad. Remarkably, minor structural changes to the common driving motif that incorporate a reciprocal pair recover robust zero-lag synchrony. The findings are observed in computational models of spiking neurons, populations of spiking neurons and neural mass models, and arise whether the oscillatory systems are periodic, chaotic, noise-free or driven by stochastic inputs. The influence of the resonance pair is also robust to parameter mismatch and asymmetrical time delays amongst the elements of the motif. We call this manner of facilitating zero-lag synchrony resonance-induced synchronization, outline the conditions for its occurrence, and propose that it may be a general mechanism to promote zero-lag synchrony in the brain.

  4. qPMS7: a fast algorithm for finding (ℓ, d-motifs in DNA and protein sequences.

    Directory of Open Access Journals (Sweden)

    Hieu Dinh

    Full Text Available Detection of rare events happening in a set of DNA/protein sequences could lead to new biological discoveries. One kind of such rare events is the presence of patterns called motifs in DNA/protein sequences. Finding motifs is a challenging problem since the general version of motif search has been proven to be intractable. Motifs discovery is an important problem in biology. For example, it is useful in the detection of transcription factor binding sites and transcriptional regulatory elements that are very crucial in understanding gene function, human disease, drug design, etc. Many versions of the motif search problem have been proposed in the literature. One such is the (ℓ, d-motif search (or Planted Motif Search (PMS. A generalized version of the PMS problem, namely, Quorum Planted Motif Search (qPMS, is shown to accurately model motifs in real data. However, solving the qPMS problem is an extremely difficult task because a special case of it, the PMS Problem, is already NP-hard, which means that any algorithm solving it can be expected to take exponential time in the worse case scenario. In this paper, we propose a novel algorithm named qPMS7 that tackles the qPMS problem on real data as well as challenging instances. Experimental results show that our Algorithm qPMS7 is on an average 5 times faster than the state-of-art algorithm. The executable program of Algorithm qPMS7 is freely available on the web at http://pms.engr.uconn.edu/downloads/qPMS7.zip. Our online motif discovery tools that use Algorithm qPMS7 are freely available at http://pms.engr.uconn.edu or http://motifsearch.com.

  5. A speedup technique for (l, d-motif finding algorithms

    Directory of Open Access Journals (Sweden)

    Dinh Hieu

    2011-03-01

    Full Text Available Abstract Background The discovery of patterns in DNA, RNA, and protein sequences has led to the solution of many vital biological problems. For instance, the identification of patterns in nucleic acid sequences has resulted in the determination of open reading frames, identification of promoter elements of genes, identification of intron/exon splicing sites, identification of SH RNAs, location of RNA degradation signals, identification of alternative splicing sites, etc. In protein sequences, patterns have proven to be extremely helpful in domain identification, location of protease cleavage sites, identification of signal peptides, protein interactions, determination of protein degradation elements, identification of protein trafficking elements, etc. Motifs are important patterns that are helpful in finding transcriptional regulatory elements, transcription factor binding sites, functional genomics, drug design, etc. As a result, numerous papers have been written to solve the motif search problem. Results Three versions of the motif search problem have been proposed in the literature: Simple Motif Search (SMS, (l, d-motif search (or Planted Motif Search (PMS, and Edit-distance-based Motif Search (EMS. In this paper we focus on PMS. Two kinds of algorithms can be found in the literature for solving the PMS problem: exact and approximate. An exact algorithm identifies the motifs always and an approximate algorithm may fail to identify some or all of the motifs. The exact version of PMS problem has been shown to be NP-hard. Exact algorithms proposed in the literature for PMS take time that is exponential in some of the underlying parameters. In this paper we propose a generic technique that can be used to speedup PMS algorithms. Conclusions We present a speedup technique that can be used on any PMS algorithm. We have tested our speedup technique on a number of algorithms. These experimental results show that our speedup technique is indeed very

  6. Transduction motif analysis of gastric cancer based on a human signaling network

    Energy Technology Data Exchange (ETDEWEB)

    Liu, G.; Li, D.Z.; Jiang, C.S.; Wang, W. [Fuzhou General Hospital of Nanjing Command, Department of Gastroenterology, Fuzhou, China, Department of Gastroenterology, Fuzhou General Hospital of Nanjing Command, Fuzhou (China)

    2014-04-04

    To investigate signal regulation models of gastric cancer, databases and literature were used to construct the signaling network in humans. Topological characteristics of the network were analyzed by CytoScape. After marking gastric cancer-related genes extracted from the CancerResource, GeneRIF, and COSMIC databases, the FANMOD software was used for the mining of gastric cancer-related motifs in a network with three vertices. The significant motif difference method was adopted to identify significantly different motifs in the normal and cancer states. Finally, we conducted a series of analyses of the significantly different motifs, including gene ontology, function annotation of genes, and model classification. A human signaling network was constructed, with 1643 nodes and 5089 regulating interactions. The network was configured to have the characteristics of other biological networks. There were 57,942 motifs marked with gastric cancer-related genes out of a total of 69,492 motifs, and 264 motifs were selected as significantly different motifs by calculating the significant motif difference (SMD) scores. Genes in significantly different motifs were mainly enriched in functions associated with cancer genesis, such as regulation of cell death, amino acid phosphorylation of proteins, and intracellular signaling cascades. The top five significantly different motifs were mainly cascade and positive feedback types. Almost all genes in the five motifs were cancer related, including EPOR, MAPK14, BCL2L1, KRT18, PTPN6, CASP3, TGFBR2, AR, and CASP7. The development of cancer might be curbed by inhibiting signal transductions upstream and downstream of the selected motifs.

  7. Rotavirus NSP1 Requires Casein Kinase II-Mediated Phosphorylation for Hijacking of Cullin-RING Ligases.

    Science.gov (United States)

    Davis, Kaitlin A; Morelli, Marco; Patton, John T

    2017-08-29

    The rotavirus nonstructural protein NSP1 repurposes cullin-RING E3 ubiquitin ligases (CRLs) to antagonize innate immune responses. By functioning as substrate adaptors of hijacked CRLs, NSP1 causes ubiquitination and proteasomal degradation of host proteins that are essential for expression of interferon (IFN) and IFN-stimulated gene products. The target of most human and porcine rotaviruses is the β-transducin repeat-containing protein (β-TrCP), a regulator of NF-κB activation. β-TrCP recognizes a phosphorylated degron (DSGΦXS) present in the inhibitor of NF-κB (IκB); phosphorylation of the IκB degron is mediated by IκB kinase (IKK). Because NSP1 contains a C-terminal IκB-like degron (ILD; DSGXS) that recruits β-TrCP, we investigated whether the NSP1 ILD is similarly activated by phosphorylation and whether this modification is required to trigger the incorporation of NSP1 into CRLs. Based on mutagenesis and phosphatase treatment studies, we found that both serine residues of the NSP1 ILD are phosphorylated, a pattern mimicking phosphorylation of IκB. A three-pronged approach using small-molecule inhibitors, small interfering RNAs, and mutagenesis demonstrated that NSP1 phosphorylation is mediated by the constitutively active casein kinase II (CKII), rather than IKK. In coimmunoprecipitation assays, we found that this modification was essential for NSP1 recruitment of β-TrCP and induced changes involving the NSP1 N-terminal RING motif that allowed formation of Cul3-NSP1 complexes. Taken together, our results indicate a highly regulated stepwise process in the formation of NSP1-Cul3 CRLs that is initiated by CKII phosphorylation of NSP1, followed by NSP1 recruitment of β-TrCP and ending with incorporation of the NSP1-β-TrCP complex into the CRL via interactions dependent on the highly conserved NSP1 RING motif. IMPORTANCE Rotavirus is a segmented double-stranded RNA virus that causes severe diarrhea in young children. A primary mechanism used by the

  8. Armadillo motifs involved in vesicular transport.

    Directory of Open Access Journals (Sweden)

    Harald Striegl

    Full Text Available Armadillo (ARM repeat proteins function in various cellular processes including vesicular transport and membrane tethering. They contain an imperfect repeating sequence motif that forms a conserved three-dimensional structure. Recently, structural and functional insight into tethering mediated by the ARM-repeat protein p115 has been provided. Here we describe the p115 ARM-motifs for reasons of clarity and nomenclature and show that both sequence and structure are highly conserved among ARM-repeat proteins. We argue that there is no need to invoke repeat types other than ARM repeats for a proper description of the structure of the p115 globular head region. Additionally, we propose to define a new subfamily of ARM-like proteins and show lack of evidence that the ARM motifs found in p115 are present in other long coiled-coil tethering factors of the golgin family.

  9. Characterizing Motif Dynamics of Electric Brain Activity Using Symbolic Analysis

    Directory of Open Access Journals (Sweden)

    Massimiliano Zanin

    2014-10-01

    Full Text Available Motifs are small recurring circuits of interactions which constitute the backbone of networked systems. Characterizing motif dynamics is therefore key to understanding the functioning of such systems. Here we propose a method to define and quantify the temporal variability and time scales of electroencephalogram (EEG motifs of resting brain activity. Given a triplet of EEG sensors, links between them are calculated by means of linear correlation; each pattern of links (i.e., each motif is then associated to a symbol, and its appearance frequency is analyzed by means of Shannon entropy. Our results show that each motif becomes observable with different coupling thresholds and evolves at its own time scale, with fronto-temporal sensors emerging at high thresholds and changing at fast time scales, and parietal ones at low thresholds and changing at slower rates. Finally, while motif dynamics differed across individuals, for each subject, it showed robustness across experimental conditions, indicating that it could represent an individual dynamical signature.

  10. Discriminative motif discovery via simulated evolution and random under-sampling.

    Directory of Open Access Journals (Sweden)

    Tao Song

    Full Text Available Conserved motifs in biological sequences are closely related to their structure and functions. Recently, discriminative motif discovery methods have attracted more and more attention. However, little attention has been devoted to the data imbalance problem, which is one of the main reasons affecting the performance of the discriminative models. In this article, a simulated evolution method is applied to solve the multi-class imbalance problem at the stage of data preprocessing, and at the stage of Hidden Markov Models (HMMs training, a random under-sampling method is introduced for the imbalance between the positive and negative datasets. It is shown that, in the task of discovering targeting motifs of nine subcellular compartments, the motifs found by our method are more conserved than the methods without considering data imbalance problem and recover the most known targeting motifs from Minimotif Miner and InterPro. Meanwhile, we use the found motifs to predict protein subcellular localization and achieve higher prediction precision and recall for the minority classes.

  11. Discriminative motif discovery via simulated evolution and random under-sampling.

    Science.gov (United States)

    Song, Tao; Gu, Hong

    2014-01-01

    Conserved motifs in biological sequences are closely related to their structure and functions. Recently, discriminative motif discovery methods have attracted more and more attention. However, little attention has been devoted to the data imbalance problem, which is one of the main reasons affecting the performance of the discriminative models. In this article, a simulated evolution method is applied to solve the multi-class imbalance problem at the stage of data preprocessing, and at the stage of Hidden Markov Models (HMMs) training, a random under-sampling method is introduced for the imbalance between the positive and negative datasets. It is shown that, in the task of discovering targeting motifs of nine subcellular compartments, the motifs found by our method are more conserved than the methods without considering data imbalance problem and recover the most known targeting motifs from Minimotif Miner and InterPro. Meanwhile, we use the found motifs to predict protein subcellular localization and achieve higher prediction precision and recall for the minority classes.

  12. Bacterial proteasome activator bpa (rv3780) is a novel ring-shaped interactor of the mycobacterial proteasome.

    Science.gov (United States)

    Delley, Cyrille L; Laederach, Juerg; Ziemski, Michal; Bolten, Marcel; Boehringer, Daniel; Weber-Ban, Eilika

    2014-01-01

    The occurrence of the proteasome in bacteria is limited to the phylum of actinobacteria, where it is maintained in parallel to the usual bacterial compartmentalizing proteases. The role it plays in these organisms is still not fully understood, but in the human pathogen Mycobacterium tuberculosis (Mtb) the proteasome supports persistence in the host. In complex with the ring-shaped ATPase Mpa (called ARC in other actinobacteria), the proteasome can degrade proteins that have been post-translationally modified with the prokaryotic ubiquitin-like protein Pup. Unlike for the eukaryotic proteasome core particle, no other bacterial proteasome interactors have been identified to date. Here we describe and characterize a novel bacterial proteasome activator of Mycobacterium tuberculosis we termed Bpa (Rv3780), using a combination of biochemical and biophysical methods. Bpa features a canonical C-terminal proteasome interaction motif referred to as the HbYX motif, and its orthologs are only found in those actinobacteria encoding the proteasomal subunits. Bpa can inhibit degradation of Pup-tagged substrates in vitro by competing with Mpa for association with the proteasome. Using negative-stain electron microscopy, we show that Bpa forms a ring-shaped homooligomer that can bind coaxially to the face of the proteasome cylinder. Interestingly, Bpa can stimulate the proteasomal degradation of the model substrate β-casein, which suggests it could play a role in the removal of non-native or damaged proteins.

  13. Indonesian Traditional Toys and the Development of Batik Motifs

    Directory of Open Access Journals (Sweden)

    Bagus Indrayana

    2016-06-01

    Full Text Available There is a wide array of traditional toys in Indonesia. In the past, traditional toys played an important role for skill and creativity development of children. Today, the position of traditional toys in the society is displaced by toys from large-scale manufacturers. Given the critical role of traditional toys for children’s motoric and social development, there is a need to develop media that can be used to promote these traditional products and strengthen their position in the public. We propose to use Batik as a way to effectively disseminate and promote traditional toys to the general public. Apart from this, using traditional toys to create new Batik motifs can have an economic value for the producers of Batik, promote Indonesian products and enrich the Indonesian Batik. This study aims to explore the variety of traditional toys, mainly from Klaten and Magelang, in the Central Java province of Indonesia, and use them as the basis for the development of Batik motif creation. This study used Trilogi Keseimbangan (or Harmony Trilogy aesthetic theory analytical approach that explains the creation of craft consists of the following phases: exploration, design, and materialization. The creation method in this study adopts Tiga Tahap Enam Langkah (Three Phases, Six Steps method offered in the theory. The finding in the field found that the traditional toys material used in Klaten and Magelang, mostly made from waste wood, plywood, and zinc. The manufacturing process is done manually by two or three craftsmen using a simple technology. The traditional toys are designed by the artisans mostly, although there may be designs from the clients. In addition, we also found that the traditional toys have never been used as a Batik motif. The traditional toys Batik motif presented in this work is researcher’s design. For the purposes of this study, we first research the variety of traditional toys available in the market today in Indonesia. We look

  14. Two-dimensional inorganic–organic hybrid semiconductors composed of double-layered ZnS and monoamines with aromatic and heterocyclic aliphatic rings: Syntheses, structures, and properties

    International Nuclear Information System (INIS)

    Wang, Sujing; Li, Jing

    2015-01-01

    As an addition to the II–VI based inorganic–organic hybrid semiconductor family, five new two-dimensional (2D) double-layered structures have been synthesized employing monoamines with different aromatic or heterocyclic aliphatic rings. Zn 2 S 2 (bza) (1), Zn 2 S 2 (mbza) (2), Zn 2 S 2 (fbza) (3), Zn 2 S 2 (pca) (4), and Zn 2 S 2 (thfa) (5) (bza=benzylamine, mbza=4-methoxybenzylamine, fbza=4-flurobenzylamine, pca=3-picolylamine, and thfa=tetrahydrofurfurylamine) are prepared by solvothermal reactions and characterized by different analytical methods, including powder X-ray diffraction, optical diffuse reflection, thermogravimetric analysis and photoluminescence spectroscopy. The powder X-ray diffraction patterns show that all five compounds adopt 2D double-layered structures. Optical diffuse reflectance spectra of these compounds suggest that they have notably lower band gaps than those of the similar compounds composed of aliphatic alkyl amines. Their photoluminescence properties and thermal stability are also analyzed. - Graphical abstract: Five new members of two-dimensional double-layered 2D-Zn 2 S 2 (L) (L=Ligand) structures employing monoamines with different aromatic or heterocyclic aliphatic rings have been designed, synthesized, and characterized. - Highlights: • A new sub-family of II-VI based hybrid semiconductors are designed, synthesized, and structurally characterized using amines with aromatic or aliphatic cyclic rings. • These compounds have notably lower band gaps than those made of aliphatic alkyl amines, greatly broadening the range of band gaps of this material family. • They emit strongly with systematically tunable emission intensity and energy

  15. Split ring containment attachment device

    International Nuclear Information System (INIS)

    Sammel, A.G.

    1996-01-01

    A containment attachment device is described for operatively connecting a glovebag to plastic sheeting covering hazardous material. The device includes an inner split ring member connected on one end to a middle ring member wherein the free end of the split ring member is inserted through a slit in the plastic sheeting to captively engage a generally circular portion of the plastic sheeting. A collar potion having an outer ring portion is provided with fastening means for securing the device together wherein the glovebag is operatively connected to the collar portion. 5 figs

  16. The 5S rDNA in two Abracris grasshoppers (Ommatolampidinae: Acrididae): molecular and chromosomal organization.

    Science.gov (United States)

    Bueno, Danilo; Palacios-Gimenez, Octavio Manuel; Martí, Dardo Andrea; Mariguela, Tatiane Casagrande; Cabral-de-Mello, Diogo Cavalcanti

    2016-08-01

    The 5S ribosomal DNA (rDNA) sequences are subject of dynamic evolution at chromosomal and molecular levels, evolving through concerted and/or birth-and-death fashion. Among grasshoppers, the chromosomal location for this sequence was established for some species, but little molecular information was obtained to infer evolutionary patterns. Here, we integrated data from chromosomal and nucleotide sequence analysis for 5S rDNA in two Abracris species aiming to identify evolutionary dynamics. For both species, two arrays were identified, a larger sequence (named type-I) that consisted of the entire 5S rDNA gene plus NTS (non-transcribed spacer) and a smaller (named type-II) with truncated 5S rDNA gene plus short NTS that was considered a pseudogene. For type-I sequences, the gene corresponding region contained the internal control region and poly-T motif and the NTS presented partial transposable elements. Between the species, nucleotide differences for type-I were noticed, while type-II was identical, suggesting pseudogenization in a common ancestor. At chromosomal point to view, the type-II was placed in one bivalent, while type-I occurred in multiple copies in distinct chromosomes. In Abracris, the evolution of 5S rDNA was apparently influenced by the chromosomal distribution of clusters (single or multiple location), resulting in a mixed mechanism integrating concerted and birth-and-death evolution depending on the unit.

  17. Overexpression of GmERF5, a new member of the soybean EAR motif-containing ERF transcription factor, enhances resistance to Phytophthora sojae in soybean.

    Science.gov (United States)

    Dong, Lidong; Cheng, Yingxin; Wu, Junjiang; Cheng, Qun; Li, Wenbin; Fan, Sujie; Jiang, Liangyu; Xu, Zhaolong; Kong, Fanjiang; Zhang, Dayong; Xu, Pengfei; Zhang, Shuzhen

    2015-05-01

    Phytophthora root and stem rot of soybean [Glycine max (L.) Merr.], caused by Phytophthora sojae Kaufmann and Gerdemann, is a destructive disease throughout the soybean planting regions in the world. Here, we report insights into the function and underlying mechanisms of a novel ethylene response factor (ERF) in soybean, namely GmERF5, in host responses to P. sojae. GmERF5-overexpressing transgenic soybean exhibited significantly enhanced resistance to P. sojae and positively regulated the expression of the PR10, PR1-1, and PR10-1 genes. Sequence analysis suggested that GmERF5 contains an AP2/ERF domain of 58 aa and a conserved ERF-associated amphiphilic repression (EAR) motif in its C-terminal region. Following stress treatments, GmERF5 was significantly induced by P. sojae, ethylene (ET), abscisic acid (ABA), and salicylic acid (SA). The activity of the GmERF5 promoter (GmERF5P) was upregulated in tobacco leaves with ET, ABA, Phytophthora nicotianae, salt, and drought treatments, suggesting that GmERF5 could be involved not only in the induced defence response but also in the ABA-mediated pathway of salt and drought tolerance. GmERF5 could bind to the GCC-box element and act as a repressor of gene transcription. It was targeted to the nucleus when transiently expressed in Arabidopsis protoplasts. GmERF5 interacted with a basic helix-loop-helix transcription factor (GmbHLH) and eukaryotic translation initiation factor (GmEIF) both in yeast cells and in planta. To the best of our knowledge, GmERF5 is the first soybean EAR motif-containing ERF transcription factor demonstrated to be involved in the response to pathogen infection. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  18. Crystal structures of 2-benzylamino-4-(4-bromophenyl-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridine-3-carbonitrile and 2-benzylamino-4-(4-chlorophenyl-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridine-3-carbonitrile

    Directory of Open Access Journals (Sweden)

    R. A. Nagalakshmi

    2015-01-01

    Full Text Available In the title compounds, C24H22BrN3, (I, and C24H22ClN3, (II, the 2-aminopyridine ring is fused with a cycloheptane ring, which adopts a half-chair conformation. The planes of the phenyl and benzene rings are inclined to that of the central pyridine ring [r.m.s. deviations = 0.0083 (1 and 0.0093 (1 Å for (I and (II, respectively] by 62.47 (17 and 72.51 (14°, respectively, in (I, and by 71.44 (9 and 54.90 (8°, respectively, in (II. The planes of the aromatic rings are inclined to one another by 53.82 (17° in (I and by 58.04 (9° in (II. In the crystals of both (I and (II, pairs of N—H...Nnitrile hydrogen bonds link the molecules, forming inversion dimers with R22(12 ring motifs. In (I, the resulting dimers are connected through C—H...Br hydrogen bonds, forming sheets parallel to (10-1, and π–π interactions [inter-centroid distance = 3.7821 (16 Å] involving inversion-related pyridine rings, forming a three-dimensional network. In (II, the resulting dimers are connected through π–π interactions [inter-centroid distance = 3.771 (2 Å] involving inversion-related pyridine rings, forming a two-dimensional network lying parallel to (001.

  19. Ionization cooling ring for muons

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    R. Palmer

    2005-06-01

    Full Text Available Practical ionization cooling rings could lead to lower cost or improved performance in neutrino factory or muon collider designs. The ring modeled here uses realistic three-dimensional fields. The performance of the ring compares favorably with the linear cooling channel used in the second U.S. Neutrino Factory Study. The normalized 6D emittance of an ideal ring is decreased by a factor of approximately 240, compared with a factor of only 15 for the linear channel. We also examine such real-world effects as windows on the absorbers and rf cavities and leaving empty lattice cells for injection and extraction. For realistic conditions the ring decreases the normalized 6D emittance by a factor of 49.

  20. Unlocked nucleic acids with a pyrene-modified uracil: Synthesis, hybridization studies, fluorescent properties and i-motif stability

    DEFF Research Database (Denmark)

    Perlíková, P.; Karlsen, K.K.; Pedersen, E.B.

    2014-01-01

    The synthesis of two new phosphoramidite building blocks for the incorporation of 5-(pyren-1-yl)uracilyl unlocked nucleic acid (UNA) monomers into oligonucleotides has been developed. Monomers containing a pyrene-modified nucleobase component were found to destabilize an i-motif structure at pH 5...... intensities upon hybridization to DNA or RNA. Efficient quenching of fluorescence of pyrene-modified UNA monomers was observed after formation of i-motif structures at pH 5.2. The stabilizing/destabilizing effect of pyrene-modified nucleic acids might be useful for designing antisense oligonucleotides...

  1. On (weakly precious rings associated to central polynomials

    Directory of Open Access Journals (Sweden)

    Hani A. Khashan

    2018-04-01

    Full Text Available Let R be an associative ring with identity and let g(x be a fixed polynomial over the center of R. We define R to be (weakly g(x-precious if for every element a∈R, there are a zero s of g(x, a unit u and a nilpotent b such that (a=±s+u+b a=s+u+b. In this paper, we investigate many examples and properties of (weakly g(x-precious rings. If a and b are in the center of R with b-a is a unit, we give a characterizations for (weakly (x-a(x-b-precious rings in terms of (weakly precious rings. In particular, we prove that if 2 is a unit, then a ring is precious if and only it is weakly precious. Finally, for n∈ℕ, we study (weakly (xⁿ-x-precious rings and clarify some of their properties.

  2. 4,6-Dichloro-2-((E-{4-[(E-3,5-dichloro-2-hydroxybenzylideneamino]butylimino}methylphenol

    Directory of Open Access Journals (Sweden)

    Hadi Kargar

    2012-07-01

    Full Text Available The asymmetric unit of the title compound, C18H16Cl4N2O2, comprises half of a potentially tetradentate Schiff base ligand. It is located about a twofold rotation axis that bisects the central C—C bond of the butane-1,4-diamine group. There are two intramolecular O—H...N hydrogen bonds making S(6 ring motifs. In the crystal, molecules are linked by pairs of weak C—H...Cl interactions, forming inversion dimers, which are further connected by C—H...O hydrogen bonds into two-dimensional frameworks that lie parallel to (001.

  3. Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

    Directory of Open Access Journals (Sweden)

    Farré Domènec

    2007-12-01

    Full Text Available Abstract Background The arrangement of regulatory motifs in gene promoters, or promoter architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of specific protein-interacting DNA motifs in gene promoters. However, little is known about the relative location and spacing of these motifs. To fill this gap, we have performed a systematic search for motifs that show significant bias at specific promoter locations in a large collection of housekeeping and tissue-specific genes. Results We observe that promoters driving housekeeping gene expression are enriched in particular motifs with strong positional bias, such as YY1, which are of little relevance in promoters driving tissue-specific expression. We also identify a large number of motifs that show positional bias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific motifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis, as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions for 559 tissue-specific motifs in mouse gene promoters. Conclusion The study shows that motif positional bias is an important feature of mammalian proximal promoters and that it affects both general and tissue-specific motifs. Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.

  4. A critical role for noncoding 5S rRNA in regulating Mdmx stability.

    Science.gov (United States)

    Li, Muyang; Gu, Wei

    2011-09-16

    Both p53 and Mdmx are ubiquitinated and degraded by the same E3 ligase Mdm2; interestingly, however, while p53 is rapidly degraded by Mdm2, Mdmx is a stable protein in most cancer cells. Thus, the mechanism by which Mdmx is degraded by Mdm2 needs further elucidation. Here, we identified the noncoding 5S rRNA as a major component of Mdmx-associated complexes from human cells. We show that 5S rRNA acts as a natural inhibitor of Mdmx degradation by Mdm2. RNAi-mediated knockdown of endogenous 5S rRNA, while not affecting p53 levels, significantly induces Mdmx degradation and, subsequently, activates p53-dependent growth arrest. Notably, 5S rRNA binds the RING domain of Mdmx and blocks its ubiquitination by Mdm2, whereas Mdm2-mediated p53 ubiquitination remains intact. These results provide insights into the differential effects on p53 and Mdmx by Mdm2 in vivo and reveal a critical role for noncoding 5S rRNA in modulating the p53-Mdmx axis. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Transmission Property of Directly Modulated Signals Enhanced by a Micro-ring Resonator

    DEFF Research Database (Denmark)

    An, Yi; Lorences Riesgo, Abel; Seoane, Jorge

    2012-01-01

    A silicon micro-ring resonator is used to enhance the modulation speed of a 10-Gbit/s directly modulated laser to 40 Gbit/s. The generated signal is transmitted error free over 4.5 km SSMF. Dispersion tolerance is also studied....

  6. Computational analyses of synergism in small molecular network motifs.

    Directory of Open Access Journals (Sweden)

    Yili Zhang

    2014-03-01

    Full Text Available Cellular functions and responses to stimuli are controlled by complex regulatory networks that comprise a large diversity of molecular components and their interactions. However, achieving an intuitive understanding of the dynamical properties and responses to stimuli of these networks is hampered by their large scale and complexity. To address this issue, analyses of regulatory networks often focus on reduced models that depict distinct, reoccurring connectivity patterns referred to as motifs. Previous modeling studies have begun to characterize the dynamics of small motifs, and to describe ways in which variations in parameters affect their responses to stimuli. The present study investigates how variations in pairs of parameters affect responses in a series of ten common network motifs, identifying concurrent variations that act synergistically (or antagonistically to alter the responses of the motifs to stimuli. Synergism (or antagonism was quantified using degrees of nonlinear blending and additive synergism. Simulations identified concurrent variations that maximized synergism, and examined the ways in which it was affected by stimulus protocols and the architecture of a motif. Only a subset of architectures exhibited synergism following paired changes in parameters. The approach was then applied to a model describing interlocked feedback loops governing the synthesis of the CREB1 and CREB2 transcription factors. The effects of motifs on synergism for this biologically realistic model were consistent with those for the abstract models of single motifs. These results have implications for the rational design of combination drug therapies with the potential for synergistic interactions.

  7. Micro-ring sensor used in the diagnosis of gastric cancer

    Science.gov (United States)

    Shi, Sichao; Cheng, Qing; Lin, Rong; Su, Da; Huang, Ying

    2016-01-01

    To find a detecting method that can be applied to the clinical screening and diagnosis, the cascaded micro-ring sensor with Vernier effect was used to distinguish gastric cancerous and normal cells. The simulation by FDTD of the cascaded microring sensor with different refractive indexes of the analyte (normal cells and gastric cancer cells) will be presented. In the simulation, with the refractive index's change Δn=0.02 for the two different analyte, the shift of sensor's resonant wavelength is 6.71nm. And the cascaded micro-ring sensor's sensitivity S is 335.5nm/RIU, and it is much larger compared to 19nm/RIU for a single ring sensor.

  8. SNS accumulator ring design and space charge considerations

    Energy Technology Data Exchange (ETDEWEB)

    Weng, W.T.

    1998-08-01

    The goal of the proposed Spallation Neutron Source (SNS) is to provide a short pulse proton beam of about 0.5 {micro}s with average beam power of 1 MW. To achieve such purpose, a proton storage ring operated at 60 Hz with 1 {times} 10{sup 14} protons per pulse at 1 GeV is required. The Accumulator Ring (AR) receives 1 msec long H{sup {minus}} beam bunches of 28 mA from a 1 GeV linac. Scope and design performance goals of the AR are presented. About 1,200 turns of charge exchange injection is needed to accumulate 1 mA in the ring. After a brief description of the lattice design and machine performance parameters, space charge related issues, such as: tune shifts, stopband corrections, halo generatino and beam collimation etc. is discussed.

  9. SNS ACCUMULATOR RING DESIGN AND SPACE CHARGE CONSIDERATIONS

    Energy Technology Data Exchange (ETDEWEB)

    WENG,W.T.

    1998-05-04

    The goal of the proposed Spallation Neutron Source (SNS) is to provide a short pulse proton beam of about 0.5{micro}s with average beam power of 1MW. To achieve such purpose, a proton storage ring operated at 60Hz with 1 x 10{sup 14} protons per pulse at 1GeV is required. The Accumulator Ring (AR) receives 1msec long H{sup {minus}} beam bunches of 28mA from a 1GeV linac. Scope and design performance goals of the AR are presented. About 1,200 turns of charge exchange injection is needed to accumulate 1mA in the ring. After a brief description of the lattice design and machine performance parameters, space charge related issues, such as: tune shifts, stopband corrections, halo generation and beam collimation etc. is discussed.

  10. Hunting Motifs in Situla Art

    Directory of Open Access Journals (Sweden)

    Andrej Preložnik

    2013-07-01

    Full Text Available Situla art developed as an echo of the toreutic style which had spread from the Near East through the Phoenicians, Greeks and Etruscans as far as the Veneti, Raeti, Histri, and their eastern neighbours in the region of Dolenjska (Lower Carniola. An Early Iron Age phenomenon (c. 600—300 BC, it rep- resents the major and most arresting form of the contemporary visual arts in an area stretching from the foot of the Apennines in the south to the Drava and Sava rivers in the east. Indeed, individual pieces have found their way across the Alpine passes and all the way north to the Danube. In the world and art of the situlae, a prominent role is accorded to ani- mals. They are displayed in numerous representations of human activities on artefacts crafted in the classic situla style – that is, between the late 6th  and early 5th centuries BC – as passive participants (e.g. in pageants or in harness or as an active element of the situla narrative. The most typical example of the latter is the hunting scene. Today we know at least four objects decorat- ed exclusively with hunting themes, and a number of situlae and other larger vessels where hunting scenes are embedded in composite narratives. All this suggests a popularity unparallelled by any other genre. Clearly recognisable are various hunting techniques and weapons, each associated with a particu- lar type of game (Fig. 1. The chase of a stag with javelin, horse and hound is depicted on the long- familiar and repeatedly published fibula of Zagorje (Fig. 2. It displays a hound mauling the stag’s back and a hunter on horseback pursuing a hind, her neck already pierced by the javelin. To judge by the (so far unnoticed shaft end un- der the stag’s muzzle, the hunter would have been brandishing a second jave- lin as well, like the warrior of the Vače fibula or the rider of the Nesactium situla, presumably himself a hunter. Many parallels to his motif are known from Greece, Etruria, and

  11. Convergent evolution and mimicry of protein linear motifs in host-pathogen interactions.

    Science.gov (United States)

    Chemes, Lucía Beatriz; de Prat-Gay, Gonzalo; Sánchez, Ignacio Enrique

    2015-06-01

    Pathogen linear motif mimics are highly evolvable elements that facilitate rewiring of host protein interaction networks. Host linear motifs and pathogen mimics differ in sequence, leading to thermodynamic and structural differences in the resulting protein-protein interactions. Moreover, the functional output of a mimic depends on the motif and domain repertoire of the pathogen protein. Regulatory evolution mediated by linear motifs can be understood by measuring evolutionary rates, quantifying positive and negative selection and performing phylogenetic reconstructions of linear motif natural history. Convergent evolution of linear motif mimics is widespread among unrelated proteins from viral, prokaryotic and eukaryotic pathogens and can also take place within individual protein phylogenies. Statistics, biochemistry and laboratory models of infection link pathogen linear motifs to phenotypic traits such as tropism, virulence and oncogenicity. In vitro evolution experiments and analysis of natural sequences suggest that changes in linear motif composition underlie pathogen adaptation to a changing environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Functional motifs responsible for human metapneumovirus M2-2-mediated innate immune evasion.

    Science.gov (United States)

    Chen, Yu; Deng, Xiaoling; Deng, Junfang; Zhou, Jiehua; Ren, Yuping; Liu, Shengxuan; Prusak, Deborah J; Wood, Thomas G; Bao, Xiaoyong

    2016-12-01

    Human metapneumovirus (hMPV) is a major cause of lower respiratory infection in young children. Repeated infections occur throughout life, but its immune evasion mechanisms are largely unknown. We recently found that hMPV M2-2 protein elicits immune evasion by targeting mitochondrial antiviral-signaling protein (MAVS), an antiviral signaling molecule. However, the molecular mechanisms underlying such inhibition are not known. Our mutagenesis studies revealed that PDZ-binding motifs, 29-DEMI-32 and 39-KEALSDGI-46, located in an immune inhibitory region of M2-2, are responsible for M2-2-mediated immune evasion. We also found both motifs prevent TRAF5 and TRAF6, the MAVS downstream adaptors, to be recruited to MAVS, while the motif 39-KEALSDGI-46 also blocks TRAF3 migrating to MAVS. In parallel, these TRAFs are important in activating transcription factors NF-kB and/or IRF-3 by hMPV. Our findings collectively demonstrate that M2-2 uses its PDZ motifs to launch the hMPV immune evasion through blocking the interaction of MAVS and its downstream TRAFs. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Methods and statistics for combining motif match scores.

    Science.gov (United States)

    Bailey, T L; Gribskov, M

    1998-01-01

    Position-specific scoring matrices are useful for representing and searching for protein sequence motifs. A sequence family can often be described by a group of one or more motifs, and an effective search must combine the scores for matching a sequence to each of the motifs in the group. We describe three methods for combining match scores and estimating the statistical significance of the combined scores and evaluate the search quality (classification accuracy) and the accuracy of the estimate of statistical significance of each. The three methods are: 1) sum of scores, 2) sum of reduced variates, 3) product of score p-values. We show that method 3) is superior to the other two methods in both regards, and that combining motif scores indeed gives better search accuracy. The MAST sequence homology search algorithm utilizing the product of p-values scoring method is available for interactive use and downloading at URL http:/(/)www.sdsc.edu/MEME.

  14. Storage Rings

    International Nuclear Information System (INIS)

    Fischer, W.

    2010-01-01

    Storage rings are circular machines that store particle beams at a constant energy. Beams are stored in rings without acceleration for a number of reasons (Tab. 1). Storage rings are used in high-energy, nuclear, atomic, and molecular physics, as well as for experiments in chemistry, material and life sciences. Parameters for storage rings such as particle species, energy, beam intensity, beam size, and store time vary widely depending on the application. The beam must be injected into a storage ring but may not be extracted (Fig. 1). Accelerator rings such as synchrotrons are used as storage rings before and after acceleration. Particles stored in rings include electrons and positrons; muons; protons and anti-protons; neutrons; light and heavy, positive and negative, atomic ions of various charge states; molecular and cluster ions, and neutral polar molecules. Spin polarized beams of electrons, positrons, and protons were stored. The kinetic energy of the stored particles ranges from 10 -6 eV to 3.5 x 10 12 eV (LHC, 7 x 10 12 eV planned), the number of stored particles from one (ESR) to 1015 (ISR). To store beam in rings requires bending (dipoles) and transverse focusing (quadrupoles). Higher order multipoles are used to correct chromatic aberrations, to suppress instabilities, and to compensate for nonlinear field errors of dipoles and quadrupoles. Magnetic multipole functions can be combined in magnets. Beams are stored bunched with radio frequency systems, and unbunched. The magnetic lattice and radio frequency system are designed to ensure the stability of transverse and longitudinal motion. New technologies allow for better storage rings. With strong focusing the beam pipe dimensions became much smaller than previously possible. For a given circumference superconducting magnets make higher energies possible, and superconducting radio frequency systems allow for efficient replenishment of synchrotron radiation losses of large current electron or positron beams

  15. MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.

    Science.gov (United States)

    Ozaki, Haruka; Iwasaki, Wataru

    2016-08-01

    As a key mechanism of gene regulation, transcription factors (TFs) bind to DNA by recognizing specific short sequence patterns that are called DNA-binding motifs. A single TF can accept ambiguity within its DNA-binding motifs, which comprise both canonical (typical) and non-canonical motifs. Clarification of such DNA-binding motif ambiguity is crucial for revealing gene regulatory networks and evaluating mutations in cis-regulatory elements. Although chromatin immunoprecipitation sequencing (ChIP-seq) now provides abundant data on the genomic sequences to which a given TF binds, existing motif discovery methods are unable to directly answer whether a given TF can bind to a specific DNA-binding motif. Here, we report a method for clarifying the DNA-binding motif ambiguity, MOCCS. Given ChIP-Seq data of any TF, MOCCS comprehensively analyzes and describes every k-mer to which that TF binds. Analysis of simulated datasets revealed that MOCCS is applicable to various ChIP-Seq datasets, requiring only a few minutes per dataset. Application to the ENCODE ChIP-Seq datasets proved that MOCCS directly evaluates whether a given TF binds to each DNA-binding motif, even if known position weight matrix models do not provide sufficient information on DNA-binding motif ambiguity. Furthermore, users are not required to provide numerous parameters or background genomic sequence models that are typically unavailable. MOCCS is implemented in Perl and R and is freely available via https://github.com/yuifu/moccs. By complementing existing motif-discovery software, MOCCS will contribute to the basic understanding of how the genome controls diverse cellular processes via DNA-protein interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Toward Detection of Exoplanetary Rings via Transit Photometry: Methodology and a Possible Candidate

    Energy Technology Data Exchange (ETDEWEB)

    Aizawa, Masataka; Masuda, Kento; Suto, Yasushi [Department of Physics, The University of Tokyo, Tokyo, 113-0033 (Japan); Uehara, Sho [Department of Physics, Tokyo Metropolitan University, Tokyo 192-4397 (Japan); Kawahara, Hajime, E-mail: aizawa@utap.phys.s.u-tokyo.ac.jp [Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033 (Japan)

    2017-04-01

    The detection of a planetary ring of exoplanets remains one of the most attractive, but challenging, goals in the field of exoplanetary science. We present a methodology that implements a systematic search for exoplanetary rings via transit photometry of long-period planets. This methodology relies on a precise integration scheme that we develop to compute a transit light curve of a ringed planet. We apply the methodology to 89 long-period planet candidates from the Kepler data so as to estimate, and/or set upper limits on, the parameters of possible rings. While the majority of our samples do not have sufficient signal-to-noise ratios (S/Ns) to place meaningful constraints on ring parameters, we find that six systems with higher S/Ns are inconsistent with the presence of a ring larger than 1.5 times the planetary radius, assuming a grazing orbit and a tilted ring. Furthermore, we identify five preliminary candidate systems whose light curves exhibit ring-like features. After removing four false positives due to the contamination from nearby stars, we identify KIC 10403228 as a reasonable candidate for a ringed planet. A systematic parameter fit of its light curve with a ringed planet model indicates two possible solutions corresponding to a Saturn-like planet with a tilted ring. There also remain two other possible scenarios accounting for the data; a circumstellar disk and a hierarchical triple. Due to large uncertain factors, we cannot choose one specific model among the three.

  17. A Ring-‘Rain’ influence for Saturn’s Cloud Albedo and Temperatures? Evidence Pro or Con from Voyager, HST, and Cassini

    Science.gov (United States)

    West, Robert A.; Li, Liming

    2015-11-01

    J. E. P. Connerney [Geophys. Res. Lett, 13, 773-776, 1986] pointed out that ‘latitudinal variations in images of Saturn’s disk, upper atmospheric temperatures, and ionospheric electron densities are found in magnetic conjugacy with features in Saturn’s ring plane’, and proposed ‘that these latitudinal variations are the result of a variable influx of water, transported along magnetic field lines from sources in Saturn’s ring plane’. Observations of H3+ support a ring-ionosphere connection [O'Donoghue et al., Nature 496, 7444, 2013]. What about cloud albedo and temperature? Connerney attributed a hemispheric asymmetry in haze and temperature to an asymmetry in water flux and predicted that ‘the presently-observed north-south asymmetry (upper tropospheric temperatures, aerosols) will persist throughout the Saturn year’. We can now test these ideas with data from the Cassini mission, from the Hubble Space Telescope, and from ground-based observations. Analyses of ground-based images and especially Hubble data established that the hemispheric asymmetry of the aerosol population does change, and seasonal effects are dominant, although non-seasonal variations are also observed [Karkoschka and Tomasko, Icarus 179, 195-221, 2005]. Upper tropospheric temperatures also vary as expected in response to seasonal forcing [Fletcher et al., Icarus 208, 337-352, 2009]. Connerney also identified dark bands in Voyager Green-filter images on magnetic conjugacy with the E ring and edges of the A and B rings. In Cassini Green-filter images there is some correspondence between dark bands and ring features in magnetic conjugacy, but collectively the correlation is not strong. Cassini 727-nm methane band images do not suggest depletion of aerosols in the upper troposphere at ring edge magnetic conjugacy latitudes as proposed by Connerney. We conclude that ring rain does not have a significant influence on upper tropospheric aerosols and temperatures on Saturn. Part of

  18. Discovery and validation of information theory-based transcription factor and cofactor binding site motifs.

    Science.gov (United States)

    Lu, Ruipeng; Mucaki, Eliseos J; Rogan, Peter K

    2017-03-17

    Data from ChIP-seq experiments can derive the genome-wide binding specificities of transcription factors (TFs) and other regulatory proteins. We analyzed 765 ENCODE ChIP-seq peak datasets of 207 human TFs with a novel motif discovery pipeline based on recursive, thresholded entropy minimization. This approach, while obviating the need to compensate for skewed nucleotide composition, distinguishes true binding motifs from noise, quantifies the strengths of individual binding sites based on computed affinity and detects adjacent cofactor binding sites that coordinate with the targets of primary, immunoprecipitated TFs. We obtained contiguous and bipartite information theory-based position weight matrices (iPWMs) for 93 sequence-specific TFs, discovered 23 cofactor motifs for 127 TFs and revealed six high-confidence novel motifs. The reliability and accuracy of these iPWMs were determined via four independent validation methods, including the detection of experimentally proven binding sites, explanation of effects of characterized SNPs, comparison with previously published motifs and statistical analyses. We also predict previously unreported TF coregulatory interactions (e.g. TF complexes). These iPWMs constitute a powerful tool for predicting the effects of sequence variants in known binding sites, performing mutation analysis on regulatory SNPs and predicting previously unrecognized binding sites and target genes. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop.

    Science.gov (United States)

    Dembska, Anna; Juskowiak, Bernard

    2015-01-01

    In this work, we present a spectral characterization of pH-sensitive system, which combines the i-motif properties with the spatially sensitive fluorescence signal of pyrene molecules attached to hairpin ends. The excimer production (fluorescence max. ∼480 nm) by pyrene labels at the ends of the molecular beacon is driven by pH-dependent i-motif formation in the loop. To illustrate the performance and reversible work of our systems, we performed the experiments with repeatedly pH cycling between pH values of 7.5±0.3 and 6.5±0.3. The sensor gives analytical response in excimer-monomer switching mode in narrow pH range (1.5 pH units) and exhibits high pH resolution (0.1 pH unit). Copyright © 2015 Elsevier B.V. All rights reserved.

  20. A cyclic nucleotide-gated channel mutation associated with canine daylight blindness provides insight into a role for the S2 segment tri-Asp motif in channel biogenesis.

    Directory of Open Access Journals (Sweden)

    Naoto Tanaka

    Full Text Available Cone cyclic nucleotide-gated channels are tetramers formed by CNGA3 and CNGB3 subunits; CNGA3 subunits function as homotetrameric channels but CNGB3 exhibits channel function only when co-expressed with CNGA3. An aspartatic acid (Asp to asparagine (Asn missense mutation at position 262 in the canine CNGB3 (D262N subunit results in loss of cone function (daylight blindness, suggesting an important role for this aspartic acid residue in channel biogenesis and/or function. Asp 262 is located in a conserved region of the second transmembrane segment containing three Asp residues designated the Tri-Asp motif. This motif is conserved in all CNG channels. Here we examine mutations in canine CNGA3 homomeric channels using a combination of experimental and computational approaches. Mutations of these conserved Asp residues result in the absence of nucleotide-activated currents in heterologous expression. A fluorescent tag on CNGA3 shows mislocalization of mutant channels. Co-expressing CNGB3 Tri-Asp mutants with wild type CNGA3 results in some functional channels, however, their electrophysiological characterization matches the properties of homomeric CNGA3 channels. This failure to record heteromeric currents suggests that Asp/Asn mutations affect heteromeric subunit assembly. A homology model of S1-S6 of the CNGA3 channel was generated and relaxed in a membrane using molecular dynamics simulations. The model predicts that the Tri-Asp motif is involved in non-specific salt bridge pairings with positive residues of S3/S4. We propose that the D262N mutation in dogs with CNGB3-day blindness results in the loss of these inter-helical interactions altering the electrostatic equilibrium within in the S1-S4 bundle. Because residues analogous to Tri-Asp in the voltage-gated Shaker potassium channel family were implicated in monomer folding, we hypothesize that destabilizing these electrostatic interactions impairs the monomer folding state in D262N mutant CNG

  1. The ITER pre-compression rings – A first in cryogenic composite technology

    International Nuclear Information System (INIS)

    Rajainmaki, Hannu; Fanthome, John; Losasso, Marcello; Foussat, Arnaud; Rodriguez, Jesus; Evans, David; Diaz, Victor

    2014-01-01

    The ITER Pre-Compression Rings represent one of the heaviest composite structures ever manufactured as a single piece and the largest - the outer diameter will be above 5.5 meters - intended for use in a cryogenic environment. With a cross section of 337 mm × 288 mm, each item will weigh more than 3,000 kg. A development program, based on filament wound and dry wound S2 glass unidirectional fibers, the latter processed by VARTM, was completed on one fifth scale rings, and these materials and techniques were shown to be satisfactory. The paper describes how a technology applied to build up primary structures of European launchers is being accommodated to produce the ITER Pre-Compression Rings, fulfilling its extremely challenging requirements. In addition, we will describe how the structural analysis is correlated with the test results of scaled down rings, as well as how the pre-compression rings’ manufacturing process will be qualified

  2. Native characterization of nucleic acid motif thermodynamics via non-covalent catalysis

    Science.gov (United States)

    Wang, Chunyan; Bae, Jin H.; Zhang, David Yu

    2016-01-01

    DNA hybridization thermodynamics is critical for accurate design of oligonucleotides for biotechnology and nanotechnology applications, but parameters currently in use are inaccurately extrapolated based on limited quantitative understanding of thermal behaviours. Here, we present a method to measure the ΔG° of DNA motifs at temperatures and buffer conditions of interest, with significantly better accuracy (6- to 14-fold lower s.e.) than prior methods. The equilibrium constant of a reaction with thermodynamics closely approximating that of a desired motif is numerically calculated from directly observed reactant and product equilibrium concentrations; a DNA catalyst is designed to accelerate equilibration. We measured the ΔG° of terminal fluorophores, single-nucleotide dangles and multinucleotide dangles, in temperatures ranging from 10 to 45 °C. PMID:26782977

  3. Observation of the strongest 5s2 5p6 5d-(5s2 5p5 5d6s+5s25p6 7p) transitions in Au XI to Bi XV ions

    International Nuclear Information System (INIS)

    Churilov, S.S.; Joshi, Y.N.

    2001-01-01

    The spectra of gold till bismuth were studied in the 90-135 A region. Nine most intense lines belonging to the 5s 2 5p 6 5d-5s 2 5p 5 5d6s array were identified in Au XI to Bi XV ions. The 5s 2 5p 6 7p 2 P 3/2,1/2 levels in Au XI and the 5s 2 5p 6 7p 2 P 3/2 level in Hg XII were also identified. The observed wavelengths and intensities agree quite well with the Hartree-Fock calculations. (orig.)

  4. Electronic de-multipliers II (ring-shape systems); Demultiplieurs electroniques II (systeme en anneau)

    Energy Technology Data Exchange (ETDEWEB)

    Raievski, V

    1948-09-01

    This report describes a new type of ring-shape fast electronic counter (de-multiplier) with a resolution capacity equivalent to the one made by Regener (Rev. of Scientific Instruments USA 1946, 17, 180-89) but requiring two-times less electronic valves. This report follows the general description of electronic de-multipliers made by J. Ailloud (CEA--001). The ring comprises 5 flip-flop circuits with two valves each. The different elements of the ring are calculated with enough details to allow the transfer of this calculation to different valve types. (J.S.)

  5. Leisure/Crime, Immaterial Labor, and the Performance of the Teenage Girl in Harmony Korine’s Spring Breakers and Sofia Coppola’s The Bling Ring

    NARCIS (Netherlands)

    Wilkinson, M.

    2017-01-01

    Harmony Korine’s Spring Breakers (2012) and Sofia Coppola’s The Bling Ring (2013) introduced audiences to girls exploring criminal behavior both for and as leisure. The films introduce an idea of leisure/crime: criminal acts that appear to develop as natural, fruitful extensions of leisure

  6. A Case Report of Early Gastric Signet Ring Cell Carcinoma

    African Journals Online (AJOL)

    2018-02-07

    gmail.com. How to cite this article: Akabah PS, Mocan S, Molnar C, Dobru D. Importance of optical diagnosis in early gastric cancer: A case report of early gastric signet ring cell carcinoma. Niger J Clin Pract 2017;20:1342-5.

  7. Design and project status of the National Synchrotron Light Source; storage rings (2.5 GeV, 0.7 GeV) for the generation of bright synchrotron radiation sources

    International Nuclear Information System (INIS)

    van Steenbergen, A.

    1980-01-01

    Two high intensity storage rings are being constructed at Brookhaven National Laboratory for the generation of intense fluxes of synchrotron radiation in the vuv wavelength region (700 MeV ring, lambda/sub c/ = 31.5 A) and in the x-ray wavelength region (2.5 GeV ring, lambda/sub c/ = 2.5 A). A description is given of the facility, the main features of the storage rings are presented and the basic parameters are enumerated. High field superconducting wigglers, to lower the short wavelength cutoff in the x-ray ring, and undulators, for flux enhancement or a free electron laser experiment will be incorporated and parameters are given here. Special design aspects to optimize the electron storage rings as dedicated synchrotron radiation sources will be emphasized and the status of the project will be given

  8. Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. I. Statics

    Science.gov (United States)

    Halverson, Jonathan D.; Lee, Won Bo; Grest, Gary S.; Grosberg, Alexander Y.; Kremer, Kurt

    2011-05-01

    Molecular dynamics simulations were conducted to investigate the structural properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N = 1600 monomers per chain which corresponds to roughly 57 entanglement lengths for comparable linear polymers. For the rings, the radius of gyration squared, , was found to scale as N4/5 for an intermediate regime and N2/3 for the larger rings indicating an overall conformation of a crumpled globule. However, almost all beads of the rings are "surface beads" interacting with beads of other rings, a result also in agreement with a primitive path analysis performed in the next paper [J. D. Halverson, W. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, J. Chem. Phys. 134, 204905 (2011)], 10.1063/1.3587138. Details of the internal conformational properties of the ring and linear polymers as well as their packing are analyzed and compared to current theoretical models.

  9. Low-dimensional morphospace of topological motifs in human fMRI brain networks

    Directory of Open Access Journals (Sweden)

    Sarah E. Morgan

    2018-06-01

    Full Text Available We present a low-dimensional morphospace of fMRI brain networks, where axes are defined in a data-driven manner based on the network motifs. The morphospace allows us to identify the key variations in healthy fMRI networks in terms of their underlying motifs, and we observe that two principal components (PCs can account for 97% of the motif variability. The first PC of the motif distribution is correlated with efficiency and inversely correlated with transitivity. Hence this axis approximately conforms to the well-known economical small-world trade-off between integration and segregation in brain networks. Finally, we show that the economical clustering generative model proposed by Vértes et al. (2012 can approximately reproduce the motif morphospace of the real fMRI brain networks, in contrast to other generative models. Overall, the motif morphospace provides a powerful way to visualize the relationships between network properties and to investigate generative or constraining factors in the formation of complex human brain functional networks. Motifs have been described as the building blocks of complex networks. Meanwhile, a morphospace allows networks to be placed in a common space and can reveal the relationships between different network properties and elucidate the driving forces behind network topology. We combine the concepts of motifs and morphospaces to create the first motif morphospace of fMRI brain networks. Crucially, the morphospace axes are defined by the motifs, in a data-driven manner. We observe strong correlations between the networks’ positions in morphospace and their global topological properties, suggesting that motif morphospaces are a powerful way to capture the topology of networks in a low-dimensional space and to compare generative models of brain networks. Motif morphospaces could also be used to study other complex networks’ topologies.

  10. Synlig læring

    DEFF Research Database (Denmark)

    Brandsen, Mads

    2017-01-01

    Introduktionen af John Hatties synlig læring i den danske skoleverden møder stadig meget kritik. Mange lærere og pædagoger oplever synlig læring som en tornado, der vil opsuge og ødelægge deres særlige danske udgave af den kontinentale dannelsestænkning, didaktik og pædagogik. Spørgsmålet er om...

  11. Wideband Circularly Polarized Printed Ring Slot Antenna for 5 GHz – 6 GHz

    Science.gov (United States)

    Nasrun Osman, Mohamed; Rahim, Mohamad Helmi A.; Jusoh, Muzammil; Sabapathy, Thennarasan; Rahim, Mohamad Kamal A.; Norlyana Azemi, Saidatul

    2018-03-01

    This paper presents the design of circularly polarized printed slot antenna operating at 5 – 6 GHz. The proposed antenna consists of L-shaped feedline on the top of structure and circular ring slot positioned at the ground plane underneath the substrate as a radiator. A radial and narrow slot in the ground plane provides coupling between the L-shaped feedline and circular ring slot. The circular polarization is realized by implementing the slits perturbation located diagonally to perturb the current flow on the slot structure. The antenna prototype is fabricated on FR4 substrate. The simulated and measured results are compared and analyzed to demonstrate the performance of the antenna. Good measured of simulated results are obtained at the targeted operating frequency. The simulated -10dB reflection coefficient bandwidths and axial ratio are 750 MHz and 165 MHz, respectively. The investigation on the affect of the important parameters towards the reflection coefficient and axial are also presented. The proposed antenna is highly potential to be used for wireless local area network (WLAN) and wireless power transfer (WPT).

  12. Memetic algorithms for de novo motif-finding in biomedical sequences.

    Science.gov (United States)

    Bi, Chengpeng

    2012-09-01

    The objectives of this study are to design and implement a new memetic algorithm for de novo motif discovery, which is then applied to detect important signals hidden in various biomedical molecular sequences. In this paper, memetic algorithms are developed and tested in de novo motif-finding problems. Several strategies in the algorithm design are employed that are to not only efficiently explore the multiple sequence local alignment space, but also effectively uncover the molecular signals. As a result, there are a number of key features in the implementation of the memetic motif-finding algorithm (MaMotif), including a chromosome replacement operator, a chromosome alteration-aware local search operator, a truncated local search strategy, and a stochastic operation of local search imposed on individual learning. To test the new algorithm, we compare MaMotif with a few of other similar algorithms using simulated and experimental data including genomic DNA, primary microRNA sequences (let-7 family), and transmembrane protein sequences. The new memetic motif-finding algorithm is successfully implemented in C++, and exhaustively tested with various simulated and real biological sequences. In the simulation, it shows that MaMotif is the most time-efficient algorithm compared with others, that is, it runs 2 times faster than the expectation maximization (EM) method and 16 times faster than the genetic algorithm-based EM hybrid. In both simulated and experimental testing, results show that the new algorithm is compared favorably or superior to other algorithms. Notably, MaMotif is able to successfully discover the transcription factors' binding sites in the chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) data, correctly uncover the RNA splicing signals in gene expression, and precisely find the highly conserved helix motif in the transmembrane protein sequences, as well as rightly detect the palindromic segments in the primary micro

  13. Two-dimensional inorganic–organic hybrid semiconductors composed of double-layered ZnS and monoamines with aromatic and heterocyclic aliphatic rings: Syntheses, structures, and properties

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Sujing; Li, Jing, E-mail: jingli@rutgers.edu

    2015-04-15

    As an addition to the II–VI based inorganic–organic hybrid semiconductor family, five new two-dimensional (2D) double-layered structures have been synthesized employing monoamines with different aromatic or heterocyclic aliphatic rings. Zn{sub 2}S{sub 2}(bza) (1), Zn{sub 2}S{sub 2}(mbza) (2), Zn{sub 2}S{sub 2}(fbza) (3), Zn{sub 2}S{sub 2}(pca) (4), and Zn{sub 2}S{sub 2}(thfa) (5) (bza=benzylamine, mbza=4-methoxybenzylamine, fbza=4-flurobenzylamine, pca=3-picolylamine, and thfa=tetrahydrofurfurylamine) are prepared by solvothermal reactions and characterized by different analytical methods, including powder X-ray diffraction, optical diffuse reflection, thermogravimetric analysis and photoluminescence spectroscopy. The powder X-ray diffraction patterns show that all five compounds adopt 2D double-layered structures. Optical diffuse reflectance spectra of these compounds suggest that they have notably lower band gaps than those of the similar compounds composed of aliphatic alkyl amines. Their photoluminescence properties and thermal stability are also analyzed. - Graphical abstract: Five new members of two-dimensional double-layered 2D-Zn{sub 2}S{sub 2}(L) (L=Ligand) structures employing monoamines with different aromatic or heterocyclic aliphatic rings have been designed, synthesized, and characterized. - Highlights: • A new sub-family of II-VI based hybrid semiconductors are designed, synthesized, and structurally characterized using amines with aromatic or aliphatic cyclic rings. • These compounds have notably lower band gaps than those made of aliphatic alkyl amines, greatly broadening the range of band gaps of this material family. • They emit strongly with systematically tunable emission intensity and energy.

  14. (5S,6R-6-Bromo-6-methyl-5-phenyl-3,4,5,6-tetrahydro-2H-cyclopenta[b]pyran-7-one

    Directory of Open Access Journals (Sweden)

    Winai Ieawsuwan

    2011-10-01

    Full Text Available The title compound, C15H15BrO2, was synthesized by a Brønsted acid-catalysed domino electrocyclization-halogenation reaction. The five-membered ring is essentially planar (r.m.s. deviation 0.006 Å and forms a dihedral angle of 72.7 (3° with the attached phenyl ring. The six-membered heterocycle adopts a half-chair conformation. The crystal packing is stabilized by a C—H...O contact.

  15. The Coagulant Type Influence on Removal Efficiency of 5- and 6-Ring Pahs During Water Coagulation Process

    Directory of Open Access Journals (Sweden)

    Nowacka Anna

    2014-12-01

    Full Text Available The article presents results on investigation of the removal efficiency of selected 5- and 6-ring polycyclic aromatic hydrocarbons (benzo[a]pyrene, benzo[b]fluoranthene, benzo[k]fluoranthene, benzo[j]fluoranthene, benzo[g,h,i]perylene, indeno[1,2,3-cd]pyrene, dibenzo[a,h]anthracene from water during coagulation and sedimentation process. Two pre-hydrolyzed aluminum coagulants: PAX XL 19H and FLOKOR 105V were chosen for research. Process was carried out at optimum process parameters: rapid-mixing - 3 min at the rotational speed of 200 rpm, slow mixing - 10 min at 30 rpm, sedimentation - 60 min. The removal effectiveness was dependant on coagulant type and its composition. Better results in the removal of 5-and 6-ring PAHs were obtained after application of FLOKOR 105V (lower aluminum content than after using PAX XL 19H.

  16. Discovering Motifs in Biological Sequences Using the Micron Automata Processor.

    Science.gov (United States)

    Roy, Indranil; Aluru, Srinivas

    2016-01-01

    Finding approximately conserved sequences, called motifs, across multiple DNA or protein sequences is an important problem in computational biology. In this paper, we consider the (l, d) motif search problem of identifying one or more motifs of length l present in at least q of the n given sequences, with each occurrence differing from the motif in at most d substitutions. The problem is known to be NP-complete, and the largest solved instance reported to date is (26,11). We propose a novel algorithm for the (l,d) motif search problem using streaming execution over a large set of non-deterministic finite automata (NFA). This solution is designed to take advantage of the micron automata processor, a new technology close to deployment that can simultaneously execute multiple NFA in parallel. We demonstrate the capability for solving much larger instances of the (l, d) motif search problem using the resources available within a single automata processor board, by estimating run-times for problem instances (39,18) and (40,17). The paper serves as a useful guide to solving problems using this new accelerator technology.

  17. PISMA: A Visual Representation of Motif Distribution in DNA Sequences

    Directory of Open Access Journals (Sweden)

    Rogelio Alcántara-Silva

    2017-03-01

    Full Text Available Background: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code–like, as a gene-map–like, and as a transcript scheme. Results: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion. Availability and Implementation: PISMA is developed in Java; it is executable in any type of hardware and in diverse operating systems. PISMA is freely available to noncommercial users. The English version and the User Manual are provided in Supplementary Files 1 and 2, and a Spanish version is available at www.biomedicas.unam.mx/wp-content/software/pisma.zip and www.biomedicas.unam.mx/wp-content/pdf/manual/pisma.pdf .

  18. Radiology of posterior lumbar apophyseal ring fractures: Report of 13 cases

    Energy Technology Data Exchange (ETDEWEB)

    Dietemann, J.L.; Beaujeux, R.; Wackenheim, A.; Runge, M.; Bonneville, J.F.; Badoz, A.; Dosch, J.C.

    1988-08-01

    The authors report radiological findings in 13 cases of avulsion of the posterior lumbar apophyseal ring. The lesion affected young adults in 10 cases and adolescents in 3 cases. The lesion involved the inferior endplate of L4 in 11, and of L5 in 2 patients. 6 patients presented with unilateral sciatica, 3 with bilateral sciatica, and 4 with low back pain. Acute spinal trauma was evident only in 2 adolescents. Radiological recognition of the lesion was possible on plain films in 9 cases. CT demonstrates association of avulsion of the posterior vertebral apophyseal ring and herniated disc in all cases. Avulsion of the posterior apophyseal ring has to be differentiated from posterior longitudinal ligament, annulus, or herniated disc calcifications, as well as from posterior degenerative ridge osteophytes. Controversy about physiopathology of the lesion remains: Weakness of the apophyseal ring during childhood and in patients with Scheuermann's disease may explain avulsion of the apophyseal ring in association with median disc herniation.

  19. Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network

    Directory of Open Access Journals (Sweden)

    Barabási Albert-László

    2004-01-01

    Full Text Available Abstract Background Transcriptional regulation of cellular functions is carried out through a complex network of interactions among transcription factors and the promoter regions of genes and operons regulated by them.To better understand the system-level function of such networks simplification of their architecture was previously achieved by identifying the motifs present in the network, which are small, overrepresented, topologically distinct regulatory interaction patterns (subgraphs. However, the interaction of such motifs with each other, and their form of integration into the full network has not been previously examined. Results By studying the transcriptional regulatory network of the bacterium, Escherichia coli, we demonstrate that the two previously identified motif types in the network (i.e., feed-forward loops and bi-fan motifs do not exist in isolation, but rather aggregate into homologous motif clusters that largely overlap with known biological functions. Moreover, these clusters further coalesce into a supercluster, thus establishing distinct topological hierarchies that show global statistical properties similar to the whole network. Targeted removal of motif links disintegrates the network into small, isolated clusters, while random disruptions of equal number of links do not cause such an effect. Conclusion Individual motifs aggregate into homologous motif clusters and a supercluster forming the backbone of the E. coli transcriptional regulatory network and play a central role in defining its global topological organization.

  20. Novel and deviant Walker A ATP-binding motifs in bacteriophage large terminase-DNA packaging proteins

    International Nuclear Information System (INIS)

    Mitchell, Michael S.; Rao, Venigalla B.

    2004-01-01

    Bacteriophage terminases constitute a very interesting class of viral-coded multifunctional ATPase 'motors' that apparently drive directional translocation of DNA into an empty viral capsid. A common Walker A motif and other conserved signatures of a critical ATPase catalytic center are identified in the N-terminal half of numerous large terminase proteins. However, several terminases, including the well-characterized λ and SPP1 terminases, seem to lack the classic Walker A in the N-terminus. Using sequence alignment approaches, we discovered the presence of deviant Walker A motifs in these and many other phage terminases. One deviation, the presence of a lysine at the beginning of P-loop, may represent a 3D equivalent of the universally conserved lysine in the Walker A GKT/S signature. This and other novel putative Walker A motifs that first came to light through this study help define the ATPase centers of phage and viral terminases as well as elicit important insights into the molecular functioning of this fundamental motif in biological systems

  1. Cave acoustics in prehistory: Exploring the association of Palaeolithic visual motifs and acoustic response.

    Science.gov (United States)

    Fazenda, Bruno; Scarre, Chris; Till, Rupert; Pasalodos, Raquel Jiménez; Guerra, Manuel Rojo; Tejedor, Cristina; Peredo, Roberto Ontañón; Watson, Aaron; Wyatt, Simon; Benito, Carlos García; Drinkall, Helen; Foulds, Frederick

    2017-09-01

    During the 1980 s, acoustic studies of Upper Palaeolithic imagery in French caves-using the technology then available-suggested a relationship between acoustic response and the location of visual motifs. This paper presents an investigation, using modern acoustic measurement techniques, into such relationships within the caves of La Garma, Las Chimeneas, La Pasiega, El Castillo, and Tito Bustillo in Northern Spain. It addresses methodological issues concerning acoustic measurement at enclosed archaeological sites and outlines a general framework for extraction of acoustic features that may be used to support archaeological hypotheses. The analysis explores possible associations between the position of visual motifs (which may be up to 40 000 yrs old) and localized acoustic responses. Results suggest that motifs, in general, and lines and dots, in particular, are statistically more likely to be found in places where reverberation is moderate and where the low frequency acoustic response has evidence of resonant behavior. The work presented suggests that an association of the location of Palaeolithic motifs with acoustic features is a statistically weak but tenable hypothesis, and that an appreciation of sound could have influenced behavior among Palaeolithic societies of this region.

  2. Ring Theory

    CERN Document Server

    Jara, Pascual; Torrecillas, Blas

    1988-01-01

    The papers in this proceedings volume are selected research papers in different areas of ring theory, including graded rings, differential operator rings, K-theory of noetherian rings, torsion theory, regular rings, cohomology of algebras, local cohomology of noncommutative rings. The book will be important for mathematicians active in research in ring theory.

  3. Dynamic motifs in socio-economic networks

    Science.gov (United States)

    Zhang, Xin; Shao, Shuai; Stanley, H. Eugene; Havlin, Shlomo

    2014-12-01

    Socio-economic networks are of central importance in economic life. We develop a method of identifying and studying motifs in socio-economic networks by focusing on “dynamic motifs,” i.e., evolutionary connection patterns that, because of “node acquaintances” in the network, occur much more frequently than random patterns. We examine two evolving bi-partite networks: i) the world-wide commercial ship chartering market and ii) the ship build-to-order market. We find similar dynamic motifs in both bipartite networks, even though they describe different economic activities. We also find that “influence” and “persistence” are strong factors in the interaction behavior of organizations. When two companies are doing business with the same customer, it is highly probable that another customer who currently only has business relationship with one of these two companies, will become customer of the second in the future. This is the effect of influence. Persistence means that companies with close business ties to customers tend to maintain their relationships over a long period of time.

  4. Compressible Vortex Ring

    Science.gov (United States)

    Elavarasan, Ramasamy; Arakeri, Jayawant; Krothapalli, Anjaneyulu

    1999-11-01

    The interaction of a high-speed vortex ring with a shock wave is one of the fundamental issues as it is a source of sound in supersonic jets. The complex flow field induced by the vortex alters the propagation of the shock wave greatly. In order to understand the process, a compressible vortex ring is studied in detail using Particle Image Velocimetry (PIV) and shadowgraphic techniques. The high-speed vortex ring is generated from a shock tube and the shock wave, which precedes the vortex, is reflected back by a plate and made to interact with the vortex. The shadowgraph images indicate that the reflected shock front is influenced by the non-uniform flow induced by the vortex and is decelerated while passing through the vortex. It appears that after the interaction the shock is "split" into two. The PIV measurements provided clear picture about the evolution of the vortex at different time interval. The centerline velocity traces show the maximum velocity to be around 350 m/s. The velocity field, unlike in incompressible rings, contains contributions from both the shock and the vortex ring. The velocity distribution across the vortex core, core diameter and circulation are also calculated from the PIV data.

  5. Ring current proton decay by charge exchange

    Science.gov (United States)

    Smith, P. H.; Hoffman, R. A.; Fritz, T.

    1975-01-01

    Explorer 45 measurements during the recovery phase of a moderate magnetic storm have confirmed that the charge exchange decay mechanism can account for the decay of the storm-time proton ring current. Data from the moderate magnetic storm of 24 February 1972 was selected for study since a symmetrical ring current had developed and effects due to asymmetric ring current losses could be eliminated. It was found that after the initial rapid decay of the proton flux, the equatorially mirroring protons in the energy range 5 to 30 keV decayed throughout the L-value range of 3.5 to 5.0 at the charge exchange decay rate calculated by Liemohn. After several days of decay, the proton fluxes reached a lower limit where an apparent equilibrium was maintained, between weak particle source mechanisms and the loss mechanisms, until fresh protons were injected into the ring current region during substorms. While other proton loss mechanisms may also be operating, the results indicate that charge exchange can entirely account for the storm-time proton ring current decay, and that this mechanism must be considered in all studies involving the loss of proton ring current particles.

  6. Scanning Tunneling Microscopic Observation of Adatom-Mediated Motifs on Gold-Thiol Self-assembled Monolayers at High Coverage

    DEFF Research Database (Denmark)

    Wang, Yun; Chi, Qijin; Hush, Noel S.

    2009-01-01

    the structural motifs observed on surfaces at low coverage and on gold nanoparticles to the observed spectroscopic properties of high-coverage SAMs formed by methanethiol. However, the significant role attributed to intermolecular steric packing effects suggests a lack of generality for the adatom-mediated motif......Self-assembled monolayers (SAMs) formed by chemisorption of a branched-chain alkanethiol, 2-methyl-1-propanethiol, on Au(111) surfaces were studied by in situ scanning tunneling microscopy (STM) under electrochemical potential control and analyzed using extensive density functional theory (DFT...... two R−S−Au−S−R adatom-mediated motifs per surface cell, with steric-induced variations in the adsorbate alignment inducing the observed STM image contrasts. Observed pits covering 5.6 ± 0.5% of the SAM surface are consistent with this structure. These results provide the missing link from...

  7. Assessing local structure motifs using order parameters for motif recognition, interstitial identification, and diffusion path characterization

    Science.gov (United States)

    Zimmermann, Nils E. R.; Horton, Matthew K.; Jain, Anubhav; Haranczyk, Maciej

    2017-11-01

    Structure-property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells) of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal closed packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP) database (61,422 compounds) for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT) facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

  8. 2-Carboxy-6-(quinolin-1-ium-8-yloxybenzoate

    Directory of Open Access Journals (Sweden)

    Jin Xie

    2012-05-01

    Full Text Available In the zwitterionic title compound, C17H11NO5, the dihedral angle between the two aromatic rings is 76.90 (7°. The dihedral angles between the carboxyl groups and the benzene ring are 64.02 (9 and 21.67 (9°, the larger angle being associated with an intramolecular N—H...Ocarboxyl hydrogen bond, resulting from proton transfer from the carboxylic acid group to the quinoline N atom and giving an S(9 ring motif. In the crystal, molecules are connected by O—H...O hydrogen bonds into chains extending along the b-axis direction. An overall two-dimensional network structure is formed through π–π interactions between the quinoline rings [minimum ring-centroid separation = 3.6068 (6 Å].

  9. Two genes in Balbiani ring 2 with metabolically different 75S transcripts

    OpenAIRE

    Galler, R.; Saiga, H.; Widmer, R. M.; Lezzi, M.; Edström, J.-E.

    1985-01-01

    Balbiani ring 2 (BR2) in salivary glands of Chironomus pallidivittatus and C. tentans (two sibling species of the subgenus Camptochironomus) is a favoured model system for studies of gene organization and transcript formation. Here we show that BR2 is more complex than hitherto believed, containing two 75S RNA-producing genes, BR2a and BR2b, present in different 35–40 kb blocks of DNA. The transcripts hybridizing to two different repeat units originating in BR2 differ in size. Further support...

  10. SOR-ring failure

    International Nuclear Information System (INIS)

    Kitamura, Hideo

    1981-01-01

    It was in the autumn of 1976 that the SOR-ring (synchrotron radiation storage ring) has commenced the regular operation. Since then, the period when the operation was interrupted due to the failures of SOR-ring itself is in total about 8 weeks. Failures and accidents have occurred most in the vacuum system. Those failure experiences are described on the vacuum, electromagnet, radio-frequency acceleration and beam transport systems with their interrupted periods. The eleven failures in the vacuum system have been reported, such as bellows breakage in a heating-evacuating period, leakage from the bellows of straight-through valves (made in U.S.A. and Japan), and leakage from the joint flange of the vacuum system. The longest interruption was 5 weeks due to the failure of a domestically manufactured straight-through valve. The failures of the electromagnet system involve the breakage in a cooling water system, short circuit of a winding in the Q magnet power transformer, blow of a fuse protecting the deflection magnet power source by the current less than the rating, and others. The failures of the RF acceleration system include the breakage of an output electronic tube the breakage of a cavity ceramic, RF voltage fluctuation due to the contact deterioration at a cavity electrode, and the failure of grid bias power source. It is necessary to select the highly reliable components for the vacuum system because the vacuum system failures require longer time for recovery, and very likely to induce secondary and tertiary failures. (Wakatsuki, Y.)

  11. Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

    Science.gov (United States)

    Kinjo, Akira R.; Nakamura, Haruki

    2012-01-01

    Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures. PMID:22347478

  12. 4-[(3-Phenyl-4,5-dihydroisoxazol-5-ylmethyl]-2H-benzo[b][1,4]thiazin-3(4H-one

    Directory of Open Access Journals (Sweden)

    Nada Kheira Sebbar

    2016-06-01

    Full Text Available In the title compound, C18H16N2O2S, the 5-dihydroisoxazol-5-yl ring and its phenyl substituent are nearly coplanar, with the largest deviation from the mean plane being 0.0184 (16 Å. The thiomorpholin-3-one ring adopts a screw-boat conformation and the attached benzene ring makes a dihedral angle of 42.26 (7° with the mean plane through the 3-phenyl-4,5-dihydroisoxazol-5-yl ring system. In the crystal, molecules are linked by pairs of C—H...N hydrogen bonds, forming inversion dimers. These dimers are linked via C—H...O hydrogen bonds, generating a three-dimensional network.

  13. Accidental ingestion of BiTine ring and a note on inefficient ring separation forceps

    Directory of Open Access Journals (Sweden)

    Baghele ON

    2011-05-01

    Full Text Available Om Nemichand Baghele1, Mangala Om Baghele21Department of Periodontology, SMBT Dental College and Hospital, Sangamner, Ahmednagar, Maharashtra, India; 2Private General Dental Practice, Mumbai, IndiaBackground: Accidental ingestion of medium-to-large instruments is relatively uncommon during dental treatment but can be potentially dangerous. A case of BiTine ring ingestion is presented with a note on inefficient ring separation forceps.Case description: A 28-year-old male patient accidentally ingested the BiTine ring (2 cm diameter, 0.5 cm outward projections while it was being applied to a distoproximal cavity in tooth # 19. The ring placement forceps were excessively flexible; bending of the beaks towards the ring combined with a poor no-slippage mechanism led to sudden disengagement of the ring and accelerated movement towards the pharynx. We followed the patient with bulk forming agents and radiographs. Fortunately the ring passed out without any complications.Clinical implications: Checking equipment and methods is as important as taking precautions against any preventable medical emergency. It is the responsibility of the clinician to check, verify and then use any instrument/equipment.Keywords: foreign bodies/radiography, foreign bodies/complications, equipment failure, dental instrument, accidental ingestion

  14. 8-{(E-[(4-Chlorophenylimino]methyl}-1,1,7,7-tetramethyl-1,2,3,5,6,7-hexahydropyrido[3,2,1-ij]quinolin-9-ol

    Directory of Open Access Journals (Sweden)

    Esen Nur Kantar

    2013-06-01

    Full Text Available The title Schiff base, C23H27ClN2O adopts the phenol–imine tautomeric form, with an intramolecular O—H...N hydrogen bond, which generates an S(6 ring motif. Three C atoms of the heterocyclic moiety of the hexahydropyridoquinoline unit, as well as the two methyl groups bonded to one of these C atoms, are disordered over two set of sites, with anoccupancy ratio of 0.740 (4:0.260 (4.

  15. (1S*,3R*,5S*,7S*-4,4,8,8-Tetrachloro-1-isopropyl-5-methyltricyclo[5.1.0.03,5]octane

    Directory of Open Access Journals (Sweden)

    Koblandy M. Turdybekov

    2014-04-01

    Full Text Available The title compound, C12H16Cl4, is a derivative of the natural product 1-isopropyl-4-methylcyclohexa-1,4-diene, and represents a diastereomer with two trans-fused cyclopropane rings. Both enantiomers are present in the non-centrosymmetric polar space group Pna21. The central cyclohexane ring is planar within 0.02 (1 Å. The C atoms of dichloromethylene groups deviate from this plane by 1.19 (1 and −1.26 (1 Å, whereas the isopropyl and methyl groups are oriented more equatorially, deviating by 0.71 (1 and −0.87 (1 Å, respectively.

  16. Probing structural changes of self assembled i-motif DNA

    KAUST Repository

    Lee, Iljoon; Patil, Sachin; Fhayli, Karim; Alsaiari, Shahad K.; Khashab, Niveen M.

    2015-01-01

    We report an i-motif structural probing system based on Thioflavin T (ThT) as a fluorescent sensor. This probe can discriminate the structural changes of RET and Rb i-motif sequences according to pH change. This journal is

  17. Report of the eRHIC Ring-Ring Working Group

    Energy Technology Data Exchange (ETDEWEB)

    Aschenauer, E. C. [Brookhaven National Lab. (BNL), Upton, NY (United States); Berg, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Blaskiewicz, M. [Brookhaven National Lab. (BNL), Upton, NY (United States); Brennan, M. [Brookhaven National Lab. (BNL), Upton, NY (United States); Fedotov, A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Fischer, W. [Brookhaven National Lab. (BNL), Upton, NY (United States); Litvinenko, V. [Brookhaven National Lab. (BNL), Upton, NY (United States); Montag, C. [Brookhaven National Lab. (BNL), Upton, NY (United States); Palmer, R. [Brookhaven National Lab. (BNL), Upton, NY (United States); Parker, B. [Brookhaven National Lab. (BNL), Upton, NY (United States); Peggs, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Ptitsyn, V. [Brookhaven National Lab. (BNL), Upton, NY (United States); Ranjbar, V. [Brookhaven National Lab. (BNL), Upton, NY (United States); Tepikian, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Trbojevic, D. [Brookhaven National Lab. (BNL), Upton, NY (United States); Willeke, F. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2015-10-13

    This report evaluates the ring-ring option for eRHIC as a lower risk alternative to the linac-ring option. The reduced risk goes along with a reduced initial luminosity performance. However, a luminosity upgrade path is kept open. This upgrade path consists of two branches, with the ultimate upgrade being either a ring-ring or a linac-ring scheme. The linac-ring upgrade could be almost identical to the proposed linac-ring scheme, which is based on an ERL in the RHIC tunnel. This linac-ring version has been studied in great detail over the past ten years, and its significant risks are known. On the other hand, no detailed work on an ultimate performance ring-ring scenario has been performed yet, other than the development of a consistent parameter set. Pursuing the ring-ring upgrade path introduces high risks and requires significant design work that is beyond the scope of this report.

  18. Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated

    Directory of Open Access Journals (Sweden)

    Down Thomas A

    2010-09-01

    Full Text Available Abstract Background DNA methylation can regulate gene expression by modulating the interaction between DNA and proteins or protein complexes. Conserved consensus motifs exist across the human genome ("predicted transcription factor binding sites": "predicted TFBS" but the large majority of these are proven by chromatin immunoprecipitation and high throughput sequencing (ChIP-seq not to be biological transcription factor binding sites ("empirical TFBS". We hypothesize that DNA methylation at conserved consensus motifs prevents promiscuous or disorderly transcription factor binding. Results Using genome-wide methylation maps of the human heart and sperm, we found that all conserved consensus motifs as well as the subset of those that reside outside CpG islands have an aggregate profile of hyper-methylation. In contrast, empirical TFBS with conserved consensus motifs have a profile of hypo-methylation. 40% of empirical TFBS with conserved consensus motifs resided in CpG islands whereas only 7% of all conserved consensus motifs were in CpG islands. Finally we further identified a minority subset of TF whose profiles are either hypo-methylated or neutral at their respective conserved consensus motifs implicating that these TF may be responsible for establishing or maintaining an un-methylated DNA state, or whose binding is not regulated by DNA methylation. Conclusions Our analysis supports the hypothesis that at least for a subset of TF, empirical binding to conserved consensus motifs genome-wide may be controlled by DNA methylation.

  19. Calcium Sensing Receptor Mutations Implicated in Pancreatitis and Idiopathic Epilepsy Syndrome Disrupt an Arginine-rich Retention Motif

    Science.gov (United States)

    Stepanchick, Ann; McKenna, Jennifer; McGovern, Olivia; Huang, Ying; Breitwieser, Gerda E.

    2010-01-01

    Calcium sensing receptor (CaSR) mutations implicated in familial hypocalciuric hypercalcemia, pancreatitis and idiopathic epilepsy syndrome map to an extended arginine-rich region in the proximal carboxyl terminus. Arginine-rich motifs mediate endoplasmic reticulum retention and/or retrieval of multisubunit proteins so we asked whether these mutations, R886P, R896H or R898Q, altered CaSR targeting to the plasma membrane. Targeting was enhanced by all three mutations, and Ca2+-stimulated ERK1/2 phosphorylation was increased for R896H and R898Q. To define the role of the extended arginine-rich region in CaSR trafficking, we independently determined the contributions of R890/R891 and/or R896/K897/R898 motifs by mutation to alanine. Disruption of the motif(s) significantly increased surface expression and function relative to wt CaSR. The arginine-rich region is flanked by phosphorylation sites at S892 (protein kinase C) and S899 (protein kinase A). The phosphorylation state of S899 regulated recognition of the arginine-rich region; S899D showed increased surface localization. CaSR assembles in the endoplasmic reticulum as a covalent disulfide-linked dimer and we determined whether retention requires the presence of arginine-rich regions in both subunits. A single arginine-rich region within the dimer was sufficient to confer intracellular retention comparable to wt CaSR. We have identified an extended arginine-rich region in the proximal carboxyl terminus of CaSR (residues R890 - R898) which fosters intracellular retention of CaSR and is regulated by phosphorylation. Mutation(s) identified in chronic pancreatitis and idiopathic epilepsy syndrome therefore increase plasma membrane targeting of CaSR, likely contributing to the altered Ca2+ signaling characteristic of these diseases. PMID:20798521

  20. Status of the SLC damping rings

    International Nuclear Information System (INIS)

    Hutton, A.M.; Davies-White, W.A.; Delahaye, J.P.

    1985-06-01

    Electron beams of full design energy 1.21 GeV and nearly full design intensity 4 x 10 10 particles/pulse (design 5 x 10 10 ) have been extracted from the Stanford Linac and successfully stored in the electron damping ring. Beams of less intensity have been extracted from the ring and reinjected into the Linac. The present intensity limits are not thought to be fundamental. The operating experience with the electron ring and the status of the construction of the positron ring will be discussed. 11 refs., 1 fig., 2 tabs

  1. Coordination of {Mo142} Ring to La3+ Provides Elliptical {Mo134La10} Ring with a Variety of Coordination Modes

    Directory of Open Access Journals (Sweden)

    Eri Ishikawa

    2009-12-01

    Full Text Available A28-electron reduced C2h-Mo-blue 34Ǻ outer ring diameter circular ring, [Mo142O429H10(H2O49(CH3CO25(C2H5CO2]30- (≡{Mo142(CH3CO25(C2H5CO2} comprising eight carboxylate-coordinated (with disorder {Mo2} linkers and six defect pockets in two inner rings (four and three for each, respectively, reacts with La3+ in aqueous solutions at pH 3.5 to yield a 28-electron reduced elliptical Ci-Mo-blue ring of formula [Mo134O416H20(H2O46{La(H2O5}4{La(H2O7}4{LaCl2(H2O5}2]10- (≡{Mo134La10}, isolated as the Na10[Mo134O416H20(H2O46{La(H2O5}4{La(H2O7}4{LaCl2(H2O5}2]·144 H2O Na+ salt. The elliptical structure of {Mo134La10} showing 36 and 31 Å long and short axes for the outer ring diameters is attributed to four (A-D modes of LaO9/LaO7Cl2 tricapped-trigonal-prismatic coordination (TTP geometries. Two different LaO2(H2O7 and one LaO2(H2O2Cl2 TTP geometries (as A-C modes for each of two inner rings result from the coordination of all three defect pockets of the inner ring for {Mo142(CH3CO25(C2H5CO2}, and two LaO4(H2O5 TTP geometries (as D mode result from the displacement of two (acetate/propionate-coordinated binuclear {Mo2} linkers with La3+ in each inner ring. The isothermal titration calorimetry (ITC of the ring modification from circle to ellipsoid, showing the endothermic reaction of [La3+]/[{Mo142(CH3CO25(C2H5CO2}] = 6/1 with DH = 22 kJ×mol-1, DS = 172 J×K-1×mol-1, DG = −28 kJ×mol-1, and K = 9.9 ´ 104 M-1 at 293 K, leads to the conclusion that the coordination of the defect pockets to La3+ precedes the replacement of the {Mo2} linkers with La3+. 139La- NMR spectrometry of the coordination of {Mo142(CH3CO25(C2H5CO2} ring to La3+ is also discussed.

  2. BlockLogo: Visualization of peptide and sequence motif conservation

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian

    2013-01-01

    BlockLogo is a web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, se...

  3. Numerical Simulations of Saturn's B Ring: Granular Friction as a Mediator between Self-gravity Wakes and Viscous Overstability

    Energy Technology Data Exchange (ETDEWEB)

    Ballouz, Ronald-Louis; Richardson, Derek C. [Department of Astronomy, University of Maryland, College Park, MD 20742-2421 (United States); Morishima, Ryuji [University of California, Los Angeles, Institute of Geophysics and Planetary Physics, Los Angeles, CA (United States)

    2017-04-01

    We study the B ring’s complex optical depth structure. The source of this structure may be the complex dynamics of the Keplerian shear and the self-gravity of the ring particles. The outcome of these dynamic effects depends sensitively on the collisional and physical properties of the particles. Two mechanisms can emerge that dominate the macroscopic physical structure of the ring: self-gravity wakes and viscous overstability. Here we study the interplay between these two mechanisms by using our recently developed particle collision method that allows us to better model the inter-particle contact physics. We find that for a constant ring surface density and particle internal density, particles with rough surfaces tend to produce axisymmetric ring features associated with the viscous overstability, while particles with smoother surfaces produce self-gravity wakes.

  4. Generalized oscillator strengths for 5s, 5s', and 5p excitations of krypton

    International Nuclear Information System (INIS)

    Li Wenbin; Zhu Linfan; Yuan Zhensheng; Sun Jianmin; Cheng Huadong; Xu Kezun; Zhong Zhiping; Liu Xiaojing

    2003-01-01

    The absolute generalized oscillator strengths (GOSs) for 5s, 5s ' , 5p [5/2] 3,2 , 5p [3/2] 1,2 , and 5p [1/2] 0 transitions of krypton have been determined in a large K 2 region at a high electron-impact energy of 2500 eV. The positions of the minima and maxima of these GOSs have been determined. The present results show that the angular resolution and pressure effect have great influence on the position and the amplitude of the minimum for the GOS of 5s+5s ' transitions. When these effects are considered, the measured minimum position for the GOS of 5s+5s ' transitions is in excellent agreement with the calculation of Chen and Msezane [J. Phys. B 33, 5397 (2000)

  5. THE MOTIF OF THE SECOND COMING IN RUSSIAN FANTASTIC FICTION

    Directory of Open Access Journals (Sweden)

    Tatyana I. Khoruzhenko

    2017-06-01

    Full Text Available The motif of the Second Coming of Christ takes a special place in Russian fantastic fiction at the turn of the millennium. In the recent decades allusions to the Gospel topic appears in increasing frequency in the genre of fantasy. The aim of the given article was to analyze the peculiarities of the depiction of the subject of Advent in Russian fantastic fiction. As the basis for the research the novels of Y. Voznesenskaya, N. Perumov, V. Khlumov, S. Lukyanenko and T. Ustimenko are of particular interest. The Advent motif appears in the story line of each of the novels in question. Though, the attitude of the authors to the image of the Savior and his second coming to the world fluctuates: from a respectful expectation (Y. Voznesenskaya, T. Ustimenko, S. Lukyanenko to the depiction of the Savior as a monster (N. Perumov. The possibility of an ambivalent interpretation of the Savior is the eloquent evidence of desacralization of this image. The profaning of the sacred is one of the tendencies of the modern popular culture. The genre of fantastic fiction, as a product of mass culture, has caught this trend quite precisely.

  6. Crystal structure of 2-hydroxyimino-2-(pyridin-2-yl-N′-[1-(pyridin-2-ylethylidene]acetohydrazide

    Directory of Open Access Journals (Sweden)

    Maxym O. Plutenko

    2014-12-01

    Full Text Available The molecule of the title compound, C14H13N5O2, is approximately planar (r.m.s deviation for all non-H atoms = 0.093 Å, with the planes of the two pyridine rings inclined to one another by 5.51 (7°. The oxime group is syn to the amide group, probably due to the formation of an intramolecular N—H...N hydrogen bond that forms an S(6 ring motif. In the crystal, molecules are linked by pairs of bifurcated O—H...(O,N hydrogen bonds, forming inversion dimers. The latter are linked via C—H...O and C—H...N hydrogen bonds, forming sheets lying parallel to (502. The sheets are linked via π–π stacking interactions [inter-centroid distance = 3.7588 (9 Å], involving the pyridine rings of inversion-related molecules, forming a three-dimensional structure.

  7. Bimodality and the formation of Saturn's ring particles

    International Nuclear Information System (INIS)

    Gehrels, T.

    1980-01-01

    The F ring appears to have an outer and an inner rim, with only the latter observed by the imaging photopolarimeter (IPP) on the Pioneer Saturn spacecraft. The inside of the G ring, near 2.49 R/sub S/, may also be seen in the optical data. 1979S1 is red as well as dark. The light scattered through the B ring is noticeably red. The A ring has a dense outer rim. The Cassini Division and the French Division (Dollfus Division) have a dark gap near their centers. The C ring becomes weaker toward the center such that outer, middle, and inner C rings can be recognized. The Pioneer and earth-based observations are explained with a model for the B and A rings to some extent of a bimodal size distributions of particles; the larger ones may be original accretions, while small debris diffuses inward through the Cassini Division and the C ring. During the formation of the ring system, differential gravitation allowed only silicaceous grains of higher density (rho> or approx. =3 g cm -3 ) to coagulate. These serve as interstitial cores for snowy carbonaceous grains, between the times of accretion from interplanetary cometary grains and liberation by collision followed by diffusion inward to Saturn and final evaporation

  8. Beam dynamic issues in TESLA damping ring

    International Nuclear Information System (INIS)

    Shiltsev, V.

    1996-05-01

    In this paper we study general requirements on impedances of the linear collider TESLA damping ring design. Quantitative consideration is performed for 17-km long ''dog-bone'' ring. Beam dynamics in alternative options of 6.3 and 2.3-km long damping rings is briefly discussed. 5 refs., 2 tabs

  9. Forandringslæring med autismediagnoser?

    DEFF Research Database (Denmark)

    Gustafson, Kari Ingrid; Mørck, Line Lerche

    2013-01-01

    Artiklen drøfter en række aktuelle spørgsmål omkring læring hos børn og unge med autisme-spektrum-forstyrrelses diagnoser. Der introduceres til en social praksisteoretisk forståelse af forandringslæring, der diskuterer forandring ikke kun i relation til en persons identitet, men også aktuelle og...... potentielle forandringer, når det gælder overskridelse af binær logik i autisme versus normalitet, samt i relation til at overskride individualiserede og dualistiske problem-forståelser af fejl og mangler ved det autistiske barn. Det illustreres, hvordan disse former for dualistisk tænkning er forankret i et...... Rasmus’ ændringer i læring, selvforståelse og tilhørsforhold perspektiveres med andre ASF-diagnostiseredes læring udforsket bl.a. gennem gruppeinterviews i regi af Asperger-foreningen. Artiklen byder således på et alternativ i form af at forstå forandringslæring som overskridende læring, med langt større...

  10. Warden’s Five-Ring System Theory: Legitimate Wartime Military Targeting or an Increased Potential to Violate the Law and Norms of Expected Behavior?

    Science.gov (United States)

    2000-04-01

    the five-ring system theory that dramatically improves the warfighters ability to systematically identify wartime targets. However, for all of its...acclaim, little has been written about Warden’s five-ring system theory . Even less has been written about the legal and moral implications of using Warden’s theory to identify wartime targets.

  11. 1-Methyl-2-[(E-2,4,5-trimethoxystyryl]pyridinium iodideThis paper is dedicated to the late His Majesty King Chulalongkorn (King Rama V of Thailand for his numerous reforms to modernize the country on the occasion of Chulalongkorn Day (Piyamaharaj Day which fell on the 23rd October.

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2010-12-01

    Full Text Available In the title compound, C17H20NO3+·I−, the cation exists in the E configuration. The pyridinium and benzene rings are close to coplanar, with a dihedral angle of 7.43 (12° between them. The three methoxy groups of 2,4,5-trimethoxyphenyl are essentially coplanar with the benzene plane, with C—O—C—C torsion angles of 1.0 (3, −1.9 (3 and 3.6 (3°. A weak intramolecular C—H...O interaction generates an S(6 ring motif. In the crystal, the cations are stacked in columns in an antiparallel manner along the a axis through π–π interactions, with a centroid–centroid distance of 3.7714 (16 Å. The iodide anion is situated between the columns and linked to the cation by a weak C—H...I interaction.

  12. Broadband impedance of the NESTOR storage ring

    International Nuclear Information System (INIS)

    Androsov, V.P.; Gladkikh, P.I.; Gvozd, A.M.; Karnaukhov, I.M.; Telegin, Yu.N.

    2011-01-01

    The contributions from lossy and inductive vacuum chamber components to the broadband impedance of the NESTOR storage ring are obtained by using both low-frequency analytical approaches and computer simulations. As was expected considering the small ring circumference (15.44m), the main contributions both to the longitudinal impedance Z || /n and the loss factor k loss come from the RF-cavity. Cavity impedance was also estimated with CST Microwave Studio (CST Studio Suite TM 2006) by simulating coaxial wire method commonly used for impedance measurements. Both estimates agree well. Finally, we performed the simulations of a number of inductive elements with CST Particle Studio 2010 by using wake field solver. We have also evaluated the bunch length in NESTOR taking the conservative estimate of 3 Ohm for the ring broadband impedance and have found that the bunch length s z = 0.5 cm could be obtained in steady state operation mode for the designed bunch current of 10 mA and RF-voltage of 250 kV.

  13. Assessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization

    Directory of Open Access Journals (Sweden)

    Nils E. R. Zimmermann

    2017-11-01

    Full Text Available Structure–property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors, as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal close packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP database (61,422 compounds for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

  14. (4bS,8aS-1-Isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octahydrophenanthren-2-yl benzoate

    Directory of Open Access Journals (Sweden)

    Radouane Oubabi

    2014-08-01

    Full Text Available The title compound, C27H34O2, was hemisynthesized through direct benzoylation of the naturally occurring meroterpene totarol. The central fused six-membered ring has a half-chair conformation, whereas the terminal six-membered ring displays a chair conformation. The dihedral angle between the fused benzene ring and the benzoyl benzene ring is 73.05 (14°. The S,S chirality of the molecule is consistent with the synthetic pathway, and confirmed by the refinement of the Flack parameter.

  15. Instrumental neutron activation analysis of tree rings for dendrochemical studies

    International Nuclear Information System (INIS)

    Schaumloffel, J.C.; Filby, R.H.

    1996-01-01

    Instrumental neutron activation analysis (INAA) was employed to determine zinc, cadmium and potassium concentrations in the growth rings of ponderosa pine (Pinus ponderosa Dougl.) trees growing along the shores of Lake Roosevelt in Washington State, U.S.A. where mineral processing activities have resulted in high burdens of zinc and cadmium in the lake sediments. The tree growing along the contaminated waterway display elevated concentrations of zinc in its growth rings relative to a tree growing along an uncontaminated tributary of Lake Roosevelt. Cadmium concentrations in the growth rings from both sites are similar from 1988 to 1993. Water quality data indicate an increased concentration of cadmium in the lake from 1984 to 1988. The increased concentrations of cadmium in the lake water were reflected in apparent increases in concentrations of cadmium in individual rings of the tree sampled at the contaminated site. This suggests that translocation of cadmium in the sapwood of heartwood-forming species does not occur in the short term, and thus may not be a limiting factor in using trees as environmental monitors for cadmium. In addition, five-year tree ring segments were analyzed and subsequently reanalyzed as individual single-year ring segments. The analytical data obtained for the pooled individual rings are essentially the same as for the five-year segments, demonstrating the utility of NAA for dendrochemical studies. (author). 24 refs., 5 figs., 2 tabs

  16. A Bacon Tone Ring on an Open-Back Banjo

    OpenAIRE

    Politzer, David

    2016-01-01

    Head taps on a new Goodtime banjo rim fitted with a reproduction Bacon Professional ff tone ring are contrasted with a new Goodtime, a 2002 Goodtime, and a 1999 Goodtime fitted with a 1/4′′ diameter brass ring. Conclusions: The 1/4" ring does what’s commonly imagined, the upgrades to the Goodtime over the years are not merely cosmetic, and the Bacon ring’s biggest effect is to damp head ringing and suppress high harmonics. Detailed comparisons of the new Goodtimes with and without the Bacon r...

  17. S-Nitrosothiols Observed Using Cavity Ring-Down Spectroscopy

    Science.gov (United States)

    Rad, Mary Lynn; Gaston, Benjamin M.; Lehmann, Kevin

    2017-06-01

    The biological importance of nitric oxide has been known for nearly forty years due to its role in cardiovascular and nervous signaling. The main carrier molecules, s-nitrosothiols (RSNOs), are of additional interest due to their role in signaling reactions. Additionally, these compounds are related to several diseases including muscular dystrophy, stroke, myocardial infarction, Alzheimer's disease, Parkinson's disease, cystic fibrosis, asthma, and pulmonary arterial hypertension. One of the main barriers to elucidating the role of these RSNOs is the low (nanomolar) concentration present in samples of low volume (typically ˜100 μL). To this end we have set up a cavity ring-down spectrometer tuned to observe ^{14}NO and ^{15}NO released from cell growth samples. To decrease the limit of detection we have implemented a laser locking scheme employing Zeeman modulation of NO in a reference cell and have tuned the polarization of the laser using a half wave plate to optimize the polarization for the inherent birefringence of the CRDS mirrors. Progress toward measuring RSNO concentration in biological samples will be presented.

  18. Dipole Magnets for the LHeC Ring-Ring Option

    CERN Document Server

    Tommasini, D; Chritin, R

    2012-01-01

    The Ring-Ring option of a Large Hadron electron Collider (LHeC) requires 3080 bending magnets, 5.35-meter-long each providing a magnetic field ranging from 0.0127 T at 10 GeV to 0.0763 T at 60 GeV. Main issues in the design of these magnets are the very low injection field, constituting a challenge in achieving a satisfactory field reproducibility from cycle to cycle, and the required compactness to fit in the existing LHC tunnel. This paper describes and discusses a design meeting these requirements, together with its experimental validation by the manufacture and measurement of a 400-mm-long magnet model.

  19. The Fine Structure of Herman Rings

    DEFF Research Database (Denmark)

    Fagella, Nuria; Henriksen, Christian

    2017-01-01

    We study the geometric structure of the boundary of Herman rings in a model family of Blaschke products of degree 3 (up to quasiconformal deformation). Shishikura’s quasiconformal surgery relates the Herman ring to the Siegel disk of a quadratic polynomial. By studying the regularity properties...

  20. Crystal structures of N-(4-chlorophenyl-2-[(4,6-diaminopyrimidin-2-ylsulfanyl]acetamide and N-(3-chlorophenyl-2-[(4,6-diaminopyrimidin-2-ylsulfanyl]acetamide

    Directory of Open Access Journals (Sweden)

    S. Subasri

    2017-04-01

    Full Text Available The title compounds, C12H12ClN5OS, (I, and C12H12ClN5OS, (II, are 2-[(diaminopyrimidin-2-ylsulfanyl]acetamides. Compound (II, crystallizes with two independent molecules (A and B in the asymmetric unit. In each of the molecules, in both (I and (II, an intramolecular N—H...N hydrogen bond forms an S(7 ring motif. The pyrimidine ring is inclined to the benzene ring by 42.25 (14° in (I, and by 59.70 (16 and 62.18 (15° in molecules A and B, respectively, of compound (II. In the crystal of (I, molecules are linked by pairs of N—H...N hydrogen bonds, forming inversion dimers with an R22(8 ring motif. The dimers are linked via bifurcated N—H...O and C—H...O hydrogen bonds, forming corrugated layers parallel to the ac plane. In the crystal of (II, the A molecules are linked through N—H...O and N—H...Cl hydrogen bonds, forming layers parallel to (100. The B molecules are also linked by N—H...O and N—H...Cl hydrogen bonds, also forming layers parallel to (100. The parallel layers of A and B molecules are linked via N—H...N hydrogen bonds, forming a three-dimensional structure.

  1. (2aR*,5S*,6aS*,8aS*,E-Ethyl 5-hydroxy-7,7,8a-trimethyl-8-oxo-2,2a,6,6a,7,8,8a,8b-octahydro-1H-pentaleno[1,6-bc]oxepine-4-carboxylate

    Directory of Open Access Journals (Sweden)

    Goverdhan Mehta

    2012-12-01

    Full Text Available The title compound, C17H24O5, featuring a 2-carbethoxy-3-oxepanone unit in its intramolecularly O—H...O hydrogen-bonded enol form, was obtained via [(CF3CO22Rh]2-catalysed intramolecular O—H bond insertion in the α-diazo-ω-hydroxy-β-ketoester, ethyl 4-[(1S,3aS,6R,6aS-6-hydroxy-2,2,3a-trimethyl-3-oxo-octahydropentalen-1-yl]-2-diazo-3-oxobutanoate. The seven-membered oxacyclic ring, thus constructed on a cis-fused diquinane platform, was found to adopt a distorted boat–sofa conformation.

  2. Planning and Prototyping for a Storage Ring Measurement of the Proton Electric Dipole Moment

    Energy Technology Data Exchange (ETDEWEB)

    Talman, Richard [Cornell Univ., Ithaca, NY (United States)

    2015-07-01

    Electron and proton EDM's can be measured in "frozen spin" (with the beam polarization always parallel to the orbit, for example) storage rings. For electrons the "magic" kinetic energy at which the beam can be frozen is 14.5 MeV. For protons the magic kinetic energy is 230 MeV. The currently measured upper limit for the electron EDM is much smaller than the proton EDM upper limit, which is very poorly known. Nevertheless, because the storage ring will be an order of magnitude cheaper, a sensible plan is to first build an all-electric electron storage ring as a prototype. Such an electron ring was successfully built at Brookhaven, in 1954, as a prototype for their AGS ring. This leaves little uncertainty concerning the cost and performance of such a ring. (This is documentedin one of the Physical Review papers mentioned above.)

  3. Rings with involution whose symmetric elements are central

    Directory of Open Access Journals (Sweden)

    Taw Pin Lim

    1980-01-01

    Full Text Available In a ring R with involution whose symmetric elements S are central, the skew-symmetric elements K form a Lie algebra over the commutative ring S. The classification of such rings which are 2-torsion free is equivalent to the classification of Lie algebras K over S equipped with a bilinear form f that is symmetric, invariant and satisfies [[x,y],z]=f(y,zx−f(z,xy. If S is a field of char ≠2, f≠0 and dimK>1 then K is a semisimple Lie algebra if and only if f is nondegenerate. Moreover, the derived algebra K′ is either the pure quaternions over S or a direct sum of mutually orthogonal abelian Lie ideals of dim≤2.

  4. Estimate of LOCA-FI plenum pressure uncertainty for a five-ring RELAP5 production reactor model

    International Nuclear Information System (INIS)

    Griggs, D.P.

    1993-03-01

    The RELAP5/MOD2.5 code (RELAP5) is used to perform best-estimate analyses of certain postulated Design Basis Accidents (DBAs) in SRS production reactors. Currently, the most limiting DBA in terms of reactor power level is an instantaneous double-ended guillotine break (DEGB) loss of coolant accident (LOCA). A six-loop RELAP5 K Reactor model is used to analyze the reactor system behavior dozing the Flow Instability (FI) phase of the LOCA, which comprises only the first 5 seconds following the DEGB. The RELAP5 K Reactor model includes tank and plenum nodalizations having five radial rings and six azimuthal sectors. The reactor system analysis provides time-dependent plenum and tank bottom pressures for use as boundary conditions in the FLOWTRAN code, which models a single fuel assembly in detail. RELAP5 also performs the system analysis for the latter phase of the LOCA, denoted the Emergency Cooling System (ECS) phase. Results from the RELAP analysis are used to provide boundary conditions to the FLOWTRAN-TF code, which is an advanced two-phase version of FLOWTRAN. The RELAP5 K Reactor model has been tested for LOCA-FI and Loss-of-Pumping Accident analyses and the results compared with equivalent analyses performed with the TRAC-PF1/MOD1 code (TRAC). An equivalent RELAP5 six-loop, five-ring, six-sector L Reactor model has been benchmarked against qualified single-phase system data from the 1989 L-Area In-Reactor Test Program. The RELAP5 K and L Reactor models have also been subjected to an independent Quality Assurance verification

  5. One motif to bind them: A small-XXX-small motif affects transmembrane domain 1 oligomerization, function, localization, and cross-talk between two yeast GPCRs.

    Science.gov (United States)

    Lock, Antonia; Forfar, Rachel; Weston, Cathryn; Bowsher, Leo; Upton, Graham J G; Reynolds, Christopher A; Ladds, Graham; Dixon, Ann M

    2014-12-01

    G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors in mammals and facilitate a range of physiological responses triggered by a variety of ligands. GPCRs were thought to function as monomers, however it is now accepted that GPCR homo- and hetero-oligomers also exist and influence receptor properties. The Schizosaccharomyces pombe GPCR Mam2 is a pheromone-sensing receptor involved in mating and has previously been shown to form oligomers in vivo. The first transmembrane domain (TMD) of Mam2 contains a small-XXX-small motif, overrepresented in membrane proteins and well-known for promoting helix-helix interactions. An ortholog of Mam2 in Saccharomyces cerevisiae, Ste2, contains an analogous small-XXX-small motif which has been shown to contribute to receptor homo-oligomerization, localization and function. Here we have used experimental and computational techniques to characterize the role of the small-XXX-small motif in function and assembly of Mam2 for the first time. We find that disruption of the motif via mutagenesis leads to reduction of Mam2 TMD1 homo-oligomerization and pheromone-responsive cellular signaling of the full-length protein. It also impairs correct targeting to the plasma membrane. Mutation of the analogous motif in Ste2 yielded similar results, suggesting a conserved mechanism for assembly. Using co-expression of the two fungal receptors in conjunction with computational models, we demonstrate a functional change in G protein specificity and propose that this is brought about through hetero-dimeric interactions of Mam2 with Ste2 via the complementary small-XXX-small motifs. This highlights the potential of these motifs to affect a range of properties that can be investigated in other GPCRs. Copyright © 2014. Published by Elsevier B.V.

  6. The kissing-loop motif is a preferred site of 5' leader recombination during replication of SL3-3 murine leukemia viruses in mice

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Mikkelsen, J G; Schmidt, J

    1999-01-01

    , and the upstream part of the 5' untranslated region, enabled us to map recombination sites, guided by distinct scattered nucleotide differences. In 30 of 44 analyzed sequences, recombination was mapped to a 33-nucleotide similarity window coinciding with the kissing-loop stem-loop motif implicated in dimerization...... of the diploid genome. Interestingly, the recombination pattern preference found in replication-competent viruses from T-cell tumors is very similar to the pattern previously reported for retroviral vectors in cell culture experiments. The data therefore sustain the hypothesis that the kissing loop, presumably...

  7. Cryptosporidium meleagridis in an Indian ring-necked parrot (Psittacula krameri).

    Science.gov (United States)

    Morgan, U M; Xiao, L; Limor, J; Gelis, S; Raidal, S R; Fayer, R; Lal, A; Elliot, A; Thompson, R C

    2000-03-01

    To perform a morphological and genetic characterisation of a Cryptosporidium infection in an Indian ring-necked parrot (Psittacula krameri) and to compare this with C meleagridis from a turkey. Tissue and intestinal sections from an Indian ring-necked parrot were examined microscopically for Cryptosporidium. The organism was also purified from the crop and intestine, the DNA extracted and a portion of the 18S rDNA gene amplified, sequenced and compared with sequence and biological information obtained for C meleagridis from a turkey as well as sequence information for other species of Cryptosporidium. Morphological examination of tissue sections from an Indian ring-necked parrot revealed large numbers of Cryptosporidium oocysts attached to the apical border of enterocytes lining the intestinal tract. Purified Cryptosporidium oocysts measured about 5.1 x 4.5 microns, which conformed morphologically to C meleagridis. The sequence obtained from this isolate was identical to sequence information obtained from a C meleagridis isolate from a turkey. Cryptosporidium meleagridis was detected in an Indian ring-necked parrot using morphological and molecular methods. This is the first time that this species of Cryptosporidium has been reported in a non-galliform host and extends the known host range of C meleagridis.

  8. Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

    LENUS (Irish Health Repository)

    Casey, Fergal

    2011-08-22

    Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.

  9. Fingerprint motifs of phytases | Fan | African Journal of Biotechnology

    African Journals Online (AJOL)

    Among the total of potential 173 phytases gained in 11 plant genomes through MAST, PAPhys are the major phytases, and HAPhys are the minor, and other phytase groups are not found in planta. Keywords: Phytase, fingerprint motif, multiple EM for motif elicitation (MEME), MAST African Journal of Biotechnology Vol.

  10. Methyl 11-hydroxy-9-[1-(4-methoxyphenyl-4-oxo-3-phenoxyazetidin-2-yl]-18-oxo-10-oxa-2-azapentacyclo[9.7.0.01,8.02,6.012,17]octadeca-12(17,13,15-triene-8-carboxylate

    Directory of Open Access Journals (Sweden)

    S. Sundaramoorthy

    2012-07-01

    Full Text Available In the title compound, C34H32N2O8, one of the pyrrolidine rings in the pyrrolizidine ring system adopts a twist conformation, whereas the other ring adopts an envelope conformation (C atom as flap. The five-membered ring in the indene ring system and the fused furan ring also adopt envelope conformations (C and O atoms as flaps, respectively. The β-lactam ring makes dihedral angles of 23.41 (2 and 25.98 (2°, respectively, with the attached methoxyphenyl and phenoxy rings. The molecular conformation is stabilized by an intramolecular O—H...N hydrogen bond, generating an S(5 motif. In the crystal, molecules are linked into C(12 chains running along the a axis by C—H...O hydrogen bonds. The structure is further consolidated by weak intermolecular C—H...π and π–π interactions [centroid–centroid distance = 3.7987 (14 Å].

  11. Solution structure of a DNA mimicking motif of an RNA aptamer against transcription factor AML1 Runt domain.

    Science.gov (United States)

    Nomura, Yusuke; Tanaka, Yoichiro; Fukunaga, Jun-ichi; Fujiwara, Kazuya; Chiba, Manabu; Iibuchi, Hiroaki; Tanaka, Taku; Nakamura, Yoshikazu; Kawai, Gota; Kozu, Tomoko; Sakamoto, Taiichi

    2013-12-01

    AML1/RUNX1 is an essential transcription factor involved in the differentiation of hematopoietic cells. AML1 binds to the Runt-binding double-stranded DNA element (RDE) of target genes through its N-terminal Runt domain. In a previous study, we obtained RNA aptamers against the AML1 Runt domain by systematic evolution of ligands by exponential enrichment and revealed that RNA aptamers exhibit higher affinity for the Runt domain than that for RDE and possess the 5'-GCGMGNN-3' and 5'-N'N'CCAC-3' conserved motif (M: A or C; N and N' form Watson-Crick base pairs) that is important for Runt domain binding. In this study, to understand the structural basis of recognition of the Runt domain by the aptamer motif, the solution structure of a 22-mer RNA was determined using nuclear magnetic resonance. The motif contains the AH(+)-C mismatch and base triple and adopts an unusual backbone structure. Structural analysis of the aptamer motif indicated that the aptamer binds to the Runt domain by mimicking the RDE sequence and structure. Our data should enhance the understanding of the structural basis of DNA mimicry by RNA molecules.

  12. Cancer caused by radioactive gold rings

    International Nuclear Information System (INIS)

    Callary, E.M.

    1989-01-01

    Two recent cases of skin cancer caused by radioactive gold rings are described. The gold was contaminated with radon daughters from hollow goldseeds used to hold radon, back in the 1930s or possibly later. Other radioactive gold rings are probably being worn. The Canadian AECB offers free testing

  13. ASSOCIATIVE RINGS SOLVED AS LIE RINGS

    Directory of Open Access Journals (Sweden)

    M. B. Smirnov

    2011-01-01

    Full Text Available The paper has proved that an associative ring which is solvable of a n- class as a Lie ring has a nilpotent ideal of the nilpotent class not more than 3×10n–2  and a corresponding quotient ring satisfies an identity [[x1, x2, [x3, x4

  14. 4-(3-Bromopropyloxy-1-hydroxy-9,10-anthraquinone

    Directory of Open Access Journals (Sweden)

    Natsumi Ohira

    2016-05-01

    Full Text Available In the molecule of the title compound, C17H13BrO4, the anthraquinone ring system is slightly bent, with a dihedral angle of 169.99 (7° between the planes of the two benzene rings. The side chain (O—C—C—C—Br has a gauche–gauche conformation, as indicated by the O—C—C—C and C—C—C—Br torsion angles of −66.9 (2 and −65.8 (2°, respectively. In addition, there is an intramolecular O—H...O hydrogen bond enclosing an S(6 ring motif. The hydrogen-bond donor is bifurcated; in the crystal, a pair of O—H...O hydrogen bonds connects two molecules, forming an inversion dimer with an R22(12 ring motif.

  15. An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom.

    Science.gov (United States)

    Vujaklija, Ivan; Bielen, Ana; Paradžik, Tina; Biđin, Siniša; Goldstein, Pavle; Vujaklija, Dušica

    2016-02-18

    The massive accumulation of protein sequences arising from the rapid development of high-throughput sequencing, coupled with automatic annotation, results in high levels of incorrect annotations. In this study, we describe an approach to decrease annotation errors of protein families characterized by low overall sequence similarity. The GDSL lipolytic family comprises proteins with multifunctional properties and high potential for pharmaceutical and industrial applications. The number of proteins assigned to this family has increased rapidly over the last few years. In particular, the natural abundance of GDSL enzymes reported recently in plants indicates that they could be a good source of novel GDSL enzymes. We noticed that a significant proportion of annotated sequences lack specific GDSL motif(s) or catalytic residue(s). Here, we applied motif-based sequence analyses to identify enzymes possessing conserved GDSL motifs in selected proteomes across the plant kingdom. Motif-based HMM scanning (Viterbi decoding-VD and posterior decoding-PD) and the here described PD/VD protocol were successfully applied on 12 selected plant proteomes to identify sequences with GDSL motifs. A significant number of identified GDSL sequences were novel. Moreover, our scanning approach successfully detected protein sequences lacking at least one of the essential motifs (171/820) annotated by Pfam profile search (PfamA) as GDSL. Based on these analyses we provide a curated list of GDSL enzymes from the selected plants. CLANS clustering and phylogenetic analysis helped us to gain a better insight into the evolutionary relationship of all identified GDSL sequences. Three novel GDSL subfamilies as well as unreported variations in GDSL motifs were discovered in this study. In addition, analyses of selected proteomes showed a remarkable expansion of GDSL enzymes in the lycophyte, Selaginella moellendorffii. Finally, we provide a general motif-HMM scanner which is easily accessible through

  16. Extensive 5.8S nrDNA polymorphism in Mammillaria (Cactaceae) with special reference to the identification of pseudogenic internal transcribed spacer regions.

    Science.gov (United States)

    Harpke, Doerte; Peterson, Angela

    2008-05-01

    The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, ITS2) represents the most widely applied nuclear marker in eukaryotic phylogenetics. Although this region has been assumed to evolve in concert, the number of investigations revealing high degrees of intra-individual polymorphism connected with the presence of pseudogenes has risen. The 5.8S rDNA is the most important diagnostic marker for functionality of the ITS region. In Mammillaria, intra-individual 5.8S rDNA polymorphisms of up to 36% and up to nine different types have been found. Twenty-eight of 30 cloned genomic Mammillaria sequences were identified as putative pseudogenes. For the identification of pseudogenic ITS regions, in addition to formal tests based on substitution rates, we attempted to focus on functional features of the 5.8S rDNA (5.8S motif, secondary structure). The importance of functional data for the identification of pseudogenes is outlined and discussed. The identification of pseudogenes is essential, because they may cause erroneous phylogenies and taxonomic problems.

  17. On zero divisor graph of unique product monoid rings over Noetherian reversible ring

    Directory of Open Access Journals (Sweden)

    Ebrahim Hashemi

    2016-02-01

    Full Text Available Let $R$ be an associative ring with identity and $Z^*(R$ be its set of non-zero zero divisors.  The zero-divisor graph of $R$, denoted by $Gamma(R$, is the graph whose vertices are the non-zero  zero-divisors of  $R$, and two distinct vertices $r$ and $s$ are adjacent if and only if $rs=0$ or $sr=0$.  In this paper, we bring some results about undirected zero-divisor graph of a monoid ring over reversible right (or left Noetherian ring $R$. We essentially classify the diameter-structure of this graph and show that $0leq mbox{diam}(Gamma(Rleq mbox{diam}(Gamma(R[M]leq 3$. Moreover, we give a characterization for the possible diam$(Gamma(R$ and diam$(Gamma(R[M]$, when $R$ is a reversible Noetherian ring and $M$ is a u.p.-monoid. Also, we study relations between the girth of $Gamma(R$ and that of $Gamma(R[M]$.

  18. Crystal structures of (Z-5-[2-(benzo[b]thiophen-2-yl-1-(3,5-dimethoxyphenylethenyl]-1H-tetrazole and (Z-5-[2-(benzo[b]thiophen-3-yl-1-(3,4,5-trimethoxyphenylethenyl]-1H-tetrazole

    Directory of Open Access Journals (Sweden)

    Narsimha Reddy Penthala

    2016-05-01

    Full Text Available (Z-5-[2-(Benzo[b]thiophen-2-yl-1-(3,5-dimethoxyphenylethenyl]-1H-tetrazole methanol monosolvate, C19H16N4O2S·CH3OH, (I, was prepared by the reaction of (Z-3-(benzo[b]thiophen-2-yl-2-(3,5-dimethoxyphenylacrylonitrile with tributyltin azide via a [3 + 2]cycloaddition azide condensation reaction. The structurally related compound (Z-5-[2-(benzo[b]thiophen-3-yl-1-(3,4,5-trimethoxyphenylethenyl]-1H-tetrazole, C20H18N4O3S, (II, was prepared by the reaction of (Z-3-(benzo[b]thiophen-3-yl-2-(3,4,5-trimethoxyphenylacrylonitrile with tributyltin azide. Crystals of (I have two molecules in the asymmetric unit (Z′ = 2, whereas crystals of (II have Z′ = 1. The benzothiophene rings in (I and (II are almost planar, with r.m.s deviations from the mean plane of 0.0084 and 0.0037 Å in (I and 0.0084 Å in (II. The tetrazole rings of (I and (II make dihedral angles with the mean planes of the benzothiophene rings of 88.81 (13 and 88.92 (13° in (I, and 60.94 (6° in (II. The dimethoxyphenyl and trimethoxyphenyl rings make dihedral angles with the benzothiophene rings of 23.91 (8 and 24.99 (8° in (I and 84.47 (3° in (II. In both structures, molecules are linked into hydrogen-bonded chains. In (I, these chains involve both tetrazole and methanol, and are parallel to the b axis. In (II, molecules are linked into chains parallel to the a axis by N—H...N hydrogen bonds between adjacent tetrazole rings.

  19. Syntheses and Tribological Property of CrMoN/MoS2 Multilayer Films on Piston Rings of Heavy Vehicle Engine

    Institute of Scientific and Technical Information of China (English)

    WANG Xiancheng; LI Qi; LI Ruoting; DI Yuelan

    2016-01-01

    In order to prolong the service life of piston rings of heavy vehicle engine and decrease the friction and wear of piston rings and cylinder liner, CrMoN/MoS2 multilayer iflms were deposited on the surface of rings by magnetron sputtering and low temperature ion sulfuration. FESEM equipped with EDX was adopted to analyze the compositions and morphologies of surface, cross-section, and wear scars of the multilayer iflms. The nano-hardness and Young’s modulus of the iflms were measured by a nano tester. Tribological properties of the iflms were tested by an SRV®4 wear tester. The experimental results indicate that the structures of the multilayer films are dense and compact. The films possess nano hardness value of approximately 26.7 GPa and superior ability of plastic deformation resistance. The multilayer iflms can activate solid lubricating, and possess an excellent antifriction and wear resistance under the conditions of heavy load, high frequency, high temperature, and dynamic load.

  20. Anion induced conformational preference of Cα NN motif residues in functional proteins.

    Science.gov (United States)

    Patra, Piya; Ghosh, Mahua; Banerjee, Raja; Chakrabarti, Jaydeb

    2017-12-01

    Among different ligand binding motifs, anion binding C α NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with C α NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping C α NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion. © 2017 Wiley Periodicals, Inc.

  1. Gene regulatory and signaling networks exhibit distinct topological distributions of motifs

    Science.gov (United States)

    Ferreira, Gustavo Rodrigues; Nakaya, Helder Imoto; Costa, Luciano da Fontoura

    2018-04-01

    The biological processes of cellular decision making and differentiation involve a plethora of signaling pathways and gene regulatory circuits. These networks in turn exhibit a multitude of motifs playing crucial parts in regulating network activity. Here we compare the topological placement of motifs in gene regulatory and signaling networks and observe that it suggests different evolutionary strategies in motif distribution for distinct cellular subnetworks.

  2. Finding a Leucine in a Haystack: Searching the Proteome for ambigous Leucine-Aspartic Acid motifs

    KAUST Repository

    Arold, Stefan T.

    2016-01-25

    Leucine-aspartic acid (LD) motifs are short helical protein-protein interaction motifs involved in cell motility, survival and communication. LD motif interactions are also implicated in cancer metastasis and are targeted by several viruses. LD motifs are notoriously difficult to detect because sequence pattern searches lead to an excessively high number of false positives. Hence, despite 20 years of research, only six LD motif–containing proteins are known in humans, three of which are close homologues of the paxillin family. To enable the proteome-wide discovery of LD motifs, we developed LD Motif Finder (LDMF), a web tool based on machine learning that combines sequence information with structural predictions to detect LD motifs with high accuracy. LDMF predicted 13 new LD motifs in humans. Using biophysical assays, we experimentally confirmed in vitro interactions for four novel LD motif proteins. Thus, LDMF allows proteome-wide discovery of LD motifs, despite a highly ambiguous sequence pattern. Functional implications will be discussed.

  3. Results of the in vitro ring trial:. Thorium and uranium isotopes in urine

    International Nuclear Information System (INIS)

    Hartmann, M.; Dalheimer, A.; Haenisch, K.

    2006-08-01

    On 22 September 2004 a workshop was held at the Berlin branch of the Federal Radiation Protection Office (BfS) on the in vitro ring trial ''Th isotopes and U isotopes in urine'' organised by the BfS head office for incorporation monitoring. The workshop was attended by 11 experts from the German, Austrian and Swiss incorporation measurement stations participating in the ring trial. The main focus of this second workshop was on the presentation of the results of the ring trial concerning Th and U isotopes in urine. According to paragraph 41 (8) of the Federal Radiation Protection Ordinance (StrlSchV 2001) one of the responsibilities of the head office for incorporation monitoring in terms of quality assurance is to have ring trials performed by the excretion analysis laboratories designated by the competent authorities as measurement stations. Section 5.2 of the Guideline on Requirements for Incorporation Monitoring Stations still in force (referred to in the following as the ''Requirements Guideline''/Guideline 1996) stipulates that incorporation measurement stations whose scope includes this type of measurement are obliged to participate in such ring trials. Inofficial and foreign incorporation measurement stations are also entitled to participate in ring trials organised by the head office. Ring trials may comprise either data acquisition or the dosimetric interpretation of data or both. By participating in ring trials measurement stations are supposed to demonstrate that the analysis and measurement methods they use are capable of supplying correct results with sufficient precision within the required time frame and of providing dosimetrically correct interpretations of activity increases

  4. A Comparison Study for DNA Motif Modeling on Protein Binding Microarray

    KAUST Repository

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin; Wong, Hau-San

    2015-01-01

    Transcription Factor Binding Sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, Protein Binding Microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k=810). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build motif models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement using di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.

  5. A Comparison Study for DNA Motif Modeling on Protein Binding Microarray

    KAUST Repository

    Wong, Ka-Chun

    2015-06-11

    Transcription Factor Binding Sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, Protein Binding Microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k=810). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build motif models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement using di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.

  6. Permuting the PGF Signature Motif Blocks both Archaeosortase-Dependent C-Terminal Cleavage and Prenyl Lipid Attachment for the Haloferax volcanii S-Layer Glycoprotein.

    Science.gov (United States)

    Abdul Halim, Mohd Farid; Karch, Kelly R; Zhou, Yitian; Haft, Daniel H; Garcia, Benjamin A; Pohlschroder, Mechthild

    2015-12-28

    For years, the S-layer glycoprotein (SLG), the sole component of many archaeal cell walls, was thought to be anchored to the cell surface by a C-terminal transmembrane segment. Recently, however, we demonstrated that the Haloferax volcanii SLG C terminus is removed by an archaeosortase (ArtA), a novel peptidase. SLG, which was previously shown to be lipid modified, contains a C-terminal tripartite structure, including a highly conserved proline-glycine-phenylalanine (PGF) motif. Here, we demonstrate that ArtA does not process an SLG variant where the PGF motif is replaced with a PFG motif (slg(G796F,F797G)). Furthermore, using radiolabeling, we show that SLG lipid modification requires the PGF motif and is ArtA dependent, lending confirmation to the use of a novel C-terminal lipid-mediated protein-anchoring mechanism by prokaryotes. Similar to the case for the ΔartA strain, the growth, cellular morphology, and cell wall of the slg(G796F,F797G) strain, in which modifications of additional H. volcanii ArtA substrates should not be altered, are adversely affected, demonstrating the importance of these posttranslational SLG modifications. Our data suggest that ArtA is either directly or indirectly involved in a novel proteolysis-coupled, covalent lipid-mediated anchoring mechanism. Given that archaeosortase homologs are encoded by a broad range of prokaryotes, it is likely that this anchoring mechanism is widely conserved. Prokaryotic proteins bound to cell surfaces through intercalation, covalent attachment, or protein-protein interactions play critical roles in essential cellular processes. Unfortunately, the molecular mechanisms that anchor proteins to archaeal cell surfaces remain poorly characterized. Here, using the archaeon H. volcanii as a model system, we report the first in vivo studies of a novel protein-anchoring pathway involving lipid modification of a peptidase-processed C terminus. Our findings not only yield important insights into poorly understood

  7. Identification of the Raptor-binding motif on Arabidopsis S6 kinase and its use as a TOR signaling suppressor.

    Science.gov (United States)

    Son, Ora; Kim, Sunghan; Hur, Yoon-Sun; Cheon, Choong-Ill

    2016-03-25

    TOR (target of rapamycin) kinase signaling plays central role as a regulator of growth and proliferation in all eukaryotic cells and its key signaling components and effectors are also conserved in plants. Unlike the mammalian and yeast counterparts, however, we found through yeast two-hybrid analysis that multiple regions of the Arabidopsis Raptor (regulatory associated protein of TOR) are required for binding to its substrate. We also identified that a 44-amino acid region at the N-terminal end of Arabidopsis ribosomal S6 kinase 1 (AtS6K1) specifically interacted with AtRaptor1, indicating that this region may contain a functional equivalent of the TOS (TOR-Signaling) motif present in the mammalian TOR substrates. Transient over-expression of this 44-amino acid fragment in Arabidopsis protoplasts resulted in significant decrease in rDNA transcription, demonstrating a feasibility of developing a new plant-specific TOR signaling inhibitor based upon perturbation of the Raptor-substrate interaction. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. A proposed vestigial translation initiation motif in VP1 of hepatitis A virus.

    Science.gov (United States)

    Kang, Jeong-Ah; Funkhouser, Ann W

    2002-07-01

    The internal ribosome entry site (IRES) of picornaviruses has a 3' polypyrimidine tract (PPT) 16-24 bases upstream of an AUG triplet (PPT/AUG motif). This motif is critical in determining the efficiency of cap-independent translation. HAV has a conserved PPT/AUG motif consisting of a nine base sequence (AGGUUUUUC) 23 bases upstream of the preferred AUG start codon. This HAV-specific PPT/AUG motif is repeated and conserved in VP1 of HAV, but not of other picornaviruses. We proposed that the PPT/AUG motif in the open reading frame initiated translation and/or had an impact on the life cycle of the virus. In vitro translation of mutant bicistronic mRNAs and growth in cell culture of mutant viruses provided no evidence that the VP1 PPT/AUG motif had any impact on either translation or growth. HAV differs from other picornaviruses in its inefficient growth in cell culture. Since the HAV-specific PPT/AUG motif is found in only 1 in 300,000 reported viral sequences outside the hepatovirus genus, this motif may be a vestigial translation initiation element and may have played a role in determining the unusual phenotype of HAV.

  9. Mutational analysis of the RecJ exonuclease of Escherichia coli: identification of phosphoesterase motifs.

    Science.gov (United States)

    Sutera, V A; Han, E S; Rajman, L A; Lovett, S T

    1999-10-01

    The recJ gene, identified in Escherichia coli, encodes a Mg(+2)-dependent 5'-to-3' exonuclease with high specificity for single-strand DNA. Genetic and biochemical experiments implicate RecJ exonuclease in homologous recombination, base excision, and methyl-directed mismatch repair. Genes encoding proteins with strong similarities to RecJ have been found in every eubacterial genome sequenced to date, with the exception of Mycoplasma and Mycobacterium tuberculosis. Multiple genes encoding proteins similar to RecJ are found in some eubacteria, including Bacillus and Helicobacter, and in the archaea. Among this divergent set of sequences, seven conserved motifs emerge. We demonstrate here that amino acids within six of these motifs are essential for both the biochemical and genetic functions of E. coli RecJ. These motifs may define interactions with Mg(2+) ions or substrate DNA. A large family of proteins more distantly related to RecJ is present in archaea, eubacteria, and eukaryotes, including a hypothetical protein in the MgPa adhesin operon of Mycoplasma, a domain of putative polyA polymerases in Synechocystis and Aquifex, PRUNE of Drosophila, and an exopolyphosphatase (PPX1) of Saccharomyces cereviseae. Because these six RecJ motifs are shared between exonucleases and exopolyphosphatases, they may constitute an ancient phosphoesterase domain now found in all kingdoms of life.

  10. 3,3,4,4-Tetrafluoro-1-[2-(3,3,4,4-tetrafluoropyrrolidin-1-ylphenyl]pyrrolidine

    Directory of Open Access Journals (Sweden)

    Jin Wang

    2011-09-01

    Full Text Available The asymmetric unit of the title compound, C14H12F8N2, contains one tetrafluoropyrrolidine system and one half-molecule of benzene; the latter, together with a second heterocyclic unit, are completed by symmetry, with a twofold crystallographic axis crossing through both the middle of the bond between the C atoms bearing the heterocyclic rings and the opposite C—C bonds of the whole benzene molecule. The pyrrolidine ring shows an envelope conformation with the apex at the N atom. The dihedral angle between the least-squares plane of this ring and the benzene ring is 36.9 (5°. There are intramolecular C—H...N interactions generating S(6 ring motifs. In the crystal structure, the molecules are linked by C—H...F interactions, forming chains parallel to [010].

  11. CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures

    Directory of Open Access Journals (Sweden)

    Hamed Bostan

    2012-01-01

    Full Text Available Computational approaches to the disulphide bonding state and its connectivity pattern prediction are based on various descriptors. One descriptor is the amino acid sequence motifs flanking the cysteine residue motifs. Despite the existence of disulphide bonding information in many databases and applications, there is no complete reference and motif query available at the moment. Cysteine motif database (CMD is the first online resource that stores all cysteine residues, their flanking motifs with their secondary structure, and propensity values assignment derived from the laboratory data. We extracted more than 3 million cysteine motifs from PDB and UniProt data, annotated with secondary structure assignment, propensity value assignment, and frequency of occurrence and coefficiency of their bonding status. Removal of redundancies generated 15875 unique flanking motifs that are always bonded and 41577 unique patterns that are always nonbonded. Queries are based on the protein ID, FASTA sequence, sequence motif, and secondary structure individually or in batch format using the provided APIs that allow remote users to query our database via third party software and/or high throughput screening/querying. The CMD offers extensive information about the bonded, free cysteine residues, and their motifs that allows in-depth characterization of the sequence motif composition.

  12. Saturn's Ring: Pre-Cassini Status and Mission Goals

    Science.gov (United States)

    Cuzzi, Jeff N.; DeVincenzi, Donald L. (Technical Monitor)

    1999-01-01

    In November 1980, and again in August 1981, identical Voyager spacecraft flew through the Saturn system, changing forever the way we think about planetary rings. Although Saturn's rings had been the only known ring system for three centuries, a ring system around Uranus had been discovered by stellar occultations from Earth in 1977, and the nearly transparent ring of Jupiter was imaged by Voyager in 1979 (the presence of material there had been inferred from charged particle experiments on Pioneer 10 and 11 several years earlier). While Saturn had thus temporarily lost its uniqueness as having the only ring system, with Voyager it handily recaptured the role of having the most fascinating one. The Voyager breakthroughs included spiral density and bending waves such as cause galactic structure; ubiquitous fine-scale radial 'irregular' structure, with the appearance of record-grooves; regional and local variations in particle color; complex, azimuthally variable ring structure; empty gaps in the rings, some containing very regular, sharp-edged, elliptical rings and one containing both a small moonlet and incomplete arcs of dusty material; and shadowy 'spokes' that flicker across the main rings. One of the paradigm shifts of this period was the realization that many aspects of planetary rings, and even the ring systems themselves, could be 'recent' on geological timescales. These early results are reviewed and summarized in the Arizona Space Science series volumes 'Saturn'. (An excellent review of ring dynamics at a formative stage is by Goldreich and Tremaine.) From the mid 1980's to the time of this writing, progress has been steady, while at a less heady pace, and some of the novel ring properties revealed by Voyager 1 and 2 are beginning to be better understood. It is clearly impossible to cite, much less review, every advance over the last decade; however, below we summarize the main advances in understanding of Saturn's rings since the mid 1980's, in the context

  13. A cyclic carbo-isosteric penta-depsipeptide: cyclo(Phe1–d-Ala2–Gly3–Phe4–APO5

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    Stéphanie M. Guéret

    2015-01-01

    Full Text Available The title compound, cyclo(Phe1–d-Ala2–Gly3–Phe4–APO5, C26H32N4O5, is the minor diastereoisomer of a cyclic penta-peptidomimetic analogue containing a novel 2-aminopropyl lactone (APO motif, which displays the same number of atoms as the native amino acid glycine and has a methyl group in place of the carbonyl O atom. The crystal structure presented here allows the analysis of the secondary structure of this unprecedented cyclic carbo-isosteric depsipeptide. The conformation of the central ring is stabilized by an intramolecular N—H...O hydrogen bond between the carbonyl O atom of the first residue (Phe1 and the amide group H atom of the fourth residue (Phe4. Based on the previously reported hydrogen bond and on the values of the torsion angles ϕ and ψ, the loop formed by the first, second, third and fourth residues (Phe1, d-Ala2, Gly3 and Phe4 can be classified as a type II′ β-turn. The loop around the new peptidomimetic motif, on the other hand, resembles an open γ-turn containing a weak N—H...O hydrogen bond between the carbonyl group O atom of the fourth residue (Phe4 and the amide unit H atom of the first residue (Phe1. In the crystal, the peptidomimetic molecules are arranged in chains along the b-axis direction. Within such a chain, the molecules of the structure are linked via N—H...O hydrogen bonds between the amide group H atom of the secondary residue (d-Ala2 and the carboxy unit O atom of the fourth residue (Phe4 in a neighboring molecule. The newly formed methyl stereocentre of the APO peptidomimetic motif (APO5 was obtained as the minor diastereoisomer in a ring-closing reductive amination reaction and adopts an R configuration.

  14. Baroclinic flows, transports, and kinematic properties in a cyclonic-anticyclonic-cyclonic ring triad in the Gulf of Mexico

    Science.gov (United States)

    Vidal, VíCtor M. V.; Vidal, Francisco V.; HernáNdez, Abel F.; Meza, Eustorgio; PéRez-Molero, José M.

    1994-04-01

    During October-November 1986 the baroclinic circulation of the central and western Gulf of Mexico was dominated by an anticyclonic ring that was being bisected by two north and south flanking cyclonic rings. The baroclinic circulation revealed a well-defined cyclonic-anticyclonic-cyclonic triad system. The anticyclone's collision against the western gulf continental slope at 22.5°N, 97°W originated the north and south flanking cyclonic rings. The weakening of the anticyclone's relative vorticity, during the collision, was compensated by along-shelf north (26 cm s-1) and south (58 cm s-1) jet currents and by the anticyclone's flanking water mass's gain of cyclonic vorticity from lateral shear contributed by east (56 cm s-1) and west (42 cm s-1) current jets with individual mass transports of ˜18 Sv. Within the 0-1000 and 0-500 dbar layers and across 96°W the magnitudes of the colliding westward transports were 17.80 and 8.59 Sv, respectively. These corresponding transports were 85 and 94% balanced by along-shelf jet currents north and south of the anticyclone's collision zone. This indicates that only minor amounts (energy from the upper to the deeper water layers. Our vertical transport estimates through the 1000-m-depth surface revealed a net vertical descending transport of 0.4 Sv for the ring triad system. This mass flux occurred primordially within the south central gulf region and most likely constituted a principal mechanism that propelled the gulf's deep horizontal circulation. The volume renewal time is ˜5 years for the ring triad system within 0-1000 dbar. The volume renewal time for the gulf's deep water layer (2000-3000 dbar), estimated as a function of its horizontal outflowing mass flux (1.96 Sv), is of the same order of magnitude and reveals that the deeper layer of the Gulf of Mexico is as well ventilated as its upper layer (0-1000 dbar). The ring triad's surface kinematic properties were derived from the sea surface baroclinic circulation field

  15. BEAM web server: a tool for structural RNA motif discovery.

    Science.gov (United States)

    Pietrosanto, Marco; Adinolfi, Marta; Casula, Riccardo; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2018-03-15

    RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. marco.pietrosanto@uniroma2.it. Supplementary data are available at Bioinformatics online.

  16. Ring Avulsion Injuries: A Systematic Review.

    Science.gov (United States)

    Bamba, Ravinder; Malhotra, Gautam; Bueno, Reuben A; Thayer, Wesley P; Shack, R Bruce

    2018-01-01

    Ring avulsion injuries can range from soft tissue injury to complete amputation. Grading systems have been developed to guide treatment, but there is controversy with high-grade injuries. Traditionally, advanced ring injuries have been treated with completion amputation, but there is evidence that severe ring injuries can be salvaged. The purpose of this systematic review was to pool the current published data on ring injuries. A systematic review of the English literature published from 1980 to 2015 in PubMed and MEDLINE databases was conducted to identify patients who underwent treatment for ring avulsion injuries. Twenty studies of ring avulsion injuries met the inclusion criteria. There were a total of 572 patients reported with ring avulsion injuries. The Urbaniak class breakdown was class I (54 patients), class II (204 patients), and class III (314 patients). The average total arc of motion (TAM) for patients with a class I injury was 201.25 (n = 40). The average 2-point discrimination was 5.6 (n = 10). The average TAM for patients with a class II injury undergoing microsurgical revascularization was 187.0 (n = 114), and the average 2-point discrimination was 8.3 (n = 40). The average TAM for patients with a class III injury undergoing microsurgical revascularization was 168.2 (n = 170), and the average 2-point discrimination was 10.5 (n = 97). Ring avulsion injuries are commonly classified with the Urbaniak class system. Outcomes are superior for class I and II injuries, and there are select class III injuries that can be treated with replantation. Shared decision making with patients is imperative to determine whether replantation is appropriate.

  17. The Tribological Performance of CrMoN/MoS2 Solid Lubrication Coating on a Piston Ring

    Directory of Open Access Journals (Sweden)

    Yuelan Di

    2017-05-01

    Full Text Available In order to improve the tribological properties of an engine piston ring and enhance its service life, magnetron sputtering technology and low temperature ion sulphurizing treatment technology were used to prepare CrMoN/MoS2 solid lubricant coating on the surface of an engine piston ring. The morphologies and compositions of the surface and cross-section of the sulfuration layer were analyzed by field emission scanning electron microscopy (FESEM, and wear property under high load, high speed and high temperature conditions were tested by a SRV®4 friction and wear testing machine. The results show that the CrMoN/MoS2 composite coatings appear as a dense grain structure, and the coating is an ideal solid lubrication layer that possesses an excellent high temperature wear resistance, reducing the engine operating temperature abrasion effectively and prolonging the service life of the engine.

  18. Methyl 4-[N-(5-bromopyrimidin-2-ylcarbamoyl]benzoate

    Directory of Open Access Journals (Sweden)

    Hui-Ling Hu

    2012-08-01

    Full Text Available In the title compound, C13H10BrN3O3, the pyrimidine and benzene rings are twisted with an interplanar angle of 58.4 (1°. The secondary amide group adopts a cis conformation with an H—N—C—O torsion angle of 14.8 (1°. In the crystal, molecules are connected into inversion dimers via pairs of N—H...N hydrogen bonds, generating an R22(8 motif. The dimers are further connected through a C—Br...O interaction [3.136 (1 Å and 169.31 (1°] into a chain along [110]. Weak C—H...N hydrogen bonds between the methyl benzoate groups and pyrimidine rings are also observed in the crystal structure.

  19. Localized AdS_{5S^{5} Black Holes.

    Science.gov (United States)

    Dias, Óscar J C; Santos, Jorge E; Way, Benson

    2016-10-07

    According to heuristic arguments, global AdS_{5S^{5} black holes are expected to undergo a phase transition in the microcanonical ensemble. At high energies, one expects black holes that respect the symmetries of the S^{5}; at low energies, one expects "localized" black holes that appear pointlike on the S^{5}. According to anti-de Sitter/conformal field theory correspondence, N=4 supersymmetric Yang-Mills (SYM) theory on a 3-sphere should therefore exhibit spontaneous R-symmetry breaking at strong coupling. In this Letter, we numerically construct these localized black holes. We extrapolate the location of this phase transition, and compute the expectation value of the broken scalar operator with lowest conformal dimension. Via the correspondence, these results offer quantitative predictions for N=4 SYM theory.

  20. Conserved XPB Core Structure and Motifs for DNA Unwinding:Implications for Pathway Selection of Transcription or ExcisionRepair

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Li; Arval, Andrew S.; Cooper, Priscilla K.; Iwai, Shigenori; Hanaoka, Fumio; Tainer, John A.

    2005-04-01

    The human xeroderma pigmentosum group B (XPB) helicase is essential for transcription, nucleotide excision repair, and TFIIH functional assembly. Here, we determined crystal structures of an Archaeoglobus fulgidus XPB homolog (AfXPB) that characterize two RecA-like XPB helicase domains and discover a DNA damage recognition domain (DRD), a unique RED motif, a flexible thumb motif (ThM), and implied conformational changes within a conserved functional core. RED motif mutations dramatically reduce helicase activity, and the DRD and ThM, which flank the RED motif, appear structurally as well as functionally analogous to the MutS mismatch recognition and DNA polymerase thumb domains. Substrate specificity is altered by DNA damage, such that AfXPB unwinds dsDNA with 3' extensions, but not blunt-ended dsDNA, unless it contains a lesion, as shown for CPD or (6-4) photoproducts. Together, these results provide an unexpected mechanism of DNA unwinding with Implications for XPB damage verification in nucleotide excision repair.

  1. Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

    Science.gov (United States)

    Fauteux, François; Strömvik, Martina V

    2009-01-01

    Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely Brassicaceae (mustards), Fabaceae (legumes) and Poaceae (grasses) using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L.) Heynh.), soybean (Glycine max (L.) Merr.) and rice (Oryza sativa L.) respectively. We have identified three conserved motifs (two RY-like and one ACGT-like) in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination of conserved motifs

  2. Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

    Directory of Open Access Journals (Sweden)

    Fauteux François

    2009-10-01

    Full Text Available Abstract Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP gene promoters from three plant families, namely Brassicaceae (mustards, Fabaceae (legumes and Poaceae (grasses using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L. Heynh., soybean (Glycine max (L. Merr. and rice (Oryza sativa L. respectively. We have identified three conserved motifs (two RY-like and one ACGT-like in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination

  3. 5-[3-(2,5-Dimethoxyphenylprop-2-enylidene]-1,3-diethyl-2-thioxohexahydropyrimidine-4,6-dione

    Directory of Open Access Journals (Sweden)

    Abdullah Mohamed Asiri

    2009-08-01

    Full Text Available 1,3-Diethyl-2-thiobarbituric acid reacts with 2,5-dimethoxybenzaldehyde to form the title Knoevenagel product, C19H22N2O4S. In the compound, the two six-membered rings at either end of the three-membered –CHCHCH– chain are nearly coplanar with this fragment (r.m.s. deviation of the two six-membered rings and the three chain atoms = 0.08 Å.

  4. Mapping Ring Particle Cooling across Saturn's Rings with Cassini CIRS

    Science.gov (United States)

    Brooks, Shawn M.; Spilker, L. J.; Edgington, S. G.; Pilorz, S. H.; Deau, E.

    2010-10-01

    Previous studies have shown that the rings' thermal inertia, a measure of their response to changes in the thermal environment, varies from ring to ring. Thermal inertia can provide insight into the physical structure of Saturn's ring particles and their regoliths. Low thermal inertia and quick temperature responses are suggestive of ring particles that have more porous or fluffy regoliths or that are riddled with cracks. Solid, coherent particles can be expected to have higher thermal inertias (Ferrari et al. 2005). Cassini's Composite Infrared Spectrometer has recorded millions of spectra of Saturn's rings since its arrival at Saturn in 2004 (personal communication, M. Segura). CIRS records far infrared radiation between 10 and 600 cm-1 (16.7 and 1000 µm) at focal plane 1 (FP1), which has a field of view of 3.9 mrad. Thermal emission from Saturn's rings peaks in this wavelength range. FP1 spectra can be used to infer ring temperatures. By tracking how ring temperatures vary, we can determine the thermal inertia of the rings. In this work we focus on CIRS observations of the shadowed portion of Saturn's rings. The thermal budget of the rings is dominated by the solar radiation absorbed by its constituent particles. When ring particles enter Saturn's shadow this source of energy is abruptly cut off. As a result, ring particles cool as they traverse Saturn's shadow. From these shadow observations we can create cooling curves at specific locations across the rings. We will show that the rings' cooling curves and thus their thermal inertia vary not only from ring to ring, but by location within the individual rings. This research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract with NASA. Copyright 2010 California Institute of Technology. Government sponsorship acknowledged.

  5. Motif-Based Text Mining of Microbial Metagenome Redundancy Profiling Data for Disease Classification.

    Science.gov (United States)

    Wang, Yin; Li, Rudong; Zhou, Yuhua; Ling, Zongxin; Guo, Xiaokui; Xie, Lu; Liu, Lei

    2016-01-01

    Text data of 16S rRNA are informative for classifications of microbiota-associated diseases. However, the raw text data need to be systematically processed so that features for classification can be defined/extracted; moreover, the high-dimension feature spaces generated by the text data also pose an additional difficulty. Here we present a Phylogenetic Tree-Based Motif Finding algorithm (PMF) to analyze 16S rRNA text data. By integrating phylogenetic rules and other statistical indexes for classification, we can effectively reduce the dimension of the large feature spaces generated by the text datasets. Using the retrieved motifs in combination with common classification methods, we can discriminate different samples of both pneumonia and dental caries better than other existing methods. We extend the phylogenetic approaches to perform supervised learning on microbiota text data to discriminate the pathological states for pneumonia and dental caries. The results have shown that PMF may enhance the efficiency and reliability in analyzing high-dimension text data.

  6. Optical fibre cavity ring down measurement of refractive index with a microchannel drilled by femtosecond laser

    Science.gov (United States)

    Zhou, Kaiming; Webb, David; Mou, Chengbo; Farries, Mark; Hayes, Neil; Bennion, Ian

    2009-10-01

    μA microchannel was inscribed in the fibre of a ring cavity which was constructed from two 0.1%:99.9% couplers and a 10m fibre loop. Cavity ring down spectroscopy (CRDS) was used to measure the refractive index (RI) of gels infused into the microchannel with high resolution. The ring down time discloses a nonlinear increase with respect to the RI of the gel and sensitivity up to 300μs/RI unit (RIU) and resolution of 5×10-4 were obtained.

  7. On the origin of distribution patterns of motifs in biological networks

    Directory of Open Access Journals (Sweden)

    Lesk Arthur M

    2008-08-01

    Full Text Available Abstract Background Inventories of small subgraphs in biological networks have identified commonly-recurring patterns, called motifs. The inference that these motifs have been selected for function rests on the idea that their occurrences are significantly more frequent than random. Results Our analysis of several large biological networks suggests, in contrast, that the frequencies of appearance of common subgraphs are similar in natural and corresponding random networks. Conclusion Indeed, certain topological features of biological networks give rise naturally to the common appearance of the motifs. We therefore question whether frequencies of occurrences are reasonable evidence that the structures of motifs have been selected for their functional contribution to the operation of networks.

  8. 2-Methylsulfanyl-5,6-dihydro-2H-1,3-dithiolo[4,5-b][1,4]dioxin-2-ium tetrafluoroborate

    Directory of Open Access Journals (Sweden)

    Guoquan Zhou

    2012-04-01

    Full Text Available The title compound, C6H7O2S3+·BF4−, consists of a planar 2-thioxo-1,3-dithiol-4,5-yl unit [maximum deviation from the ring plane = 0.020 (3 Å], with an ethylenedioxy group fused at the 4,5-positions; the ethylenedioxy C atoms are disordered over two positions with site-occupancy factors of 0.5. The 1,4-dioxine ring has a twist-chair conformation. Weak cation–anion S...F interactions [3.022 (4–3.095 (4 Å] and an S...O [3.247 (4 Å] interaction are present.

  9. The Cryogenic Storage Ring CSR

    OpenAIRE

    von Hahn, Robert; Becker, Arno; Berg, Felix; Blaum, Klaus; Breitenfeldt, Christian; Fadil, Hisham; Fellenberger, Florian; Froese, Michael; George, Sebastian; Göck, Jürgen; Grieser, Manfred; Grussie, Florian; Guerin, Elisabeth A.; Heber, Oded; Herwig, Philipp

    2016-01-01

    An electrostatic cryogenic storage ring, CSR, for beams of anions and cations with up to 300 keV kinetic energy per unit charge has been designed, constructed, and put into operation. With a circumference of 35 m, the ion-beam vacuum chambers and all beam optics are in a cryostat and cooled by a closed-cycle liquid helium system. At temperatures as low as (5.5 ± 1) K inside the ring, storage time constants of several minutes up to almost an hour were observed for atomic and molecular, anion a...

  10. Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences

    Science.gov (United States)

    König, Sebastian L. B.; Huppert, Julian L.; Sigel, Roland K. O.; Evans, Amanda C.

    2013-01-01

    G-quadruplexes and i-motifs are complementary examples of non-canonical nucleic acid substructure conformations. G-quadruplex thermodynamic stability has been extensively studied for a variety of base sequences, but the degree of duplex destabilization that adjacent quadruplex structure formation can cause has yet to be fully addressed. Stable in vivo formation of these alternative nucleic acid structures is likely to be highly dependent on whether sufficient spacing exists between neighbouring duplex- and quadruplex-/i-motif-forming regions to accommodate quadruplexes or i-motifs without disrupting duplex stability. Prediction of putative G-quadruplex-forming regions is likely to be assisted by further understanding of what distance (number of base pairs) is required for duplexes to remain stable as quadruplexes or i-motifs form. Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions. The undermining effect that quadruplex formation can have on duplex stability is mitigated with increased distance from the duplex region: a spacing of five base pairs or more is sufficient to maintain duplex stability proximal to predicted quadruplex/i-motif-forming regions. PMID:23771141

  11. Systematic comparison of the response properties of protein and RNA mediated gene regulatory motifs.

    Science.gov (United States)

    Iyengar, Bharat Ravi; Pillai, Beena; Venkatesh, K V; Gadgil, Chetan J

    2017-05-30

    We present a framework enabling the dissection of the effects of motif structure (feedback or feedforward), the nature of the controller (RNA or protein), and the regulation mode (transcriptional, post-transcriptional or translational) on the response to a step change in the input. We have used a common model framework for gene expression where both motif structures have an activating input and repressing regulator, with the same set of parameters, to enable a comparison of the responses. We studied the global sensitivity of the system properties, such as steady-state gain, overshoot, peak time, and peak duration, to parameters. We find that, in all motifs, overshoot correlated negatively whereas peak duration varied concavely with peak time. Differences in the other system properties were found to be mainly dependent on the nature of the controller rather than the motif structure. Protein mediated motifs showed a higher degree of adaptation i.e. a tendency to return to baseline levels; in particular, feedforward motifs exhibited perfect adaptation. RNA mediated motifs had a mild regulatory effect; they also exhibited a lower peaking tendency and mean overshoot. Protein mediated feedforward motifs showed higher overshoot and lower peak time compared to the corresponding feedback motifs.

  12. Folded three-spin string solutions in AdS5 x S5

    International Nuclear Information System (INIS)

    Ryang Shijong

    2004-01-01

    We construct a spinning closed string solution in AdS 5 x S 5 which is folded in the radial direction and has two equal spins in AdS 5 and a spin in S 5 . The energy expression of the three-spin solution specified by the folding and winding numbers for the small S 5 spin shows a logarithmic behavior and a one-third power behavior of the large total AdS 5 spin, in the long string and in the short string located near the boundary of AdS 5 respectively. It exhibits the non-regular expansion in the 't Hooft coupling constant, while it takes the regular one when the S 5 spin becomes large. (author)

  13. Stability of driven systems with growing gaps, quantum rings, and Wannier ladders

    Czech Academy of Sciences Publication Activity Database

    Asch, J.; Duclos, P.; Exner, Pavel

    1998-01-01

    Roč. 92, 5/6 (1998), s. 1053-1070 ISSN 0022-4715 R&D Projects: GA AV ČR(CZ) IAA148409 Keywords : quantum stability * energy expectations * driven rings Subject RIV: BE - Theoretical Physics Impact factor: 1.469, year: 1998

  14. Fast social-like learning of complex behaviors based on motor motifs

    Science.gov (United States)

    Calvo Tapia, Carlos; Tyukin, Ivan Y.; Makarov, Valeri A.

    2018-05-01

    Social learning is widely observed in many species. Less experienced agents copy successful behaviors exhibited by more experienced individuals. Nevertheless, the dynamical mechanisms behind this process remain largely unknown. Here we assume that a complex behavior can be decomposed into a sequence of n motor motifs. Then a neural network capable of activating motor motifs in a given sequence can drive an agent. To account for (n -1 )! possible sequences of motifs in a neural network, we employ the winnerless competition approach. We then consider a teacher-learner situation: one agent exhibits a complex movement, while another one aims at mimicking the teacher's behavior. Despite the huge variety of possible motif sequences we show that the learner, equipped with the provided learning model, can rewire "on the fly" its synaptic couplings in no more than (n -1 ) learning cycles and converge exponentially to the durations of the teacher's motifs. We validate the learning model on mobile robots. Experimental results show that the learner is indeed capable of copying the teacher's behavior composed of six motor motifs in a few learning cycles. The reported mechanism of learning is general and can be used for replicating different functions, including, for example, sound patterns or speech.

  15. Adsorption and ring-opening of lactide on the chiral metal surface Pt(321){sup S} studied by density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Franke, J.-H.; Kosov, D. S. [Department of Physics, Campus Plaine - CP 231, Universite Libre de Bruxelles, 1050 Brussels (Belgium)

    2015-01-28

    We study the adsorption and ring-opening of lactide on the naturally chiral metal surface Pt(321){sup S}. Lactide is a precursor for polylactic acid ring-opening polymerization, and Pt is a well known catalyst surface. We study, here, the energetics of the ring-opening of lactide on a surface that has a high density of kink atoms. These sites are expected to be present on a realistic Pt surface and show enhanced catalytic activity. The use of a naturally chiral surface also enables us to study potential chiral selectivity effects of the reaction at the same time. Using density functional theory with a functional that includes the van der Waals forces in a first-principles manner, we find modest adsorption energies of around 1.4 eV for the pristine molecule and different ring-opened states. The energy barrier to be overcome in the ring-opening reaction is found to be very small at 0.32 eV and 0.30 eV for LL- and its chiral partner DD-lactide, respectively. These energies are much smaller than the activation energy for a dehydrogenation reaction of 0.78 eV. Our results thus indicate that (a) ring-opening reactions of lactide on Pt(321) can be expected already at very low temperatures, and Pt might be a very effective catalyst for this reaction; (b) the ring-opening reaction rate shows noticeable enantioselectivity.

  16. Crystal structure of 2-hy-droxy-imino-2-(pyridin-2-yl)-N'-[1-(pyridin-2-yl)ethyl-idene]acetohydrazide.

    Science.gov (United States)

    Plutenko, Maxym O; Lampeka, Rostislav D; Haukka, Matti; Nordlander, Ebbe

    2014-12-01

    The mol-ecule of the title compound, C14H13N5O2, is approximately planar (r.m.s deviation for all non-H atoms = 0.093 Å), with the planes of the two pyridine rings inclined to one another by 5.51 (7)°. The oxime group is syn to the amide group, probably due to the formation of an intra-molecular N-H⋯N hydrogen bond that forms an S(6) ring motif. In the crystal, mol-ecules are linked by pairs of bifurcated O-H⋯(O,N) hydrogen bonds, forming inversion dimers. The latter are linked via C-H⋯O and C-H⋯N hydrogen bonds, forming sheets lying parallel to (502). The sheets are linked via π-π stacking inter-actions [inter-centroid distance = 3.7588 (9) Å], involving the pyridine rings of inversion-related mol-ecules, forming a three-dimensional structure.

  17. Crystal structure of 2-hy­droxy­imino-2-(pyridin-2-yl)-N′-[1-(pyridin-2-yl)ethyl­idene]acetohydrazide

    Science.gov (United States)

    Plutenko, Maxym O.; Lampeka, Rostislav D.; Haukka, Matti; Nordlander, Ebbe

    2014-01-01

    The mol­ecule of the title compound, C14H13N5O2, is approximately planar (r.m.s deviation for all non-H atoms = 0.093 Å), with the planes of the two pyridine rings inclined to one another by 5.51 (7)°. The oxime group is syn to the amide group, probably due to the formation of an intra­molecular N—H⋯N hydrogen bond that forms an S(6) ring motif. In the crystal, mol­ecules are linked by pairs of bifurcated O—H⋯(O,N) hydrogen bonds, forming inversion dimers. The latter are linked via C—H⋯O and C—H⋯N hydrogen bonds, forming sheets lying parallel to (502). The sheets are linked via π–π stacking inter­actions [inter-centroid distance = 3.7588 (9) Å], involving the pyridine rings of inversion-related mol­ecules, forming a three-dimensional structure. PMID:25552998

  18. 2-(4-Methylphenyl-7-(2-methylpropoxy-4H-chromen-4-one–6-chloro-2-(4-methylphenyl-7-(2-methylpropoxy-4H-chromen-4-one (19/1

    Directory of Open Access Journals (Sweden)

    Vijay M. Barot

    2012-08-01

    Full Text Available The title co-crystal, 0.95C20H20O3·0.05C20H19ClO3, arises as the chloride carried over during the synthesis shares a position with an aromatic H atom; the partial occupancies are 0.947 (2 and 0.053 (2 for H and Cl, respectively. The molecular structure is stabilized by intramolecular C—H...O contacts, forming pseudo five- and six-membered rings with S(5 and S(6 graph-set motifs, respectively. The crystal structure features π–π stacking interactions between the centroids of the central fused ring systems [centroid–centroid distance = 3.501 (2 Å].

  19. WildSpan: mining structured motifs from protein sequences

    Directory of Open Access Journals (Sweden)

    Chen Chien-Yu

    2011-03-01

    Full Text Available Abstract Background Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. For proteins, it is desired to discover sequence motifs containing a large number of wildcard symbols, as the residues associated with functional sites are usually largely separated in sequences. Discovering such patterns is time-consuming because abundant combinations exist when long gaps (a gap consists of one or more successive wildcards are considered. Mining algorithms often employ constraints to narrow down the search space in order to increase efficiency. However, improper constraint models might degrade the sensitivity and specificity of the motifs discovered by computational methods. We previously proposed a new constraint model to handle large wildcard regions for discovering functional motifs of proteins. The patterns that satisfy the proposed constraint model are called W-patterns. A W-pattern is a structured motif that groups motif symbols into pattern blocks interleaved with large irregular gaps. Considering large gaps reflects the fact that functional residues are not always from a single region of protein sequences, and restricting motif symbols into clusters corresponds to the observation that short motifs are frequently present within protein families. To efficiently discover W-patterns for large-scale sequence annotation and function prediction, this paper first formally introduces the problem to solve and proposes an algorithm named WildSpan (sequential pattern mining across large wildcard regions that incorporates several pruning strategies to largely reduce the mining cost. Results WildSpan is shown to efficiently find W-patterns containing conserved residues that are far separated in sequences. We conducted experiments with two mining strategies, protein-based and family-based mining, to evaluate the usefulness of W-patterns and performance of WildSpan. The protein-based mining mode

  20. IMAGING AN 80 au RADIUS DUST RING AROUND THE F5V STAR HD 157587

    International Nuclear Information System (INIS)

    Millar-Blanchaer, Maxwell A.; Moon, Dae-Sik; Wang, Jason J.; Kalas, Paul; Graham, James R.; Duchêne, Gaspard; Rosa, Robert J. De; Nielsen, Eric L.; Perrin, Marshall; Chen, Christine H.; Padgett, Deborah; Metchev, Stanimir; Bruzzone, Sebastian; Ammons, S. Mark; Bailey, Vanessa P.; Barman, Travis; Bulger, Joanna; Chilcote, Jeffrey; Cotten, Tara; Doyon, Rene

    2016-01-01

    We present H -band near-infrared polarimetric imaging observations of the F5V star HD 157587 obtained with the Gemini Planet Imager (GPI) that reveal the debris disk as a bright ring structure at a separation of ∼80–100 au. The new GPI data complement recent Hubble Space Telescope /STIS observations that show the disk extending out to over 500 au. The GPI image displays a strong asymmetry along the projected minor axis as well as a fainter asymmetry along the projected major axis. We associate the minor and major axis asymmetries with polarized forward scattering and a possible stellocentric offset, respectively. To constrain the disk geometry, we fit two separate disk models to the polarized image, each using a different scattering phase function. Both models favor a disk inclination of ∼70° and a 1.5 ± 0.6 au stellar offset in the plane of the sky along the projected major axis of the disk. We find that the stellar offset in the disk plane, perpendicular to the projected major axis is degenerate with the form of the scattering phase function and remains poorly constrained. The disk is not recovered in total intensity due in part to strong adaptive optics residuals, but we recover three point sources. Considering the system’s proximity to the galactic plane and the point sources’ positions relative to the disk, we consider it likely that they are background objects and unrelated to the disk’s offset from the star.

  1. IMAGING AN 80 au RADIUS DUST RING AROUND THE F5V STAR HD 157587

    Energy Technology Data Exchange (ETDEWEB)

    Millar-Blanchaer, Maxwell A.; Moon, Dae-Sik [Department of Astronomy and Astrophysics, University of Toronto, Toronto, ON M5S 3H4 (Canada); Wang, Jason J.; Kalas, Paul; Graham, James R.; Duchêne, Gaspard; Rosa, Robert J. De [Astronomy Department, University of California Berkeley, Berkeley, CA 94720 (United States); Nielsen, Eric L. [SETI Institute, Carl Sagan Center, 189 Bernardo Avenue, Mountain View, CA 94043 (United States); Perrin, Marshall; Chen, Christine H. [Space Telescope Science Institute, Baltimore, MD 21218 (United States); Padgett, Deborah [Goddard Space Flight Center, 8800 Greenbelt Road, Greenbelt, MD 20771 (United States); Metchev, Stanimir; Bruzzone, Sebastian [Department of Physics and Astronomy, Centre for Planetary Science and Exploration, The University of Western Ontario, London, ON N6A 3K7 (Canada); Ammons, S. Mark [Lawrence Livermore National Laboratory, Livermore, CA 94551 (United States); Bailey, Vanessa P. [Kavli Institute for Particle Astrophysics and Cosmology, Department of Physics, Stanford University, Stanford, CA, 94305 (United States); Barman, Travis [Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ 85721 (United States); Bulger, Joanna [Subaru Telescope, NAOJ, 650 North A’ohoku Place, Hilo, HI 96720 (United States); Chilcote, Jeffrey [Dunlap Institute for Astronomy and Astrophysics, University of Toronto, Toronto, ON M5S 3H4 (Canada); Cotten, Tara [Department of Physics and Astronomy, University of Georgia, Athens, GA 30602 (United States); Doyon, Rene, E-mail: maxmb@astro.utoronto.ca [Institut de Recherche sur les Exoplanètes, Départment de Physique, Université de Montréal, Montréal QC H3C 3J7 (Canada); and others

    2016-11-01

    We present H -band near-infrared polarimetric imaging observations of the F5V star HD 157587 obtained with the Gemini Planet Imager (GPI) that reveal the debris disk as a bright ring structure at a separation of ∼80–100 au. The new GPI data complement recent Hubble Space Telescope /STIS observations that show the disk extending out to over 500 au. The GPI image displays a strong asymmetry along the projected minor axis as well as a fainter asymmetry along the projected major axis. We associate the minor and major axis asymmetries with polarized forward scattering and a possible stellocentric offset, respectively. To constrain the disk geometry, we fit two separate disk models to the polarized image, each using a different scattering phase function. Both models favor a disk inclination of ∼70° and a 1.5 ± 0.6 au stellar offset in the plane of the sky along the projected major axis of the disk. We find that the stellar offset in the disk plane, perpendicular to the projected major axis is degenerate with the form of the scattering phase function and remains poorly constrained. The disk is not recovered in total intensity due in part to strong adaptive optics residuals, but we recover three point sources. Considering the system’s proximity to the galactic plane and the point sources’ positions relative to the disk, we consider it likely that they are background objects and unrelated to the disk’s offset from the star.

  2. Motif formation and industry specific topologies in the Japanese business firm network

    Science.gov (United States)

    Maluck, Julian; Donner, Reik V.; Takayasu, Hideki; Takayasu, Misako

    2017-05-01

    Motifs and roles are basic quantities for the characterization of interactions among 3-node subsets in complex networks. In this work, we investigate how the distribution of 3-node motifs can be influenced by modifying the rules of an evolving network model while keeping the statistics of simpler network characteristics, such as the link density and the degree distribution, invariant. We exemplify this problem for the special case of the Japanese Business Firm Network, where a well-studied and relatively simple yet realistic evolving network model is available, and compare the resulting motif distribution in the real-world and simulated networks. To better approximate the motif distribution of the real-world network in the model, we introduce both subgraph dependent and global additional rules. We find that a specific rule that allows only for the merging process between nodes with similar link directionality patterns reduces the observed excess of densely connected motifs with bidirectional links. Our study improves the mechanistic understanding of motif formation in evolving network models to better describe the characteristic features of real-world networks with a scale-free topology.

  3. Unusual Ring Contration by Substitution of 4-O-activated-pentono-1,5-lactams with cyanide. Stereospecific Synthesis of 6-Amino-1,4,5,6-tetradeoxy-1,4-imino-hexitols

    DEFF Research Database (Denmark)

    Godskesen, Michael Anders; Lundt, Inge; Søtofte, Inger

    2000-01-01

    Reaction of 4-O-sulfonylated 2,3-O-isopropylidene-D-ribo- or -D-lyxo-1,5-lactams with tetrabutylammonium cyanide gave 4-amino-5-C-cyano-4,5-dideoxy-2,3-O-isopropylidene-L-lyxo-5 or -L-ribo-15-1,4-lactams, respectively. A stereospecific ring contraction with inversion at C-4 had taken place in each...

  4. Binding properties of SUMO-interacting motifs (SIMs) in yeast.

    Science.gov (United States)

    Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

    2015-03-01

    Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

  5. De Novo Discovery of Structured ncRNA Motifs in Genomic Sequences

    DEFF Research Database (Denmark)

    Ruzzo, Walter L; Gorodkin, Jan

    2014-01-01

    De novo discovery of "motifs" capturing the commonalities among related noncoding ncRNA structured RNAs is among the most difficult problems in computational biology. This chapter outlines the challenges presented by this problem, together with some approaches towards solving them, with an emphas...... on an approach based on the CMfinder CMfinder program as a case study. Applications to genomic screens for novel de novo structured ncRNA ncRNA s, including structured RNA elements in untranslated portions of protein-coding genes, are presented.......De novo discovery of "motifs" capturing the commonalities among related noncoding ncRNA structured RNAs is among the most difficult problems in computational biology. This chapter outlines the challenges presented by this problem, together with some approaches towards solving them, with an emphasis...

  6. Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells

    KAUST Repository

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin

    2015-01-01

    Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.

  7. Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells

    KAUST Repository

    Wong, Ka-Chun

    2015-09-27

    Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.

  8. Mutational analysis of TRAF6 reveals a conserved functional role of the RING dimerization interface and a potentially necessary but insufficient role of RING-dependent TRAF6 polyubiquitination towards NF-κB activation.

    Science.gov (United States)

    Megas, Charilaos; Hatzivassiliou, Eudoxia G; Yin, Qian; Marinopoulou, Elli; Hadweh, Paul; Vignali, Dario A A; Mosialos, George

    2011-05-01

    TRAF6 is an E3 ubiquitin ligase that plays a pivotal role in the activation of NF-κB by innate and adaptive immunity stimuli. TRAF6 consists of a highly conserved carboxyl terminal TRAF-C domain which is preceded by a coiled coil domain and an amino terminal region that contains a RING domain and a series of putative zinc-finger motifs. The TRAF-C domain contributes to TRAF6 oligomerization and mediates the interaction of TRAF6 with upstream signaling molecules whereas the RING domain comprises the core of the ubiquitin ligase catalytic domain. In order to identify structural elements that are important for TRAF6-induced NF-κB activation, mutational analysis of the TRAF-C and RING domains was performed. Alterations of highly conserved residues of the TRAF-C domain of TRAF6 did not affect significantly the ability of the protein to activate NF-κB. On the other hand a number of functionally important residues (L77, Q82, R88, F118, N121 and E126) for the activation of NF-κB were identified within the RING domain of TRAF6. Interestingly, several homologues of these residues in TRAF2 were shown to have a conserved functional role in TRAF2-induced NF-κB activation and lie at the dimerization interface of the RING domain. Finally, whereas alteration of Q82, R88 and F118 compromised both the K63-linked polyubiquitination of TRAF6 and its ability to activate NF-κB, alteration of L77, N121 and E126 diminished the NF-κB activating function of TRAF6 without affecting TRAF6 K63-linked polyubiquitination. Our results support a conserved functional role of the TRAF RING domain dimerization interface and a potentially necessary but insufficient role for RING-dependent TRAF6 K63-linked polyubiquitination towards NF-κB activation in cells. Copyright © 2010 Elsevier Inc. All rights reserved.

  9. A 6-Nucleotide Regulatory Motif within the AbcR Small RNAs of Brucella abortus Mediates Host-Pathogen Interactions.

    Science.gov (United States)

    Sheehan, Lauren M; Caswell, Clayton C

    2017-06-06

    In Brucella abortus , two small RNAs (sRNAs), AbcR1 and AbcR2, are responsible for regulating transcripts encoding ABC-type transport systems. AbcR1 and AbcR2 are required for Brucella virulence, as a double chromosomal deletion of both sRNAs results in attenuation in mice. Although these sRNAs are responsible for targeting transcripts for degradation, the mechanism utilized by the AbcR sRNAs to regulate mRNA in Brucella has not been described. Here, two motifs (M1 and M2) were identified in AbcR1 and AbcR2, and complementary motif sequences were defined in AbcR-regulated transcripts. Site-directed mutagenesis of M1 or M2 or of both M1 and M2 in the sRNAs revealed transcripts to be targeted by one or both motifs. Electrophoretic mobility shift assays revealed direct, concentration-dependent binding of both AbcR sRNAs to a target mRNA sequence. These experiments genetically and biochemically characterized two indispensable motifs within the AbcR sRNAs that bind to and regulate transcripts. Additionally, cellular and animal models of infection demonstrated that only M2 in the AbcR sRNAs is required for Brucella virulence. Furthermore, one of the M2-regulated targets, BAB2_0612, was found to be critical for the virulence of B. abortus in a mouse model of infection. Although these sRNAs are highly conserved among Alphaproteobacteria , the present report displays how gene regulation mediated by the AbcR sRNAs has diverged to meet the intricate regulatory requirements of each particular organism and its unique biological niche. IMPORTANCE Small RNAs (sRNAs) are important components of bacterial regulation, allowing organisms to quickly adapt to changes in their environments. The AbcR sRNAs are highly conserved throughout the Alphaproteobacteria and negatively regulate myriad transcripts, many encoding ABC-type transport systems. In Brucella abortus , AbcR1 and AbcR2 are functionally redundant, as only a double abcR1 abcR2 ( abcR1 / 2 ) deletion results in attenuation in

  10. Preparation of nucleoside-pyridine hybrids and pyridine attached acylureas from an unexpected uracil ring-opening and pyridine ring-forming sequence

    Institute of Scientific and Technical Information of China (English)

    Xue Sen Fan; Xia Wang; Xin Ying Zhang; Dong Feng; Ying Ying Qu

    2009-01-01

    Novel pyrimidine nucleoside-3,5-dicyanopyridine hybrids (4) or pyridine attached acylureas (5) were selectively and efficiently prepared from the reaction of 2'-deoxyuridin-5-yl-methylene malonortitrile (1), malononitrile (2) and thiophenol (3) or from an unexpected uracil ring-opening and pyridine ring-forming sequence via the reaction of 1 and 3. It is the first time such a sequence has ever been reported.

  11. Catch history of ringed seals (Phoca hispida in Canada

    Directory of Open Access Journals (Sweden)

    Randall R Reeves

    1998-06-01

    Full Text Available The ringed seal (Phoca hispida has always been a staple in the diet and household economy of Inuit in Canada. The present paper was prepared at the request of the NAMMCO Scientific Committee to support their assessment of ringed seal stocks in the North Atlantic Basin and adjacent arctic and subarctic waters. Specifically, our objective was to evaluate recent and current levels of use of ringed seals by Canadian Inuit. Annual removals probably were highest (possibly greater than 100,000 in the 1960s and 1970s, a period when sealskin prices were particularly strong. Catches declined substantially in the 1980s following a collapse in sealskin prices, presumably related to the European trade ban on skins from newborn harp and hooded seals (Phoca groenlandica and Cystophora cristata, respectively. Recent catch levels throughout Canada (1980s and early 1990s are believed to be in the order of 50,000 to 65,000 ringed seals, with a total average annual kill (including hunting loss in the high tens of thousands. No reliable system is in place to monitor catches of ringed seals, so any estimate must be derived from a heterogeneous array of sources.

  12. Phospholipid composition and a polybasic motif determine D6 PROTEIN KINASE polar association with the plasma membrane and tropic responses.

    Science.gov (United States)

    Barbosa, Inês C R; Shikata, Hiromasa; Zourelidou, Melina; Heilmann, Mareike; Heilmann, Ingo; Schwechheimer, Claus

    2016-12-15

    Polar transport of the phytohormone auxin through PIN-FORMED (PIN) auxin efflux carriers is essential for the spatiotemporal control of plant development. The Arabidopsis thaliana serine/threonine kinase D6 PROTEIN KINASE (D6PK) is polarly localized at the plasma membrane of many cells where it colocalizes with PINs and activates PIN-mediated auxin efflux. Here, we show that the association of D6PK with the basal plasma membrane and PINs is dependent on the phospholipid composition of the plasma membrane as well as on the phosphatidylinositol phosphate 5-kinases PIP5K1 and PIP5K2 in epidermis cells of the primary root. We further show that D6PK directly binds polyacidic phospholipids through a polybasic lysine-rich motif in the middle domain of the kinase. The lysine-rich motif is required for proper PIN3 phosphorylation and for auxin transport-dependent tropic growth. Polybasic motifs are also present at a conserved position in other D6PK-related kinases and required for membrane and phospholipid binding. Thus, phospholipid-dependent recruitment to membranes through polybasic motifs might not only be required for D6PK-mediated auxin transport but also other processes regulated by these, as yet, functionally uncharacterized kinases. © 2016. Published by The Company of Biologists Ltd.

  13. Efficient sequential and parallel algorithms for finding edit distance based motifs.

    Science.gov (United States)

    Pal, Soumitra; Xiao, Peng; Rajasekaran, Sanguthevar

    2016-08-18

    Motif search is an important step in extracting meaningful patterns from biological data. The general problem of motif search is intractable and there is a pressing need to develop efficient, exact and approximation algorithms to solve this problem. In this paper, we present several novel, exact, sequential and parallel algorithms for solving the (l,d) Edit-distance-based Motif Search (EMS) problem: given two integers l,d and n biological strings, find all strings of length l that appear in each input string with atmost d errors of types substitution, insertion and deletion. One popular technique to solve the problem is to explore for each input string the set of all possible l-mers that belong to the d-neighborhood of any substring of the input string and output those which are common for all input strings. We introduce a novel and provably efficient neighborhood exploration technique. We show that it is enough to consider the candidates in neighborhood which are at a distance exactly d. We compactly represent these candidate motifs using wildcard characters and efficiently explore them with very few repetitions. Our sequential algorithm uses a trie based data structure to efficiently store and sort the candidate motifs. Our parallel algorithm in a multi-core shared memory setting uses arrays for storing and a novel modification of radix-sort for sorting the candidate motifs. The algorithms for EMS are customarily evaluated on several challenging instances such as (8,1), (12,2), (16,3), (20,4), and so on. The best previously known algorithm, EMS1, is sequential and in estimated 3 days solves up to instance (16,3). Our sequential algorithms are more than 20 times faster on (16,3). On other hard instances such as (9,2), (11,3), (13,4), our algorithms are much faster. Our parallel algorithm has more than 600 % scaling performance while using 16 threads. Our algorithms have pushed up the state-of-the-art of EMS solvers and we believe that the techniques introduced in

  14. Buthalital and methitural – 5,5-substituted derivatives of 2-thiobarbituric acid forming the same type of hydrogen-bonded chain

    Directory of Open Access Journals (Sweden)

    Thomas Gelbrich

    2017-12-01

    Full Text Available The molecule of buthalital, (I [systematic name: 5-(2-methylpropyl-5-(prop-2-en-1-yl-2-sulfanylidene-1,3-diazinane-4,6-dione], C11H16N2O2S, exhibits a planar pyrimidine ring, whereas the pyrimidine ring of methitural, (II [systematic name: 5-(1-methylbutyl-5-[2-(methylsulfanylethyl]-2-sulfanylidene-1,3-diazinane-4,6-dione], C12H20N2O2S2, is slightly puckered. (I and (II contain the same hydrogen-bonded chain structure in which each molecule is connected, via four N—H...O=C hydrogen bonds, to two other molecules, resulting in a hydrogen-bonded chain displaying a sequence of R22(8 rings. The same type of N—H...O=C hydrogen-bonded chain has previously been found in several 5,5-disubstituted derivatives of barbituric acid which are chemically closely related to (I and (II.

  15. Physical-chemical property based sequence motifs and methods regarding same

    Science.gov (United States)

    Braun, Werner [Friendswood, TX; Mathura, Venkatarajan S [Sarasota, FL; Schein, Catherine H [Friendswood, TX

    2008-09-09

    A data analysis system, program, and/or method, e.g., a data mining/data exploration method, using physical-chemical property motifs. For example, a sequence database may be searched for identifying segments thereof having physical-chemical properties similar to the physical-chemical property motifs.

  16. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.

    Science.gov (United States)

    Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude

    2011-06-20

    One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

  17. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2011-06-01

    Full Text Available Abstract Background One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet, which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i ubiquitous motifs, shared by several superfamilies and (ii superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P and SAH/SAM. Conclusions Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

  18. Spectral Properties of Novel 1,3-oxazol-5(4H)-ones With Substituted Benzylidene and Phenyl Rings

    DEFF Research Database (Denmark)

    Palcut, Marián

    2009-01-01

    In the present work, five novel (4Z)-4-benzylidene-2-phenyl-1,3-oxazol-5(4H)-ones (azlactones) were investigated by the infra-red (IR) and nuclear magnetic resonance spectroscopy (NMR) of the 1H and 13C nuclei. The spectral properties of the oxazolone ring were monitored with respect to the subst...

  19. Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks.

    Science.gov (United States)

    Gorochowski, Thomas E; Grierson, Claire S; di Bernardo, Mario

    2018-03-01

    Network motifs are significantly overrepresented subgraphs that have been proposed as building blocks for natural and engineered networks. Detailed functional analysis has been performed for many types of motif in isolation, but less is known about how motifs work together to perform complex tasks. To address this issue, we measure the aggregation of network motifs via methods that extract precisely how these structures are connected. Applying this approach to a broad spectrum of networked systems and focusing on the widespread feed-forward loop motif, we uncover striking differences in motif organization. The types of connection are often highly constrained, differ between domains, and clearly capture architectural principles. We show how this information can be used to effectively predict functionally important nodes in the metabolic network of Escherichia coli . Our findings have implications for understanding how networked systems are constructed from motif parts and elucidate constraints that guide their evolution.

  20. Introduction of N-cadherin-binding motif to alginate hydrogels for controlled stem cell differentiation.

    Science.gov (United States)

    Lee, Jae Won; An, Hyoseok; Lee, Kuen Yong

    2017-07-01

    Control of stem cell fate and phenotype using biomimetic synthetic extracellular matrices (ECMs) is an important tissue engineering approach. Many studies have focused on improving cell-matrix interactions. However, proper control of cell-cell interactions using synthetic ECMs could be critical for tissue engineering, especially with undifferentiated stem cells. In this study, alginate hydrogels were modified with a peptide derived from the low-density lipoprotein receptor-related protein 5 (LRP5), which is known to bind to N-cadherin, as a cell-cell interaction motif. In vitro changes in the morphology and differentiation of mouse bone marrow stromal cells (D1 stem cells) cultured in LRP5-alginate hydrogels were investigated. LRP5-alginate gels successfully induced stem cell aggregation and enhanced chondrogenic differentiation of D1 stem cells, compared to RGD-alginate gels, at low cell density. This approach to tailoring synthetic biomimetic ECMs using cell-cell interaction motifs may be critical in tissue engineering approaches using stem cells. Copyright © 2017 Elsevier B.V. All rights reserved.